diff --git a/apps/app/src/App.tsx b/apps/app/src/App.tsx
index 2283307a3..692fd15c8 100644
--- a/apps/app/src/App.tsx
+++ b/apps/app/src/App.tsx
@@ -20,6 +20,7 @@ import {
   PROJECT_ARCHIVED_ROUTE_PATH,
   PROJECTLESS_THREAD_DETAIL_ROUTE_PATH,
   PROJECT_SETTINGS_ROUTE_PATH,
+  STANDALONE_APP_ROUTE_PATH,
   THREAD_DETAIL_ROUTE_PATH,
 } from "./lib/app-route-paths";
 
@@ -46,6 +47,11 @@ const InternalReplayListView = lazy(() =>
     default: m.InternalReplayListView,
   })),
 );
+const StandaloneAppView = lazy(() =>
+  import("./views/standalone-app/StandaloneAppView").then((m) => ({
+    default: m.StandaloneAppView,
+  })),
+);
 
 function AppRoutes() {
   return (
@@ -54,6 +60,10 @@ function AppRoutes() {
         <Routes>
           <Route path={APP_ROOT_ROUTE_PATH} element={<RootComposeRoute />} />
           <Route path={APP_SETTINGS_ROUTE_PATH} element={<AppSettingsView />} />
+          <Route
+            path={STANDALONE_APP_ROUTE_PATH}
+            element={<StandaloneAppView />}
+          />
           {import.meta.env.DEV ? (
             <Route
               path={DEVELOPMENT_REPLAY_ROUTE_PATH}
diff --git a/apps/app/src/components/app-viewer/AppViewer.tsx b/apps/app/src/components/app-viewer/AppViewer.tsx
new file mode 100644
index 000000000..01d149a61
--- /dev/null
+++ b/apps/app/src/components/app-viewer/AppViewer.tsx
@@ -0,0 +1,167 @@
+import { useMemo } from "react";
+import { useApp, useAppMarkdownPreview } from "@/hooks/queries/thread-queries";
+import {
+  buildAppEntryUrl,
+  buildAppPublicBaseUrl,
+} from "@/lib/file-content-urls";
+import { createAssetMarkdownUrlTransform } from "@/lib/markdown-url-transform";
+import { FilePreview as FilePreviewSurface } from "@/components/secondary-panel/FilePreview";
+
+const APP_HEADER_MODE = "none";
+
+export interface AppViewerProps {
+  applicationId: string;
+  /**
+   * Thread the app posts into via its `message` capability. `null` on the
+   * standalone surface, where the app renders without a host thread.
+   */
+  targetThreadId: string | null;
+}
+
+/**
+ * Canonical renderer for a global app's entry. Resolves the app manifest, then
+ * serves the HTML entry through the injected `/api/v1/apps/:id/` iframe (the
+ * same route the in-thread tab uses) or renders a markdown entry statically.
+ * Shared by the in-thread `AppTabContent` panel and the standalone app route so
+ * there is a single app-rendering path.
+ */
+export function AppViewer({ applicationId, targetThreadId }: AppViewerProps) {
+  const appDetail = useApp(applicationId);
+  const markdownEntryPath =
+    appDetail.data?.entry.kind === "md" ? appDetail.data.entry.path : null;
+  const markdownPreview = useAppMarkdownPreview(
+    applicationId,
+    markdownEntryPath,
+    {
+      enabled: markdownEntryPath !== null,
+    },
+  );
+  const markdownAssetBaseUrl = useMemo(() => {
+    if (markdownEntryPath === null) {
+      return null;
+    }
+    return buildAppPublicBaseUrl(applicationId, markdownEntryPath);
+  }, [applicationId, markdownEntryPath]);
+  const markdownUrlTransform = useMemo(() => {
+    if (markdownAssetBaseUrl === null) {
+      return undefined;
+    }
+    return createAssetMarkdownUrlTransform(markdownAssetBaseUrl);
+  }, [markdownAssetBaseUrl]);
+  const htmlEntryUrl = useMemo(
+    () =>
+      buildAppEntryUrl({
+        applicationId,
+        targetThreadId,
+        reloadToken: appDetail.dataUpdatedAt,
+      }),
+    [appDetail.dataUpdatedAt, applicationId, targetThreadId],
+  );
+
+  if (appDetail.isError) {
+    return (
+      <FilePreviewSurface
+        path={applicationId}
+        headerMode={APP_HEADER_MODE}
+        state={{
+          kind: "error",
+          message:
+            appDetail.error instanceof Error
+              ? appDetail.error.message
+              : "Failed to load app.",
+        }}
+      />
+    );
+  }
+
+  if (!appDetail.data) {
+    return (
+      <FilePreviewSurface
+        path={applicationId}
+        headerMode={APP_HEADER_MODE}
+        state={{ kind: "loading" }}
+      />
+    );
+  }
+
+  if (appDetail.data.entry.kind === "html") {
+    return (
+      <FilePreviewSurface
+        path={appDetail.data.name}
+        headerMode={APP_HEADER_MODE}
+        state={{
+          kind: "iframe",
+          sandbox: null,
+          title: appDetail.data.name,
+          url: htmlEntryUrl,
+        }}
+      />
+    );
+  }
+
+  if (markdownPreview.isError) {
+    return (
+      <FilePreviewSurface
+        path={appDetail.data.name}
+        headerMode={APP_HEADER_MODE}
+        state={{
+          kind: "error",
+          message:
+            markdownPreview.error instanceof Error
+              ? markdownPreview.error.message
+              : "Failed to load app entry.",
+        }}
+      />
+    );
+  }
+
+  if (!markdownPreview.data) {
+    return (
+      <FilePreviewSurface
+        path={appDetail.data.name}
+        headerMode={APP_HEADER_MODE}
+        state={{ kind: "loading" }}
+      />
+    );
+  }
+
+  if (markdownPreview.data.kind !== "text") {
+    return (
+      <FilePreviewSurface
+        path={appDetail.data.name}
+        headerMode={APP_HEADER_MODE}
+        state={{
+          kind: "error",
+          message: `Preview not available for ${markdownPreview.data.mimeType}.`,
+        }}
+      />
+    );
+  }
+
+  if (markdownPreview.data.content.length === 0) {
+    return (
+      <FilePreviewSurface
+        path={appDetail.data.name}
+        headerMode={APP_HEADER_MODE}
+        state={{ kind: "empty" }}
+      />
+    );
+  }
+
+  return (
+    <FilePreviewSurface
+      path={appDetail.data.name}
+      headerMode={APP_HEADER_MODE}
+      state={{
+        kind: "ready",
+        lineNumber: null,
+        showMarkdownModeToggle: false,
+        markdownUrlTransform,
+        file: {
+          name: markdownPreview.data.name ?? appDetail.data.entry.path,
+          contents: markdownPreview.data.content,
+        },
+      }}
+    />
+  );
+}
diff --git a/apps/app/src/components/layout/AppLayout.test.tsx b/apps/app/src/components/layout/AppLayout.test.tsx
index 093741282..0d9853275 100644
--- a/apps/app/src/components/layout/AppLayout.test.tsx
+++ b/apps/app/src/components/layout/AppLayout.test.tsx
@@ -351,12 +351,12 @@ describe("AppLayout desktop chrome", () => {
       await renderAppLayout({
         desktopInfo: null,
         initialEntry: "/projects/proj_sidebar_resize",
-        children: <iframe title="Status app" />,
+        children: <iframe title="Review Board app" />,
       });
 
       const appLayoutRoot = await screen.findByTestId("app-layout-root");
       const resizeHandle = screen.getByTestId("app-sidebar-resize-handle");
-      const iframe = screen.getByTitle("Status app");
+      const iframe = screen.getByTitle("Review Board app");
 
       expect(appLayoutRoot.contains(iframe)).toBe(true);
       expect(screen.queryByTestId("iframe-drag-guard-overlay")).toBeNull();
diff --git a/apps/app/src/components/layout/AppLayout.tsx b/apps/app/src/components/layout/AppLayout.tsx
index f6c0004ec..dd1b55716 100644
--- a/apps/app/src/components/layout/AppLayout.tsx
+++ b/apps/app/src/components/layout/AppLayout.tsx
@@ -24,6 +24,7 @@ import {
   stripProjectThreads,
 } from "@/hooks/queries/project-queries";
 import {
+  useApp,
   useThread,
   useThreadDetailBootstrap,
 } from "@/hooks/queries/thread-queries";
@@ -53,6 +54,7 @@ import { useQuickCreateProjectController } from "@/hooks/useQuickCreateProject";
 import { useStandardManagerTimelinePreference } from "@/lib/manager-timeline-view-preference";
 import { useSetRootComposeProjectId } from "@/lib/root-compose-selection";
 import { IframeDragGuardOverlay } from "@/lib/iframe-drag-guard";
+import { dispatchBrowserViewBoundsSync } from "@/lib/browser-view-bounds-sync";
 
 const SIDEBAR_WIDTH_KEY = "bb.sidebar.width";
 const SIDEBAR_OPEN_KEY = "bb.sidebar.open";
@@ -112,6 +114,7 @@ interface SidebarStateBridgeProps {
 }
 
 type SidebarResizeMouseEvent = ReactMouseEvent<HTMLDivElement>;
+type SidebarOpenChangeHandler = (open: boolean) => void;
 
 type SidebarProviderStyle = CSSProperties & {
   "--sidebar-width": string;
@@ -124,6 +127,13 @@ function SidebarStateBridge({
   children,
 }: SidebarStateBridgeProps) {
   const [open, setOpen] = useAtom(sidebarOpenAtom);
+  const handleOpenChange = useCallback<SidebarOpenChangeHandler>(
+    (nextOpen) => {
+      setOpen(nextOpen);
+      window.requestAnimationFrame(dispatchBrowserViewBoundsSync);
+    },
+    [setOpen],
+  );
   return (
     <SidebarProvider
       ref={providerRef}
@@ -131,7 +141,7 @@ function SidebarStateBridge({
       className={className}
       data-testid="app-layout-root"
       open={open}
-      onOpenChange={setOpen}
+      onOpenChange={handleOpenChange}
     >
       {children}
     </SidebarProvider>
@@ -340,6 +350,8 @@ export function AppLayout({ children }: AppLayoutProps) {
   const {
     projectId,
     threadId,
+    applicationId,
+    isAppView,
     isThreadView,
     isArchivedView,
     isSettingsView,
@@ -400,6 +412,11 @@ export function AppLayout({ children }: AppLayoutProps) {
     : threadId
       ? `Thread ${threadId.slice(0, 8)}`
       : "Thread";
+  // The standalone app route has no thread/project chrome, so the global header
+  // carries the app name (resolved from the manifest) the way it carries thread
+  // and project titles elsewhere.
+  const { data: app } = useApp(applicationId, { enabled: isAppView });
+  const appDisplayTitle = app?.name ?? "App";
   useEffect(() => {
     if (!thread?.projectId) return;
     setRootComposeProjectId(thread.projectId);
@@ -409,7 +426,12 @@ export function AppLayout({ children }: AppLayoutProps) {
         title: thread ? getThreadDisplayTitle(thread) : "Thread",
         subtitle: undefined,
       }
-    : isArchivedView && projectId
+    : isAppView
+      ? {
+          title: appDisplayTitle,
+          subtitle: undefined,
+        }
+      : isArchivedView && projectId
       ? {
           title: "",
           subtitle: undefined,
@@ -444,6 +466,9 @@ export function AppLayout({ children }: AppLayoutProps) {
     if (isThreadView) {
       return threadDisplayTitle;
     }
+    if (isAppView) {
+      return appDisplayTitle;
+    }
     if (isArchivedView && projectId) {
       return `${projectLabel ?? projectId} · Archived`;
     }
@@ -479,6 +504,7 @@ export function AppLayout({ children }: AppLayoutProps) {
       "--sidebar-width",
       `${liveWidthRef.current}px`,
     );
+    dispatchBrowserViewBoundsSync();
     setSidebarWidth(liveWidthRef.current);
     setIsSidebarResizing(false);
     resetSidebarResizeDocumentState();
@@ -493,6 +519,7 @@ export function AppLayout({ children }: AppLayoutProps) {
         "--sidebar-width",
         `${liveWidthRef.current}px`,
       );
+      dispatchBrowserViewBoundsSync();
     };
 
     const handleMouseMove = (event: MouseEvent) => {
diff --git a/apps/app/src/components/secondary-panel/AppTabContent.test.tsx b/apps/app/src/components/secondary-panel/AppTabContent.test.tsx
index 21c48d36a..0c9ee5686 100644
--- a/apps/app/src/components/secondary-panel/AppTabContent.test.tsx
+++ b/apps/app/src/components/secondary-panel/AppTabContent.test.tsx
@@ -1,13 +1,10 @@
 // @vitest-environment jsdom
 
 import { act, cleanup, render, screen, waitFor } from "@testing-library/react";
-import type { AppDetail, AppSummary } from "@bb/server-contract";
+import type { AppDetail } from "@bb/server-contract";
 import * as api from "@/lib/api";
 import { afterEach, describe, expect, it, vi } from "vitest";
-import {
-  threadAppQueryKey,
-  threadAppsQueryKey,
-} from "@/hooks/queries/query-keys";
+import { appQueryKey } from "@/hooks/queries/query-keys";
 import { createQueryClientTestHarness } from "@/test/queryClientTestHarness";
 import { AppTabContent } from "./AppTabContent";
 
@@ -16,25 +13,31 @@ vi.mock("@/lib/api", async (importOriginal) => {
 
   return {
     ...actual,
-    getThreadApp: vi.fn(),
-    getThreadAppMarkdownPreview: vi.fn(),
+    getApp: vi.fn(),
+    getAppMarkdownPreview: vi.fn(),
   };
 });
 
 const HTML_APP: AppDetail = {
-  id: "status",
-  name: "Status",
+  applicationId: "status",
+  name: "Review Board",
   entry: { path: "index.html", kind: "html" },
   capabilities: ["data", "message"],
   icon: { kind: "builtin", name: "ListTodo" },
+  appsRootPath: "/tmp/bb-data/apps",
+  appRootPath: "/tmp/bb-data/apps/status",
+  appDataPath: "/tmp/bb-data/apps/status/data",
 };
 
 const MARKDOWN_APP: AppDetail = {
-  id: "readme",
+  applicationId: "readme",
   name: "Readme",
   entry: { path: "docs/index.md", kind: "md" },
   capabilities: [],
   icon: { kind: "builtin", name: "GridView" },
+  appsRootPath: "/tmp/bb-data/apps",
+  appRootPath: "/tmp/bb-data/apps/readme",
+  appDataPath: "/tmp/bb-data/apps/readme/data",
 };
 
 afterEach(() => {
@@ -44,58 +47,42 @@ afterEach(() => {
 });
 
 describe("AppTabContent", () => {
-  it("renders app-list metadata while the detail refetch is still pending", () => {
-    vi.mocked(api.getThreadApp).mockReturnValue(new Promise(() => {}));
-    const { queryClient, wrapper } = createQueryClientTestHarness();
-    queryClient.setQueryData<AppSummary[]>(threadAppsQueryKey("thr_1"), [
-      HTML_APP,
-    ]);
-
-    render(<AppTabContent threadId="thr_1" appId="status" />, { wrapper });
-
-    const frame = screen.getByTitle("Status");
-    expect(frame.getAttribute("src")).toMatch(
-      /^\/api\/v1\/threads\/thr_1\/apps\/status\/\?v=\d+$/u,
-    );
-    expect(api.getThreadApp).toHaveBeenCalledWith(
-      "thr_1",
-      "status",
-      expect.any(AbortSignal),
-    );
-  });
-
   it("renders HTML apps in the injected app iframe route", async () => {
-    vi.mocked(api.getThreadApp).mockResolvedValue(HTML_APP);
+    vi.mocked(api.getApp).mockResolvedValue(HTML_APP);
     const { wrapper } = createQueryClientTestHarness();
 
-    render(<AppTabContent threadId="thr_1" appId="status" />, { wrapper });
+    render(<AppTabContent threadId="thr_1" applicationId="status" />, {
+      wrapper,
+    });
 
-    const frame = await screen.findByTitle("Status");
+    const frame = await screen.findByTitle("Review Board");
     expect(frame.getAttribute("src")).toMatch(
-      /^\/api\/v1\/threads\/thr_1\/apps\/status\/\?v=\d+$/u,
+      /^\/api\/v1\/apps\/status\/\?targetThreadId=thr_1&v=\d+$/u,
     );
     expect(frame.getAttribute("sandbox")).toBeNull();
-    expect(api.getThreadAppMarkdownPreview).not.toHaveBeenCalled();
+    expect(api.getAppMarkdownPreview).not.toHaveBeenCalled();
   });
 
   it("reloads HTML app iframes when app detail data refreshes", async () => {
-    vi.mocked(api.getThreadApp).mockReturnValue(new Promise(() => {}));
+    vi.mocked(api.getApp).mockReturnValue(new Promise(() => {}));
     const { queryClient, wrapper } = createQueryClientTestHarness();
-    const appQueryKey = threadAppQueryKey("thr_1", "status");
-    queryClient.setQueryData<AppDetail>(appQueryKey, HTML_APP, {
+    const queryKey = appQueryKey("status");
+    queryClient.setQueryData<AppDetail>(queryKey, HTML_APP, {
       updatedAt: 1_000,
     });
 
-    render(<AppTabContent threadId="thr_1" appId="status" />, { wrapper });
+    render(<AppTabContent threadId="thr_1" applicationId="status" />, {
+      wrapper,
+    });
 
-    const firstFrame = screen.getByTitle("Status");
+    const firstFrame = screen.getByTitle("Review Board");
     const firstSrc = firstFrame.getAttribute("src");
     act(() => {
       queryClient.setQueryData<AppDetail>(
-        appQueryKey,
+        queryKey,
         {
           ...HTML_APP,
-          name: "Status",
+          name: "Review Board",
         },
         {
           updatedAt: 2_000,
@@ -104,30 +91,31 @@ describe("AppTabContent", () => {
     });
 
     await waitFor(() => {
-      expect(screen.getByTitle("Status").getAttribute("src")).not.toBe(
+      expect(screen.getByTitle("Review Board").getAttribute("src")).not.toBe(
         firstSrc,
       );
     });
   });
 
   it("renders markdown apps through the static markdown preview path", async () => {
-    vi.mocked(api.getThreadApp).mockResolvedValue(MARKDOWN_APP);
-    vi.mocked(api.getThreadAppMarkdownPreview).mockResolvedValue({
+    vi.mocked(api.getApp).mockResolvedValue(MARKDOWN_APP);
+    vi.mocked(api.getAppMarkdownPreview).mockResolvedValue({
       kind: "text",
       path: "docs/index.md",
       name: "index.md",
-      url: "/api/v1/threads/thr_1/apps/readme/docs/index.md",
+      url: "/api/v1/apps/readme/docs/index.md",
       mimeType: "text/markdown",
       content: "# App Notes\n\nStatic content.",
     });
     const { wrapper } = createQueryClientTestHarness();
 
-    render(<AppTabContent threadId="thr_1" appId="readme" />, { wrapper });
+    render(<AppTabContent threadId="thr_1" applicationId="readme" />, {
+      wrapper,
+    });
 
     expect(await screen.findByText("App Notes")).toBeTruthy();
     expect(screen.getByText("Static content.")).toBeTruthy();
-    expect(api.getThreadAppMarkdownPreview).toHaveBeenCalledWith(
-      "thr_1",
+    expect(api.getAppMarkdownPreview).toHaveBeenCalledWith(
       "readme",
       "docs/index.md",
       expect.any(AbortSignal),
diff --git a/apps/app/src/components/secondary-panel/AppTabContent.tsx b/apps/app/src/components/secondary-panel/AppTabContent.tsx
index 4fe39a9b1..a5ed9c7ef 100644
--- a/apps/app/src/components/secondary-panel/AppTabContent.tsx
+++ b/apps/app/src/components/secondary-panel/AppTabContent.tsx
@@ -1,176 +1,15 @@
-import { useMemo } from "react";
-import {
-  useThreadApp,
-  useThreadAppMarkdownPreview,
-} from "@/hooks/queries/thread-queries";
-import {
-  buildThreadAppAssetBaseUrl,
-  buildThreadAppEntryUrl,
-} from "@/lib/file-content-urls";
-import { createAssetMarkdownUrlTransform } from "@/lib/markdown-url-transform";
-import { FilePreview as FilePreviewSurface } from "./FilePreview";
-
-const APP_HEADER_MODE = "none";
-
-interface BuildReloadableAppEntryUrlArgs {
-  appId: string;
-  reloadToken: number;
-  threadId: string;
-}
+import { AppViewer } from "@/components/app-viewer/AppViewer";
 
 export interface AppTabContentProps {
-  appId: string;
+  applicationId: string;
   threadId: string;
 }
 
-function buildReloadableAppEntryUrl({
-  appId,
-  reloadToken,
-  threadId,
-}: BuildReloadableAppEntryUrlArgs): string {
-  return `${buildThreadAppEntryUrl(threadId, appId)}?v=${encodeURIComponent(
-    String(reloadToken),
-  )}`;
-}
-
-export function AppTabContent({ appId, threadId }: AppTabContentProps) {
-  const appDetail = useThreadApp(threadId, appId);
-  const markdownEntryPath =
-    appDetail.data?.entry.kind === "md" ? appDetail.data.entry.path : null;
-  const markdownPreview = useThreadAppMarkdownPreview(
-    threadId,
-    appId,
-    markdownEntryPath,
-    {
-      enabled: markdownEntryPath !== null,
-    },
-  );
-  const markdownAssetBaseUrl = useMemo(() => {
-    if (markdownEntryPath === null) {
-      return null;
-    }
-    return buildThreadAppAssetBaseUrl(threadId, appId, markdownEntryPath);
-  }, [appId, markdownEntryPath, threadId]);
-  const markdownUrlTransform = useMemo(() => {
-    if (markdownAssetBaseUrl === null) {
-      return undefined;
-    }
-    return createAssetMarkdownUrlTransform(markdownAssetBaseUrl);
-  }, [markdownAssetBaseUrl]);
-  const htmlEntryUrl = useMemo(
-    () =>
-      buildReloadableAppEntryUrl({
-        appId,
-        reloadToken: appDetail.dataUpdatedAt,
-        threadId,
-      }),
-    [appDetail.dataUpdatedAt, appId, threadId],
-  );
-
-  if (appDetail.isError) {
-    return (
-      <FilePreviewSurface
-        path={appId}
-        headerMode={APP_HEADER_MODE}
-        state={{
-          kind: "error",
-          message:
-            appDetail.error instanceof Error
-              ? appDetail.error.message
-              : "Failed to load app.",
-        }}
-      />
-    );
-  }
-
-  if (!appDetail.data) {
-    return (
-      <FilePreviewSurface
-        path={appId}
-        headerMode={APP_HEADER_MODE}
-        state={{ kind: "loading" }}
-      />
-    );
-  }
-
-  if (appDetail.data.entry.kind === "html") {
-    return (
-      <FilePreviewSurface
-        path={appDetail.data.name}
-        headerMode={APP_HEADER_MODE}
-        state={{
-          kind: "iframe",
-          sandbox: null,
-          title: appDetail.data.name,
-          url: htmlEntryUrl,
-        }}
-      />
-    );
-  }
-
-  if (markdownPreview.isError) {
-    return (
-      <FilePreviewSurface
-        path={appDetail.data.name}
-        headerMode={APP_HEADER_MODE}
-        state={{
-          kind: "error",
-          message:
-            markdownPreview.error instanceof Error
-              ? markdownPreview.error.message
-              : "Failed to load app entry.",
-        }}
-      />
-    );
-  }
-
-  if (!markdownPreview.data) {
-    return (
-      <FilePreviewSurface
-        path={appDetail.data.name}
-        headerMode={APP_HEADER_MODE}
-        state={{ kind: "loading" }}
-      />
-    );
-  }
-
-  if (markdownPreview.data.kind !== "text") {
-    return (
-      <FilePreviewSurface
-        path={appDetail.data.name}
-        headerMode={APP_HEADER_MODE}
-        state={{
-          kind: "error",
-          message: `Preview not available for ${markdownPreview.data.mimeType}.`,
-        }}
-      />
-    );
-  }
-
-  if (markdownPreview.data.content.length === 0) {
-    return (
-      <FilePreviewSurface
-        path={appDetail.data.name}
-        headerMode={APP_HEADER_MODE}
-        state={{ kind: "empty" }}
-      />
-    );
-  }
-
-  return (
-    <FilePreviewSurface
-      path={appDetail.data.name}
-      headerMode={APP_HEADER_MODE}
-      state={{
-        kind: "ready",
-        lineNumber: null,
-        showMarkdownModeToggle: false,
-        markdownUrlTransform,
-        file: {
-          name: markdownPreview.data.name ?? appDetail.data.entry.path,
-          contents: markdownPreview.data.content,
-        },
-      }}
-    />
-  );
+/**
+ * In-thread secondary-panel host for a global app. Delegates to the shared
+ * {@link AppViewer}, targeting the panel's thread so the app's `message`
+ * capability posts into that thread.
+ */
+export function AppTabContent({ applicationId, threadId }: AppTabContentProps) {
+  return <AppViewer applicationId={applicationId} targetThreadId={threadId} />;
 }
diff --git a/apps/app/src/components/secondary-panel/BrowserTabContent.tsx b/apps/app/src/components/secondary-panel/BrowserTabContent.tsx
index fe0a6858c..79e7ffca8 100644
--- a/apps/app/src/components/secondary-panel/BrowserTabContent.tsx
+++ b/apps/app/src/components/secondary-panel/BrowserTabContent.tsx
@@ -10,8 +10,10 @@ import {
 import type {
   BbDesktopBrowserApi,
   BbDesktopBrowserState,
+  BbDesktopBrowserViewportBounds,
   BbDesktopBrowserViewBounds,
 } from "@bb/server-contract";
+import { clampBbDesktopBrowserViewBounds } from "@bb/server-contract";
 import { Icon } from "@/components/ui/icon.js";
 import { getDesktopBrowserApi } from "@/lib/bb-desktop";
 import {
@@ -19,8 +21,12 @@ import {
   resolveBrowserAddressInput,
 } from "@/lib/browser-url";
 import { useBrowserHistory } from "@/lib/browser-history";
+import { BROWSER_VIEW_BOUNDS_SYNC_EVENT } from "@/lib/browser-view-bounds-sync";
 import { BrowserNewTabScreen } from "./BrowserNewTabScreen";
-import type { BrowserViewVisibilityCoordinator } from "./browserViewVisibilityCoordinator";
+import {
+  registerBrowserView,
+  type BrowserViewVisibilityCoordinator,
+} from "./browserViewVisibilityCoordinator";
 import type { UpdateBrowserTabArgs } from "./useThreadFileTabs";
 
 export interface BrowserTabContentProps {
@@ -38,6 +44,7 @@ export interface BrowserTabContentProps {
    * visible at once). Null on the web build, where there is no native view.
    */
   visibilityCoordinator: BrowserViewVisibilityCoordinator | null;
+  environmentId: string | null;
   threadId: string;
   onUpdate: (args: UpdateBrowserTabArgs) => void;
 }
@@ -63,6 +70,17 @@ interface NavButtonProps {
   onClick: () => void;
 }
 
+interface BrowserViewBoundsFromElementArgs {
+  element: HTMLElement;
+}
+
+const EMPTY_BROWSER_VIEW_BOUNDS: BbDesktopBrowserViewBounds = {
+  x: 0,
+  y: 0,
+  width: 0,
+  height: 0,
+};
+
 function roundedBoundsFromRect(rect: DOMRect): BbDesktopBrowserViewBounds {
   return {
     x: Math.round(rect.left),
@@ -72,6 +90,22 @@ function roundedBoundsFromRect(rect: DOMRect): BbDesktopBrowserViewBounds {
   };
 }
 
+function browserViewportBounds(): BbDesktopBrowserViewportBounds {
+  return {
+    width: window.innerWidth,
+    height: window.innerHeight,
+  };
+}
+
+function browserViewBoundsFromElement(
+  args: BrowserViewBoundsFromElementArgs,
+): BbDesktopBrowserViewBounds {
+  return clampBbDesktopBrowserViewBounds({
+    bounds: roundedBoundsFromRect(args.element.getBoundingClientRect()),
+    viewport: browserViewportBounds(),
+  });
+}
+
 function NavButton({ icon, label, disabled, onClick }: NavButtonProps) {
   return (
     <button
@@ -189,6 +223,7 @@ export function BrowserTabContent({
   initialUrl,
   isActive,
   visibilityCoordinator,
+  environmentId,
   threadId,
   onUpdate,
 }: BrowserTabContentProps) {
@@ -221,24 +256,45 @@ export function BrowserTabContent({
   isActiveRef.current = isActive;
 
   const hasPage = currentUrl.length > 0;
-
   // Pending rAF handle for the coalesced bounds sync, so a burst of resize ticks
   // collapses to a single native setBounds per frame.
   const boundsSyncFrameRef = useRef<number | null>(null);
 
+  const readBounds = useCallback(() => {
+    const element = contentRef.current;
+    if (element === null) {
+      return null;
+    }
+    return browserViewBoundsFromElement({ element });
+  }, []);
+
+  const sendBounds = useCallback(
+    (bounds: BbDesktopBrowserViewBounds) => {
+      if (desktopBrowser === null) {
+        return;
+      }
+      desktopBrowser.setBounds({
+        tabId,
+        bounds,
+      });
+    },
+    [desktopBrowser, tabId],
+  );
+
   // Push the current content-rect to the native overlay immediately. The
   // coordinator's show() calls this synchronously so bounds always land before
   // the view is made visible (never a stale/zero-bounds flash on activation).
   const syncBounds = useCallback(() => {
-    const element = contentRef.current;
-    if (element === null || desktopBrowser === null) {
+    const bounds = readBounds();
+    if (bounds === null) {
       return;
     }
-    desktopBrowser.setBounds({
-      tabId,
-      bounds: roundedBoundsFromRect(element.getBoundingClientRect()),
-    });
-  }, [desktopBrowser, tabId]);
+    sendBounds(bounds);
+  }, [readBounds, sendBounds]);
+
+  const syncInitialBounds = useCallback(() => {
+    return readBounds() ?? EMPTY_BROWSER_VIEW_BOUNDS;
+  }, [readBounds]);
 
   // rAF-coalesced bounds sync for live resize tracking. A drag-resize fires the
   // ResizeObserver (and `window` resize) repeatedly; batching to one setBounds
@@ -254,21 +310,17 @@ export function BrowserTabContent({
     });
   }, [syncBounds]);
 
-  // Create the native view on mount, stream navigation state back, and tear it
-  // down on unmount. Because the deck keeps every open browser tab mounted, this
-  // unmounts only when the tab is CLOSED (or the panel/thread unmounts) — never
-  // on mere deactivation — so the view (and its page + scroll) survives tab
-  // switches. Destroying on unmount keeps the lifecycle leak-free.
+  // Create (or re-attach to) the native view on mount and stream navigation
+  // state back. Unmount is not ownership teardown: switching threads unmounts
+  // the deck, but the native view is intentionally retained so returning to the
+  // thread can show the existing page without recreating/reloading it.
   useEffect(() => {
     if (desktopBrowser === null) {
       return;
     }
-    const element = contentRef.current;
-    const initialBounds =
-      element !== null
-        ? roundedBoundsFromRect(element.getBoundingClientRect())
-        : { x: 0, y: 0, width: 0, height: 0 };
+    const initialBounds = syncInitialBounds();
     const mountUrl = initialUrlRef.current;
+    registerBrowserView({ environmentId, tabId, threadId });
     desktopBrowser.attach({
       tabId,
       url: mountUrl,
@@ -299,12 +351,19 @@ export function BrowserTabContent({
 
     return () => {
       unsubscribe();
-      // Forget this tab before destroying its view so a subsequent show on
-      // another tab does not try to hide a view that no longer exists.
+      // The native view survives this unmount. Only explicit tab close/thread
+      // deletion owns detach; unmount just disconnects this component's state
+      // listener and forgets any stale visibility ownership.
       visibilityCoordinator?.release(tabId);
-      desktopBrowser.detach(tabId);
     };
-  }, [desktopBrowser, visibilityCoordinator, tabId]);
+  }, [
+    desktopBrowser,
+    environmentId,
+    syncInitialBounds,
+    visibilityCoordinator,
+    tabId,
+    threadId,
+  ]);
 
   // Track the panel content rect so the native overlay stays aligned — including
   // throughout a drag-resize, where the rect changes every frame. Coalesced via
@@ -329,13 +388,29 @@ export function BrowserTabContent({
     };
   }, [desktopBrowser, scheduleBoundsSync]);
 
+  // ResizeObserver only reports size changes; dragging the left sidebar can
+  // move this content rect without changing its width. AppLayout emits this
+  // event from the same rAF that applies the live sidebar width, so the native
+  // view is re-pinned to the content edge even on position-only layout shifts.
+  useEffect(() => {
+    if (desktopBrowser === null) {
+      return;
+    }
+
+    window.addEventListener(BROWSER_VIEW_BOUNDS_SYNC_EVENT, syncBounds);
+
+    return () => {
+      window.removeEventListener(BROWSER_VIEW_BOUNDS_SYNC_EVENT, syncBounds);
+    };
+  }, [desktopBrowser, syncBounds]);
+
   // The native view is shown whenever this tab is the active panel tab and has a
   // page. It is NOT hidden during a drag-resize — the overlay tracks the live
-  // bounds (see the ResizeObserver effect) so it follows the panel smoothly
-  // instead of blanking and flashing. It stays attached when hidden, so
-  // deactivation never reloads it. (Collapse/expand of the panel toggles
-  // `isActive`, which hides the view outright rather than chasing a CSS
-  // transition the overlay cannot clip to.)
+  // bounds (see the ResizeObserver and layout-sync effects) so it follows
+  // the panel smoothly instead of blanking and flashing. It stays attached when
+  // hidden, so deactivation never reloads it. (Collapse/expand of the panel
+  // toggles `isActive`, which hides the view outright rather than chasing a
+  // CSS transition the overlay cannot clip to.)
   const isViewVisible = isActive && hasPage;
   // A layout effect (pre-paint) declares visibility so showing/hiding lands in
   // the same frame as the DOM tab swap — no flash. Ordering across tabs (hide
@@ -348,7 +423,9 @@ export function BrowserTabContent({
     }
     if (isViewVisible) {
       visibilityCoordinator.show(tabId, syncBounds);
-      return;
+      return () => {
+        visibilityCoordinator.hide(tabId);
+      };
     }
     visibilityCoordinator.hide(tabId);
   }, [visibilityCoordinator, tabId, isViewVisible, syncBounds]);
diff --git a/apps/app/src/components/secondary-panel/BrowserTabDeck.test.tsx b/apps/app/src/components/secondary-panel/BrowserTabDeck.test.tsx
index 3dbc07583..6048b647c 100644
--- a/apps/app/src/components/secondary-panel/BrowserTabDeck.test.tsx
+++ b/apps/app/src/components/secondary-panel/BrowserTabDeck.test.tsx
@@ -6,15 +6,19 @@ import { afterEach, describe, expect, it, vi } from "vitest";
 import type {
   BbDesktopApi,
   BbDesktopBrowserApi,
+  BbDesktopBrowserViewBounds,
   BbDesktopInfo,
   BbDesktopInfoChangeHandler,
 } from "@bb/server-contract";
 import type { BrowserFixedPanelTab } from "@/lib/fixed-panel-tabs-state";
+import { BROWSER_VIEW_BOUNDS_SYNC_EVENT } from "@/lib/browser-view-bounds-sync";
 import { BrowserTabDeck } from "./BrowserTabDeck";
+import { resetBrowserViewPersistence } from "./browserViewVisibilityCoordinator";
 import { threadSecondaryPanelResizingAtom } from "./threadSecondaryPanelAtoms";
 
 interface RecordedBrowserCall {
   method: "attach" | "detach" | "setVisible" | "setBounds" | "navigate";
+  bounds: BbDesktopBrowserViewBounds | null;
   tabId: string;
   visible: boolean | null;
 }
@@ -40,26 +44,38 @@ function createRecordingBrowserApi(): RecordingBrowserApi {
     attach(request) {
       calls.push({
         method: "attach",
+        bounds: request.bounds,
         tabId: request.tabId,
         visible: request.visible,
       });
     },
     detach(tabId) {
-      calls.push({ method: "detach", tabId, visible: null });
+      calls.push({ method: "detach", bounds: null, tabId, visible: null });
     },
     navigate(request) {
-      calls.push({ method: "navigate", tabId: request.tabId, visible: null });
+      calls.push({
+        method: "navigate",
+        bounds: null,
+        tabId: request.tabId,
+        visible: null,
+      });
     },
     goBack() {},
     goForward() {},
     reload() {},
     stop() {},
     setBounds(request) {
-      calls.push({ method: "setBounds", tabId: request.tabId, visible: null });
+      calls.push({
+        method: "setBounds",
+        bounds: request.bounds,
+        tabId: request.tabId,
+        visible: null,
+      });
     },
     setVisible(request) {
       calls.push({
         method: "setVisible",
+        bounds: null,
         tabId: request.tabId,
         visible: request.visible,
       });
@@ -101,6 +117,56 @@ function browserTab(id: string, url: string): BrowserFixedPanelTab {
 
 const TAB_A = browserTab("browser:a", "https://a.example/");
 const TAB_B = browserTab("browser:b", "https://b.example/");
+const TAB_C = browserTab("browser:c", "https://c.example/");
+
+type RestoreHandler = () => void;
+
+interface BrowserContentRect {
+  height: number;
+  left: number;
+  top: number;
+  width: number;
+}
+
+interface BrowserViewportSize {
+  height: number;
+  width: number;
+}
+
+interface QueuedAnimationFrame {
+  callback: FrameRequestCallback;
+  canceled: boolean;
+  id: number;
+}
+
+interface QueuedAnimationFrameController {
+  flushNext(): void;
+  restore(): void;
+}
+
+interface ThreadDeckHostProps {
+  activeBrowserTabId: string | null;
+  browserTabs: readonly BrowserFixedPanelTab[];
+  threadId: string;
+}
+
+function ThreadDeckHost({
+  activeBrowserTabId,
+  browserTabs,
+  threadId,
+}: ThreadDeckHostProps) {
+  return (
+    <BrowserTabDeck
+      key={threadId}
+      browserTabs={browserTabs}
+      activeBrowserTabId={activeBrowserTabId}
+      environmentId="env_test"
+      isPanelOpen
+      threadId={threadId}
+      onUpdate={() => {}}
+    />
+  );
+}
 
 function visibilityFor(
   calls: readonly RecordedBrowserCall[],
@@ -140,9 +206,106 @@ function maxConcurrentVisible(calls: readonly RecordedBrowserCall[]): number {
   return max;
 }
 
+function installBrowserContentRect(
+  rect: BrowserContentRect,
+): RestoreHandler {
+  const rectMock = vi
+    .spyOn(HTMLElement.prototype, "getBoundingClientRect")
+    .mockImplementation(
+      () => new DOMRect(rect.left, rect.top, rect.width, rect.height),
+    );
+  return () => rectMock.mockRestore();
+}
+
+function installViewportSize(size: BrowserViewportSize): RestoreHandler {
+  const previousWidth = window.innerWidth;
+  const previousHeight = window.innerHeight;
+  Object.defineProperty(window, "innerWidth", {
+    configurable: true,
+    value: size.width,
+  });
+  Object.defineProperty(window, "innerHeight", {
+    configurable: true,
+    value: size.height,
+  });
+  return () => {
+    Object.defineProperty(window, "innerWidth", {
+      configurable: true,
+      value: previousWidth,
+    });
+    Object.defineProperty(window, "innerHeight", {
+      configurable: true,
+      value: previousHeight,
+    });
+  };
+}
+
+function installQueuedAnimationFrame(): QueuedAnimationFrameController {
+  const frames: QueuedAnimationFrame[] = [];
+  let nextId = 1;
+  const requestFrame = vi
+    .spyOn(window, "requestAnimationFrame")
+    .mockImplementation((callback) => {
+      const frame: QueuedAnimationFrame = {
+        callback,
+        canceled: false,
+        id: nextId,
+      };
+      nextId += 1;
+      frames.push(frame);
+      return frame.id;
+    });
+  const cancelFrame = vi
+    .spyOn(window, "cancelAnimationFrame")
+    .mockImplementation((id) => {
+      const frame = frames.find((candidate) => candidate.id === id);
+      if (frame !== undefined) {
+        frame.canceled = true;
+      }
+    });
+
+  return {
+    flushNext() {
+      const frame = frames.shift();
+      if (frame === undefined || frame.canceled) {
+        return;
+      }
+      frame.callback(0);
+    },
+    restore() {
+      requestFrame.mockRestore();
+      cancelFrame.mockRestore();
+    },
+  };
+}
+
+function lastSetBoundsFor(
+  calls: readonly RecordedBrowserCall[],
+  tabId: string,
+): BbDesktopBrowserViewBounds | null {
+  for (let index = calls.length - 1; index >= 0; index -= 1) {
+    const call = calls[index];
+    if (call?.method === "setBounds" && call.tabId === tabId) {
+      return call.bounds;
+    }
+  }
+  return null;
+}
+
+function attachBoundsFor(
+  calls: readonly RecordedBrowserCall[],
+  tabId: string,
+): BbDesktopBrowserViewBounds | null {
+  const call = calls.find(
+    (candidate) => candidate.method === "attach" && candidate.tabId === tabId,
+  );
+  return call?.bounds ?? null;
+}
+
 afterEach(() => {
   cleanup();
   delete window.bbDesktop;
+  resetBrowserViewPersistence();
   window.localStorage.clear();
   // The resizing flag lives in the default jotai store, which persists across
   // tests in this module; reset it so a resize test never leaks into the next.
@@ -158,6 +321,7 @@ describe("BrowserTabDeck", () => {
       <BrowserTabDeck
         browserTabs={[TAB_A, TAB_B]}
         activeBrowserTabId={TAB_A.id}
+        environmentId="env_test"
         isPanelOpen
         threadId="thr_test"
         onUpdate={() => {}}
@@ -182,6 +346,7 @@ describe("BrowserTabDeck", () => {
       <BrowserTabDeck
         browserTabs={[TAB_A, TAB_B]}
         activeBrowserTabId={TAB_A.id}
+        environmentId="env_test"
         isPanelOpen
         threadId="thr_test"
         onUpdate={() => {}}
@@ -195,6 +360,7 @@ describe("BrowserTabDeck", () => {
       <BrowserTabDeck
         browserTabs={[TAB_A, TAB_B]}
         activeBrowserTabId={TAB_B.id}
+        environmentId="env_test"
         isPanelOpen
         threadId="thr_test"
         onUpdate={() => {}}
@@ -204,6 +370,7 @@ describe("BrowserTabDeck", () => {
       <BrowserTabDeck
         browserTabs={[TAB_A, TAB_B]}
         activeBrowserTabId={TAB_A.id}
+        environmentId="env_test"
         isPanelOpen
         threadId="thr_test"
         onUpdate={() => {}}
@@ -218,6 +385,76 @@ describe("BrowserTabDeck", () => {
     expect(visibilityFor(calls, TAB_B.id)).toBe(false);
   });
 
+  it("hides but does not destroy the active view when a thread deck unmounts", () => {
+    const { api, calls } = createRecordingBrowserApi();
+    installDesktopBrowserApi(api);
+
+    const { unmount } = render(
+      <BrowserTabDeck
+        browserTabs={[TAB_A]}
+        activeBrowserTabId={TAB_A.id}
+        environmentId="env_test"
+        isPanelOpen
+        threadId="thr_one"
+        onUpdate={() => {}}
+      />,
+    );
+
+    calls.length = 0;
+
+    unmount();
+
+    expect(calls.some((call) => call.method === "detach")).toBe(false);
+    expect(visibilityFor(calls, TAB_A.id)).toBe(false);
+  });
+
+  it("switches thread decks by hiding the old thread before showing the new one", () => {
+    const { api, calls } = createRecordingBrowserApi();
+    installDesktopBrowserApi(api);
+
+    const { rerender } = render(
+      <ThreadDeckHost
+        browserTabs={[TAB_A]}
+        activeBrowserTabId={TAB_A.id}
+        threadId="thr_one"
+      />,
+    );
+
+    calls.length = 0;
+
+    rerender(
+      <ThreadDeckHost
+        browserTabs={[TAB_C]}
+        activeBrowserTabId={TAB_C.id}
+        threadId="thr_two"
+      />,
+    );
+
+    const hideOldThread = calls.findIndex(
+      (call) =>
+        call.method === "setVisible" &&
+        call.tabId === TAB_A.id &&
+        call.visible === false,
+    );
+    const newThreadBounds = calls.findIndex(
+      (call) => call.method === "setBounds" && call.tabId === TAB_C.id,
+    );
+    const showNewThread = calls.findIndex(
+      (call) =>
+        call.method === "setVisible" &&
+        call.tabId === TAB_C.id &&
+        call.visible === true,
+    );
+
+    expect(hideOldThread).toBeGreaterThanOrEqual(0);
+    expect(newThreadBounds).toBeGreaterThanOrEqual(0);
+    expect(showNewThread).toBeGreaterThanOrEqual(0);
+    expect(hideOldThread).toBeLessThan(showNewThread);
+    expect(newThreadBounds).toBeLessThan(showNewThread);
+    expect(calls.some((call) => call.method === "detach")).toBe(false);
+    expect(maxConcurrentVisible(calls)).toBe(1);
+  });
+
   it("syncs bounds before showing a newly-activated view (no stale-bounds flash)", () => {
     const { api, calls } = createRecordingBrowserApi();
     installDesktopBrowserApi(api);
@@ -226,6 +463,7 @@ describe("BrowserTabDeck", () => {
       <BrowserTabDeck
         browserTabs={[TAB_A, TAB_B]}
         activeBrowserTabId={TAB_A.id}
+        environmentId="env_test"
         isPanelOpen
         threadId="thr_test"
         onUpdate={() => {}}
@@ -238,6 +476,7 @@ describe("BrowserTabDeck", () => {
       <BrowserTabDeck
         browserTabs={[TAB_A, TAB_B]}
         activeBrowserTabId={TAB_B.id}
+        environmentId="env_test"
         isPanelOpen
         threadId="thr_test"
         onUpdate={() => {}}
@@ -256,6 +495,85 @@ describe("BrowserTabDeck", () => {
     expect(setBoundsIndex).toBeLessThan(showIndex);
   });
 
+  it("resyncs bounds when the panel position changes without resizing", () => {
+    const { api, calls } = createRecordingBrowserApi();
+    installDesktopBrowserApi(api);
+    const rect: BrowserContentRect = {
+      left: 320,
+      top: 96,
+      width: 480,
+      height: 360,
+    };
+    const restoreRect = installBrowserContentRect(rect);
+    try {
+      render(
+        <BrowserTabDeck
+          browserTabs={[TAB_A]}
+          activeBrowserTabId={TAB_A.id}
+          environmentId="env_test"
+          isPanelOpen
+          threadId="thr_test"
+          onUpdate={() => {}}
+        />,
+      );
+
+      calls.length = 0;
+
+      rect.left = 248;
+      rect.top = 88;
+
+      act(() => {
+        window.dispatchEvent(new Event(BROWSER_VIEW_BOUNDS_SYNC_EVENT));
+      });
+
+      expect(lastSetBoundsFor(calls, TAB_A.id)).toEqual({
+        x: 248,
+        y: 88,
+        width: 480,
+        height: 360,
+      });
+    } finally {
+      restoreRect();
+    }
+  });
+
+  it("anchors browser bounds to the content left edge and clamps them to the viewport", () => {
+    const { api, calls } = createRecordingBrowserApi();
+    installDesktopBrowserApi(api);
+    const restoreViewport = installViewportSize({ width: 500, height: 360 });
+    const restoreRect = installBrowserContentRect({
+      left: 180,
+      top: 48,
+      width: 400,
+      height: 420,
+    });
+
+    try {
+      render(
+        <BrowserTabDeck
+          browserTabs={[TAB_A]}
+          activeBrowserTabId={TAB_A.id}
+          environmentId="env_test"
+          isPanelOpen
+          threadId="thr_test"
+          onUpdate={() => {}}
+        />,
+      );
+
+      const expectedBounds: BbDesktopBrowserViewBounds = {
+        x: 180,
+        y: 48,
+        width: 320,
+        height: 312,
+      };
+      expect(attachBoundsFor(calls, TAB_A.id)).toEqual(expectedBounds);
+      expect(lastSetBoundsFor(calls, TAB_A.id)).toEqual(expectedBounds);
+    } finally {
+      restoreRect();
+      restoreViewport();
+    }
+  });
+
   it("hides the later view before showing the earlier one when switching B -> A", () => {
     const { api, calls } = createRecordingBrowserApi();
     installDesktopBrowserApi(api);
@@ -264,6 +582,7 @@ describe("BrowserTabDeck", () => {
       <BrowserTabDeck
         browserTabs={[TAB_A, TAB_B]}
         activeBrowserTabId={TAB_A.id}
+        environmentId="env_test"
         isPanelOpen
         threadId="thr_test"
         onUpdate={() => {}}
@@ -276,6 +595,7 @@ describe("BrowserTabDeck", () => {
       <BrowserTabDeck
         browserTabs={[TAB_A, TAB_B]}
         activeBrowserTabId={TAB_B.id}
+        environmentId="env_test"
         isPanelOpen
         threadId="thr_test"
         onUpdate={() => {}}
@@ -288,6 +608,7 @@ describe("BrowserTabDeck", () => {
       <BrowserTabDeck
         browserTabs={[TAB_A, TAB_B]}
         activeBrowserTabId={TAB_A.id}
+        environmentId="env_test"
         isPanelOpen
         threadId="thr_test"
         onUpdate={() => {}}
@@ -320,6 +641,7 @@ describe("BrowserTabDeck", () => {
       <BrowserTabDeck
         browserTabs={[TAB_A, TAB_B]}
         activeBrowserTabId={TAB_A.id}
+        environmentId="env_test"
         isPanelOpen
         threadId="thr_test"
         onUpdate={() => {}}
@@ -331,6 +653,7 @@ describe("BrowserTabDeck", () => {
         <BrowserTabDeck
           browserTabs={[TAB_A, TAB_B]}
           activeBrowserTabId={activeId}
+          environmentId="env_test"
           isPanelOpen
           threadId="thr_test"
           onUpdate={() => {}}
@@ -349,6 +672,7 @@ describe("BrowserTabDeck", () => {
       <BrowserTabDeck
         browserTabs={[TAB_A, TAB_B]}
         activeBrowserTabId={TAB_B.id}
+        environmentId="env_test"
         isPanelOpen
         threadId="thr_test"
         onUpdate={() => {}}
@@ -362,6 +686,7 @@ describe("BrowserTabDeck", () => {
       <BrowserTabDeck
         browserTabs={[TAB_B]}
         activeBrowserTabId={TAB_B.id}
+        environmentId="env_test"
         isPanelOpen
         threadId="thr_test"
         onUpdate={() => {}}
@@ -380,6 +705,7 @@ describe("BrowserTabDeck", () => {
       <BrowserTabDeck
         browserTabs={[TAB_A]}
         activeBrowserTabId={TAB_A.id}
+        environmentId="env_test"
         isPanelOpen
         threadId="thr_test"
         onUpdate={() => {}}
@@ -392,6 +718,7 @@ describe("BrowserTabDeck", () => {
       <BrowserTabDeck
         browserTabs={[TAB_A]}
         activeBrowserTabId={TAB_A.id}
+        environmentId="env_test"
         isPanelOpen={false}
         threadId="thr_test"
         onUpdate={() => {}}
@@ -421,19 +748,13 @@ describe("BrowserTabDeck", () => {
       disconnect() {}
     }
     vi.stubGlobal("ResizeObserver", CapturingResizeObserver);
-    // Run the rAF-coalesced bounds sync synchronously so the resize tick lands a
-    // setBounds within this test's `act` scope.
-    const requestFrame = vi
-      .spyOn(window, "requestAnimationFrame")
-      .mockImplementation((callback) => {
-        callback(0);
-        return 0;
-      });
+    const animationFrame = installQueuedAnimationFrame();
 
     render(
       <BrowserTabDeck
         browserTabs={[TAB_A]}
         activeBrowserTabId={TAB_A.id}
+        environmentId="env_test"
         isPanelOpen
         threadId="thr_test"
         onUpdate={() => {}}
@@ -449,6 +770,8 @@ describe("BrowserTabDeck", () => {
       for (const fireResizeTick of resizeCallbacks) {
         fireResizeTick();
       }
+      animationFrame.flushNext();
+      animationFrame.flushNext();
     });
     const duringResize = calls.slice(resizeStart);
 
@@ -471,7 +794,7 @@ describe("BrowserTabDeck", () => {
     // Net effect: the active view stays visible throughout the resize.
     expect(visibilityFor(calls, TAB_A.id)).toBe(true);
 
-    requestFrame.mockRestore();
+    animationFrame.restore();
     vi.unstubAllGlobals();
   });
 });
diff --git a/apps/app/src/components/secondary-panel/BrowserTabDeck.tsx b/apps/app/src/components/secondary-panel/BrowserTabDeck.tsx
index b8d04803e..ade72db8a 100644
--- a/apps/app/src/components/secondary-panel/BrowserTabDeck.tsx
+++ b/apps/app/src/components/secondary-panel/BrowserTabDeck.tsx
@@ -1,31 +1,47 @@
-import { useMemo, useRef } from "react";
+import { useEffect, useMemo, useRef } from "react";
 import type { BrowserFixedPanelTab } from "@/lib/fixed-panel-tabs-state";
 import { getDesktopBrowserApi } from "@/lib/bb-desktop";
 import { cn } from "@/lib/utils";
 import { BrowserTabContent } from "./BrowserTabContent";
 import {
-  createBrowserViewVisibilityCoordinator,
-  type BrowserViewVisibilityCoordinator,
+  destroyPersistedBrowserView,
+  getBrowserViewVisibilityCoordinator,
 } from "./browserViewVisibilityCoordinator";
 import type { UpdateBrowserTabArgs } from "./useThreadFileTabs";
 
 export interface BrowserTabDeckProps {
   browserTabs: readonly BrowserFixedPanelTab[];
   activeBrowserTabId: string | null;
+  environmentId: string | null;
   /** Whether the secondary panel is open; gates the active view's visibility. */
   isPanelOpen: boolean;
   threadId: string;
   onUpdate: (args: UpdateBrowserTabArgs) => void;
 }
 
+interface BrowserTabIdSnapshot {
+  tabIds: ReadonlySet<string>;
+  threadId: string;
+}
+
+interface BuildBrowserTabIdSetArgs {
+  browserTabs: readonly BrowserFixedPanelTab[];
+}
+
+function buildBrowserTabIdSet({
+  browserTabs,
+}: BuildBrowserTabIdSetArgs): ReadonlySet<string> {
+  return new Set(browserTabs.map((tab) => tab.id));
+}
+
 /**
  * Renders every open browser tab at once, keeping each tab's native
  * `WebContentsView` mounted (and its page + scroll intact) for the tab's whole
  * lifetime. Only the active tab is laid out and visible; the rest are
  * `display:none` with their views hidden — so switching tabs is a visibility
- * toggle, never a destroy/recreate + reload. A tab's view is torn down only when
- * its `BrowserTabContent` unmounts, i.e. when the tab is closed or the panel /
- * thread unmounts.
+ * toggle, never a destroy/recreate + reload. A tab's view is torn down when it
+ * leaves this thread's open-tab list; thread navigation only unmounts this deck,
+ * so retained views stay alive for when the user returns.
  *
  * Mounted regardless of which panel tab is active so the views survive switching
  * to a non-browser tab; the whole deck collapses to `display:none` when no
@@ -34,19 +50,34 @@ export interface BrowserTabDeckProps {
 export function BrowserTabDeck({
   browserTabs,
   activeBrowserTabId,
+  environmentId,
   isPanelOpen,
   threadId,
   onUpdate,
 }: BrowserTabDeckProps) {
   const desktopBrowser = useMemo(() => getDesktopBrowserApi(), []);
-  // One coordinator per deck owns the cross-tab visibility ordering for the
-  // lifetime of the panel; created once (the native bridge identity is stable).
-  const coordinatorRef = useRef<BrowserViewVisibilityCoordinator | null>(null);
-  if (desktopBrowser !== null && coordinatorRef.current === null) {
-    coordinatorRef.current =
-      createBrowserViewVisibilityCoordinator(desktopBrowser);
-  }
-  const visibilityCoordinator = coordinatorRef.current;
+  const previousTabIdsRef = useRef<BrowserTabIdSnapshot | null>(null);
+  const visibilityCoordinator =
+    desktopBrowser === null
+      ? null
+      : getBrowserViewVisibilityCoordinator(desktopBrowser);
+
+  useEffect(() => {
+    const tabIds = buildBrowserTabIdSet({ browserTabs });
+    const previous = previousTabIdsRef.current;
+    if (
+      desktopBrowser !== null &&
+      previous !== null &&
+      previous.threadId === threadId
+    ) {
+      for (const tabId of previous.tabIds) {
+        if (!tabIds.has(tabId)) {
+          destroyPersistedBrowserView({ desktopBrowser, tabId });
+        }
+      }
+    }
+    previousTabIdsRef.current = { tabIds, threadId };
+  }, [browserTabs, desktopBrowser, threadId]);
 
   if (browserTabs.length === 0) {
     return null;
@@ -71,6 +102,7 @@ export function BrowserTabDeck({
               initialUrl={tab.url}
               isActive={isActive && isPanelOpen}
               visibilityCoordinator={visibilityCoordinator}
+              environmentId={environmentId}
               threadId={threadId}
               onUpdate={onUpdate}
             />
diff --git a/apps/app/src/components/secondary-panel/FilePreview.test.tsx b/apps/app/src/components/secondary-panel/FilePreview.test.tsx
index 15b39bba2..f904ebb49 100644
--- a/apps/app/src/components/secondary-panel/FilePreview.test.tsx
+++ b/apps/app/src/components/secondary-panel/FilePreview.test.tsx
@@ -26,8 +26,8 @@ describe("FilePreview", () => {
         state={{
           kind: "iframe",
           sandbox: null,
-          title: "Status",
-          url: "/api/v1/threads/thr_1/apps/status/",
+          title: "Review Board",
+          url: "/api/v1/apps/review-board/?targetThreadId=thr_1",
         }}
       />,
     );
@@ -54,13 +54,13 @@ describe("FilePreview", () => {
         state={{
           kind: "iframe",
           sandbox: null,
-          title: "Status",
-          url: "/api/v1/threads/thr_1/apps/status/",
+          title: "Review Board",
+          url: "/api/v1/apps/review-board/?targetThreadId=thr_1",
         }}
       />,
     );
 
-    fireEvent.load(screen.getByTitle("Status"));
+    fireEvent.load(screen.getByTitle("Review Board"));
     act(() => {
       vi.advanceTimersByTime(160);
     });
diff --git a/apps/app/src/components/secondary-panel/ManagerThreadStorageBrowser.stories.tsx b/apps/app/src/components/secondary-panel/ManagerThreadStorageBrowser.stories.tsx
index dc1fe0d6a..72d6d6be1 100644
--- a/apps/app/src/components/secondary-panel/ManagerThreadStorageBrowser.stories.tsx
+++ b/apps/app/src/components/secondary-panel/ManagerThreadStorageBrowser.stories.tsx
@@ -28,8 +28,8 @@ function makeFile(path: string): WorkspaceFile {
 
 const FILES: WorkspaceFile[] = [
   makeFile("ASYNC.md"),
-  makeFile("apps/status/manifest.json"),
-  makeFile("apps/status/data/state.json"),
+  makeFile("notes/current-work.md"),
+  makeFile("plans/kickoff.md"),
   makeFile("PREFERENCES.md"),
 ];
 
diff --git a/apps/app/src/components/secondary-panel/NewTabFileSearch.tsx b/apps/app/src/components/secondary-panel/NewTabFileSearch.tsx
index 39327117c..9848e167c 100644
--- a/apps/app/src/components/secondary-panel/NewTabFileSearch.tsx
+++ b/apps/app/src/components/secondary-panel/NewTabFileSearch.tsx
@@ -33,16 +33,16 @@ import { isDesktopBrowserAvailable } from "@/lib/bb-desktop";
 import { formatRelativeTime } from "@/lib/relative-time";
 import { isPromptDraftEmpty, type PromptDraftState } from "@/lib/prompt-draft";
 
-export const CREATE_APP_PROMPT_TEMPLATE = `You are creating a new bb app for this thread.
+export const CREATE_APP_PROMPT_TEMPLATE = `You are creating a new global bb app.
 
 Apps system reference — run \`bb guide app\` for full detail. Layout:
-- apps/<id>/manifest.json — { manifestVersion: 1, id, name, icon | logo.svg, entry, contributions: ["thread.app"], capabilities: ["data"?, "message"?] }
-- apps/<id>/assets/index.html — self-contained static HTML/CSS/JS/SVG served by bb; use inline/relative files, no web server, npm, or build step
-- apps/<id>/data/state.json — initial state if the app uses window.bb.data
+- <dataDir>/apps/<applicationId>/manifest.json — { manifestVersion: 1, id: applicationId, name?, icon | logo.svg, entry, capabilities: ["data"?, "message"?] }
+- <dataDir>/apps/<applicationId>/public/index.html — self-contained static HTML/CSS/JS/SVG served by bb; use inline/relative files, no web server, npm, or build step
+- <dataDir>/apps/<applicationId>/data/state.json — state if the app uses window.bb.data
 
 In the page, use window.bb.data for live state (read / write / delete / list / onChange; onChange replays + streams) and window.bb.message(text) to send the thread a prompt. Guard with \`window.bb?.data?.…\` since capabilities are advisory.
 
-Scaffold with \`bb app new\` — the default styling is wired up already, so build on top of it and keep the UI polished, accessible, and dense like the rest of bb.
+Scaffold with \`bb app new --name "Name"\` or \`bb app new --slug my-app\`; inside an app-capable runtime, inspect \`bb app current --json\` and write directly to \`BB_APP_ROOT\` / \`BB_APP_DATA_PATH\`. The application id is the lowercase slug folder name; display names are optional labels, not identifiers.
 
 What I want:
 
@@ -217,14 +217,6 @@ const RECENT_CHIP_ICON_NAME = {
 } satisfies Record<RecentFileChip, IconName>;
 const RECENT_ENTRY_ID_PREFIX = "file-search-result-recent";
 
-function slugifyAppName(name: string): string {
-  return name
-    .trim()
-    .toLowerCase()
-    .replace(/[^a-z0-9]+/g, "-")
-    .replace(/^-+|-+$/g, "");
-}
-
 function getAvailableFileSearchSources({
   projectId,
   currentThreadId,
@@ -245,7 +237,7 @@ function getAvailableFileSearchSources({
 
 function getFileSearchResultId(suggestion: FileSearchSuggestion): string {
   const idSegment =
-    suggestion.entryKind === "app" ? suggestion.appId : suggestion.path;
+    suggestion.entryKind === "app" ? suggestion.applicationId : suggestion.path;
   return `file-search-result-${suggestion.source}-${encodeURIComponent(
     idSegment,
   )}`;
@@ -442,8 +434,6 @@ function AppResultRow({
   const handleSelect = useCallback(() => {
     onSelect(suggestion);
   }, [onSelect, suggestion]);
-  const showAppId = suggestion.appId !== slugifyAppName(suggestion.name);
-
   return (
     <LauncherTile
       id={id}
@@ -460,16 +450,12 @@ function AppResultRow({
       </span>
       <span className="flex min-w-0 flex-1 items-center gap-1.5">
         <span className="truncate text-foreground">{suggestion.name}</span>
-        {showAppId ? (
-          <>
-            <span className="shrink-0 text-muted-foreground opacity-50" aria-hidden>
-              ·
-            </span>
-            <span className="truncate font-mono text-muted-foreground">
-              {suggestion.appId}
-            </span>
-          </>
-        ) : null}
+        <span className="shrink-0 text-muted-foreground opacity-50" aria-hidden>
+          ·
+        </span>
+        <span className="truncate font-mono text-muted-foreground">
+          {suggestion.applicationId}
+        </span>
       </span>
     </LauncherTile>
   );
@@ -597,7 +583,10 @@ function RecentResultRow({
   const { chip, label } = resolveRecentFileKind(item.path);
   const name = getRecentItemName(item.path);
   const { directory } = splitPath(item.path);
-  const relativeTime = formatRelativeTime({ timestamp: item.openedAt, now: nowMs });
+  const relativeTime = formatRelativeTime({
+    timestamp: item.openedAt,
+    now: nowMs,
+  });
 
   return (
     <LauncherTile
@@ -716,7 +705,8 @@ export function NewTabFileSearch({
     !isUnavailable &&
     onOpenBrowser !== undefined &&
     isDesktopBrowserAvailable() &&
-    (!hasQuery || OPEN_BROWSER_ENTRY_KEYWORDS.includes(trimmedQuery.toLowerCase()));
+    (!hasQuery ||
+      OPEN_BROWSER_ENTRY_KEYWORDS.includes(trimmedQuery.toLowerCase()));
   const normalizedRecentQuery = hasQuery ? trimmedQuery.toLowerCase() : "";
   const matchingRecentItems = useMemo(
     () =>
@@ -757,9 +747,7 @@ export function NewTabFileSearch({
   );
   const navigableEntries = useMemo(
     () =>
-      sections.flatMap((section) =>
-        section.items.map(({ entry }) => entry),
-      ),
+      sections.flatMap((section) => section.items.map(({ entry }) => entry)),
     [sections],
   );
   const activeEntry = useMemo(
@@ -787,7 +775,7 @@ export function NewTabFileSearch({
 
   const handleAppSelect = useCallback(
     (suggestion: AppSearchSuggestion) => {
-      onSelect({ source: "app", appId: suggestion.appId });
+      onSelect({ source: "app", applicationId: suggestion.applicationId });
     },
     [onSelect],
   );
@@ -1006,7 +994,8 @@ function NewTabResults({
   const showAppsSection = appsSection !== undefined;
   const showOpenSection = openSection !== undefined;
   const showFilesSection = filesSection !== undefined;
-  const showRecentSection = recentSection !== undefined || recent.emptyHintVisible;
+  const showRecentSection =
+    recentSection !== undefined || recent.emptyHintVisible;
   const hasSectionsAbove =
     showAppsSection || showOpenSection || showFilesSection;
   const showLoading = isLoading && !showFilesSection;
@@ -1067,7 +1056,7 @@ function NewTabResults({
               const suggestion = entry.suggestion;
               return (
                 <AppResultRow
-                  key={`app:${suggestion.appId}`}
+                  key={`app:${suggestion.applicationId}`}
                   id={getFileSearchEntryId(entry)}
                   suggestion={suggestion}
                   isActive={index === activeIndex}
diff --git a/apps/app/src/components/secondary-panel/NewTabPage.test.tsx b/apps/app/src/components/secondary-panel/NewTabPage.test.tsx
index df6d3bcc5..36a8e67bc 100644
--- a/apps/app/src/components/secondary-panel/NewTabPage.test.tsx
+++ b/apps/app/src/components/secondary-panel/NewTabPage.test.tsx
@@ -1,6 +1,12 @@
 // @vitest-environment jsdom
 
-import { cleanup, fireEvent, render, screen, within } from "@testing-library/react";
+import {
+  cleanup,
+  fireEvent,
+  render,
+  screen,
+  within,
+} from "@testing-library/react";
 import type { AppSummary, WorkspacePathEntry } from "@bb/server-contract";
 import * as api from "@/lib/api";
 import {
@@ -24,7 +30,7 @@ vi.mock("@/lib/api", async (importOriginal) => {
   return {
     ...actual,
     searchProjectPaths: vi.fn(),
-    listThreadApps: vi.fn(),
+    listApps: vi.fn(),
     listThreadStoragePaths: vi.fn(),
   };
 });
@@ -74,9 +80,9 @@ function makePathResponse(
   };
 }
 
-const STATUS_APP: AppSummary = {
-  id: "status",
-  name: "Status",
+const APP: AppSummary = {
+  applicationId: "status",
+  name: "Review Board",
   entry: { path: "index.html", kind: "html" },
   capabilities: ["data", "message"],
   icon: { kind: "builtin", name: "ListTodo" },
@@ -124,7 +130,7 @@ function seedRecentItems(threadId: string, items: ThreadRecentItem[]): void {
 }
 
 function mockEmptySearchSources(): void {
-  vi.mocked(api.listThreadApps).mockResolvedValue([]);
+  vi.mocked(api.listApps).mockResolvedValue([]);
   vi.mocked(api.searchProjectPaths).mockResolvedValue(makePathResponse([]));
   vi.mocked(api.listThreadStoragePaths).mockResolvedValue({
     ...makePathResponse([]),
@@ -162,7 +168,7 @@ afterEach(() => {
 
 describe("NewTabPage", () => {
   it("autofocuses search and selects a workspace result", async () => {
-    vi.mocked(api.listThreadApps).mockResolvedValue([]);
+    vi.mocked(api.listApps).mockResolvedValue([]);
     vi.mocked(api.searchProjectPaths).mockResolvedValue(
       makePathResponse([
         {
@@ -192,23 +198,25 @@ describe("NewTabPage", () => {
   });
 
   it("lists apps and opens an app selection", async () => {
-    vi.mocked(api.listThreadApps).mockResolvedValue([STATUS_APP]);
+    vi.mocked(api.listApps).mockResolvedValue([APP]);
     const { onSelect } = renderNewTabPage({
       currentThreadId: "thr-manager",
       currentThreadType: "manager",
     });
 
     expect(await screen.findByText("Apps")).toBeTruthy();
-    fireEvent.click(await screen.findByRole("option", { name: /Status/u }));
+    fireEvent.click(
+      await screen.findByRole("option", { name: /Review Board/u }),
+    );
 
     expect(onSelect).toHaveBeenCalledWith({
       source: "app",
-      appId: "status",
+      applicationId: "status",
     });
   });
 
   it("prefills the composer draft with the create-app prompt", () => {
-    vi.mocked(api.listThreadApps).mockResolvedValue([]);
+    vi.mocked(api.listApps).mockResolvedValue([]);
     renderNewTabPage({ projectId: "proj-1" });
 
     fireEvent.click(screen.getByRole("option", { name: /Create App/u }));
@@ -233,7 +241,7 @@ describe("NewTabPage", () => {
   });
 
   it("leaves a non-empty composer draft unchanged when replacement is canceled", () => {
-    vi.mocked(api.listThreadApps).mockResolvedValue([]);
+    vi.mocked(api.listApps).mockResolvedValue([]);
     vi.spyOn(window, "confirm").mockReturnValue(false);
     setStoredThreadDraft(DRAFT_WITH_ATTACHMENT);
     renderNewTabPage({ projectId: "proj-1" });
@@ -244,7 +252,7 @@ describe("NewTabPage", () => {
   });
 
   it("replaces non-empty composer text and attachments after confirmation", () => {
-    vi.mocked(api.listThreadApps).mockResolvedValue([]);
+    vi.mocked(api.listApps).mockResolvedValue([]);
     vi.spyOn(window, "confirm").mockReturnValue(true);
     setStoredThreadDraft(DRAFT_WITH_ATTACHMENT);
     renderNewTabPage({ projectId: "proj-1" });
@@ -258,13 +266,15 @@ describe("NewTabPage", () => {
   });
 
   it("arrows past the app rows onto the create-app entry as the last option", async () => {
-    vi.mocked(api.listThreadApps).mockResolvedValue([STATUS_APP]);
+    vi.mocked(api.listApps).mockResolvedValue([APP]);
     renderNewTabPage({ projectId: "proj-1" });
 
     const input = screen.getByRole("textbox", {
       name: "Search apps and files",
     });
-    const appOption = await screen.findByRole("option", { name: /Status/u });
+    const appOption = await screen.findByRole("option", {
+      name: /Review Board/u,
+    });
     const createAppOption = screen.getByRole("option", {
       name: /Create App/u,
     });
@@ -286,13 +296,13 @@ describe("NewTabPage", () => {
   });
 
   it("prefills the composer draft when the create-app entry is activated by Enter", async () => {
-    vi.mocked(api.listThreadApps).mockResolvedValue([STATUS_APP]);
+    vi.mocked(api.listApps).mockResolvedValue([APP]);
     renderNewTabPage({ projectId: "proj-1" });
 
     const input = screen.getByRole("textbox", {
       name: "Search apps and files",
     });
-    await screen.findByRole("option", { name: /Status/u });
+    await screen.findByRole("option", { name: /Review Board/u });
 
     fireEvent.keyDown(input, { key: "ArrowDown" });
     fireEvent.keyDown(input, { key: "Enter" });
@@ -304,7 +314,7 @@ describe("NewTabPage", () => {
   });
 
   it("selects a manager thread-storage result with the keyboard", async () => {
-    vi.mocked(api.listThreadApps).mockResolvedValue([]);
+    vi.mocked(api.listApps).mockResolvedValue([]);
     vi.mocked(api.searchProjectPaths).mockResolvedValue(
       makePathResponse([
         {
@@ -351,7 +361,7 @@ describe("NewTabPage", () => {
       screen.getByText("No searchable app or file source is available."),
     ).toBeTruthy();
     expect(api.searchProjectPaths).not.toHaveBeenCalled();
-    expect(api.listThreadApps).not.toHaveBeenCalled();
+    expect(api.listApps).not.toHaveBeenCalled();
     expect(api.listThreadStoragePaths).not.toHaveBeenCalled();
   });
 });
@@ -467,7 +477,7 @@ describe("NewTabPage recent section", () => {
 
   it("reaches a recent row via keyboard navigation", async () => {
     mockEmptySearchSources();
-    vi.mocked(api.listThreadApps).mockResolvedValue([STATUS_APP]);
+    vi.mocked(api.listApps).mockResolvedValue([APP]);
     const threadId = "thr-recent-keys";
     seedRecentItems(threadId, [
       {
@@ -488,7 +498,9 @@ describe("NewTabPage recent section", () => {
     // Await the app row so the async sources have settled and the active-index
     // reset no longer fires; the recent row trails Apps + Create App in one
     // shared index space, so ArrowUp wraps onto it from the first entry.
-    const appOption = await screen.findByRole("option", { name: /Status/u });
+    const appOption = await screen.findByRole("option", {
+      name: /Review Board/u,
+    });
     const recentOption = screen.getByRole("option", {
       name: /swap-model\.md/u,
     });
diff --git a/apps/app/src/components/secondary-panel/ThreadSecondaryPanel.test.tsx b/apps/app/src/components/secondary-panel/ThreadSecondaryPanel.test.tsx
index 64028215a..b51c3bfec 100644
--- a/apps/app/src/components/secondary-panel/ThreadSecondaryPanel.test.tsx
+++ b/apps/app/src/components/secondary-panel/ThreadSecondaryPanel.test.tsx
@@ -189,13 +189,13 @@ afterEach(() => {
 describe("ThreadSecondaryPanel", () => {
   it.each<SecondaryPanelChromeDragScenario>([
     {
-      name: "status app iframe",
+      name: "app iframe",
       activeTab: buildActiveFileTab({
-        id: "app:status",
-        filename: "Status",
+        id: "app:review-board",
+        filename: "Review Board",
         isPinned: true,
       }),
-      iframeTitle: "Status app",
+      iframeTitle: "Review Board app",
       closeButtonLabel: null,
     },
     {
@@ -275,9 +275,9 @@ describe("ThreadSecondaryPanel", () => {
   ])(
     "keeps iframe previews interactable after secondary panel resize ends via $name",
     async ({ finishDrag }) => {
-      const activeStatusTab: SecondaryPanelFileTab = {
-        id: "app:status",
-        filename: "Status",
+      const activeAppTab: SecondaryPanelFileTab = {
+        id: "app:review-board",
+        filename: "Review Board",
         isActive: true,
         isPinned: true,
         statusLabel: null,
@@ -286,8 +286,8 @@ describe("ThreadSecondaryPanel", () => {
       };
 
       renderPanel({
-        fileTabs: [activeStatusTab],
-        fileTabContent: <iframe title="Status app" />,
+        fileTabs: [activeAppTab],
+        fileTabContent: <iframe title="Review Board app" />,
         renderAsDrawer: false,
       });
 
@@ -317,7 +317,9 @@ describe("ThreadSecondaryPanel", () => {
       // Regression guard: the drag must be intercepted by the overlay, never by
       // disabling the iframe's pointer-events — that detaches the iframe's
       // compositor scroll node in Chromium and kills wheel-scroll after resize.
-      expect(aside?.className).not.toContain(IFRAME_POINTER_EVENTS_TOGGLE_CLASS);
+      expect(aside?.className).not.toContain(
+        IFRAME_POINTER_EVENTS_TOGGLE_CLASS,
+      );
 
       finishDrag();
 
@@ -348,7 +350,9 @@ describe("ThreadSecondaryPanel", () => {
     renderPanel({ reserveLeftForDesktopTrafficLights: false });
 
     const topChrome = screen.getByTestId("thread-secondary-panel-top-chrome");
-    expect(topChrome.className).not.toContain(MACOS_TRAFFIC_LIGHT_RESERVE_CLASS);
+    expect(topChrome.className).not.toContain(
+      MACOS_TRAFFIC_LIGHT_RESERVE_CLASS,
+    );
   });
 
   it("shows the resize seam hairline while the conversation is expanded", () => {
@@ -367,7 +371,11 @@ describe("ThreadSecondaryPanel", () => {
       isBrowserTabActive: true,
       browserDeck: <div>browser deck</div>,
       fileTabs: [
-        buildActiveFileTab({ id: "browser:a", filename: "Example", isPinned: false }),
+        buildActiveFileTab({
+          id: "browser:a",
+          filename: "Example",
+          isPinned: false,
+        }),
       ],
       fileTabContent: <div>file tab content</div>,
     });
@@ -382,7 +390,11 @@ describe("ThreadSecondaryPanel", () => {
       isBrowserTabActive: false,
       browserDeck: <div>browser deck</div>,
       fileTabs: [
-        buildActiveFileTab({ id: "app:status", filename: "Status", isPinned: true }),
+        buildActiveFileTab({
+          id: "app:status",
+          filename: "Status",
+          isPinned: true,
+        }),
       ],
       fileTabContent: <div>file tab content</div>,
     });
@@ -427,7 +439,7 @@ describe("ThreadSecondaryPanel", () => {
     expect(
       Boolean(
         toggle.compareDocumentPosition(hideButton) &
-          Node.DOCUMENT_POSITION_FOLLOWING,
+        Node.DOCUMENT_POSITION_FOLLOWING,
       ),
     ).toBe(true);
 
diff --git a/apps/app/src/components/secondary-panel/ThreadSecondaryPanelNewTab.stories.tsx b/apps/app/src/components/secondary-panel/ThreadSecondaryPanelNewTab.stories.tsx
index 78499f26c..abe847731 100644
--- a/apps/app/src/components/secondary-panel/ThreadSecondaryPanelNewTab.stories.tsx
+++ b/apps/app/src/components/secondary-panel/ThreadSecondaryPanelNewTab.stories.tsx
@@ -10,8 +10,8 @@ import type {
 import { StoryCard, StoryRow } from "../../../.ladle/story-card";
 import { createAppQueryClient } from "@/lib/query-client";
 import {
+  appsQueryKey,
   projectPathsQueryKey,
-  threadAppsQueryKey,
   threadStoragePathsQueryKey,
 } from "@/hooks/queries/query-keys";
 import { ThreadSecondaryPanel } from "./ThreadSecondaryPanel";
@@ -87,10 +87,10 @@ const THREAD_STORAGE_PATH_RESULTS: WorkspacePathEntry[] = [
   },
 ];
 
-const THREAD_APPS_RESPONSE: AppSummary[] = [
+const APPS_RESPONSE: AppSummary[] = [
   {
-    id: "status",
-    name: "Status",
+    applicationId: "story-review-board",
+    name: "Review Board",
     entry: { path: "index.html", kind: "html" },
     capabilities: ["data", "message"],
     icon: { kind: "builtin", name: "ListTodo" },
@@ -99,21 +99,21 @@ const THREAD_APPS_RESPONSE: AppSummary[] = [
 
 const APPS_ROW_APPS: AppSummary[] = [
   {
-    id: "status",
+    applicationId: "app_status",
     name: "Status",
     entry: { path: "index.html", kind: "html" },
     capabilities: ["data", "message"],
     icon: { kind: "builtin", name: "ListTodo" },
   },
   {
-    id: "workspace-map",
+    applicationId: "app_workspace_map",
     name: "Workspace Map",
     entry: { path: "index.html", kind: "html" },
     capabilities: ["data"],
     icon: { kind: "builtin", name: "GridView" },
   },
   {
-    id: "release-notes",
+    applicationId: "app_release_notes",
     name: "Release Notes",
     entry: { path: "index.html", kind: "html" },
     capabilities: ["message"],
@@ -259,9 +259,7 @@ function useStoryQueryClient({
       ),
       makeWorkspacePathResponse(workspacePaths),
     );
-    if (currentThreadId.length > 0) {
-      queryClient.setQueryData(threadAppsQueryKey(currentThreadId), apps);
-    }
+    queryClient.setQueryData(appsQueryKey(), apps);
     queryClient.setQueryData(
       threadStoragePathsQueryKey(currentThreadId, {
         limit: STORY_SOURCE_LIMIT,
@@ -333,11 +331,11 @@ function NewTabPanelStory({
             {
               id:
                 selection.source === "app"
-                  ? `app:${selection.appId}`
+                  ? `app:${selection.applicationId}`
                   : `${selection.source}:${selection.path}`,
               filename:
                 selection.source === "app"
-                  ? selection.appId
+                  ? selection.applicationId
                   : (selection.path.split("/").at(-1) ?? selection.path),
               isActive: true,
               statusLabel: null,
@@ -370,7 +368,9 @@ function NewTabPanelStory({
               : "thread storage file"}
         </p>
         <p className="pt-1 font-mono text-xs text-muted-foreground">
-          {selection.source === "app" ? selection.appId : selection.path}
+          {selection.source === "app"
+            ? selection.applicationId
+            : selection.path}
         </p>
       </div>
     );
@@ -454,7 +454,7 @@ export function NewTab() {
         hint="active New tab seeded with workspace and manager thread-storage matches"
       >
         <NewTabPanelStory
-          apps={THREAD_APPS_RESPONSE}
+          apps={APPS_RESPONSE}
           currentThreadId={SEARCH_THREAD_ID}
           currentThreadType="manager"
           initialQuery="thread"
diff --git a/apps/app/src/components/secondary-panel/browserViewVisibilityCoordinator.test.ts b/apps/app/src/components/secondary-panel/browserViewVisibilityCoordinator.test.ts
index b5b2af86b..b7631be0c 100644
--- a/apps/app/src/components/secondary-panel/browserViewVisibilityCoordinator.test.ts
+++ b/apps/app/src/components/secondary-panel/browserViewVisibilityCoordinator.test.ts
@@ -1,27 +1,45 @@
-import { describe, expect, it } from "vitest";
+import { afterEach, describe, expect, it } from "vitest";
 import type { BbDesktopBrowserApi } from "@bb/server-contract";
 import { createNoopDesktopBrowserApi } from "@/test/bb-desktop-test-utils";
-import { createBrowserViewVisibilityCoordinator } from "./browserViewVisibilityCoordinator";
+import {
+  createBrowserViewVisibilityCoordinator,
+  destroyPersistedBrowserViewsForEnvironment,
+  destroyPersistedBrowserViewsForThread,
+  getBrowserViewVisibilityCoordinator,
+  registerBrowserView,
+  resetBrowserViewPersistence,
+} from "./browserViewVisibilityCoordinator";
 
 interface VisibilityCall {
   tabId: string;
   visible: boolean;
 }
 
-function createRecordingApi(): {
+interface RecordingApi {
   api: BbDesktopBrowserApi;
+  detachments: string[];
   visibility: VisibilityCall[];
-} {
+}
+
+function createRecordingApi(): RecordingApi {
+  const detachments: string[] = [];
   const visibility: VisibilityCall[] = [];
   const api: BbDesktopBrowserApi = {
     ...createNoopDesktopBrowserApi(),
+    detach(tabId) {
+      detachments.push(tabId);
+    },
     setVisible(request) {
       visibility.push({ tabId: request.tabId, visible: request.visible });
     },
   };
-  return { api, visibility };
+  return { api, detachments, visibility };
 }
 
+afterEach(() => {
+  resetBrowserViewPersistence();
+});
+
 describe("browserViewVisibilityCoordinator", () => {
   it("hides the previously-visible view before showing the next one", () => {
     const { api, visibility } = createRecordingApi();
@@ -82,4 +100,68 @@ describe("browserViewVisibilityCoordinator", () => {
       { tabId: "b", visible: true },
     ]);
   });
+
+  it("shares visibility ownership across browser decks in one renderer window", () => {
+    const { api, visibility } = createRecordingApi();
+    const firstDeckCoordinator = getBrowserViewVisibilityCoordinator(api);
+    const secondDeckCoordinator = getBrowserViewVisibilityCoordinator(api);
+
+    firstDeckCoordinator.show("thread-a-tab", () => {});
+    secondDeckCoordinator.show("thread-b-tab", () => {});
+
+    expect(secondDeckCoordinator).toBe(firstDeckCoordinator);
+    expect(visibility).toEqual([
+      { tabId: "thread-a-tab", visible: true },
+      { tabId: "thread-a-tab", visible: false },
+      { tabId: "thread-b-tab", visible: true },
+    ]);
+  });
+
+  it("destroys registered views for a deleted thread only", () => {
+    const { api, detachments, visibility } = createRecordingApi();
+    registerBrowserView({
+      environmentId: "environment-a",
+      tabId: "thread-a-tab",
+      threadId: "thread-a",
+    });
+    registerBrowserView({
+      environmentId: "environment-b",
+      tabId: "thread-b-tab",
+      threadId: "thread-b",
+    });
+
+    destroyPersistedBrowserViewsForThread({
+      desktopBrowser: api,
+      threadId: "thread-a",
+    });
+
+    expect(visibility).toEqual([
+      { tabId: "thread-a-tab", visible: false },
+    ]);
+    expect(detachments).toEqual(["thread-a-tab"]);
+  });
+
+  it("destroys registered views for a deleted environment only", () => {
+    const { api, detachments, visibility } = createRecordingApi();
+    registerBrowserView({
+      environmentId: "environment-a",
+      tabId: "thread-a-tab",
+      threadId: "thread-a",
+    });
+    registerBrowserView({
+      environmentId: "environment-b",
+      tabId: "thread-b-tab",
+      threadId: "thread-b",
+    });
+
+    destroyPersistedBrowserViewsForEnvironment({
+      desktopBrowser: api,
+      environmentId: "environment-b",
+    });
+
+    expect(visibility).toEqual([
+      { tabId: "thread-b-tab", visible: false },
+    ]);
+    expect(detachments).toEqual(["thread-b-tab"]);
+  });
 });
diff --git a/apps/app/src/components/secondary-panel/browserViewVisibilityCoordinator.ts b/apps/app/src/components/secondary-panel/browserViewVisibilityCoordinator.ts
index 55024f637..26a8a451b 100644
--- a/apps/app/src/components/secondary-panel/browserViewVisibilityCoordinator.ts
+++ b/apps/app/src/components/secondary-panel/browserViewVisibilityCoordinator.ts
@@ -30,6 +30,37 @@ export interface BrowserViewVisibilityCoordinator {
   release(tabId: string): void;
 }
 
+interface BrowserViewRecord {
+  environmentId: string | null;
+  tabId: string;
+  threadId: string;
+}
+
+interface RegisterBrowserViewArgs {
+  environmentId: string | null;
+  tabId: string;
+  threadId: string;
+}
+
+interface DestroyPersistedBrowserViewArgs {
+  desktopBrowser: BbDesktopBrowserApi;
+  tabId: string;
+}
+
+interface DestroyPersistedBrowserViewsForThreadArgs {
+  desktopBrowser: BbDesktopBrowserApi | null;
+  threadId: string;
+}
+
+interface DestroyPersistedBrowserViewsForEnvironmentArgs {
+  desktopBrowser: BbDesktopBrowserApi | null;
+  environmentId: string;
+}
+
+const browserViewRecords = new Map<string, BrowserViewRecord>();
+let sharedDesktopBrowser: BbDesktopBrowserApi | null = null;
+let sharedCoordinator: BrowserViewVisibilityCoordinator | null = null;
+
 export function createBrowserViewVisibilityCoordinator(
   desktopBrowser: BbDesktopBrowserApi,
 ): BrowserViewVisibilityCoordinator {
@@ -57,3 +88,68 @@ export function createBrowserViewVisibilityCoordinator(
     },
   };
 }
+
+export function getBrowserViewVisibilityCoordinator(
+  desktopBrowser: BbDesktopBrowserApi,
+): BrowserViewVisibilityCoordinator {
+  if (sharedDesktopBrowser !== desktopBrowser || sharedCoordinator === null) {
+    sharedDesktopBrowser = desktopBrowser;
+    sharedCoordinator = createBrowserViewVisibilityCoordinator(desktopBrowser);
+  }
+  return sharedCoordinator;
+}
+
+export function registerBrowserView({
+  environmentId,
+  tabId,
+  threadId,
+}: RegisterBrowserViewArgs): void {
+  browserViewRecords.set(tabId, { environmentId, tabId, threadId });
+}
+
+export function destroyPersistedBrowserView({
+  desktopBrowser,
+  tabId,
+}: DestroyPersistedBrowserViewArgs): void {
+  const coordinator = getBrowserViewVisibilityCoordinator(desktopBrowser);
+  coordinator.hide(tabId);
+  coordinator.release(tabId);
+  desktopBrowser.detach(tabId);
+  browserViewRecords.delete(tabId);
+}
+
+export function destroyPersistedBrowserViewsForThread({
+  desktopBrowser,
+  threadId,
+}: DestroyPersistedBrowserViewsForThreadArgs): void {
+  if (desktopBrowser === null) {
+    return;
+  }
+  const records = [...browserViewRecords.values()];
+  for (const record of records) {
+    if (record.threadId === threadId) {
+      destroyPersistedBrowserView({ desktopBrowser, tabId: record.tabId });
+    }
+  }
+}
+
+export function destroyPersistedBrowserViewsForEnvironment({
+  desktopBrowser,
+  environmentId,
+}: DestroyPersistedBrowserViewsForEnvironmentArgs): void {
+  if (desktopBrowser === null) {
+    return;
+  }
+  const records = [...browserViewRecords.values()];
+  for (const record of records) {
+    if (record.environmentId === environmentId) {
+      destroyPersistedBrowserView({ desktopBrowser, tabId: record.tabId });
+    }
+  }
+}
+
+export function resetBrowserViewPersistence(): void {
+  browserViewRecords.clear();
+  sharedDesktopBrowser = null;
+  sharedCoordinator = null;
+}
diff --git a/apps/app/src/components/secondary-panel/threadSecondaryPanelAtoms.test.ts b/apps/app/src/components/secondary-panel/threadSecondaryPanelAtoms.test.ts
index e643fafe7..eb84e4225 100644
--- a/apps/app/src/components/secondary-panel/threadSecondaryPanelAtoms.test.ts
+++ b/apps/app/src/components/secondary-panel/threadSecondaryPanelAtoms.test.ts
@@ -5,6 +5,8 @@ import { afterEach, describe, expect, it, vi } from "vitest";
 import {
   getThreadConversationCollapsedAtom,
   getThreadConversationCollapsedStorageKey,
+  getThreadSecondaryPanelOpenAtom,
+  getThreadSecondaryPanelOpenStorageKey,
 } from "./threadSecondaryPanelAtoms";
 
 const THREAD_A = "thr_a";
@@ -15,6 +17,81 @@ afterEach(() => {
   vi.resetModules();
 });
 
+describe("getThreadSecondaryPanelOpenAtom", () => {
+  it("defaults to open=false and persists toggles to a per-thread key", () => {
+    const store = createStore();
+    const atomA = getThreadSecondaryPanelOpenAtom(THREAD_A);
+    expect(store.get(atomA)).toBe(false);
+
+    store.set(atomA, true);
+    expect(store.get(atomA)).toBe(true);
+    expect(
+      window.localStorage.getItem(
+        getThreadSecondaryPanelOpenStorageKey({ threadId: THREAD_A }),
+      ),
+    ).toBe("true");
+
+    store.set(atomA, false);
+    expect(store.get(atomA)).toBe(false);
+    expect(
+      window.localStorage.getItem(
+        getThreadSecondaryPanelOpenStorageKey({ threadId: THREAD_A }),
+      ),
+    ).toBe("false");
+  });
+
+  it("keeps each thread's open state isolated", () => {
+    const store = createStore();
+    const atomA = getThreadSecondaryPanelOpenAtom(THREAD_A);
+    const atomB = getThreadSecondaryPanelOpenAtom(THREAD_B);
+
+    store.set(atomA, true);
+
+    expect(store.get(atomA)).toBe(true);
+    expect(store.get(atomB)).toBe(false);
+    expect(
+      window.localStorage.getItem(
+        getThreadSecondaryPanelOpenStorageKey({ threadId: THREAD_B }),
+      ),
+    ).toBeNull();
+
+    store.set(atomB, false);
+    expect(store.get(atomA)).toBe(true);
+  });
+
+  it("returns a stable atom reference per thread id", () => {
+    expect(getThreadSecondaryPanelOpenAtom(THREAD_A)).toBe(
+      getThreadSecondaryPanelOpenAtom(THREAD_A),
+    );
+    expect(getThreadSecondaryPanelOpenAtom(THREAD_A)).not.toBe(
+      getThreadSecondaryPanelOpenAtom(THREAD_B),
+    );
+  });
+
+  it("falls back to a non-persisted disabled atom without a thread id", () => {
+    const store = createStore();
+    const disabled = getThreadSecondaryPanelOpenAtom(undefined);
+    expect(getThreadSecondaryPanelOpenAtom(null)).toBe(disabled);
+    expect(store.get(disabled)).toBe(false);
+
+    store.set(disabled, true);
+    expect(window.localStorage.length).toBe(0);
+  });
+
+  it("hydrates a thread's persisted open state when its atom initializes", async () => {
+    const { getThreadSecondaryPanelOpenStorageKey: seedKey } = await import(
+      "./threadSecondaryPanelAtoms"
+    );
+    window.localStorage.setItem(seedKey({ threadId: THREAD_A }), "true");
+    vi.resetModules();
+    const { getThreadSecondaryPanelOpenAtom: hydratedGetter } = await import(
+      "./threadSecondaryPanelAtoms"
+    );
+
+    expect(createStore().get(hydratedGetter(THREAD_A))).toBe(true);
+  });
+});
+
 describe("getThreadConversationCollapsedAtom", () => {
   it("defaults to collapsed=false and persists toggles to a per-thread key", () => {
     const store = createStore();
diff --git a/apps/app/src/components/secondary-panel/threadSecondaryPanelAtoms.ts b/apps/app/src/components/secondary-panel/threadSecondaryPanelAtoms.ts
index 56125159e..cfbc270bd 100644
--- a/apps/app/src/components/secondary-panel/threadSecondaryPanelAtoms.ts
+++ b/apps/app/src/components/secondary-panel/threadSecondaryPanelAtoms.ts
@@ -5,6 +5,24 @@ import { createLocalStorageSyncStorage } from "@/lib/browser-storage";
 
 export const threadSecondaryPanelResizingAtom = atom(false);
 
+type ResolvedThreadSecondaryPanelThreadId = string;
+type ThreadSecondaryPanelThreadId =
+  | ResolvedThreadSecondaryPanelThreadId
+  | null
+  | undefined;
+
+interface ThreadSecondaryPanelStorageKeyArgs {
+  prefix: string;
+  threadId: ResolvedThreadSecondaryPanelThreadId;
+}
+
+function getThreadSecondaryPanelStorageKey({
+  prefix,
+  threadId,
+}: ThreadSecondaryPanelStorageKeyArgs): string {
+  return `${prefix}-${encodeURIComponent(threadId)}`;
+}
+
 /**
  * User's preferred secondary panel width as a percentage of the surrounding
  * PanelGroup. Persisted across reloads. The default (50) is used when the
@@ -28,6 +46,76 @@ export const secondaryPanelWidthPercentAtom = atomWithStorage<number>(
   { getOnInit: true },
 );
 
+const threadSecondaryPanelBooleanStorage =
+  createLocalStorageSyncStorage<boolean>({
+    parse: (storedValue, initialValue) => {
+      if (storedValue === "true") return true;
+      if (storedValue === "false") return false;
+      return initialValue;
+    },
+    serialize: (value) => String(value),
+  });
+
+/**
+ * Whether a given thread's secondary panel is open on wide viewports. Stored
+ * separately from the tab list so the user's right-panel layout choice is
+ * restored per thread even as app/fullscreen and conversation-collapse flows
+ * mutate the selected tab. Defaults closed for threads with no stored value,
+ * matching the empty fixed-panel state.
+ */
+const THREAD_SECONDARY_PANEL_OPEN_STORAGE_PREFIX =
+  "bb.thread.secondaryPanel.open";
+
+interface ThreadSecondaryPanelOpenStorageKeyArgs {
+  threadId: ResolvedThreadSecondaryPanelThreadId;
+}
+
+export function getThreadSecondaryPanelOpenStorageKey({
+  threadId,
+}: ThreadSecondaryPanelOpenStorageKeyArgs): string {
+  return getThreadSecondaryPanelStorageKey({
+    prefix: THREAD_SECONDARY_PANEL_OPEN_STORAGE_PREFIX,
+    threadId,
+  });
+}
+
+const threadSecondaryPanelOpenAtomFamily = atomFamily(
+  (threadId: ResolvedThreadSecondaryPanelThreadId) =>
+    atomWithStorage<boolean>(
+      getThreadSecondaryPanelOpenStorageKey({ threadId }),
+      false,
+      threadSecondaryPanelBooleanStorage,
+      { getOnInit: true },
+    ),
+);
+
+// Fallback for callers without a resolved thread id (e.g. before routing
+// settles). It stays false and any write lands on this throwaway atom, so no
+// real thread's panel-open state is affected.
+const disabledThreadSecondaryPanelOpenAtom = atom(false);
+
+function hasThreadId(
+  threadId: ThreadSecondaryPanelThreadId,
+): threadId is ResolvedThreadSecondaryPanelThreadId {
+  return threadId !== null && threadId !== undefined && threadId.length > 0;
+}
+
+/**
+ * The panel-open atom for a specific thread. `atomFamily` memoizes by threadId,
+ * so repeated calls with the same id return a stable atom reference safe to
+ * pass straight to `useAtom`/`useSetAtom`/`useAtomValue`.
+ */
+export function getThreadSecondaryPanelOpenAtom(
+  threadId: ThreadSecondaryPanelThreadId,
+) {
+  return hasThreadId(threadId)
+    ? threadSecondaryPanelOpenAtomFamily(threadId)
+    : disabledThreadSecondaryPanelOpenAtom;
+}
+
+const THREAD_CONVERSATION_COLLAPSED_STORAGE_PREFIX =
+  "bb.thread.conversation.collapsed";
+
 /**
  * Whether a given thread's conversation/timeline pane is collapsed so the
  * secondary panel fills the whole content area. Keyed per thread (like the
@@ -37,37 +125,29 @@ export const secondaryPanelWidthPercentAtom = atomWithStorage<number>(
  * Persisted per thread; only takes effect while the secondary panel is open on
  * a wide viewport — see ThreadDetailSecondaryContent for the gating.
  */
-const THREAD_CONVERSATION_COLLAPSED_STORAGE_PREFIX =
-  "bb.thread.conversation.collapsed";
-
 interface ThreadConversationCollapsedStorageKeyArgs {
-  threadId: string;
+  threadId: ResolvedThreadSecondaryPanelThreadId;
 }
 
 export function getThreadConversationCollapsedStorageKey({
   threadId,
 }: ThreadConversationCollapsedStorageKeyArgs): string {
-  return `${THREAD_CONVERSATION_COLLAPSED_STORAGE_PREFIX}-${encodeURIComponent(
+  return getThreadSecondaryPanelStorageKey({
+    prefix: THREAD_CONVERSATION_COLLAPSED_STORAGE_PREFIX,
     threadId,
-  )}`;
+  });
 }
 
-const conversationCollapsedStorage = createLocalStorageSyncStorage<boolean>({
-  parse: (storedValue, initialValue) => {
-    if (storedValue === "true") return true;
-    if (storedValue === "false") return false;
-    return initialValue;
-  },
-  serialize: (value) => String(value),
-});
+const conversationCollapsedStorage = threadSecondaryPanelBooleanStorage;
 
-const threadConversationCollapsedAtomFamily = atomFamily((threadId: string) =>
-  atomWithStorage<boolean>(
-    getThreadConversationCollapsedStorageKey({ threadId }),
-    false,
-    conversationCollapsedStorage,
-    { getOnInit: true },
-  ),
+const threadConversationCollapsedAtomFamily = atomFamily(
+  (threadId: ResolvedThreadSecondaryPanelThreadId) =>
+    atomWithStorage<boolean>(
+      getThreadConversationCollapsedStorageKey({ threadId }),
+      false,
+      conversationCollapsedStorage,
+      { getOnInit: true },
+    ),
 );
 
 // Fallback for callers without a resolved thread id (e.g. before routing
@@ -75,17 +155,13 @@ const threadConversationCollapsedAtomFamily = atomFamily((threadId: string) =>
 // real thread's collapse state is affected.
 const disabledThreadConversationCollapsedAtom = atom(false);
 
-function hasThreadId(threadId: string | null | undefined): threadId is string {
-  return threadId !== null && threadId !== undefined && threadId.length > 0;
-}
-
 /**
  * The conversation-collapsed atom for a specific thread. `atomFamily` memoizes
  * by threadId, so repeated calls with the same id return a stable atom
  * reference safe to pass straight to `useAtom`/`useSetAtom`/`useAtomValue`.
  */
 export function getThreadConversationCollapsedAtom(
-  threadId: string | null | undefined,
+  threadId: ThreadSecondaryPanelThreadId,
 ) {
   return hasThreadId(threadId)
     ? threadConversationCollapsedAtomFamily(threadId)
diff --git a/apps/app/src/components/secondary-panel/useThreadFileTabs.test.tsx b/apps/app/src/components/secondary-panel/useThreadFileTabs.test.tsx
index 4e95d2507..2a323e621 100644
--- a/apps/app/src/components/secondary-panel/useThreadFileTabs.test.tsx
+++ b/apps/app/src/components/secondary-panel/useThreadFileTabs.test.tsx
@@ -26,7 +26,7 @@ import {
   type WorkspaceFilePreviewFixedPanelTab,
 } from "@/lib/fixed-panel-tabs-state";
 import { useFixedPanelTabsState } from "@/lib/fixed-panel-tabs";
-import { STATUS_APP_ID, useThreadFileTabs } from "./useThreadFileTabs";
+import { useThreadFileTabs } from "./useThreadFileTabs";
 import { useThreadRecentItems } from "./threadRecentItems";
 
 const NOW = 1_700_000_000_000;
@@ -44,7 +44,7 @@ interface TestWrapperProps {
 }
 
 interface HookProps {
-  apps?: readonly { id: string }[];
+  apps?: readonly { applicationId: string }[];
   environmentId: string | null | undefined;
   storageFiles: readonly { path: string }[] | undefined;
   threadId: string;
@@ -148,7 +148,7 @@ function storageFilePaths(
 }
 
 function appTabIds(tabs: readonly SecondaryFileFixedPanelTab[]): string[] {
-  return tabs.filter(isAppTab).map((tab) => tab.appId);
+  return tabs.filter(isAppTab).map((tab) => tab.applicationId);
 }
 
 function tabIds(tabs: readonly SecondaryFileFixedPanelTab[]): string[] {
@@ -167,8 +167,8 @@ function hostFileTabId(path: string): string {
   return `host-file-preview:${encodeURIComponent(path)}`;
 }
 
-function appTabId(appId: string): string {
-  return `app:${encodeURIComponent(appId)}`;
+function appTabId(applicationId: string): string {
+  return `app:${encodeURIComponent(applicationId)}`;
 }
 
 function newTabId(): string {
@@ -236,7 +236,7 @@ function getStoredStoragePaths(state: FixedPanelTabsState): string[] {
 }
 
 function getStoredAppIds(state: FixedPanelTabsState): string[] {
-  return state.secondary.tabs.filter(isAppTab).map((tab) => tab.appId);
+  return state.secondary.tabs.filter(isAppTab).map((tab) => tab.applicationId);
 }
 
 afterEach(() => {
@@ -434,22 +434,17 @@ describe("useThreadFileTabs", () => {
     expect(result.current.activeHostFilePath).toBeNull();
   });
 
-  it("orders file tabs by open order with the pinned status app first", async () => {
+  it("orders file tabs by open order", () => {
     const { result } = renderThreadFileTabsHook({
-      apps: [{ id: STATUS_APP_ID }],
+      apps: [{ applicationId: "review" }],
       environmentId: "env-one",
       threadType: "manager",
       storageFiles: [{ path: "notes.md" }],
       threadId: "thr-manager-open-order",
     });
 
-    await waitFor(() => {
-      expect(appTabIds(result.current.orderedSecondaryFileTabs)).toEqual([
-        STATUS_APP_ID,
-      ]);
-    });
-
     act(() => {
+      result.current.openApp("review");
       result.current.openWorkspaceFile(
         buildWorkspaceFileTab({ lineNumber: null, path: "src/app.ts" }),
       );
@@ -458,7 +453,7 @@ describe("useThreadFileTabs", () => {
     });
 
     expect(tabIds(result.current.orderedSecondaryFileTabs)).toEqual([
-      appTabId(STATUS_APP_ID),
+      appTabId("review"),
       workspaceFileTabId("src/app.ts"),
       storageFileTabId("notes.md"),
       hostFileTabId("/tmp/host.md"),
@@ -783,35 +778,35 @@ describe("useThreadFileTabs", () => {
     expect(result.current.activeStorageFilePath).toBeNull();
   });
 
-  it("opens the status app tab for managers and keeps it pinned", async () => {
+  it("closes app tabs", () => {
     const { result } = renderThreadFileTabsHook({
-      apps: [{ id: STATUS_APP_ID }],
+      apps: [{ applicationId: "review" }],
       environmentId: null,
       threadType: "manager",
       storageFiles: undefined,
-      threadId: "thr-manager-status-app",
-    });
-
-    await waitFor(() => {
-      expect(appTabIds(result.current.orderedSecondaryFileTabs)).toEqual([
-        STATUS_APP_ID,
-      ]);
+      threadId: "thr-manager-app",
     });
-    expect(result.current.activeAppId).toBe(STATUS_APP_ID);
 
     act(() => {
-      result.current.closeAppTab(STATUS_APP_ID);
+      result.current.openApp("review");
     });
 
     expect(appTabIds(result.current.orderedSecondaryFileTabs)).toEqual([
-      STATUS_APP_ID,
+      "review",
     ]);
-    expect(result.current.activeAppId).toBe(STATUS_APP_ID);
+    expect(result.current.activeAppId).toBe("review");
+
+    act(() => {
+      result.current.closeAppTab("review");
+    });
+
+    expect(appTabIds(result.current.orderedSecondaryFileTabs)).toEqual([]);
+    expect(result.current.activeAppId).toBeNull();
   });
 
   it("opens an app tab from launcher search selection", () => {
     const { result } = renderThreadFileTabsHook({
-      apps: [{ id: "demo" }],
+      apps: [{ applicationId: "demo" }],
       environmentId: "env-one",
       threadType: "standard",
       storageFiles: undefined,
@@ -822,7 +817,7 @@ describe("useThreadFileTabs", () => {
       result.current.openNewTab();
       result.current.selectFileSearchResult({
         source: "app",
-        appId: "demo",
+        applicationId: "demo",
       });
     });
 
@@ -1012,9 +1007,9 @@ describe("useThreadFileTabs — browser tabs", () => {
     });
 
     expect(result.current.activeBrowserTab?.title).toBe("Example");
-    const persisted = readStoredState(
-      "thr-browser-update",
-    ).secondary.tabs.find((entry) => entry.kind === "browser");
+    const persisted = readStoredState("thr-browser-update").secondary.tabs.find(
+      (entry) => entry.kind === "browser",
+    );
     expect(persisted?.kind === "browser" ? persisted.url : null).toBe(
       "https://example.com",
     );
diff --git a/apps/app/src/components/secondary-panel/useThreadFileTabs.ts b/apps/app/src/components/secondary-panel/useThreadFileTabs.ts
index c41dbe9c8..3d92648d2 100644
--- a/apps/app/src/components/secondary-panel/useThreadFileTabs.ts
+++ b/apps/app/src/components/secondary-panel/useThreadFileTabs.ts
@@ -1,4 +1,5 @@
 import { useCallback, useEffect, useMemo } from "react";
+import { useSetAtom } from "jotai";
 import type { ThreadType } from "@bb/domain";
 import {
   useFixedPanelTabsState,
@@ -27,16 +28,15 @@ import {
   type HostFileTabState,
   type WorkspaceFileTabState,
 } from "@/lib/file-preview";
+import { getThreadSecondaryPanelOpenAtom } from "./threadSecondaryPanelAtoms";
 import { useRecordThreadRecentItem } from "./threadRecentItems";
 
-export const STATUS_APP_ID = "status";
-
-interface ThreadAppTabDescriptor {
-  id: string;
+interface AppTabDescriptor {
+  applicationId: string;
 }
 
 interface UseThreadFileTabsParams {
-  apps?: readonly ThreadAppTabDescriptor[] | undefined;
+  apps?: readonly AppTabDescriptor[] | undefined;
   threadId: string | null | undefined;
   environmentId: string | null | undefined;
   threadType: ThreadType | undefined;
@@ -67,7 +67,7 @@ export interface FileSearchThreadStorageSelection {
 
 export interface FileSearchAppSelection {
   source: "app";
-  appId: string;
+  applicationId: string;
 }
 
 export type FileSearchSelection =
@@ -200,10 +200,11 @@ function pruneStorageTabs(
 
 function pruneAppTabs(
   tabs: readonly FixedPanelTab[],
-  knownAppIds: ReadonlySet<string>,
+  knownApplicationIds: ReadonlySet<string>,
 ): readonly FixedPanelTab[] {
   const nextTabs = tabs.filter(
-    (tab) => !isAppTab(tab) || knownAppIds.has(tab.appId),
+    (tab) =>
+      !isAppTab(tab) || knownApplicationIds.has(tab.applicationId),
   );
   return nextTabs.length === tabs.length ? tabs : nextTabs;
 }
@@ -222,8 +223,8 @@ function createStorageTab(path: string): ThreadStorageFilePreviewFixedPanelTab {
   });
 }
 
-function createAppTab(appId: string): AppFixedPanelTab {
-  return createAppFixedPanelTab({ appId });
+function createAppTab(applicationId: string): AppFixedPanelTab {
+  return createAppFixedPanelTab({ applicationId });
 }
 
 function findWorkspaceTab(
@@ -264,10 +265,10 @@ function findStorageFileTab(
 
 function findAppTab(
   tabs: readonly FixedPanelTab[],
-  appId: string,
+  applicationId: string,
 ): AppFixedPanelTab | null {
   for (const tab of tabs) {
-    if (isAppTab(tab) && tab.appId === appId) {
+    if (isAppTab(tab) && tab.applicationId === applicationId) {
       return tab;
     }
   }
@@ -340,19 +341,10 @@ interface BuildOrderedSecondaryFileTabsArgs {
   isManagerThread: boolean;
 }
 
-function isPinnedAppTab(tab: SecondaryFileFixedPanelTab): boolean {
-  return tab.kind === "app" && tab.appId === STATUS_APP_ID;
-}
-
-function isPinnedSecondaryFileTab(tab: SecondaryFileFixedPanelTab): boolean {
-  return isPinnedAppTab(tab);
-}
-
 /**
  * Flattens the secondary panel's tabs into the closable file-tab strip, in the
- * order the user opened them. The pinned manager status app is floated to the
- * front; everything else (workspace, host, storage, new tab) keeps its
- * insertion order regardless of type.
+ * order the user opened them. Workspace, host, storage, app, browser, and new
+ * tabs keep their insertion order regardless of type.
  */
 function buildOrderedSecondaryFileTabs({
   tabs,
@@ -387,10 +379,7 @@ function buildOrderedSecondaryFileTabs({
         break;
     }
   }
-  return [
-    ...displayable.filter(isPinnedSecondaryFileTab),
-    ...displayable.filter((tab) => !isPinnedSecondaryFileTab(tab)),
-  ];
+  return displayable;
 }
 
 /**
@@ -402,11 +391,15 @@ function buildOrderedSecondaryFileTabs({
  */
 export function useOpenThreadAppTab(
   threadId: string | null | undefined,
-): (appId: string) => void {
+): (applicationId: string) => void {
   const updateFixedPanelTabsState = useUpdateFixedPanelTabsState(threadId);
+  const setThreadSecondaryPanelOpen = useSetAtom(
+    getThreadSecondaryPanelOpenAtom(threadId),
+  );
   return useCallback(
-    (appId: string) => {
-      const nextTab = createAppTab(appId);
+    (applicationId: string) => {
+      const nextTab = createAppTab(applicationId);
+      setThreadSecondaryPanelOpen(true);
       updateFixedPanelTabsState((state) => {
         const tabs = upsertSecondaryTab(state.secondary.tabs, nextTab);
         if (
@@ -424,7 +417,7 @@ export function useOpenThreadAppTab(
         });
       });
     },
-    [updateFixedPanelTabsState],
+    [setThreadSecondaryPanelOpen, updateFixedPanelTabsState],
   );
 }
 
@@ -437,14 +430,17 @@ export function useThreadFileTabs({
 }: UseThreadFileTabsParams) {
   const fixedPanelTabsState = useFixedPanelTabsState(threadId);
   const updateFixedPanelTabsState = useUpdateFixedPanelTabsState(threadId);
+  const setThreadSecondaryPanelOpen = useSetAtom(
+    getThreadSecondaryPanelOpenAtom(threadId),
+  );
   const recordRecentItem = useRecordThreadRecentItem(threadId);
   const isThreadResolved = threadType !== undefined;
   const isManagerThread = threadType === "manager";
   const resolvedEnvironmentId = isThreadResolved
     ? (environmentId ?? null)
     : undefined;
-  const appIds = useMemo(
-    () => (apps ? new Set(apps.map((app) => app.id)) : null),
+  const applicationIds = useMemo(
+    () => (apps ? new Set(apps.map((app) => app.applicationId)) : null),
     [apps],
   );
 
@@ -519,9 +515,9 @@ export function useThreadFileTabs({
   ]);
 
   useEffect(() => {
-    if (!isThreadResolved || appIds === null) return;
+    if (!isThreadResolved || applicationIds === null) return;
     updateFixedPanelTabsState((state) => {
-      const tabs = pruneAppTabs(state.secondary.tabs, appIds);
+      const tabs = pruneAppTabs(state.secondary.tabs, applicationIds);
       const activeTabId = isActiveTabStillOpen(
         tabs,
         state.secondary.activeTabId,
@@ -535,33 +531,12 @@ export function useThreadFileTabs({
         tabs,
       });
     });
-  }, [appIds, isThreadResolved, updateFixedPanelTabsState]);
-
-  useEffect(() => {
-    if (!isManagerThread || appIds === null || !appIds.has(STATUS_APP_ID)) {
-      return;
-    }
-    updateFixedPanelTabsState((state) => {
-      const statusAppTab = createAppTab(STATUS_APP_ID);
-      const tabs = upsertSecondaryTab(state.secondary.tabs, statusAppTab);
-      const activeTabId = isActiveTabStillOpen(
-        tabs,
-        state.secondary.activeTabId,
-      )
-        ? state.secondary.activeTabId
-        : statusAppTab.id;
-      return setSecondaryTabs({
-        activeTabId,
-        isOpen: state.secondary.isOpen,
-        state,
-        tabs,
-      });
-    });
-  }, [appIds, isManagerThread, updateFixedPanelTabsState]);
+  }, [applicationIds, isThreadResolved, updateFixedPanelTabsState]);
 
   const openWorkspaceFile = useCallback(
     ({ lineNumber, path, source, statusLabel }: WorkspaceFileTabState) => {
       if (resolvedEnvironmentId === undefined) return;
+      setThreadSecondaryPanelOpen(true);
       // Only working-tree opens are recorded as recent: a recent row reopens the
       // live file, so diff-only previews (head/merge-base) would reopen to the
       // wrong content.
@@ -599,7 +574,12 @@ export function useThreadFileTabs({
         });
       });
     },
-    [recordRecentItem, resolvedEnvironmentId, updateFixedPanelTabsState],
+    [
+      recordRecentItem,
+      resolvedEnvironmentId,
+      setThreadSecondaryPanelOpen,
+      updateFixedPanelTabsState,
+    ],
   );
 
   const closeWorkspaceFileTab = useCallback(
@@ -626,6 +606,10 @@ export function useThreadFileTabs({
 
   const activateWorkspaceFileTab = useCallback(
     (path: string) => {
+      if (findWorkspaceTab(fixedPanelTabsState.secondary.tabs, path) === null) {
+        return;
+      }
+      setThreadSecondaryPanelOpen(true);
       updateFixedPanelTabsState((state) => {
         const tab = findWorkspaceTab(state.secondary.tabs, path);
         if (!tab) {
@@ -642,12 +626,17 @@ export function useThreadFileTabs({
         });
       });
     },
-    [updateFixedPanelTabsState],
+    [
+      fixedPanelTabsState.secondary.tabs,
+      setThreadSecondaryPanelOpen,
+      updateFixedPanelTabsState,
+    ],
   );
 
   const openStorageFile = useCallback(
     (path: string) => {
       if (!isManagerThread) return;
+      setThreadSecondaryPanelOpen(true);
       recordRecentItem({ source: "thread-storage", path });
       const nextTab = createStorageTab(path);
       updateFixedPanelTabsState((state) => {
@@ -667,12 +656,18 @@ export function useThreadFileTabs({
         });
       });
     },
-    [isManagerThread, recordRecentItem, updateFixedPanelTabsState],
+    [
+      isManagerThread,
+      recordRecentItem,
+      setThreadSecondaryPanelOpen,
+      updateFixedPanelTabsState,
+    ],
   );
 
   const openHostFile = useCallback(
     ({ lineNumber, path }: HostFileTabState) => {
       if (!threadId) return;
+      setThreadSecondaryPanelOpen(true);
       const nextTab = createHostFilePreviewFixedPanelTab({
         lineNumber,
         path,
@@ -696,7 +691,7 @@ export function useThreadFileTabs({
         });
       });
     },
-    [threadId, updateFixedPanelTabsState],
+    [setThreadSecondaryPanelOpen, threadId, updateFixedPanelTabsState],
   );
 
   const closeHostFileTab = useCallback(
@@ -723,6 +718,10 @@ export function useThreadFileTabs({
 
   const activateHostFileTab = useCallback(
     (path: string) => {
+      if (findHostFileTab(fixedPanelTabsState.secondary.tabs, path) === null) {
+        return;
+      }
+      setThreadSecondaryPanelOpen(true);
       updateFixedPanelTabsState((state) => {
         const tab = findHostFileTab(state.secondary.tabs, path);
         if (!tab) {
@@ -739,16 +738,19 @@ export function useThreadFileTabs({
         });
       });
     },
-    [updateFixedPanelTabsState],
+    [
+      fixedPanelTabsState.secondary.tabs,
+      setThreadSecondaryPanelOpen,
+      updateFixedPanelTabsState,
+    ],
   );
 
   const openApp = useOpenThreadAppTab(threadId);
 
   const closeAppTab = useCallback(
-    (appId: string) => {
-      if (appId === STATUS_APP_ID) return;
+    (applicationId: string) => {
       updateFixedPanelTabsState((state) => {
-        const tab = findAppTab(state.secondary.tabs, appId);
+        const tab = findAppTab(state.secondary.tabs, applicationId);
         if (!tab) {
           return state;
         }
@@ -768,9 +770,15 @@ export function useThreadFileTabs({
   );
 
   const activateAppTab = useCallback(
-    (appId: string) => {
+    (applicationId: string) => {
+      if (
+        findAppTab(fixedPanelTabsState.secondary.tabs, applicationId) === null
+      ) {
+        return;
+      }
+      setThreadSecondaryPanelOpen(true);
       updateFixedPanelTabsState((state) => {
-        const tab = findAppTab(state.secondary.tabs, appId);
+        const tab = findAppTab(state.secondary.tabs, applicationId);
         if (!tab) {
           return state;
         }
@@ -785,7 +793,11 @@ export function useThreadFileTabs({
         });
       });
     },
-    [updateFixedPanelTabsState],
+    [
+      fixedPanelTabsState.secondary.tabs,
+      setThreadSecondaryPanelOpen,
+      updateFixedPanelTabsState,
+    ],
   );
 
   // Opening a browser tab swaps the transient new-tab in place (like selecting
@@ -795,13 +807,18 @@ export function useThreadFileTabs({
   const openBrowserTab = useCallback(
     (url?: string) => {
       const nextTab = createBrowserFixedPanelTab({ url: url ?? "" });
+      setThreadSecondaryPanelOpen(true);
       updateFixedPanelTabsState((state) => replaceNewTab({ nextTab, state }));
     },
-    [updateFixedPanelTabsState],
+    [setThreadSecondaryPanelOpen, updateFixedPanelTabsState],
   );
 
   const activateBrowserTab = useCallback(
     (tabId: string) => {
+      if (findBrowserTab(fixedPanelTabsState.secondary.tabs, tabId) === null) {
+        return;
+      }
+      setThreadSecondaryPanelOpen(true);
       updateFixedPanelTabsState((state) => {
         const tab = findBrowserTab(state.secondary.tabs, tabId);
         if (!tab) {
@@ -818,7 +835,11 @@ export function useThreadFileTabs({
         });
       });
     },
-    [updateFixedPanelTabsState],
+    [
+      fixedPanelTabsState.secondary.tabs,
+      setThreadSecondaryPanelOpen,
+      updateFixedPanelTabsState,
+    ],
   );
 
   const closeBrowserTab = useCallback(
@@ -899,6 +920,10 @@ export function useThreadFileTabs({
   const activateStorageFileTab = useCallback(
     (path: string) => {
       if (!isManagerThread) return;
+      if (findStorageFileTab(fixedPanelTabsState.secondary.tabs, path) === null) {
+        return;
+      }
+      setThreadSecondaryPanelOpen(true);
       updateFixedPanelTabsState((state) => {
         const tab = findStorageFileTab(state.secondary.tabs, path);
         if (!tab) {
@@ -915,11 +940,17 @@ export function useThreadFileTabs({
         });
       });
     },
-    [isManagerThread, updateFixedPanelTabsState],
+    [
+      fixedPanelTabsState.secondary.tabs,
+      isManagerThread,
+      setThreadSecondaryPanelOpen,
+      updateFixedPanelTabsState,
+    ],
   );
 
   const openNewTab = useCallback(() => {
     const newTab = createNewTabFixedPanelTab();
+    setThreadSecondaryPanelOpen(true);
     updateFixedPanelTabsState((state) => {
       const tabs = upsertSecondaryTab(state.secondary.tabs, newTab);
       if (
@@ -936,10 +967,14 @@ export function useThreadFileTabs({
         tabs,
       });
     });
-  }, [updateFixedPanelTabsState]);
+  }, [setThreadSecondaryPanelOpen, updateFixedPanelTabsState]);
 
   const activateNewTab = useCallback(() => {
     const newTab = createNewTabFixedPanelTab();
+    if (findNewTab(fixedPanelTabsState.secondary.tabs) === null) {
+      return;
+    }
+    setThreadSecondaryPanelOpen(true);
     updateFixedPanelTabsState((state) => {
       const existingTab = findNewTab(state.secondary.tabs);
       if (!existingTab) {
@@ -955,7 +990,11 @@ export function useThreadFileTabs({
         tabs: state.secondary.tabs,
       });
     });
-  }, [updateFixedPanelTabsState]);
+  }, [
+    fixedPanelTabsState.secondary.tabs,
+    setThreadSecondaryPanelOpen,
+    updateFixedPanelTabsState,
+  ]);
 
   const closeNewTab = useCallback(() => {
     const newTab = createNewTabFixedPanelTab();
@@ -979,13 +1018,15 @@ export function useThreadFileTabs({
   const selectFileSearchResult = useCallback(
     (selection: FileSearchSelection) => {
       if (selection.source === "app") {
-        const nextTab = createAppTab(selection.appId);
+        const nextTab = createAppTab(selection.applicationId);
+        setThreadSecondaryPanelOpen(true);
         updateFixedPanelTabsState((state) => replaceNewTab({ nextTab, state }));
         return;
       }
 
       if (selection.source === "workspace") {
         if (resolvedEnvironmentId === undefined) return;
+        setThreadSecondaryPanelOpen(true);
         recordRecentItem({ source: "workspace", path: selection.path });
         const nextTab = createWorkspaceFilePreviewFixedPanelTab({
           environmentId: resolvedEnvironmentId,
@@ -1001,6 +1042,7 @@ export function useThreadFileTabs({
       }
 
       if (!isManagerThread) return;
+      setThreadSecondaryPanelOpen(true);
       recordRecentItem({ source: "thread-storage", path: selection.path });
       const nextTab = createStorageTab(selection.path);
       updateFixedPanelTabsState((state) => replaceNewTab({ nextTab, state }));
@@ -1009,6 +1051,7 @@ export function useThreadFileTabs({
       isManagerThread,
       recordRecentItem,
       resolvedEnvironmentId,
+      setThreadSecondaryPanelOpen,
       updateFixedPanelTabsState,
     ],
   );
@@ -1072,7 +1115,7 @@ export function useThreadFileTabs({
     activateHostFileTab,
     activateStorageFileTab,
     activateWorkspaceFileTab,
-    activeAppId: activeAppTab?.appId ?? null,
+    activeAppId: activeAppTab?.applicationId ?? null,
     activeBrowserTab,
     activeHostFileLineNumber: activeHostFileTab?.lineNumber ?? null,
     activeHostFilePath: activeHostFileTab?.path ?? null,
diff --git a/apps/app/src/components/sidebar/ProjectList.test.tsx b/apps/app/src/components/sidebar/ProjectList.test.tsx
index 9b6035e90..de2d5782d 100644
--- a/apps/app/src/components/sidebar/ProjectList.test.tsx
+++ b/apps/app/src/components/sidebar/ProjectList.test.tsx
@@ -15,7 +15,6 @@ import {
   waitFor,
 } from "@testing-library/react";
 import { BrowserRouter } from "react-router-dom";
-import { useAtom } from "jotai";
 import type { QueryClient } from "@tanstack/react-query";
 import { PERSONAL_PROJECT_ID } from "@bb/domain";
 import type {
@@ -29,10 +28,12 @@ import {
   resetFakeReconnectingWebSockets,
 } from "@/test/fake-reconnecting-websocket";
 import { createQueryClientTestHarness } from "@/test/queryClientTestHarness";
-import { installFetchRoutes, jsonResponse } from "@/test/http-test-utils";
+import {
+  installFetchRoutes,
+  jsonResponse,
+  type FetchRoute,
+} from "@/test/http-test-utils";
 import { wsManager } from "@/lib/ws";
-import { useFixedPanelTabsState } from "@/lib/fixed-panel-tabs";
-import { getThreadConversationCollapsedAtom } from "@/components/secondary-panel/threadSecondaryPanelAtoms";
 import { useRootComposeReuseEnvironment } from "@/lib/root-compose-selection";
 import { encodeReuseValue } from "@/components/pickers/environment-picker-value";
 import {
@@ -72,7 +73,7 @@ type ProjectThreadListEntryOverrides = Partial<ProjectThreadListEntry>;
 type ProjectWithThreadsOverrides = Partial<ProjectWithThreadsResponse>;
 
 interface MakeAppArgs {
-  id: string;
+  applicationId: string;
   name: string;
   icon: AppSummary["icon"];
 }
@@ -137,9 +138,26 @@ function makeThreadListEntry(
   };
 }
 
-function makeApp({ id, name, icon }: MakeAppArgs): AppSummary {
+// The sidebar now lists global apps unconditionally, so every render hits
+// `GET /api/v1/apps`. Default it to an empty list when a test doesn't care about
+// apps, so those tests don't have to register the route by hand.
+function installProjectListFetchRoutes(routes: FetchRoute[]) {
+  const hasAppsRoute = routes.some(
+    (route) => route.pathname === "/api/v1/apps",
+  );
+  return installFetchRoutes(
+    hasAppsRoute
+      ? routes
+      : [
+          ...routes,
+          { pathname: "/api/v1/apps", handler: () => jsonResponse([]) },
+        ],
+  );
+}
+
+function makeApp({ applicationId, name, icon }: MakeAppArgs): AppSummary {
   return {
-    id,
+    applicationId,
     name,
     entry: { path: "index.html", kind: "html" },
     capabilities: [],
@@ -147,20 +165,21 @@ function makeApp({ id, name, icon }: MakeAppArgs): AppSummary {
   };
 }
 
-const STATUS_APP = makeApp({
-  id: "status",
-  name: "Status",
+const REVIEW_BOARD_APP = makeApp({
+  applicationId: "review-board",
+  name: "Review Board",
   icon: { kind: "builtin", name: "ListTodo" },
 });
 
-// Manager app rows render after sidebar bootstrap plus a per-manager app query.
-const MANAGER_APP_ROW_TIMEOUT_MS = 5_000;
+// App rows render after the global app query resolves, which trails the sidebar
+// bootstrap, so allow a little extra time when finding one.
+const APP_ROW_TIMEOUT_MS = 5_000;
 
-function findStatusAppButton() {
+function findReviewBoardAppButton() {
   return screen.findByRole(
     "button",
-    { name: "Open Status app" },
-    { timeout: MANAGER_APP_ROW_TIMEOUT_MS },
+    { name: "Open Review Board app" },
+    { timeout: APP_ROW_TIMEOUT_MS },
   );
 }
 
@@ -174,10 +193,6 @@ interface RootComposeReuseProbeProps {
   onValue: (value: string | null) => void;
 }
 
-interface PanelStateProbeProps {
-  threadId: string;
-}
-
 function buildProjectListHandler(args: ProjectListHandlerArgs) {
   return (request: Request) => {
     const url = new URL(request.url);
@@ -247,44 +262,6 @@ function RootComposeReuseProbe({
   return null;
 }
 
-function PanelStateProbe({ threadId }: PanelStateProbeProps) {
-  const state = useFixedPanelTabsState(threadId);
-  return (
-    <div data-testid="panel-state">
-      {JSON.stringify({
-        activeTabId: state.secondary.activeTabId,
-        isOpen: state.secondary.isOpen,
-      })}
-    </div>
-  );
-}
-
-interface ConversationCollapseProbeProps {
-  threadId: string;
-}
-
-// Mirrors one thread's conversation-collapse preference the thread detail view
-// reads/writes, and exposes a button that stands in for the collapsed rail's
-// expand control so a sidebar-only test can drive the same state. Keyed by
-// threadId so a test can probe several threads independently.
-function ConversationCollapseProbe({
-  threadId,
-}: ConversationCollapseProbeProps) {
-  const [collapsed, setCollapsed] = useAtom(
-    getThreadConversationCollapsedAtom(threadId),
-  );
-  return (
-    <div>
-      <div data-testid={`conversation-collapsed:${threadId}`}>
-        {String(collapsed)}
-      </div>
-      <button type="button" onClick={() => setCollapsed(false)}>
-        {`expand-conversation:${threadId}`}
-      </button>
-    </div>
-  );
-}
-
 async function renderProjectList(
   props: ProjectListRenderProps = {},
   options: ProjectListRenderOptions = {},
@@ -346,7 +323,7 @@ describe("ProjectList", () => {
       projects,
       threadsByProjectId,
     });
-    installFetchRoutes([
+    installProjectListFetchRoutes([
       {
         pathname: "/api/v1/sidebar-bootstrap",
         handler: () => {
@@ -417,7 +394,7 @@ describe("ProjectList", () => {
   });
 
   it("does not show project error or empty states before the websocket connects", async () => {
-    const fetchMock = installFetchRoutes([
+    const fetchMock = installProjectListFetchRoutes([
       {
         pathname: "/api/v1/sidebar-bootstrap",
         handler: () => new Response("starting", { status: 503 }),
@@ -469,7 +446,7 @@ describe("ProjectList", () => {
       name: "Personal",
       threads: [],
     });
-    installFetchRoutes([
+    installProjectListFetchRoutes([
       {
         pathname: "/api/v1/sidebar-bootstrap",
         handler: () =>
@@ -525,7 +502,7 @@ describe("ProjectList", () => {
     expect(screen.getByText("Project Thread")).toBeTruthy();
   });
 
-  it("renders manager app rows directly under their owning manager", async () => {
+  it("lists global apps once in a top-level Apps section, not nested under managers", async () => {
     const project = makeProjectResponse({
       id: "project-1",
       name: "Project One",
@@ -548,7 +525,7 @@ describe("ProjectList", () => {
       name: "Personal",
       threads: [],
     });
-    installFetchRoutes([
+    installProjectListFetchRoutes([
       {
         pathname: "/api/v1/sidebar-bootstrap",
         handler: () =>
@@ -563,8 +540,8 @@ describe("ProjectList", () => {
           ),
       },
       {
-        pathname: `/api/v1/threads/${managerThread.id}/apps`,
-        handler: () => jsonResponse([STATUS_APP]),
+        pathname: "/api/v1/apps",
+        handler: () => jsonResponse([REVIEW_BOARD_APP]),
       },
       {
         pathname: "/api/v1/projects",
@@ -590,27 +567,34 @@ describe("ProjectList", () => {
 
     await renderProjectList();
 
-    const appRow = await findStatusAppButton();
+    const appRow = await findReviewBoardAppButton();
+    const appsLabel = screen.getByText("Apps");
     const managerLabel = screen.getByText("Sidebar Manager");
-    const workerLabel = screen.getByText("Worker Thread");
 
-    expect(appRow.classList.contains("pl-14")).toBe(true);
-    expect(appRow.parentElement?.className).toContain("before:left-10");
+    // One global app → exactly one app row, regardless of the manager present.
+    expect(
+      screen.getAllByRole("button", { name: "Open Review Board app" }),
+    ).toHaveLength(1);
+    // Top-level indent (pl-2), not the manager-nested indent (pl-14).
+    expect(appRow.classList.contains("pl-2")).toBe(true);
+    expect(appRow.classList.contains("pl-14")).toBe(false);
+    // The row lives in the standalone Apps section, after the manager that is
+    // listed under Projects — it is not a child of the manager group.
     expect(
       Boolean(
-        managerLabel.compareDocumentPosition(appRow) &
+        managerLabel.compareDocumentPosition(appsLabel) &
         Node.DOCUMENT_POSITION_FOLLOWING,
       ),
     ).toBe(true);
     expect(
       Boolean(
-        appRow.compareDocumentPosition(workerLabel) &
+        appsLabel.compareDocumentPosition(appRow) &
         Node.DOCUMENT_POSITION_FOLLOWING,
       ),
     ).toBe(true);
   });
 
-  it("opens a manager app row in the owning thread secondary panel", async () => {
+  it("opens a global app on its standalone route", async () => {
     const project = makeProjectResponse({
       id: "project-1",
       name: "Project One",
@@ -627,7 +611,7 @@ describe("ProjectList", () => {
       name: "Personal",
       threads: [],
     });
-    installFetchRoutes([
+    installProjectListFetchRoutes([
       {
         pathname: "/api/v1/sidebar-bootstrap",
         handler: () =>
@@ -640,8 +624,8 @@ describe("ProjectList", () => {
           ),
       },
       {
-        pathname: `/api/v1/threads/${managerThread.id}/apps`,
-        handler: () => jsonResponse([STATUS_APP]),
+        pathname: "/api/v1/apps",
+        handler: () => jsonResponse([REVIEW_BOARD_APP]),
       },
       {
         pathname: "/api/v1/projects",
@@ -665,26 +649,87 @@ describe("ProjectList", () => {
       },
     ]);
 
-    await renderProjectList(
-      {},
-      { extraUi: <PanelStateProbe threadId={managerThread.id} /> },
+    // Apps open on their own route regardless of the thread in view.
+    window.history.pushState(
+      null,
+      "",
+      `/projects/${project.id}/threads/${managerThread.id}`,
     );
 
-    fireEvent.click(
-      await findStatusAppButton(),
-    );
+    await renderProjectList();
+
+    fireEvent.click(await findReviewBoardAppButton());
 
     await waitFor(() => {
-      const probe = screen.getByTestId("panel-state");
-      expect(probe.textContent).toContain('"activeTabId":"app:status"');
-      expect(probe.textContent).toContain('"isOpen":true');
+      expect(window.location.pathname).toBe("/apps/review-board");
+    });
+  });
+
+  it("keeps global app rows enabled and routable when no thread is selected", async () => {
+    const project = makeProjectResponse({
+      id: "project-1",
+      name: "Project One",
+    });
+    const personalProject = makeProjectWithThreadsResponse({
+      id: PERSONAL_PROJECT_ID,
+      kind: "personal",
+      name: "Personal",
+      threads: [],
+    });
+    installProjectListFetchRoutes([
+      {
+        pathname: "/api/v1/sidebar-bootstrap",
+        handler: () =>
+          jsonResponse(
+            buildSidebarNavigationResponse({
+              personalProject,
+              projects: [project],
+            }),
+          ),
+      },
+      {
+        pathname: "/api/v1/apps",
+        handler: () => jsonResponse([REVIEW_BOARD_APP]),
+      },
+      {
+        pathname: "/api/v1/projects",
+        handler: () => jsonResponse([project]),
+      },
+      {
+        pathname: "/api/v1/threads",
+        handler: () => jsonResponse([]),
+      },
+      {
+        pathname: "/api/v1/system/config",
+        handler: () =>
+          jsonResponse({
+            hostDaemonPort: null,
+            voiceTranscriptionEnabled: false,
+          }),
+      },
+      {
+        pathname: "/api/v1/hosts",
+        handler: () => jsonResponse([]),
+      },
+    ]);
+
+    // Root view: no thread selected. The app still opens via its standalone
+    // route, so the row is interactive rather than disabled.
+    window.history.pushState(null, "", "/");
+
+    await renderProjectList();
+
+    const appRow = await findReviewBoardAppButton();
+    expect(appRow).toHaveProperty("disabled", false);
+
+    fireEvent.click(appRow);
+
+    await waitFor(() => {
+      expect(window.location.pathname).toBe("/apps/review-board");
     });
-    expect(window.location.pathname).toBe(
-      `/projects/${project.id}/threads/${managerThread.id}`,
-    );
   });
 
-  it("hides manager app rows when the owning manager is collapsed", async () => {
+  it("keeps the Apps section visible when a manager is collapsed", async () => {
     const project = makeProjectResponse({
       id: "project-1",
       name: "Project One",
@@ -707,7 +752,7 @@ describe("ProjectList", () => {
       name: "Personal",
       threads: [],
     });
-    installFetchRoutes([
+    installProjectListFetchRoutes([
       {
         pathname: "/api/v1/sidebar-bootstrap",
         handler: () =>
@@ -722,8 +767,8 @@ describe("ProjectList", () => {
           ),
       },
       {
-        pathname: `/api/v1/threads/${managerThread.id}/apps`,
-        handler: () => jsonResponse([STATUS_APP]),
+        pathname: "/api/v1/apps",
+        handler: () => jsonResponse([REVIEW_BOARD_APP]),
       },
       {
         pathname: "/api/v1/projects",
@@ -749,21 +794,21 @@ describe("ProjectList", () => {
 
     await renderProjectList();
 
-    expect(
-      await findStatusAppButton(),
-    ).toBeTruthy();
+    expect(await findReviewBoardAppButton()).toBeTruthy();
     expect(screen.getByText("Worker Thread")).toBeTruthy();
 
+    // Apps are no longer nested under managers, so collapsing the manager hides
+    // its worker thread but leaves the global Apps section untouched.
     fireEvent.click(
       screen.getByRole("button", {
         name: "Collapse Sidebar Manager threads",
       }),
     );
 
-    expect(
-      screen.queryByRole("button", { name: "Open Status app" }),
-    ).toBeNull();
     expect(screen.queryByText("Worker Thread")).toBeNull();
+    expect(
+      screen.getByRole("button", { name: "Open Review Board app" }),
+    ).toBeTruthy();
   });
 
   it("orders project hover actions as menu, new manager, then new thread", async () => {
@@ -780,7 +825,7 @@ describe("ProjectList", () => {
     });
     const reuseValues: (string | null)[] = [];
     const staleReuseValue = encodeReuseValue("env-stale");
-    installFetchRoutes([
+    installProjectListFetchRoutes([
       {
         pathname: "/api/v1/sidebar-bootstrap",
         handler: () =>
@@ -890,7 +935,7 @@ describe("ProjectList", () => {
       name: "Personal",
       threads: [],
     });
-    installFetchRoutes([
+    installProjectListFetchRoutes([
       {
         pathname: "/api/v1/sidebar-bootstrap",
         handler: () =>
@@ -967,7 +1012,7 @@ describe("ProjectList", () => {
   });
 
   it("shows projects unavailable when the project request fails after the websocket connects", async () => {
-    installFetchRoutes([
+    installProjectListFetchRoutes([
       {
         pathname: "/api/v1/sidebar-bootstrap",
         handler: () => new Response("starting", { status: 503 }),
@@ -1001,7 +1046,7 @@ describe("ProjectList", () => {
 
   it("shows threads unavailable when the sidebar navigation fails after the websocket connects", async () => {
     const project = makeProjectResponse();
-    installFetchRoutes([
+    installProjectListFetchRoutes([
       {
         pathname: "/api/v1/sidebar-bootstrap",
         handler: () => new Response("starting", { status: 503 }),
@@ -1051,7 +1096,7 @@ describe("ProjectList", () => {
       name: "Personal",
       threads: [projectlessThread],
     });
-    installFetchRoutes([
+    installProjectListFetchRoutes([
       {
         pathname: "/api/v1/sidebar-bootstrap",
         handler: () =>
@@ -1117,7 +1162,7 @@ describe("ProjectList", () => {
       name: "Personal",
       threads: [],
     });
-    installFetchRoutes([
+    installProjectListFetchRoutes([
       {
         pathname: "/api/v1/sidebar-bootstrap",
         handler: () =>
@@ -1177,7 +1222,7 @@ describe("ProjectList", () => {
       name: "Personal",
       threads: [],
     });
-    installFetchRoutes([
+    installProjectListFetchRoutes([
       {
         pathname: "/api/v1/sidebar-bootstrap",
         handler: () =>
@@ -1245,7 +1290,7 @@ describe("ProjectList", () => {
       name: "Personal",
       threads: [],
     });
-    installFetchRoutes([
+    installProjectListFetchRoutes([
       {
         pathname: "/api/v1/sidebar-bootstrap",
         handler: () =>
@@ -1311,7 +1356,7 @@ describe("ProjectList", () => {
       name: "Personal",
       threads: [projectlessManager, projectlessChild, projectlessThread],
     });
-    installFetchRoutes([
+    installProjectListFetchRoutes([
       {
         pathname: "/api/v1/sidebar-bootstrap",
         handler: () =>
@@ -1323,7 +1368,7 @@ describe("ProjectList", () => {
           ),
       },
       {
-        pathname: `/api/v1/threads/${projectlessManager.id}/apps`,
+        pathname: "/api/v1/apps",
         handler: () => jsonResponse([]),
       },
       {
@@ -1378,7 +1423,7 @@ describe("ProjectList", () => {
       name: "Personal",
       threads: [projectlessThread],
     });
-    installFetchRoutes([
+    installProjectListFetchRoutes([
       {
         pathname: "/api/v1/sidebar-bootstrap",
         handler: () =>
@@ -1432,7 +1477,7 @@ describe("ProjectList", () => {
       name: "Personal",
       threads: [],
     });
-    installFetchRoutes([
+    installProjectListFetchRoutes([
       {
         pathname: "/api/v1/sidebar-bootstrap",
         handler: () =>
@@ -1512,7 +1557,7 @@ describe("ProjectList", () => {
       name: "Personal",
       threads: [],
     });
-    installFetchRoutes([
+    installProjectListFetchRoutes([
       {
         pathname: "/api/v1/sidebar-bootstrap",
         handler: () =>
@@ -1556,327 +1601,4 @@ describe("ProjectList", () => {
       ),
     ).toBe(true);
   });
-
-  it("collapses the conversation and moves the single selection to the opened app row", async () => {
-    const project = makeProjectResponse({
-      id: "project-1",
-      name: "Project One",
-    });
-    const managerThread = makeThreadListEntry(project.id, 10, {
-      id: "thread-manager-app-select",
-      title: "Sidebar Manager",
-      titleFallback: "Sidebar Manager",
-      type: "manager",
-    });
-    const personalProject = makeProjectWithThreadsResponse({
-      id: PERSONAL_PROJECT_ID,
-      kind: "personal",
-      name: "Personal",
-      threads: [],
-    });
-    installFetchRoutes([
-      {
-        pathname: "/api/v1/sidebar-bootstrap",
-        handler: () =>
-          jsonResponse(
-            buildSidebarNavigationResponse({
-              personalProject,
-              projects: [project],
-              threadsByProjectId: new Map([[project.id, [managerThread]]]),
-            }),
-          ),
-      },
-      {
-        pathname: `/api/v1/threads/${managerThread.id}/apps`,
-        handler: () => jsonResponse([STATUS_APP]),
-      },
-      {
-        pathname: "/api/v1/projects",
-        handler: () => jsonResponse([project]),
-      },
-      {
-        pathname: "/api/v1/threads",
-        handler: () => jsonResponse([]),
-      },
-      {
-        pathname: "/api/v1/system/config",
-        handler: () =>
-          jsonResponse({
-            hostDaemonPort: null,
-            voiceTranscriptionEnabled: false,
-          }),
-      },
-      {
-        pathname: "/api/v1/hosts",
-        handler: () => jsonResponse([]),
-      },
-    ]);
-
-    // Start on the manager thread route so its row is the selected surface.
-    window.history.pushState(
-      null,
-      "",
-      `/projects/${project.id}/threads/${managerThread.id}`,
-    );
-
-    await renderProjectList(
-      {},
-      { extraUi: <ConversationCollapseProbe threadId={managerThread.id} /> },
-    );
-
-    const appRow = await findStatusAppButton();
-    const findManagerRow = () =>
-      screen
-        .getByText("Sidebar Manager")
-        .closest("[data-sidebar-sticky-tier='manager']");
-
-    // Conversation active: the manager row owns the single selected highlight
-    // and no app row is highlighted.
-    expect(findManagerRow()?.className).toContain("bg-sidebar-border");
-    expect(appRow.className).not.toContain("bg-sidebar-border");
-    expect(
-      screen.getByTestId(`conversation-collapsed:${managerThread.id}`)
-        .textContent,
-    ).toBe("false");
-
-    fireEvent.click(appRow);
-
-    // App opened: the conversation collapses and the app row becomes the single
-    // selected row; the manager row drops its selected background.
-    await waitFor(() => {
-      expect(
-        screen.getByTestId(`conversation-collapsed:${managerThread.id}`)
-          .textContent,
-      ).toBe("true");
-    });
-    expect(
-      screen.getByRole("button", { name: "Open Status app" }).className,
-    ).toContain("bg-sidebar-border");
-    expect(findManagerRow()?.className).not.toContain("bg-sidebar-border");
-
-    // Expanding the conversation flips the selection back to the manager row.
-    fireEvent.click(
-      screen.getByRole("button", {
-        name: `expand-conversation:${managerThread.id}`,
-      }),
-    );
-
-    await waitFor(() => {
-      expect(findManagerRow()?.className).toContain("bg-sidebar-border");
-    });
-    expect(
-      screen.getByRole("button", { name: "Open Status app" }).className,
-    ).not.toContain("bg-sidebar-border");
-  });
-
-  it("restores the conversation when its thread row is selected while collapsed", async () => {
-    const project = makeProjectResponse({
-      id: "project-1",
-      name: "Project One",
-    });
-    const managerThread = makeThreadListEntry(project.id, 10, {
-      id: "thread-manager-row-restore",
-      title: "Sidebar Manager",
-      titleFallback: "Sidebar Manager",
-      type: "manager",
-    });
-    const personalProject = makeProjectWithThreadsResponse({
-      id: PERSONAL_PROJECT_ID,
-      kind: "personal",
-      name: "Personal",
-      threads: [],
-    });
-    installFetchRoutes([
-      {
-        pathname: "/api/v1/sidebar-bootstrap",
-        handler: () =>
-          jsonResponse(
-            buildSidebarNavigationResponse({
-              personalProject,
-              projects: [project],
-              threadsByProjectId: new Map([[project.id, [managerThread]]]),
-            }),
-          ),
-      },
-      {
-        pathname: `/api/v1/threads/${managerThread.id}/apps`,
-        handler: () => jsonResponse([STATUS_APP]),
-      },
-      {
-        pathname: "/api/v1/projects",
-        handler: () => jsonResponse([project]),
-      },
-      {
-        pathname: "/api/v1/threads",
-        handler: () => jsonResponse([]),
-      },
-      {
-        pathname: "/api/v1/system/config",
-        handler: () =>
-          jsonResponse({
-            hostDaemonPort: null,
-            voiceTranscriptionEnabled: false,
-          }),
-      },
-      {
-        pathname: "/api/v1/hosts",
-        handler: () => jsonResponse([]),
-      },
-    ]);
-
-    // Start on the manager thread route so its row is the selected surface.
-    window.history.pushState(
-      null,
-      "",
-      `/projects/${project.id}/threads/${managerThread.id}`,
-    );
-
-    await renderProjectList(
-      {},
-      { extraUi: <ConversationCollapseProbe threadId={managerThread.id} /> },
-    );
-
-    // Opening the app collapses the conversation so the app fills the view.
-    fireEvent.click(
-      await findStatusAppButton(),
-    );
-    await waitFor(() => {
-      expect(
-        screen.getByTestId(`conversation-collapsed:${managerThread.id}`)
-          .textContent,
-      ).toBe("true");
-    });
-
-    // Selecting the agent/thread row is the inverse: it restores the
-    // conversation by clearing this thread's own collapse flag.
-    fireEvent.click(screen.getByRole("link", { name: "Open Sidebar Manager" }));
-
-    await waitFor(() => {
-      expect(
-        screen.getByTestId(`conversation-collapsed:${managerThread.id}`)
-          .textContent,
-      ).toBe("false");
-    });
-  });
-
-  it("keeps each thread's collapse state isolated when selecting another thread", async () => {
-    const project = makeProjectResponse({
-      id: "project-1",
-      name: "Project One",
-    });
-    const managerA = makeThreadListEntry(project.id, 10, {
-      id: "thread-manager-a",
-      title: "Manager A",
-      titleFallback: "Manager A",
-      type: "manager",
-    });
-    const managerB = makeThreadListEntry(project.id, 9, {
-      id: "thread-manager-b",
-      title: "Manager B",
-      titleFallback: "Manager B",
-      type: "manager",
-    });
-    const personalProject = makeProjectWithThreadsResponse({
-      id: PERSONAL_PROJECT_ID,
-      kind: "personal",
-      name: "Personal",
-      threads: [],
-    });
-    installFetchRoutes([
-      {
-        pathname: "/api/v1/sidebar-bootstrap",
-        handler: () =>
-          jsonResponse(
-            buildSidebarNavigationResponse({
-              personalProject,
-              projects: [project],
-              threadsByProjectId: new Map([[project.id, [managerA, managerB]]]),
-            }),
-          ),
-      },
-      {
-        pathname: `/api/v1/threads/${managerA.id}/apps`,
-        handler: () => jsonResponse([STATUS_APP]),
-      },
-      {
-        pathname: `/api/v1/threads/${managerB.id}/apps`,
-        handler: () => jsonResponse([]),
-      },
-      {
-        pathname: "/api/v1/projects",
-        handler: () => jsonResponse([project]),
-      },
-      {
-        pathname: "/api/v1/threads",
-        handler: () => jsonResponse([]),
-      },
-      {
-        pathname: "/api/v1/system/config",
-        handler: () =>
-          jsonResponse({
-            hostDaemonPort: null,
-            voiceTranscriptionEnabled: false,
-          }),
-      },
-      {
-        pathname: "/api/v1/hosts",
-        handler: () => jsonResponse([]),
-      },
-    ]);
-
-    // Start on Manager A so opening its app targets A's thread.
-    window.history.pushState(
-      null,
-      "",
-      `/projects/${project.id}/threads/${managerA.id}`,
-    );
-
-    await renderProjectList(
-      {},
-      {
-        extraUi: (
-          <>
-            <ConversationCollapseProbe threadId={managerA.id} />
-            <ConversationCollapseProbe threadId={managerB.id} />
-          </>
-        ),
-      },
-    );
-
-    // Collapse A's conversation by opening its app full-screen.
-    fireEvent.click(
-      await findStatusAppButton(),
-    );
-    await waitFor(() => {
-      expect(
-        screen.getByTestId(`conversation-collapsed:${managerA.id}`).textContent,
-      ).toBe("true");
-    });
-    // B was never collapsed.
-    expect(
-      screen.getByTestId(`conversation-collapsed:${managerB.id}`).textContent,
-    ).toBe("false");
-
-    // Selecting B's row restores only B and leaves A collapsed (full-screen app).
-    fireEvent.click(screen.getByRole("link", { name: "Open Manager B" }));
-    await waitFor(() => {
-      expect(window.location.pathname).toBe(
-        `/projects/${project.id}/threads/${managerB.id}`,
-      );
-    });
-    expect(
-      screen.getByTestId(`conversation-collapsed:${managerB.id}`).textContent,
-    ).toBe("false");
-    expect(
-      screen.getByTestId(`conversation-collapsed:${managerA.id}`).textContent,
-    ).toBe("true");
-
-    // Reselecting A restores only A.
-    fireEvent.click(screen.getByRole("link", { name: "Open Manager A" }));
-    await waitFor(() => {
-      expect(
-        screen.getByTestId(`conversation-collapsed:${managerA.id}`).textContent,
-      ).toBe("false");
-    });
-  });
 });
diff --git a/apps/app/src/components/sidebar/ProjectList.tsx b/apps/app/src/components/sidebar/ProjectList.tsx
index bbd99ffb4..5a6bbb0f2 100644
--- a/apps/app/src/components/sidebar/ProjectList.tsx
+++ b/apps/app/src/components/sidebar/ProjectList.tsx
@@ -33,13 +33,14 @@ import {
   verticalListSortingStrategy,
 } from "@dnd-kit/sortable";
 import { CSS } from "@dnd-kit/utilities";
-import type { ProjectResponse } from "@bb/server-contract";
+import type { AppSummary, ProjectResponse } from "@bb/server-contract";
 import {
   findLocalPathProjectSourceForHost,
   PERSONAL_PROJECT_ID,
   type ThreadListEntry,
 } from "@bb/domain";
 import { useAppRoute } from "@/hooks/useAppRoute";
+import { useApps } from "@/hooks/queries/thread-queries";
 import {
   useConnectionAwareQueryState,
   type ConnectionAwareQueryStatus,
@@ -86,6 +87,7 @@ import {
   COARSE_POINTER_ROW_HEIGHT_CLASS,
 } from "@/components/ui/coarse-pointer-sizing.js";
 import { ProjectRow, ProjectThreadTree } from "./ProjectRow";
+import { SidebarAppsSection } from "./SidebarAppsSection";
 import type {
   ProjectRowDragBindings,
   ProjectRowProps,
@@ -244,7 +246,12 @@ function hasSameSidebarSectionOrder(
 }
 
 function isSidebarSectionId(value: string): value is SidebarSectionId {
-  return value === "pinned" || value === "projects" || value === "threads";
+  return (
+    value === "pinned" ||
+    value === "projects" ||
+    value === "threads" ||
+    value === "apps"
+  );
 }
 
 function normalizeSidebarSectionOrder(
@@ -276,6 +283,8 @@ const EMPTY_PROJECT_THREAD_LIST_STATE: ProjectThreadListState = {
   status: "loading",
 };
 
+const EMPTY_APPS: readonly AppSummary[] = [];
+
 function getProjectThreadListState({
   status,
   threads,
@@ -618,6 +627,8 @@ function ProjectListComponent({
   const setRootComposeMode = useSetRootComposeMode();
   const sidebarNavigationQuery = useSidebarNavigation();
   const sidebarNavigation = sidebarNavigationQuery.data;
+  const appsQuery = useApps();
+  const apps = appsQuery.data ?? EMPTY_APPS;
   const projects = useMemo(
     () => sidebarNavigation?.projects.map(stripProjectThreads),
     [sidebarNavigation],
@@ -894,12 +905,17 @@ function ProjectListComponent({
     [threads],
   );
   const hasPinnedSection = pinnedSidebarState.rootItems.length > 0;
+  // No apps → no section: the empty Apps list adds nothing, so it stays hidden
+  // (like the Pinned section) until at least one global app exists.
+  const hasAppsSection = apps.length > 0;
   const visibleSidebarSectionOrder = useMemo(
     () =>
-      sidebarSectionOrder.filter(
-        (sectionId) => sectionId !== "pinned" || hasPinnedSection,
-      ),
-    [hasPinnedSection, sidebarSectionOrder],
+      sidebarSectionOrder.filter((sectionId) => {
+        if (sectionId === "pinned") return hasPinnedSection;
+        if (sectionId === "apps") return hasAppsSection;
+        return true;
+      }),
+    [hasAppsSection, hasPinnedSection, sidebarSectionOrder],
   );
   const threadsByProject = useMemo(() => {
     const grouped = new Map<string, ThreadListEntry[]>();
@@ -1159,6 +1175,7 @@ function ProjectListComponent({
       onReorderManager={handleReorderManager}
     />
   );
+  const appsSectionContent = <SidebarAppsSection apps={apps} />;
   const projectsSectionActions = onNewProject ? (
     <ProjectListProjectsSectionActions
       onNewProject={onNewProject}
@@ -1215,7 +1232,7 @@ function ProjectListComponent({
                 >
                   {projectsSectionContent}
                 </SortableSidebarSection>
-              ) : (
+              ) : sectionId === "threads" ? (
                 <SortableSidebarSection
                   key={sectionId}
                   id={sectionId}
@@ -1228,6 +1245,18 @@ function ProjectListComponent({
                 >
                   {threadsSectionContent}
                 </SortableSidebarSection>
+              ) : (
+                <SortableSidebarSection
+                  key={sectionId}
+                  id={sectionId}
+                  label="Apps"
+                  disabled={visibleSidebarSectionOrder.length < 2}
+                  consumeClickSuppression={
+                    consumeSidebarSectionClickSuppression
+                  }
+                >
+                  {appsSectionContent}
+                </SortableSidebarSection>
               ),
             )}
           </div>
diff --git a/apps/app/src/components/sidebar/ProjectRow.tsx b/apps/app/src/components/sidebar/ProjectRow.tsx
index d51e51ed7..789c86e18 100644
--- a/apps/app/src/components/sidebar/ProjectRow.tsx
+++ b/apps/app/src/components/sidebar/ProjectRow.tsx
@@ -9,7 +9,6 @@ import {
   type ReactNode,
 } from "react";
 import { flushSync } from "react-dom";
-import { useAtomValue } from "jotai";
 import {
   closestCenter,
   DndContext,
@@ -31,11 +30,10 @@ import {
 } from "@dnd-kit/sortable";
 import { CSS } from "@dnd-kit/utilities";
 import type { ThreadListEntry } from "@bb/domain";
-import type { AppSummary, ProjectResponse } from "@bb/server-contract";
+import type { ProjectResponse } from "@bb/server-contract";
 import { NavLink, useNavigate } from "react-router-dom";
 import { useCreateThreadInWorktree } from "@/hooks/useCreateThreadInWorktree";
 import { useArchiveEnvironmentThreads } from "@/hooks/mutations/environment-mutations";
-import { useThreadApps } from "@/hooks/queries/thread-queries";
 import { Button } from "@/components/ui/button.js";
 import {
   DropdownMenu,
@@ -75,9 +73,6 @@ import {
 import { cn } from "@/lib/utils";
 import { getEnvironmentWorkspaceLabelIconName } from "@/lib/environment-workspace-display";
 import { getProjectSettingsRoutePath } from "@/lib/app-route-paths";
-import { useFixedPanelTabsState } from "@/lib/fixed-panel-tabs";
-import type { FixedPanelTabsState } from "@/lib/fixed-panel-tabs-state";
-import { getThreadConversationCollapsedAtom } from "@/components/secondary-panel/threadSecondaryPanelAtoms";
 import {
   applyNeighborReorder,
   buildNeighborReorderRequest,
@@ -90,7 +85,6 @@ import {
   type ThreadRowDragBindings,
   type ThreadRowOptions,
 } from "./ThreadRow";
-import { ThreadAppRow } from "./ThreadAppRow";
 import {
   buildProjectThreadGroups,
   type EnvironmentThreadGroup,
@@ -109,7 +103,6 @@ import {
   SIDEBAR_SECTION_GROUP_LINE_CLASS,
   SIDEBAR_SECTION_LINE_CONTINUATION_CLASS,
   SIDEBAR_STANDARD_ROW_PADDING_CLASS,
-  type SidebarThreadRowIndent,
 } from "./sidebarRowClasses";
 import { SIDEBAR_SORTABLE_TRANSITION } from "./sortableMotion";
 import {
@@ -230,7 +223,6 @@ type ProjectItemClickCaptureHandler = MouseEventHandler<HTMLLIElement>;
 type ProjectThreadListClickCaptureHandler = MouseEventHandler<HTMLDivElement>;
 
 const EMPTY_PROJECT_THREADS: ThreadListEntry[] = [];
-const EMPTY_THREAD_APPS: readonly AppSummary[] = [];
 const PROJECT_ROW_LEADING_SLOT_CLASS =
   "h-7 w-8 max-md:pointer-coarse:h-10 max-md:pointer-coarse:w-10";
 
@@ -244,13 +236,6 @@ interface ManagerThreadOrderEntry {
   id: string;
 }
 
-interface ActiveThreadAppIdArgs {
-  fixedPanelTabsState: FixedPanelTabsState;
-  isConversationCollapsed: boolean;
-  selectedThreadId?: string;
-  threadId: string;
-}
-
 function getManagerThreadGroupId(
   managerThreadGroup: ManagerThreadGroup,
 ): string {
@@ -334,12 +319,6 @@ function getProjectThreadTreeManagedChildOptions(
     : THREAD_ROW_PROJECT_MANAGED_CHILD_OPTIONS;
 }
 
-function getProjectThreadTreeManagedAppIndent(
-  variant: ProjectThreadTreeVariant,
-): SidebarThreadRowIndent {
-  return variant === "section" ? "project-child" : "nested-child";
-}
-
 function getProjectThreadTreeEnvGroupedChildOptions(
   variant: ProjectThreadTreeVariant,
 ): ThreadRowOptions {
@@ -388,29 +367,6 @@ function getProjectThreadTreeManagerLineContinuationClassName(
     : SIDEBAR_MANAGER_LINE_CONTINUATION_CLASS;
 }
 
-function getActiveThreadAppId({
-  fixedPanelTabsState,
-  isConversationCollapsed,
-  selectedThreadId,
-  threadId,
-}: ActiveThreadAppIdArgs): string | null {
-  // An app is the active surface only for the open thread, and only while the
-  // conversation is tucked into the collapsed rail with the panel showing the
-  // app full. With the conversation visible it stays the selected surface, so
-  // no app row is highlighted and the manager row reads as selected instead.
-  if (selectedThreadId !== threadId || !isConversationCollapsed) {
-    return null;
-  }
-
-  const { activeTabId, isOpen, tabs } = fixedPanelTabsState.secondary;
-  if (!isOpen || activeTabId === null) {
-    return null;
-  }
-
-  const activeTab = tabs.find((tab) => tab.id === activeTabId);
-  return activeTab?.kind === "app" ? activeTab.appId : null;
-}
-
 function ProjectThreadTreeGroup({
   children,
   variant,
@@ -894,20 +850,7 @@ export const ManagerThreadGroupRow = memo(function ManagerThreadGroupRow({
   sortableStyle,
 }: ManagerThreadGroupRowProps) {
   const { managerThread, managedItems, stats } = managerThreadGroup;
-  const managerAppsQuery = useThreadApps(managerThread.id);
-  const managerApps = managerAppsQuery.data ?? EMPTY_THREAD_APPS;
-  const fixedPanelTabsState = useFixedPanelTabsState(managerThread.id);
-  const isConversationCollapsed = useAtomValue(
-    getThreadConversationCollapsedAtom(managerThread.id),
-  );
-  const activeAppId = getActiveThreadAppId({
-    fixedPanelTabsState,
-    isConversationCollapsed,
-    selectedThreadId,
-    threadId: managerThread.id,
-  });
-  const nestedChildCount = stats.managedChildCount + managerApps.length;
-  const appIndent = getProjectThreadTreeManagedAppIndent(variant);
+  const nestedChildCount = stats.managedChildCount;
   const managerOptions = useMemo<ThreadRowOptions>(
     () => ({
       kind: "manager",
@@ -939,10 +882,10 @@ export const ManagerThreadGroupRow = memo(function ManagerThreadGroupRow({
       <ThreadRow
         projectId={projectId}
         thread={managerThread}
-        // When one of this manager's apps is the active surface, that app row
-        // owns the single selected highlight; the manager row drops its full
-        // selected background (its nesting still shows context).
-        isActive={selectedThreadId === managerThread.id && activeAppId === null}
+        // The thread row itself drops its selected background when this thread
+        // shows a full-screen app (the app's sidebar row owns the highlight),
+        // so the manager row only needs to track route selection here.
+        isActive={selectedThreadId === managerThread.id}
         onProjectSelect={onProjectSelect}
         options={managerOptions}
       />
@@ -953,16 +896,6 @@ export const ManagerThreadGroupRow = memo(function ManagerThreadGroupRow({
             getProjectThreadTreeChildGroupLineClassName(variant),
           )}
         >
-          {managerApps.map((app) => (
-            <ThreadAppRow
-              key={`app:${app.id}`}
-              app={app}
-              indent={appIndent}
-              isActive={activeAppId === app.id}
-              projectId={projectId}
-              threadId={managerThread.id}
-            />
-          ))}
           {managedItems.map((item) =>
             item.kind === "thread" ? (
               <ThreadRow
diff --git a/apps/app/src/components/sidebar/SidebarAppsSection.test.tsx b/apps/app/src/components/sidebar/SidebarAppsSection.test.tsx
new file mode 100644
index 000000000..409d23fb8
--- /dev/null
+++ b/apps/app/src/components/sidebar/SidebarAppsSection.test.tsx
@@ -0,0 +1,67 @@
+// @vitest-environment jsdom
+
+import { cleanup, fireEvent, render, screen } from "@testing-library/react";
+import { MemoryRouter, useLocation } from "react-router-dom";
+import type { AppSummary } from "@bb/server-contract";
+import { afterEach, describe, expect, it } from "vitest";
+import { SidebarAppsSection } from "./SidebarAppsSection";
+
+const APPS: AppSummary[] = [
+  {
+    applicationId: "alpha",
+    name: "Alpha",
+    entry: { path: "index.html", kind: "html" },
+    capabilities: ["data"],
+    icon: { kind: "builtin", name: "GridView" },
+  },
+  {
+    applicationId: "beta",
+    name: "Beta",
+    entry: { path: "index.html", kind: "html" },
+    capabilities: ["data"],
+    icon: { kind: "builtin", name: "GridView" },
+  },
+];
+
+function LocationDisplay() {
+  const location = useLocation();
+  return <div data-testid="location">{location.pathname}</div>;
+}
+
+function renderSection(initialEntry: string) {
+  return render(
+    <MemoryRouter initialEntries={[initialEntry]}>
+      <SidebarAppsSection apps={APPS} />
+      <LocationDisplay />
+    </MemoryRouter>,
+  );
+}
+
+afterEach(() => {
+  cleanup();
+});
+
+describe("SidebarAppsSection", () => {
+  it("navigates to the standalone app route and stays enabled without a thread", () => {
+    // Root compose screen — no thread/project selected.
+    renderSection("/");
+
+    const row = screen.getByRole("button", { name: "Open Alpha app" });
+    // The row is no longer gated on a selected thread.
+    expect((row as HTMLButtonElement).disabled).toBe(false);
+
+    fireEvent.click(row);
+
+    expect(screen.getByTestId("location").textContent).toBe("/apps/alpha");
+  });
+
+  it("marks the row for the active app route as current", () => {
+    renderSection("/apps/beta");
+
+    const activeRow = screen.getByRole("button", { name: "Open Beta app" });
+    const inactiveRow = screen.getByRole("button", { name: "Open Alpha app" });
+
+    expect(activeRow.getAttribute("aria-current")).toBe("page");
+    expect(inactiveRow.getAttribute("aria-current")).toBeNull();
+  });
+});
diff --git a/apps/app/src/components/sidebar/ThreadAppRow.tsx b/apps/app/src/components/sidebar/SidebarAppsSection.tsx
similarity index 50%
rename from apps/app/src/components/sidebar/ThreadAppRow.tsx
rename to apps/app/src/components/sidebar/SidebarAppsSection.tsx
index 4cb9ed985..4121b987c 100644
--- a/apps/app/src/components/sidebar/ThreadAppRow.tsx
+++ b/apps/app/src/components/sidebar/SidebarAppsSection.tsx
@@ -1,71 +1,54 @@
 import { memo, useCallback } from "react";
 import { useNavigate } from "react-router-dom";
-import { useSetAtom } from "jotai";
 import type { AppSummary } from "@bb/server-contract";
 import { ResolvedAppIcon } from "@/components/secondary-panel/AppIcon";
-import { useOpenThreadAppTab } from "@/components/secondary-panel/useThreadFileTabs";
-import { getThreadConversationCollapsedAtom } from "@/components/secondary-panel/threadSecondaryPanelAtoms";
 import {
   COARSE_POINTER_COMPACT_ROW_HEIGHT_CLASS,
   COARSE_POINTER_GLYPH_BOX_CLASS,
   COARSE_POINTER_ICON_SIZE_CLASS,
 } from "@/components/ui/coarse-pointer-sizing.js";
-import { getThreadRoutePath } from "@/lib/app-route-paths";
+import { useAppRoute } from "@/hooks/useAppRoute";
+import { getStandaloneAppRoutePath } from "@/lib/app-route-paths";
 import { cn } from "@/lib/utils";
 import {
   SIDEBAR_ROW_BASE_CLASS,
   SIDEBAR_ROW_GLYPH_SLOT_CLASS,
   SIDEBAR_ROW_INTERACTIVE_STATE_CLASS,
-  getSidebarThreadRowPaddingClass,
-  type SidebarThreadRowIndent,
+  SIDEBAR_STANDARD_ROW_PADDING_CLASS,
 } from "./sidebarRowClasses";
 
-interface ThreadAppRowProps {
+interface SidebarAppsSectionProps {
+  apps: readonly AppSummary[];
+}
+
+interface SidebarAppRowProps {
   app: AppSummary;
-  indent: SidebarThreadRowIndent;
   isActive: boolean;
-  projectId: string;
-  threadId: string;
 }
 
-function ThreadAppRowComponent({
+const SidebarAppRow = memo(function SidebarAppRow({
   app,
-  indent,
   isActive,
-  projectId,
-  threadId,
-}: ThreadAppRowProps) {
+}: SidebarAppRowProps) {
   const navigate = useNavigate();
-  const openThreadAppTab = useOpenThreadAppTab(threadId);
-  const setConversationCollapsed = useSetAtom(
-    getThreadConversationCollapsedAtom(threadId),
-  );
+  // Global apps open on their own thread-independent route, so the row simply
+  // navigates there — no thread required, and the active highlight follows the
+  // current `/apps/:applicationId` route.
   const openApp = useCallback(() => {
-    // Opening an app makes it the active surface: reveal its tab in the
-    // secondary panel (openThreadAppTab also opens the panel) and tuck the
-    // conversation into the collapsed rail so the app fills the view.
-    openThreadAppTab(app.id);
-    setConversationCollapsed(true);
-    navigate(getThreadRoutePath({ projectId, threadId }));
-  }, [
-    app.id,
-    navigate,
-    openThreadAppTab,
-    projectId,
-    setConversationCollapsed,
-    threadId,
-  ]);
+    navigate(getStandaloneAppRoutePath(app.applicationId));
+  }, [app.applicationId, navigate]);
 
   return (
     <button
       type="button"
       aria-label={`Open ${app.name} app`}
       title={`${app.name} app`}
+      aria-current={isActive ? "page" : undefined}
       className={cn(
-        "group/thread-app-row",
+        "group/sidebar-app-row",
         SIDEBAR_ROW_BASE_CLASS,
         COARSE_POINTER_COMPACT_ROW_HEIGHT_CLASS,
-        getSidebarThreadRowPaddingClass(indent),
+        SIDEBAR_STANDARD_ROW_PADDING_CLASS,
         "cursor-pointer pr-2 text-left outline-none ring-sidebar-ring focus-visible:ring-2",
         isActive
           ? "bg-sidebar-border text-sidebar-foreground"
@@ -89,6 +72,29 @@ function ThreadAppRowComponent({
       <span className="relative z-10 min-w-0 flex-1 truncate">{app.name}</span>
     </button>
   );
-}
+});
 
-export const ThreadAppRow = memo(ThreadAppRowComponent);
+/**
+ * Top-level sidebar list of the global apps. Apps are not nested under any
+ * project or manager: there is one canonical list, sourced from `useApps()` by
+ * the caller. Opening an app routes to its standalone surface
+ * (`/apps/:applicationId`), which is thread-independent, so rows stay active
+ * even with no thread selected. The highlight follows the current app route.
+ */
+export const SidebarAppsSection = memo(function SidebarAppsSection({
+  apps,
+}: SidebarAppsSectionProps) {
+  const { applicationId: activeApplicationId } = useAppRoute();
+
+  return (
+    <div className="space-y-px group-data-[collapsible=icon]:hidden">
+      {apps.map((app) => (
+        <SidebarAppRow
+          key={app.applicationId}
+          app={app}
+          isActive={activeApplicationId === app.applicationId}
+        />
+      ))}
+    </div>
+  );
+});
diff --git a/apps/app/src/components/sidebar/ThreadRow.tsx b/apps/app/src/components/sidebar/ThreadRow.tsx
index e11ccdbb9..7ee6d9b6e 100644
--- a/apps/app/src/components/sidebar/ThreadRow.tsx
+++ b/apps/app/src/components/sidebar/ThreadRow.tsx
@@ -1,11 +1,16 @@
 import { memo, useCallback, useState, type MouseEventHandler } from "react";
-import { useSetAtom } from "jotai";
+import { useAtomValue, useSetAtom } from "jotai";
 import type {
   DraggableAttributes,
   DraggableSyntheticListeners,
 } from "@dnd-kit/core";
 import type { ThreadListEntry } from "@bb/domain";
-import { getThreadConversationCollapsedAtom } from "@/components/secondary-panel/threadSecondaryPanelAtoms";
+import {
+  getThreadConversationCollapsedAtom,
+  getThreadSecondaryPanelOpenAtom,
+} from "@/components/secondary-panel/threadSecondaryPanelAtoms";
+import { useFixedPanelTabsState } from "@/lib/fixed-panel-tabs";
+import { getActiveSecondaryAppId } from "@/lib/fixed-panel-tabs-state";
 import { Icon, type IconName } from "@/components/ui/icon.js";
 import { SidebarStickyTier } from "@/components/ui/sidebar.js";
 import { NavLink } from "react-router-dom";
@@ -300,6 +305,24 @@ function ThreadRowComponent({
   const setConversationCollapsed = useSetAtom(
     getThreadConversationCollapsedAtom(thread.id),
   );
+  // When this thread tucks its conversation into the collapsed rail to show an
+  // app full-screen, the app's sidebar row owns the single selected highlight,
+  // so this row drops its own selected background even though it is the route's
+  // selected thread. Keeps exactly one row highlighted across the sidebar.
+  const isConversationCollapsed = useAtomValue(
+    getThreadConversationCollapsedAtom(thread.id),
+  );
+  const isSecondaryPanelOpen = useAtomValue(
+    getThreadSecondaryPanelOpenAtom(thread.id),
+  );
+  const fixedPanelTabsState = useFixedPanelTabsState(thread.id);
+  const appOwnsSurface =
+    isConversationCollapsed &&
+    getActiveSecondaryAppId({
+      isSecondaryPanelOpen,
+      state: fixedPanelTabsState,
+    }) !== null;
+  const showActive = isActive && !appOwnsSurface;
   const hasPendingInteraction = thread.hasPendingInteraction;
   const threadIsBusy = isBusyThread(thread) && !hasPendingInteraction;
   const showUnreadBadge = !hasPendingInteraction && isUnreadDoneThread(thread);
@@ -353,7 +376,7 @@ function ThreadRowComponent({
       ? COARSE_POINTER_COMPACT_ROW_HEIGHT_CLASS
       : COARSE_POINTER_ROW_HEIGHT_CLASS,
     getSidebarThreadRowPaddingClass(options.indent),
-    isActive
+    showActive
       ? "bg-sidebar-border text-sidebar-foreground"
       : SIDEBAR_ROW_INTERACTIVE_STATE_CLASS,
   );
@@ -377,8 +400,8 @@ function ThreadRowComponent({
         onClick={() => {
           // Selecting a thread/agent row restores its conversation: the inverse
           // of opening an app row, which tucks the conversation into the
-          // collapsed rail so the app fills the view (see ThreadAppRow). Both
-          // write this thread's own collapse flag, so selecting one thread
+          // collapsed rail so the app fills the view (see SidebarAppsSection).
+          // Both write this thread's own collapse flag, so selecting one thread
           // never disturbs another's full-screen-app state.
           setConversationCollapsed(false);
           onProjectSelect?.();
diff --git a/apps/app/src/components/sidebar/sidebarCollapsedAtoms.ts b/apps/app/src/components/sidebar/sidebarCollapsedAtoms.ts
index 4e3b90ca9..df0bec3ad 100644
--- a/apps/app/src/components/sidebar/sidebarCollapsedAtoms.ts
+++ b/apps/app/src/components/sidebar/sidebarCollapsedAtoms.ts
@@ -6,12 +6,13 @@ const COLLAPSED_MANAGERS_STORAGE_KEY = "bb.sidebar.collapsedManagers";
 const COLLAPSED_ENVIRONMENTS_STORAGE_KEY = "bb.sidebar.collapsedEnvironments";
 const SIDEBAR_SECTION_ORDER_STORAGE_KEY = "bb.sidebar.sectionOrder";
 
-export type SidebarSectionId = "pinned" | "projects" | "threads";
+export type SidebarSectionId = "pinned" | "projects" | "threads" | "apps";
 
 export const DEFAULT_SIDEBAR_SECTION_ORDER: readonly SidebarSectionId[] = [
   "pinned",
   "projects",
   "threads",
+  "apps",
 ];
 
 export const collapsedProjectIdsAtom = atomWithStorage<string[]>(
diff --git a/apps/app/src/components/thread/ThreadActionsProvider.tsx b/apps/app/src/components/thread/ThreadActionsProvider.tsx
index e4d0b71c6..ba731cf3f 100644
--- a/apps/app/src/components/thread/ThreadActionsProvider.tsx
+++ b/apps/app/src/components/thread/ThreadActionsProvider.tsx
@@ -37,8 +37,10 @@ import {
   ThreadDeleteDialog,
   type ThreadDeleteDialogTarget,
 } from "@/components/dialogs/ThreadDeleteDialog";
+import { destroyPersistedBrowserViewsForThread } from "@/components/secondary-panel/browserViewVisibilityCoordinator";
 import { getThreadReadToggleAction } from "@/components/sidebar/threadReadState";
 import { getRootComposeRoutePath } from "@/lib/app-route-paths";
+import { getDesktopBrowserApi } from "@/lib/bb-desktop";
 import { useSetRootComposeProjectId } from "@/lib/root-compose-selection";
 
 export interface ThreadActionsContextValue {
@@ -232,6 +234,10 @@ export function ThreadActionsProvider({
         { id: thread.id, managerChildThreadsConfirmed },
         {
           onSuccess: () => {
+            destroyPersistedBrowserViewsForThread({
+              desktopBrowser: getDesktopBrowserApi(),
+              threadId: thread.id,
+            });
             closeDialog();
             navigateAwayIfViewing(thread);
           },
diff --git a/apps/app/src/hooks/cache-owners/cache-owner-registry.test.ts b/apps/app/src/hooks/cache-owners/cache-owner-registry.test.ts
index 5086bf6e7..11039ecdb 100644
--- a/apps/app/src/hooks/cache-owners/cache-owner-registry.test.ts
+++ b/apps/app/src/hooks/cache-owners/cache-owner-registry.test.ts
@@ -130,6 +130,9 @@ const CACHE_OWNER_QUERY_KEY_IMPORTS: CacheOwnerQueryKeyImportRegistry = {
   ],
   "hooks/cache-owners/realtime-cache-registry.ts": [
     "allHostQueryKeyPrefix",
+    "allAppMarkdownPreviewQueryKeyPrefix",
+    "allAppQueryKeyPrefix",
+    "allAppsQueryKeyPrefix",
     "allSystemExecutionOptionsQueryKeyPrefix",
     "allThreadQueryKeyPrefix",
     "allThreadTerminalsQueryKeyPrefix",
@@ -139,9 +142,6 @@ const CACHE_OWNER_QUERY_KEY_IMPORTS: CacheOwnerQueryKeyImportRegistry = {
     "hostsQueryKey",
     "sidebarNavigationQueryKey",
     "systemProvidersQueryKey",
-    "threadAppMarkdownPreviewQueryKeyPrefix",
-    "threadAppQueryKeyPrefix",
-    "threadAppsQueryKey",
     "threadListQueryKey",
     "threadQueryKey",
     "threadStorageFilePreviewQueryKeyPrefix",
@@ -157,11 +157,11 @@ const CACHE_OWNER_QUERY_KEY_IMPORTS: CacheOwnerQueryKeyImportRegistry = {
     "allEnvironmentQueryKeyPrefix",
     "allEnvironmentWorkStatusQueryKeyPrefix",
     "allHostQueryKeyPrefix",
+    "allAppMarkdownPreviewQueryKeyPrefix",
+    "allAppQueryKeyPrefix",
+    "allAppsQueryKeyPrefix",
     "allProjectPathsQueryKeyPrefix",
     "allSystemExecutionOptionsQueryKeyPrefix",
-    "allThreadAppMarkdownPreviewQueryKeyPrefix",
-    "allThreadAppQueryKeyPrefix",
-    "allThreadAppsQueryKeyPrefix",
     "allThreadDefaultExecutionOptionsQueryKeyPrefix",
     "allThreadPendingInteractionsQueryKeyPrefix",
     "allThreadQueryKeyPrefix",
diff --git a/apps/app/src/hooks/cache-owners/realtime-cache-registry.ts b/apps/app/src/hooks/cache-owners/realtime-cache-registry.ts
index 6fa2ab45e..539986c36 100644
--- a/apps/app/src/hooks/cache-owners/realtime-cache-registry.ts
+++ b/apps/app/src/hooks/cache-owners/realtime-cache-registry.ts
@@ -22,6 +22,9 @@ import {
 } from "./thread-list-cache-data";
 import {
   allHostQueryKeyPrefix,
+  allAppMarkdownPreviewQueryKeyPrefix,
+  allAppQueryKeyPrefix,
+  allAppsQueryKeyPrefix,
   allSystemExecutionOptionsQueryKeyPrefix,
   allThreadQueryKeyPrefix,
   allThreadTerminalsQueryKeyPrefix,
@@ -31,9 +34,6 @@ import {
   hostsQueryKey,
   sidebarNavigationQueryKey,
   systemProvidersQueryKey,
-  threadAppMarkdownPreviewQueryKeyPrefix,
-  threadAppQueryKeyPrefix,
-  threadAppsQueryKey,
   threadListQueryKey,
   threadQueryKey,
   threadTerminalsQueryKey,
@@ -273,6 +273,9 @@ export const REALTIME_SYSTEM_CHANGE_REGISTRY = {
   "config-changed": {
     dirty: [dirtySystemProviderQueries, dirtySystemExecutionOptionQueries],
   },
+  "apps-changed": {
+    dirty: [dirtyAppListQueries],
+  },
 } satisfies SystemChangeRegistry;
 
 export type ThreadChangeFlushPriority = "debounced" | "immediate";
@@ -577,9 +580,6 @@ function dirtyThreadStorageQueriesForEnvironment({
     queryKeys.push(threadStorageFilesForThreadQueryKeyPrefix(threadId));
     queryKeys.push(threadStoragePathsForThreadQueryKeyPrefix(threadId));
     queryKeys.push(threadStorageFilePreviewQueryKeyPrefix(threadId));
-    queryKeys.push(threadAppsQueryKey(threadId));
-    queryKeys.push(threadAppQueryKeyPrefix(threadId));
-    queryKeys.push(threadAppMarkdownPreviewQueryKeyPrefix(threadId));
   }
   return queryKeys;
 }
@@ -605,3 +605,11 @@ function dirtySystemProviderQueries(): QueryKey[] {
 function dirtySystemExecutionOptionQueries(): QueryKey[] {
   return [allSystemExecutionOptionsQueryKeyPrefix()];
 }
+
+function dirtyAppListQueries(): QueryKey[] {
+  return [
+    allAppsQueryKeyPrefix(),
+    allAppQueryKeyPrefix(),
+    allAppMarkdownPreviewQueryKeyPrefix(),
+  ];
+}
diff --git a/apps/app/src/hooks/cache-owners/resource-route-owner.test.tsx b/apps/app/src/hooks/cache-owners/resource-route-owner.test.tsx
index f3a3c5d7d..69683f438 100644
--- a/apps/app/src/hooks/cache-owners/resource-route-owner.test.tsx
+++ b/apps/app/src/hooks/cache-owners/resource-route-owner.test.tsx
@@ -6,6 +6,16 @@ import { QueryClientProvider } from "@tanstack/react-query";
 import type { ChangedMessage, ThreadWithRuntime } from "@bb/domain";
 import { afterEach, describe, expect, it } from "vitest";
 import { MemoryRouter, useLocation } from "react-router-dom";
+import type {
+  BbDesktopApi,
+  BbDesktopBrowserApi,
+  BbDesktopInfo,
+  BbDesktopInfoChangeHandler,
+} from "@bb/server-contract";
+import {
+  registerBrowserView,
+  resetBrowserViewPersistence,
+} from "@/components/secondary-panel/browserViewVisibilityCoordinator";
 import { collapsedProjectIdsAtom } from "@/components/sidebar/sidebarCollapsedAtoms";
 import { createAppQueryClient } from "@/lib/query-client";
 import {
@@ -13,6 +23,7 @@ import {
   getThreadRoutePath,
 } from "@/lib/app-route-paths";
 import { useRootComposeProjectId } from "@/lib/root-compose-selection";
+import { createNoopDesktopBrowserApi } from "@/test/bb-desktop-test-utils";
 import { threadQueryKey } from "../queries/query-keys";
 import {
   useDeletedResourceRouteOwner,
@@ -29,6 +40,22 @@ interface RenderRouteOwnerResult {
   queryClient: ReturnType<typeof createAppQueryClient>;
 }
 
+interface RecordedBrowserCall {
+  method: "detach" | "setVisible";
+  tabId: string;
+  visible: boolean | null;
+}
+
+const DESKTOP_INFO: BbDesktopInfo = {
+  lastCheckedAt: null,
+  latestVersion: null,
+  pendingVersion: null,
+  platform: "macos",
+  updateAvailable: false,
+  updateDownloaded: false,
+  version: "0.0.1",
+};
+
 function makeThread(
   overrides: Partial<ThreadWithRuntime> = {},
 ): ThreadWithRuntime {
@@ -59,6 +86,42 @@ function makeThread(
   };
 }
 
+function installRecordingDesktopBrowser(): RecordedBrowserCall[] {
+  const calls: RecordedBrowserCall[] = [];
+  const browser: BbDesktopBrowserApi = {
+    ...createNoopDesktopBrowserApi(),
+    detach(tabId) {
+      calls.push({ method: "detach", tabId, visible: null });
+    },
+    setVisible(request) {
+      calls.push({
+        method: "setVisible",
+        tabId: request.tabId,
+        visible: request.visible,
+      });
+    },
+  };
+  const desktop: BbDesktopApi = {
+    ...DESKTOP_INFO,
+    browser,
+    async checkForUpdates() {
+      return DESKTOP_INFO;
+    },
+    async getInfo() {
+      return DESKTOP_INFO;
+    },
+    async installUpdate() {
+      return undefined;
+    },
+    onChange(_listener: BbDesktopInfoChangeHandler) {
+      return () => undefined;
+    },
+    setTheme() {},
+  };
+  window.bbDesktop = desktop;
+  return calls;
+}
+
 function RouteProbe() {
   const location = useLocation();
   const [rootComposeProjectId] = useRootComposeProjectId();
@@ -117,6 +180,8 @@ function renderRouteOwner({
 
 afterEach(() => {
   cleanup();
+  delete window.bbDesktop;
+  resetBrowserViewPersistence();
 });
 
 describe("useDeletedResourceRouteOwner", () => {
@@ -231,4 +296,48 @@ describe("useDeletedResourceRouteOwner", () => {
     );
     expect(jotaiStore.get(collapsedProjectIdsAtom)).toEqual([activeProjectId]);
   });
+
+  it("releases retained browser views when an environment is deleted remotely", () => {
+    const calls = installRecordingDesktopBrowser();
+    registerBrowserView({
+      environmentId: "env_deleted",
+      tabId: "browser:deleted-environment",
+      threadId: "thr_deleted_environment",
+    });
+    registerBrowserView({
+      environmentId: "env_other",
+      tabId: "browser:other-environment",
+      threadId: "thr_other_environment",
+    });
+    const activeProjectRoute = getLegacyProjectComposeRoutePath("proj_1");
+    const { handleChanged } = renderRouteOwner({
+      initialEntry: activeProjectRoute,
+    });
+    const message: ChangedMessage = {
+      type: "changed",
+      entity: "environment",
+      id: "env_deleted",
+      changes: ["environment-deleted"],
+    };
+
+    act(() => {
+      handleChanged()(message);
+    });
+
+    expect(calls).toEqual([
+      {
+        method: "setVisible",
+        tabId: "browser:deleted-environment",
+        visible: false,
+      },
+      {
+        method: "detach",
+        tabId: "browser:deleted-environment",
+        visible: null,
+      },
+    ]);
+    expect(screen.getByTestId("location").textContent).toBe(
+      activeProjectRoute,
+    );
+  });
 });
diff --git a/apps/app/src/hooks/cache-owners/resource-route-owner.ts b/apps/app/src/hooks/cache-owners/resource-route-owner.ts
index 8cb583c31..bedb32713 100644
--- a/apps/app/src/hooks/cache-owners/resource-route-owner.ts
+++ b/apps/app/src/hooks/cache-owners/resource-route-owner.ts
@@ -4,11 +4,17 @@ import { useNavigate } from "react-router-dom";
 import { useQueryClient } from "@tanstack/react-query";
 import type {
   ChangedMessage,
+  EnvironmentChangedMessage,
   ProjectChangedMessage,
   ThreadChangedMessage,
 } from "@bb/domain";
+import {
+  destroyPersistedBrowserViewsForEnvironment,
+  destroyPersistedBrowserViewsForThread,
+} from "@/components/secondary-panel/browserViewVisibilityCoordinator";
 import { collapsedProjectIdsAtom } from "@/components/sidebar/sidebarCollapsedAtoms";
 import { getRootComposeRoutePath } from "@/lib/app-route-paths";
+import { getDesktopBrowserApi } from "@/lib/bb-desktop";
 import { useSetRootComposeProjectId } from "@/lib/root-compose-selection";
 import { useAppRoute } from "../useAppRoute";
 import { getCachedThreadProjectId } from "./thread-detail-cache-owner";
@@ -37,6 +43,16 @@ function isDeletedThreadMessage(
   );
 }
 
+function isDeletedEnvironmentMessage(
+  message: ChangedMessage,
+): message is EnvironmentChangedMessage & { id: string } {
+  return (
+    message.entity === "environment" &&
+    message.id !== undefined &&
+    message.changes.includes("environment-deleted")
+  );
+}
+
 export function useDeletedResourceRouteOwner(): DeletedResourceRouteChangeHandler {
   const navigate = useNavigate();
   const queryClient = useQueryClient();
@@ -58,9 +74,19 @@ export function useDeletedResourceRouteOwner(): DeletedResourceRouteChangeHandle
       }
 
       if (!isDeletedThreadMessage(message)) {
+        if (isDeletedEnvironmentMessage(message)) {
+          destroyPersistedBrowserViewsForEnvironment({
+            desktopBrowser: getDesktopBrowserApi(),
+            environmentId: message.id,
+          });
+        }
         return;
       }
       const deletedThreadId = message.id;
+      destroyPersistedBrowserViewsForThread({
+        desktopBrowser: getDesktopBrowserApi(),
+        threadId: deletedThreadId,
+      });
       if (routeThreadId !== deletedThreadId) {
         return;
       }
diff --git a/apps/app/src/hooks/cache-owners/system-cache-effects.ts b/apps/app/src/hooks/cache-owners/system-cache-effects.ts
index 63b253360..08656253a 100644
--- a/apps/app/src/hooks/cache-owners/system-cache-effects.ts
+++ b/apps/app/src/hooks/cache-owners/system-cache-effects.ts
@@ -10,9 +10,9 @@ import {
   allProjectPathsQueryKeyPrefix,
   allSystemExecutionOptionsQueryKeyPrefix,
   allThreadDefaultExecutionOptionsQueryKeyPrefix,
-  allThreadAppMarkdownPreviewQueryKeyPrefix,
-  allThreadAppQueryKeyPrefix,
-  allThreadAppsQueryKeyPrefix,
+  allAppMarkdownPreviewQueryKeyPrefix,
+  allAppQueryKeyPrefix,
+  allAppsQueryKeyPrefix,
   allThreadQueuedMessagesQueryKeyPrefix,
   allThreadPendingInteractionsQueryKeyPrefix,
   allThreadQueryKeyPrefix,
@@ -121,9 +121,9 @@ function getServerReconnectInvalidationQueryKeys(): QueryKey[] {
     threadPromptHistoryQueryKeyPrefix(),
     allThreadPendingInteractionsQueryKeyPrefix(),
     allThreadDefaultExecutionOptionsQueryKeyPrefix(),
-    allThreadAppsQueryKeyPrefix(),
-    allThreadAppQueryKeyPrefix(),
-    allThreadAppMarkdownPreviewQueryKeyPrefix(),
+    allAppsQueryKeyPrefix(),
+    allAppQueryKeyPrefix(),
+    allAppMarkdownPreviewQueryKeyPrefix(),
     allThreadStorageFilesQueryKeyPrefix(),
     allThreadStoragePathsQueryKeyPrefix(),
     allThreadStorageFilePreviewQueryKeyPrefix(),
diff --git a/apps/app/src/hooks/queries/query-keys.ts b/apps/app/src/hooks/queries/query-keys.ts
index 3a1dc1159..a186e7a94 100644
--- a/apps/app/src/hooks/queries/query-keys.ts
+++ b/apps/app/src/hooks/queries/query-keys.ts
@@ -36,9 +36,9 @@ export const THREAD_TERMINALS_QUERY_KEY = "threadTerminals";
 export const THREAD_STORAGE_FILES_QUERY_KEY = "threadStorageFiles";
 export const THREAD_STORAGE_PATHS_QUERY_KEY = "threadStoragePaths";
 export const THREAD_STORAGE_FILE_PREVIEW_QUERY_KEY = "threadStorageFilePreview";
-export const THREAD_APPS_QUERY_KEY = "threadApps";
-export const THREAD_APP_QUERY_KEY = "threadApp";
-export const THREAD_APP_MARKDOWN_PREVIEW_QUERY_KEY = "threadAppMarkdownPreview";
+export const APPS_QUERY_KEY = "apps";
+export const APP_QUERY_KEY = "app";
+export const APP_MARKDOWN_PREVIEW_QUERY_KEY = "appMarkdownPreview";
 export const THREAD_HOST_FILE_PREVIEW_QUERY_KEY = "threadHostFilePreview";
 export const ENVIRONMENT_QUERY_KEY = "environment";
 export const ENVIRONMENT_WORK_STATUS_QUERY_KEY = "environmentWorkStatus";
@@ -238,35 +238,21 @@ export type ThreadStorageFilePreviewQueryKeyPrefix = readonly [
   typeof THREAD_STORAGE_FILE_PREVIEW_QUERY_KEY,
   string,
 ];
-export type AllThreadAppsQueryKeyPrefix = readonly [
-  typeof THREAD_APPS_QUERY_KEY,
+export type AllAppsQueryKeyPrefix = readonly [typeof APPS_QUERY_KEY];
+export type AppsQueryKey = readonly [typeof APPS_QUERY_KEY];
+export type AllAppQueryKeyPrefix = readonly [typeof APP_QUERY_KEY];
+export type AppQueryKey = readonly [typeof APP_QUERY_KEY, string];
+export type AppQueryKeyPrefix = readonly [typeof APP_QUERY_KEY];
+export type AllAppMarkdownPreviewQueryKeyPrefix = readonly [
+  typeof APP_MARKDOWN_PREVIEW_QUERY_KEY,
 ];
-export type ThreadAppsQueryKey = readonly [
-  typeof THREAD_APPS_QUERY_KEY,
-  string,
-];
-export type AllThreadAppQueryKeyPrefix = readonly [typeof THREAD_APP_QUERY_KEY];
-export type ThreadAppQueryKey = readonly [
-  typeof THREAD_APP_QUERY_KEY,
-  string,
-  string,
-];
-export type ThreadAppQueryKeyPrefix = readonly [
-  typeof THREAD_APP_QUERY_KEY,
-  string,
-];
-export type AllThreadAppMarkdownPreviewQueryKeyPrefix = readonly [
-  typeof THREAD_APP_MARKDOWN_PREVIEW_QUERY_KEY,
-];
-export type ThreadAppMarkdownPreviewQueryKey = readonly [
-  typeof THREAD_APP_MARKDOWN_PREVIEW_QUERY_KEY,
-  string,
+export type AppMarkdownPreviewQueryKey = readonly [
+  typeof APP_MARKDOWN_PREVIEW_QUERY_KEY,
   string,
   string | null | undefined,
 ];
-export type ThreadAppMarkdownPreviewQueryKeyPrefix = readonly [
-  typeof THREAD_APP_MARKDOWN_PREVIEW_QUERY_KEY,
-  string,
+export type AppMarkdownPreviewQueryKeyPrefix = readonly [
+  typeof APP_MARKDOWN_PREVIEW_QUERY_KEY,
 ];
 export type ThreadHostFilePreviewQueryKey = readonly [
   typeof THREAD_HOST_FILE_PREVIEW_QUERY_KEY,
@@ -670,47 +656,39 @@ export function threadStorageFilePreviewQueryKeyPrefix(
   return [THREAD_STORAGE_FILE_PREVIEW_QUERY_KEY, threadId];
 }
 
-export function allThreadAppsQueryKeyPrefix(): AllThreadAppsQueryKeyPrefix {
-  return [THREAD_APPS_QUERY_KEY];
+export function allAppsQueryKeyPrefix(): AllAppsQueryKeyPrefix {
+  return [APPS_QUERY_KEY];
 }
 
-export function threadAppsQueryKey(threadId: string): ThreadAppsQueryKey {
-  return [THREAD_APPS_QUERY_KEY, threadId];
+export function appsQueryKey(): AppsQueryKey {
+  return [APPS_QUERY_KEY];
 }
 
-export function allThreadAppQueryKeyPrefix(): AllThreadAppQueryKeyPrefix {
-  return [THREAD_APP_QUERY_KEY];
+export function allAppQueryKeyPrefix(): AllAppQueryKeyPrefix {
+  return [APP_QUERY_KEY];
 }
 
-export function threadAppQueryKey(
-  threadId: string,
-  appId: string,
-): ThreadAppQueryKey {
-  return [THREAD_APP_QUERY_KEY, threadId, appId];
+export function appQueryKey(applicationId: string): AppQueryKey {
+  return [APP_QUERY_KEY, applicationId];
 }
 
-export function threadAppQueryKeyPrefix(
-  threadId: string,
-): ThreadAppQueryKeyPrefix {
-  return [THREAD_APP_QUERY_KEY, threadId];
+export function appQueryKeyPrefix(): AppQueryKeyPrefix {
+  return [APP_QUERY_KEY];
 }
 
-export function allThreadAppMarkdownPreviewQueryKeyPrefix(): AllThreadAppMarkdownPreviewQueryKeyPrefix {
-  return [THREAD_APP_MARKDOWN_PREVIEW_QUERY_KEY];
+export function allAppMarkdownPreviewQueryKeyPrefix(): AllAppMarkdownPreviewQueryKeyPrefix {
+  return [APP_MARKDOWN_PREVIEW_QUERY_KEY];
 }
 
-export function threadAppMarkdownPreviewQueryKey(
-  threadId: string,
-  appId: string,
+export function appMarkdownPreviewQueryKey(
+  applicationId: string,
   entryPath: string | null | undefined,
-): ThreadAppMarkdownPreviewQueryKey {
-  return [THREAD_APP_MARKDOWN_PREVIEW_QUERY_KEY, threadId, appId, entryPath];
+): AppMarkdownPreviewQueryKey {
+  return [APP_MARKDOWN_PREVIEW_QUERY_KEY, applicationId, entryPath];
 }
 
-export function threadAppMarkdownPreviewQueryKeyPrefix(
-  threadId: string,
-): ThreadAppMarkdownPreviewQueryKeyPrefix {
-  return [THREAD_APP_MARKDOWN_PREVIEW_QUERY_KEY, threadId];
+export function appMarkdownPreviewQueryKeyPrefix(): AppMarkdownPreviewQueryKeyPrefix {
+  return [APP_MARKDOWN_PREVIEW_QUERY_KEY];
 }
 
 export function threadHostFilePreviewQueryKey(
diff --git a/apps/app/src/hooks/queries/thread-queries.ts b/apps/app/src/hooks/queries/thread-queries.ts
index 8dc4204b9..b3fa366c2 100644
--- a/apps/app/src/hooks/queries/thread-queries.ts
+++ b/apps/app/src/hooks/queries/thread-queries.ts
@@ -49,9 +49,9 @@ import {
   threadStorageFilesQueryKey,
   threadStoragePathsQueryKey,
   threadStorageFilePreviewQueryKey,
-  threadAppMarkdownPreviewQueryKey,
-  threadAppQueryKey,
-  threadAppsQueryKey,
+  appMarkdownPreviewQueryKey,
+  appQueryKey,
+  appsQueryKey,
   threadHostFilePreviewQueryKey,
   threadTimelineQueryKey,
   threadTimelineTurnSummaryDetailsQueryKey,
@@ -528,70 +528,51 @@ export function useThreadStorageFilePreview(
 }
 
 /**
- * Thread apps rarely change within a session and are read from both the sidebar
- * (a query per manager row) and the thread detail view. A shared default stale
- * window lets navigation reuse a recent sidebar fetch instead of refetching on
- * detail mount; callers can still override `staleTime` explicitly.
+ * Apps rarely change within a session and are read from both the sidebar and
+ * thread detail view. A shared default stale window lets navigation reuse a
+ * recent fetch instead of refetching on detail mount; callers can still
+ * override `staleTime` explicitly.
  */
-const THREAD_APPS_STALE_TIME_MS = 30_000;
+const APPS_STALE_TIME_MS = 30_000;
 
-export function useThreadApps(id: string, options?: QueryOptions) {
+export function useApps(options?: QueryOptions) {
   return useQuery<AppSummary[]>({
-    queryKey: threadAppsQueryKey(id),
-    queryFn: ({ signal }) =>
-      api.listThreadApps(requireThreadId(id, "useThreadApps"), signal),
-    enabled: (options?.enabled ?? true) && Boolean(id),
+    queryKey: appsQueryKey(),
+    queryFn: ({ signal }) => api.listApps(signal),
+    enabled: options?.enabled ?? true,
     refetchOnMount: options?.refetchOnMount ?? true,
     refetchOnWindowFocus: false,
-    staleTime: options?.staleTime ?? THREAD_APPS_STALE_TIME_MS,
+    staleTime: options?.staleTime ?? APPS_STALE_TIME_MS,
   });
 }
 
-export function useThreadApp(
-  id: string,
-  appId: string | null | undefined,
+export function useApp(
+  applicationId: string | null | undefined,
   options?: QueryOptions,
 ) {
-  const queryClient = useQueryClient();
-
   return useQuery<AppDetail>({
-    queryKey: threadAppQueryKey(id, appId ?? ""),
+    queryKey: appQueryKey(applicationId ?? ""),
     queryFn: ({ signal }) =>
-      api.getThreadApp(
-        requireThreadId(id, "useThreadApp"),
-        appId ?? "",
-        signal,
-      ),
-    enabled: (options?.enabled ?? true) && Boolean(id) && Boolean(appId),
+      api.getApp(applicationId ?? "", signal),
+    enabled: (options?.enabled ?? true) && Boolean(applicationId),
     refetchOnMount: options?.refetchOnMount ?? true,
     refetchOnWindowFocus: false,
-    placeholderData: () =>
-      queryClient
-        .getQueryData<AppSummary[]>(threadAppsQueryKey(id))
-        ?.find((app) => app.id === appId),
     staleTime: options?.staleTime,
   });
 }
 
-export function useThreadAppMarkdownPreview(
-  id: string,
-  appId: string | null | undefined,
+export function useAppMarkdownPreview(
+  applicationId: string | null | undefined,
   entryPath: string | null | undefined,
   options?: QueryOptions,
 ) {
   return useQuery<FilePreview>({
-    queryKey: threadAppMarkdownPreviewQueryKey(id, appId ?? "", entryPath),
+    queryKey: appMarkdownPreviewQueryKey(applicationId ?? "", entryPath),
     queryFn: ({ signal }) =>
-      api.getThreadAppMarkdownPreview(
-        requireThreadId(id, "useThreadAppMarkdownPreview"),
-        appId ?? "",
-        entryPath ?? "",
-        signal,
-      ),
+      api.getAppMarkdownPreview(applicationId ?? "", entryPath ?? "", signal),
     enabled:
       (options?.enabled ?? true) &&
-      Boolean(id) &&
-      Boolean(appId) &&
+      Boolean(applicationId) &&
       Boolean(entryPath),
     refetchOnWindowFocus: false,
     staleTime: options?.staleTime,
diff --git a/apps/app/src/hooks/realtime-cache-effects.test.ts b/apps/app/src/hooks/realtime-cache-effects.test.ts
index 3c4ceacde..c9aea770b 100644
--- a/apps/app/src/hooks/realtime-cache-effects.test.ts
+++ b/apps/app/src/hooks/realtime-cache-effects.test.ts
@@ -4,11 +4,13 @@ import {
   ENVIRONMENT_CHANGE_KINDS,
   HOST_CHANGE_KINDS,
   PROJECT_CHANGE_KINDS,
+  SYSTEM_CHANGE_KINDS,
   THREAD_CHANGE_KINDS,
 } from "@bb/domain";
 import { createAppQueryClient } from "@/lib/query-client";
 import {
   archivedThreadsListQueryKey,
+  appsQueryKey,
   environmentGitDiffQueryKey,
   environmentWorkStatusQueryKey,
   localPathExistenceQueryKey,
@@ -17,9 +19,6 @@ import {
   projectSourceBranchesQueryKey,
   projectsQueryKey,
   sidebarNavigationQueryKey,
-  threadAppMarkdownPreviewQueryKey,
-  threadAppQueryKey,
-  threadAppsQueryKey,
   threadQueuedMessagesQueryKey,
   threadListQueryKey,
   threadPromptHistoryQueryKey,
@@ -33,6 +32,7 @@ import {
   REALTIME_ENVIRONMENT_CHANGE_REGISTRY,
   REALTIME_HOST_CHANGE_REGISTRY,
   REALTIME_PROJECT_CHANGE_REGISTRY,
+  REALTIME_SYSTEM_CHANGE_REGISTRY,
   REALTIME_THREAD_CHANGE_REGISTRY,
 } from "./cache-owners/realtime-cache-registry";
 
@@ -127,6 +127,14 @@ describe("createRealtimeCacheEffects", () => {
     }
   });
 
+  it("maps every realtime system change to at least one dirty handler", () => {
+    for (const changeKind of SYSTEM_CHANGE_KINDS) {
+      expect(
+        REALTIME_SYSTEM_CHANGE_REGISTRY[changeKind].dirty.length,
+      ).toBeGreaterThan(0);
+    }
+  });
+
   it.each(PROJECT_PROMPT_HISTORY_THREAD_CHANGES)(
     "invalidates all cached project prompt histories for %s thread events",
     (change) => {
@@ -583,89 +591,6 @@ describe("createRealtimeCacheEffects", () => {
     effects.dispose();
   });
 
-  it("refetches active thread app queries for thread storage changes", async () => {
-    vi.useFakeTimers();
-    const { effects, queryClient } = createRealtimeEffectsTestContext();
-    const threadKey = threadQueryKey("thr_1");
-    const appListKey = threadAppsQueryKey("thr_1");
-    const appDetailKey = threadAppQueryKey("thr_1", "status");
-    const markdownPreviewKey = threadAppMarkdownPreviewQueryKey(
-      "thr_1",
-      "status",
-      "index.md",
-    );
-    const nextAppDetail = {
-      id: "status",
-      name: "Status",
-      entry: { path: "index.html", kind: "html" },
-      capabilities: ["data"],
-      icon: { kind: "builtin", name: "ListTodo" },
-    };
-    const nextMarkdownPreview = {
-      kind: "text",
-      content: "new",
-      mimeType: "text/markdown",
-      path: "index.md",
-      url: "/new",
-    };
-    queryClient.setQueryData(threadKey, {
-      id: "thr_1",
-      environmentId: "env-1",
-    });
-    queryClient.setQueryData(appListKey, []);
-    queryClient.setQueryData(appDetailKey, {
-      ...nextAppDetail,
-      name: "Old Status",
-    });
-    queryClient.setQueryData(markdownPreviewKey, {
-      ...nextMarkdownPreview,
-      content: "old",
-    });
-    const appListQueryFn = vi.fn(async () => [nextAppDetail]);
-    const appDetailQueryFn = vi.fn(async () => nextAppDetail);
-    const markdownPreviewQueryFn = vi.fn(async () => nextMarkdownPreview);
-    const appListObserver = new QueryObserver(queryClient, {
-      queryKey: appListKey,
-      queryFn: appListQueryFn,
-      staleTime: Infinity,
-    });
-    const appDetailObserver = new QueryObserver(queryClient, {
-      queryKey: appDetailKey,
-      queryFn: appDetailQueryFn,
-      staleTime: Infinity,
-    });
-    const markdownPreviewObserver = new QueryObserver(queryClient, {
-      queryKey: markdownPreviewKey,
-      queryFn: markdownPreviewQueryFn,
-      staleTime: Infinity,
-    });
-    const unsubscribeAppList = appListObserver.subscribe(() => {});
-    const unsubscribeAppDetail = appDetailObserver.subscribe(() => {});
-    const unsubscribeMarkdownPreview = markdownPreviewObserver.subscribe(
-      () => {},
-    );
-    appListQueryFn.mockClear();
-    appDetailQueryFn.mockClear();
-    markdownPreviewQueryFn.mockClear();
-
-    effects.handleChanged({
-      type: "changed",
-      entity: "environment",
-      id: "env-1",
-      changes: ["thread-storage-changed"],
-    });
-    await vi.advanceTimersByTimeAsync(250);
-
-    expect(appListQueryFn).toHaveBeenCalledTimes(1);
-    expect(appDetailQueryFn).toHaveBeenCalledTimes(1);
-    expect(markdownPreviewQueryFn).toHaveBeenCalledTimes(1);
-
-    unsubscribeAppList();
-    unsubscribeAppDetail();
-    unsubscribeMarkdownPreview();
-    effects.dispose();
-  });
-
   it("does not invalidate timeline queries for status-only thread changes", () => {
     const { effects, queryClient } = createRealtimeEffectsTestContext();
     const timelineKey = threadTimelineQueryKey("thr_1", undefined);
@@ -1069,6 +994,31 @@ describe("createRealtimeCacheEffects", () => {
     effects.dispose();
   });
 
+  it("refetches active app list queries for app list changes without reconnect", async () => {
+    const { effects, queryClient } = createRealtimeEffectsTestContext();
+    const appsKey = appsQueryKey();
+    queryClient.setQueryData(appsKey, []);
+    const appsQueryFn = vi.fn(async () => []);
+    const appsObserver = new QueryObserver(queryClient, {
+      queryKey: appsKey,
+      queryFn: appsQueryFn,
+      staleTime: Infinity,
+    });
+    const unsubscribeApps = appsObserver.subscribe(() => {});
+    appsQueryFn.mockClear();
+
+    effects.handleChanged({
+      type: "changed",
+      entity: "system",
+      changes: ["apps-changed"],
+    });
+
+    await vi.waitFor(() => expect(appsQueryFn).toHaveBeenCalledTimes(1));
+
+    unsubscribeApps();
+    effects.dispose();
+  });
+
   it("invalidates cached thread terminals for terminal changes", () => {
     vi.useFakeTimers();
     const { effects, queryClient, terminalKey } =
diff --git a/apps/app/src/hooks/useAppRoute.test.tsx b/apps/app/src/hooks/useAppRoute.test.tsx
index d9a6ca76c..506287b2a 100644
--- a/apps/app/src/hooks/useAppRoute.test.tsx
+++ b/apps/app/src/hooks/useAppRoute.test.tsx
@@ -85,6 +85,16 @@ describe("useAppRoute", () => {
     expect(route.isProjectlessView).toBe(false);
   });
 
+  it("recognizes the standalone app route", () => {
+    const route = renderRouteCapture({ initialEntry: "/apps/alpha" });
+
+    expect(route.applicationId).toBe("alpha");
+    expect(route.isAppView).toBe(true);
+    expect(route.threadId).toBeUndefined();
+    expect(route.projectId).toBeUndefined();
+    expect(route.isThreadView).toBe(false);
+  });
+
   it("does not accept personal project thread routes", () => {
     const route = renderRouteCapture({
       initialEntry: `/projects/${PERSONAL_PROJECT_ID}/threads/thr_personal`,
diff --git a/apps/app/src/hooks/useAppRoute.ts b/apps/app/src/hooks/useAppRoute.ts
index 66c420b45..707578af4 100644
--- a/apps/app/src/hooks/useAppRoute.ts
+++ b/apps/app/src/hooks/useAppRoute.ts
@@ -6,6 +6,10 @@ export interface AppRouteState {
   projectId: string | undefined;
   /** ID of the thread in view (thread detail only), else undefined. */
   threadId: string | undefined;
+  /** ID of the global app in view (standalone app route only), else undefined. */
+  applicationId: string | undefined;
+  /** On the standalone app surface (`/apps/:applicationId`). */
+  isAppView: boolean;
   /** On a thread detail URL. */
   isThreadView: boolean;
   /** On the project's archived threads list. */
@@ -35,6 +39,7 @@ export function useAppRoute(): AppRouteState {
   const projectlessThreadMatch = useMatch("/threads/:threadId/*");
   const projectArchivedMatch = useMatch("/projects/:projectId/archived");
   const projectSettingsMatch = useMatch("/projects/:projectId/settings");
+  const appMatch = useMatch("/apps/:applicationId");
   const isRootView = location.pathname === "/";
   const isUnsupportedPersonalProjectThread =
     projectThreadMatch?.params.projectId === PERSONAL_PROJECT_ID;
@@ -55,6 +60,8 @@ export function useAppRoute(): AppRouteState {
   return {
     projectId,
     threadId,
+    applicationId: appMatch?.params.applicationId,
+    isAppView: Boolean(appMatch),
     isThreadView:
       Boolean(projectlessThreadMatch) ||
       (Boolean(projectThreadMatch) && !isUnsupportedPersonalProjectThread),
diff --git a/apps/app/src/hooks/useFileSearchSuggestions.test.tsx b/apps/app/src/hooks/useFileSearchSuggestions.test.tsx
index c2937f257..a3253110e 100644
--- a/apps/app/src/hooks/useFileSearchSuggestions.test.tsx
+++ b/apps/app/src/hooks/useFileSearchSuggestions.test.tsx
@@ -17,7 +17,7 @@ vi.mock("@/lib/api", async (importOriginal) => {
   return {
     ...actual,
     searchProjectPaths: vi.fn(),
-    listThreadApps: vi.fn(),
+    listApps: vi.fn(),
     listThreadStoragePaths: vi.fn(),
   };
 });
@@ -63,9 +63,9 @@ function isFilePathSearchSuggestion(
   return suggestion.entryKind === "file";
 }
 
-const STATUS_APP: AppSummary = {
-  id: "status",
-  name: "Status",
+const APP: AppSummary = {
+  applicationId: "status",
+  name: "Review Board",
   entry: { path: "index.html", kind: "html" },
   capabilities: ["data", "message"],
   icon: { kind: "builtin", name: "ListTodo" },
@@ -78,7 +78,7 @@ afterEach(() => {
 
 describe("useFileSearchSuggestions", () => {
   it("merges workspace and manager thread-storage file results", async () => {
-    vi.mocked(api.listThreadApps).mockResolvedValue([]);
+    vi.mocked(api.listApps).mockResolvedValue([]);
     vi.mocked(api.searchProjectPaths).mockResolvedValue(
       makePathResponse([
         {
@@ -145,7 +145,7 @@ describe("useFileSearchSuggestions", () => {
   });
 
   it("returns matching apps before files", async () => {
-    vi.mocked(api.listThreadApps).mockResolvedValue([STATUS_APP]);
+    vi.mocked(api.listApps).mockResolvedValue([APP]);
     vi.mocked(api.searchProjectPaths).mockResolvedValue(
       makePathResponse([
         {
@@ -180,8 +180,8 @@ describe("useFileSearchSuggestions", () => {
     expect(result.current.suggestions[0]).toMatchObject({
       source: "app",
       entryKind: "app",
-      appId: "status",
-      name: "Status",
+      applicationId: "status",
+      name: "Review Board",
     });
     expect(result.current.suggestions[1]).toMatchObject({
       source: "workspace",
diff --git a/apps/app/src/hooks/useFileSearchSuggestions.ts b/apps/app/src/hooks/useFileSearchSuggestions.ts
index af7c4e4b6..2317d5640 100644
--- a/apps/app/src/hooks/useFileSearchSuggestions.ts
+++ b/apps/app/src/hooks/useFileSearchSuggestions.ts
@@ -6,7 +6,7 @@ import {
   type PathSuggestion,
   type PathSuggestionSource,
 } from "./usePathSuggestions";
-import { useThreadApps } from "./queries/thread-queries";
+import { useApps } from "./queries/thread-queries";
 
 const DEFAULT_FILE_SEARCH_SUGGESTION_LIMIT = 8;
 
@@ -14,7 +14,7 @@ export interface AppSearchSuggestion {
   source: "app";
   entryKind: "app";
   app: AppSummary;
-  appId: string;
+  applicationId: string;
   name: string;
   score: number;
 }
@@ -84,7 +84,7 @@ function scoreAppSearchMatch(app: AppSummary, normalizedQuery: string): number {
   }
 
   const normalizedName = app.name.toLowerCase();
-  const normalizedId = app.id.toLowerCase();
+  const normalizedId = app.applicationId.toLowerCase();
   if (normalizedName === normalizedQuery || normalizedId === normalizedQuery) {
     return 100;
   }
@@ -119,7 +119,7 @@ function buildAppSearchSuggestions({
       source: "app",
       entryKind: "app",
       app,
-      appId: app.id,
+      applicationId: app.applicationId,
       name: app.name,
       score,
     });
@@ -149,17 +149,17 @@ export function useFileSearchSuggestions(
     includeDirectories: false,
   });
   const canSearchApps = Boolean(args.currentThreadId);
-  const threadApps = useThreadApps(args.currentThreadId ?? "", {
+  const apps = useApps({
     enabled: canSearchApps,
   });
   const appSuggestions = useMemo<AppSearchSuggestion[]>(
     () =>
       buildAppSearchSuggestions({
-        apps: threadApps.data ?? [],
+        apps: apps.data ?? [],
         limit,
         query: args.query ?? "",
       }),
-    [args.query, limit, threadApps.data],
+    [args.query, apps.data, limit],
   );
   const fileSuggestions = useMemo<FilePathSearchSuggestion[]>(
     () =>
@@ -180,8 +180,8 @@ export function useFileSearchSuggestions(
     suggestions,
     isLoading:
       suggestions.length === 0 &&
-      (pathSuggestions.isLoading || (canSearchApps && threadApps.isLoading)),
-    isError: pathSuggestions.isError || (canSearchApps && threadApps.isError),
+      (pathSuggestions.isLoading || (canSearchApps && apps.isLoading)),
+    isError: pathSuggestions.isError || (canSearchApps && apps.isError),
     isDebouncing: pathSuggestions.isDebouncing,
     isUnavailable: !canSearchApps && !canSearchWorkspace && !canSearchThreadStorage,
   };
diff --git a/apps/app/src/lib/api.ts b/apps/app/src/lib/api.ts
index f64088b1e..063ff3cf1 100644
--- a/apps/app/src/lib/api.ts
+++ b/apps/app/src/lib/api.ts
@@ -92,7 +92,7 @@ import {
   type FilePreviewTarget,
 } from "./file-preview";
 import {
-  buildThreadAppAssetUrl,
+  buildAppPublicFileUrl,
   buildThreadHostFileContentUrl,
   buildThreadStorageContentUrl,
 } from "./file-content-urls";
@@ -886,34 +886,28 @@ export async function getThreadStorageFilePreview(
   );
 }
 
-export async function listThreadApps(
-  id: string,
+export async function listApps(
   signal?: AbortSignal,
 ): Promise<AppSummary[]> {
   return request<AppSummary[]>(
-    apiClient.threads[":id"].apps.$get(
-      { param: { id } },
-      requestOptions(signal),
-    ),
+    apiClient.apps.$get({}, requestOptions(signal)),
   );
 }
 
-export async function getThreadApp(
-  id: string,
-  appId: string,
+export async function getApp(
+  applicationId: string,
   signal?: AbortSignal,
 ): Promise<AppDetail> {
   return request<AppDetail>(
-    apiClient.threads[":id"].apps[":appId"].$get(
-      { param: { id, appId } },
+    apiClient.apps[":applicationId"].$get(
+      { param: { applicationId } },
       requestOptions(signal),
     ),
   );
 }
 
-export async function getThreadAppMarkdownPreview(
-  id: string,
-  appId: string,
+export async function getAppMarkdownPreview(
+  applicationId: string,
   path: string,
   signal?: AbortSignal,
 ): Promise<FilePreview> {
@@ -921,7 +915,7 @@ export async function getThreadAppMarkdownPreview(
     {
       name: path.split("/").at(-1),
       path,
-      url: buildThreadAppAssetUrl(id, appId, path),
+      url: buildAppPublicFileUrl(applicationId, path),
     },
     signal,
   );
diff --git a/apps/app/src/lib/app-route-paths.ts b/apps/app/src/lib/app-route-paths.ts
index a3c098e29..edeab3972 100644
--- a/apps/app/src/lib/app-route-paths.ts
+++ b/apps/app/src/lib/app-route-paths.ts
@@ -5,6 +5,7 @@ export const AUTH_CALLBACK_ROUTE_PATH = "/auth/callback";
 export const APP_SETTINGS_ROUTE_PATH = "/settings";
 export const DEVELOPMENT_REPLAY_ROUTE_PATH = "/development-only/replay";
 export const ROOT_COMPOSE_ROUTE_PATH = APP_ROOT_ROUTE_PATH;
+export const STANDALONE_APP_ROUTE_PATH = "/apps/:applicationId";
 export const LEGACY_PROJECT_COMPOSE_ROUTE_PATH = "/projects/:projectId";
 export const PROJECTLESS_THREAD_DETAIL_ROUTE_PATH = "/threads/:threadId";
 export const PROJECT_SETTINGS_ROUTE_PATH = "/projects/:projectId/settings";
@@ -45,10 +46,15 @@ export function getThreadRoutePath(args: ThreadRoutePathArgs): string {
     : `/projects/${args.projectId}/threads/${args.threadId}`;
 }
 
+export function getStandaloneAppRoutePath(applicationId: string): string {
+  return `/apps/${applicationId}`;
+}
+
 const baseAppRoutePatterns: readonly string[] = [
   APP_ROOT_ROUTE_PATH,
   AUTH_CALLBACK_ROUTE_PATH,
   APP_SETTINGS_ROUTE_PATH,
+  STANDALONE_APP_ROUTE_PATH,
   LEGACY_PROJECT_COMPOSE_ROUTE_PATH,
   PROJECT_SETTINGS_ROUTE_PATH,
   PROJECT_ARCHIVED_ROUTE_PATH,
diff --git a/apps/app/src/lib/browser-view-bounds-sync.ts b/apps/app/src/lib/browser-view-bounds-sync.ts
new file mode 100644
index 000000000..7b879f1ae
--- /dev/null
+++ b/apps/app/src/lib/browser-view-bounds-sync.ts
@@ -0,0 +1,5 @@
+export const BROWSER_VIEW_BOUNDS_SYNC_EVENT = "bb:browser-view-bounds-sync";
+
+export function dispatchBrowserViewBoundsSync(): void {
+  window.dispatchEvent(new Event(BROWSER_VIEW_BOUNDS_SYNC_EVENT));
+}
diff --git a/apps/app/src/lib/file-content-urls.ts b/apps/app/src/lib/file-content-urls.ts
index 13ee9726b..04437f1ec 100644
--- a/apps/app/src/lib/file-content-urls.ts
+++ b/apps/app/src/lib/file-content-urls.ts
@@ -35,33 +35,56 @@ export function buildThreadStorageRawContentUrl(
   return `/api/v1/threads/${encodeURIComponent(threadId)}/thread-storage/files/${encodePathSegments(path)}`;
 }
 
-export function buildThreadAppEntryUrl(
-  threadId: string,
-  appId: string,
-): string {
-  return `/api/v1/threads/${encodeURIComponent(
-    threadId,
-  )}/apps/${encodeURIComponent(appId)}/`;
+export interface AppEntryUrlArgs {
+  applicationId: string;
+  /**
+   * Thread the app should target for its `message` capability. `null` for the
+   * standalone surface, where the app renders thread-independently and has no
+   * thread to post into.
+   */
+  targetThreadId: string | null;
+  /**
+   * Cache-busting token (typically the app detail's `dataUpdatedAt`) so the
+   * iframe reloads when the underlying app changes. Omitted when no reload
+   * tracking is needed.
+   */
+  reloadToken?: number | string;
 }
 
-export function buildThreadAppAssetUrl(
-  threadId: string,
-  appId: string,
+export function buildAppEntryUrl({
+  applicationId,
+  targetThreadId,
+  reloadToken,
+}: AppEntryUrlArgs): string {
+  const params = new URLSearchParams();
+  if (targetThreadId !== null) {
+    params.set("targetThreadId", targetThreadId);
+  }
+  if (reloadToken !== undefined) {
+    params.set("v", String(reloadToken));
+  }
+  const query = params.toString();
+  return `/api/v1/apps/${encodeURIComponent(applicationId)}/${
+    query ? `?${query}` : ""
+  }`;
+}
+
+export function buildAppPublicFileUrl(
+  applicationId: string,
   path: string,
 ): string {
-  return `/api/v1/threads/${encodeURIComponent(
-    threadId,
-  )}/apps/${encodeURIComponent(appId)}/${encodePathSegments(path)}`;
+  return `/api/v1/apps/${encodeURIComponent(
+    applicationId,
+  )}/${encodePathSegments(path)}`;
 }
 
-export function buildThreadAppAssetBaseUrl(
-  threadId: string,
-  appId: string,
+export function buildAppPublicBaseUrl(
+  applicationId: string,
   entryPath: string,
 ): string {
   const lastSlash = entryPath.lastIndexOf("/");
   const basePath = lastSlash === -1 ? "" : entryPath.slice(0, lastSlash + 1);
-  return buildThreadAppAssetUrl(threadId, appId, basePath);
+  return buildAppPublicFileUrl(applicationId, basePath);
 }
 
 export function buildThreadHostFileContentUrl(
diff --git a/apps/app/src/lib/fixed-panel-tabs-state.test.ts b/apps/app/src/lib/fixed-panel-tabs-state.test.ts
index 7368e46d8..6dff9884c 100644
--- a/apps/app/src/lib/fixed-panel-tabs-state.test.ts
+++ b/apps/app/src/lib/fixed-panel-tabs-state.test.ts
@@ -70,7 +70,6 @@ function makeFixedPanelTabsState(
   });
 }
 
-
 describe("fixed panel tabs state storage", () => {
   it("round-trips valid state", () => {
     const state = makeFixedPanelTabsState();
@@ -86,7 +85,7 @@ describe("fixed panel tabs state storage", () => {
   });
 
   it("round-trips app tabs", () => {
-    const appTab = createAppFixedPanelTab({ appId: "status" });
+    const appTab = createAppFixedPanelTab({ applicationId: "status" });
     const state = makeFixedPanelTabsState({
       secondary: {
         tabs: [appTab],
diff --git a/apps/app/src/lib/fixed-panel-tabs-state.ts b/apps/app/src/lib/fixed-panel-tabs-state.ts
index 39ad99a13..d3557c099 100644
--- a/apps/app/src/lib/fixed-panel-tabs-state.ts
+++ b/apps/app/src/lib/fixed-panel-tabs-state.ts
@@ -82,7 +82,7 @@ const threadStorageFilePreviewFixedPanelTabSchema = z
   .strict();
 const appFixedPanelTabSchema = z
   .object({
-    appId: z.string().min(1),
+    applicationId: z.string().min(1),
     id: z.string().min(1),
     kind: z.literal("app"),
   })
@@ -194,7 +194,7 @@ export interface ThreadStorageFilePreviewFixedPanelTab {
 }
 
 export interface AppFixedPanelTab {
-  appId: string;
+  applicationId: string;
   id: string;
   kind: "app";
 }
@@ -268,6 +268,28 @@ export interface FixedPanelTabsState {
   lastUsedAt: number;
 }
 
+interface GetActiveSecondaryAppIdArgs {
+  isSecondaryPanelOpen: boolean;
+  state: FixedPanelTabsState;
+}
+
+/**
+ * The application id of the secondary panel's active tab when that tab is an
+ * app and the panel is open, else null. Lets sidebar rows tell whether a
+ * thread's panel is currently showing a given app without reaching into the
+ * tab list shape themselves.
+ */
+export function getActiveSecondaryAppId(
+  { isSecondaryPanelOpen, state }: GetActiveSecondaryAppIdArgs,
+): string | null {
+  const { activeTabId, tabs } = state.secondary;
+  if (!isSecondaryPanelOpen || activeTabId === null) {
+    return null;
+  }
+  const activeTab = tabs.find((tab) => tab.id === activeTabId);
+  return activeTab?.kind === "app" ? activeTab.applicationId : null;
+}
+
 interface FixedPanelTabsStorageKeyArgs {
   threadId: string;
 }
@@ -317,7 +339,7 @@ interface CreateThreadStorageFilePreviewFixedPanelTabArgs {
 }
 
 interface CreateAppFixedPanelTabArgs {
-  appId: string;
+  applicationId: string;
 }
 
 interface CreateBrowserFixedPanelTabArgs {
@@ -401,11 +423,11 @@ export function createThreadStorageFilePreviewFixedPanelTab({
 }
 
 export function createAppFixedPanelTab({
-  appId,
+  applicationId,
 }: CreateAppFixedPanelTabArgs): AppFixedPanelTab {
   return {
-    appId,
-    id: `app:${encodeURIComponent(appId)}`,
+    applicationId,
+    id: `app:${encodeURIComponent(applicationId)}`,
     kind: "app",
   };
 }
@@ -413,7 +435,7 @@ export function createAppFixedPanelTab({
 /**
  * Browser tabs get a fresh unique id per instance — the URL is mutable (it
  * changes on every navigation), so it cannot serve as a stable identity the way
- * an app id or file path does.
+ * an application id or file path does.
  */
 export function createBrowserFixedPanelTab({
   url,
@@ -697,7 +719,7 @@ export function areFixedPanelTabsEquivalent(
         a.path === b.path
       );
     case "app":
-      return b.kind === "app" && a.appId === b.appId;
+      return b.kind === "app" && a.applicationId === b.applicationId;
     case "browser":
       return b.kind === "browser" && a.url === b.url && a.title === b.title;
     case "thread-storage-file-preview":
diff --git a/apps/app/src/lib/fixed-panel-tabs.ts b/apps/app/src/lib/fixed-panel-tabs.ts
index 82eb2771c..68b26caf7 100644
--- a/apps/app/src/lib/fixed-panel-tabs.ts
+++ b/apps/app/src/lib/fixed-panel-tabs.ts
@@ -38,6 +38,7 @@ interface LastFixedPanelTabsTouch {
 }
 
 type FixedPanelSecondaryPanelSetter = (panel: ThreadSecondaryPanel) => void;
+type FixedPanelSecondaryPanelOpener = () => void;
 type FixedPanelSecondaryPanelCloser = () => void;
 type FixedPanelSecondaryPanelToggler = () => void;
 type FixedPanelTerminalIdSetter = (terminalId: string | null) => void;
@@ -304,6 +305,15 @@ export function useCloseFixedSecondaryPanel(
   }, [updateState]);
 }
 
+export function useOpenFixedSecondaryPanel(
+  threadId: FixedPanelTabsThreadId,
+): FixedPanelSecondaryPanelOpener {
+  const updateState = useUpdateFixedPanelTabsState(threadId);
+  return useCallback(() => {
+    updateState(openFixedSecondaryPanelState);
+  }, [updateState]);
+}
+
 export function useToggleFixedSecondaryPanel(
   threadId: string | null | undefined,
 ): FixedPanelSecondaryPanelToggler {
diff --git a/apps/app/src/views/standalone-app/StandaloneAppView.test.tsx b/apps/app/src/views/standalone-app/StandaloneAppView.test.tsx
new file mode 100644
index 000000000..6c0ad755f
--- /dev/null
+++ b/apps/app/src/views/standalone-app/StandaloneAppView.test.tsx
@@ -0,0 +1,97 @@
+// @vitest-environment jsdom
+
+import { cleanup, render, screen } from "@testing-library/react";
+import { MemoryRouter, Route, Routes } from "react-router-dom";
+import type { AppDetail } from "@bb/server-contract";
+import { afterEach, describe, expect, it, vi } from "vitest";
+import * as api from "@/lib/api";
+import { HttpError } from "@/lib/api";
+import { STANDALONE_APP_ROUTE_PATH } from "@/lib/app-route-paths";
+import { createQueryClientTestHarness } from "@/test/queryClientTestHarness";
+import { StandaloneAppView } from "./StandaloneAppView";
+
+vi.mock("@/lib/api", async (importOriginal) => {
+  const actual = await importOriginal<typeof import("@/lib/api")>();
+
+  return {
+    ...actual,
+    getApp: vi.fn(),
+    getAppMarkdownPreview: vi.fn(),
+  };
+});
+
+const HTML_APP: AppDetail = {
+  applicationId: "status",
+  name: "Review Board",
+  entry: { path: "index.html", kind: "html" },
+  capabilities: ["data", "message"],
+  icon: { kind: "builtin", name: "ListTodo" },
+  appsRootPath: "/tmp/bb-data/apps",
+  appRootPath: "/tmp/bb-data/apps/status",
+  appDataPath: "/tmp/bb-data/apps/status/data",
+};
+
+function renderStandaloneApp(applicationId: string) {
+  const { wrapper } = createQueryClientTestHarness();
+  return render(
+    <MemoryRouter initialEntries={[`/apps/${applicationId}`]}>
+      <Routes>
+        <Route
+          path={STANDALONE_APP_ROUTE_PATH}
+          element={<StandaloneAppView />}
+        />
+      </Routes>
+    </MemoryRouter>,
+    { wrapper },
+  );
+}
+
+afterEach(() => {
+  cleanup();
+  vi.clearAllMocks();
+});
+
+describe("StandaloneAppView", () => {
+  it("renders the app surface in a thread-independent iframe", async () => {
+    vi.mocked(api.getApp).mockResolvedValue(HTML_APP);
+
+    renderStandaloneApp("status");
+
+    const frame = await screen.findByTitle("Review Board");
+    // No targetThreadId on the standalone surface — the app renders without a
+    // host thread.
+    expect(frame.getAttribute("src")).toMatch(
+      /^\/api\/v1\/apps\/status\/\?v=\d+$/u,
+    );
+  });
+
+  it("shows a clean not-found state when the app is missing", async () => {
+    vi.mocked(api.getApp).mockRejectedValue(
+      new HttpError({
+        status: 404,
+        code: "app_missing",
+        message: "App not found",
+      }),
+    );
+
+    renderStandaloneApp("gone");
+
+    expect(await screen.findByText("App not found.")).toBeTruthy();
+  });
+
+  it("surfaces an invalid manifest error", async () => {
+    vi.mocked(api.getApp).mockRejectedValue(
+      new HttpError({
+        status: 422,
+        code: "invalid_manifest",
+        message: "App manifest failed validation.",
+      }),
+    );
+
+    renderStandaloneApp("broken");
+
+    expect(
+      await screen.findByText("This app's manifest is invalid."),
+    ).toBeTruthy();
+  });
+});
diff --git a/apps/app/src/views/standalone-app/StandaloneAppView.tsx b/apps/app/src/views/standalone-app/StandaloneAppView.tsx
new file mode 100644
index 000000000..3ff88e620
--- /dev/null
+++ b/apps/app/src/views/standalone-app/StandaloneAppView.tsx
@@ -0,0 +1,89 @@
+import { useApp } from "@/hooks/queries/thread-queries";
+import { useAppRoute } from "@/hooks/useAppRoute";
+import { AppViewer } from "@/components/app-viewer/AppViewer";
+import { EmptyState } from "@/components/ui/empty-state.js";
+import { Skeleton } from "@/components/ui/skeleton.js";
+import { HttpError } from "@/lib/api";
+import type { IconName } from "@/components/ui/icon.js";
+
+// Counters the padded `<main>` so the app fills the surface edge to edge below
+// the global header, matching how other full surfaces (PageShell) bleed.
+const STANDALONE_SHELL_CLASS =
+  "-m-4 flex h-full min-h-0 flex-1 flex-col overflow-hidden md:-m-5";
+
+interface StandaloneAppMessageState {
+  icon: IconName;
+  message: string;
+}
+
+function resolveStandaloneAppErrorState(
+  error: unknown,
+): StandaloneAppMessageState {
+  const code = error instanceof HttpError ? error.code : undefined;
+  if (code === "app_missing") {
+    return { icon: "FileQuestion", message: "App not found." };
+  }
+  if (code === "invalid_manifest") {
+    return {
+      icon: "AlertTriangle",
+      message: "This app's manifest is invalid.",
+    };
+  }
+  return {
+    icon: "AlertTriangle",
+    message: error instanceof Error ? error.message : "Failed to load app.",
+  };
+}
+
+function StandaloneAppMessage({ icon, message }: StandaloneAppMessageState) {
+  return (
+    <div className="flex h-full flex-1 items-center justify-center p-8">
+      <EmptyState icon={icon} message={message} />
+    </div>
+  );
+}
+
+function StandaloneAppLoading() {
+  return (
+    <div className="space-y-2 p-6" aria-busy>
+      <Skeleton className="h-3 w-1/3 rounded-sm" />
+      <Skeleton className="h-3 w-full rounded-sm" />
+      <Skeleton className="h-3 w-5/6 rounded-sm" />
+      <Skeleton className="h-3 w-2/3 rounded-sm" />
+    </div>
+  );
+}
+
+/**
+ * Standalone, thread-independent surface for a global app at
+ * `/apps/:applicationId`. The app name is shown in the global header (see
+ * AppLayout); this view owns the missing/invalid/loading states and delegates
+ * the rendered app to the shared {@link AppViewer}. Deep-linking here loads the
+ * app with no thread or project context.
+ */
+export function StandaloneAppView() {
+  const { applicationId } = useAppRoute();
+  const appDetail = useApp(applicationId);
+
+  if (applicationId === undefined) {
+    return (
+      <div className={STANDALONE_SHELL_CLASS}>
+        <StandaloneAppMessage icon="FileQuestion" message="App not found." />
+      </div>
+    );
+  }
+
+  return (
+    <div className={STANDALONE_SHELL_CLASS}>
+      {appDetail.isError ? (
+        <StandaloneAppMessage
+          {...resolveStandaloneAppErrorState(appDetail.error)}
+        />
+      ) : appDetail.isPending ? (
+        <StandaloneAppLoading />
+      ) : (
+        <AppViewer applicationId={applicationId} targetThreadId={null} />
+      )}
+    </div>
+  );
+}
diff --git a/apps/app/src/views/thread-detail/ThreadDetailView.tsx b/apps/app/src/views/thread-detail/ThreadDetailView.tsx
index 4b98086c3..f89329ed1 100644
--- a/apps/app/src/views/thread-detail/ThreadDetailView.tsx
+++ b/apps/app/src/views/thread-detail/ThreadDetailView.tsx
@@ -31,9 +31,9 @@ import {
 } from "../../hooks/queries/environment-queries";
 import {
   getLatestPendingInteraction,
+  useApps,
   useProjectThreadSubset,
   useThread,
-  useThreadApps,
   useThreadComposerBootstrap,
   useThreadDetailBootstrap,
   useThreadPendingInteractions,
@@ -78,7 +78,10 @@ import { ThreadDetailSecondaryContent } from "./ThreadDetailSecondaryContent";
 import { useThreadSecondaryPanelVisibility } from "./useThreadSecondaryPanelVisibility";
 import type { HostConnectionNotice } from "./ThreadTimelinePane";
 import { useThreadStorageViewer } from "@/components/secondary-panel/useThreadStorageViewer";
-import { getThreadConversationCollapsedAtom } from "@/components/secondary-panel/threadSecondaryPanelAtoms";
+import {
+  getThreadConversationCollapsedAtom,
+  getThreadSecondaryPanelOpenAtom,
+} from "@/components/secondary-panel/threadSecondaryPanelAtoms";
 import {
   HostFilePreviewTabContent,
   ThreadStorageFilePreviewTabContent,
@@ -99,10 +102,7 @@ import {
 import { getBrowserUrlHost } from "@/lib/browser-url";
 import { ResolvedAppIcon } from "@/components/secondary-panel/AppIcon";
 import { useManagerStorageBrowser } from "@/components/secondary-panel/useManagerStorageBrowser";
-import {
-  STATUS_APP_ID,
-  useThreadFileTabs,
-} from "@/components/secondary-panel/useThreadFileTabs";
+import { useThreadFileTabs } from "@/components/secondary-panel/useThreadFileTabs";
 import type { SecondaryPanelFileTab } from "@/components/secondary-panel/ThreadSecondaryPanel";
 import { useEnvironmentMergeBase } from "@/components/secondary-panel/git-diff/useEnvironmentMergeBase";
 import { useThreadGitActions } from "./useThreadGitActions";
@@ -194,6 +194,9 @@ export function ThreadDetailView() {
   useFixedPanelTabsStorageMaintenance(threadId);
   useThreadTerminalPanelStorageMaintenance(threadId);
   const fixedPanelTabsState = useFixedPanelTabsState(threadId);
+  const isPersistedSecondaryPanelOpen = useAtomValue(
+    getThreadSecondaryPanelOpenAtom(threadId),
+  );
   const terminalPanelState = useThreadTerminalPanelState(threadId);
   const activeFixedSecondaryTab = getActiveFixedSecondaryTab({
     fixedPanelTabsState,
@@ -202,7 +205,7 @@ export function ThreadDetailView() {
     activeFixedSecondaryTab,
   });
   const activeSecondaryPanel = getActiveThreadSecondaryPanel({
-    fixedPanelTabsState,
+    isSecondaryPanelOpen: isPersistedSecondaryPanelOpen,
     selectedSecondaryPanel,
   });
   const renderSecondaryPanelAsDrawer = useIsCompactViewport();
@@ -306,8 +309,8 @@ export function ThreadDetailView() {
     threadId,
     threadType: thread?.type,
   });
-  const threadAppsQuery = useThreadApps(threadId ?? "", {
-    enabled: Boolean(threadId) && thread !== undefined,
+  const appsQuery = useApps({
+    enabled: thread !== undefined,
   });
   const {
     activateAppTab,
@@ -336,7 +339,6 @@ export function ThreadDetailView() {
     isNewTabActive,
     openBrowserTab,
     openNewTab,
-    openApp,
     openHostFile,
     openStorageFile,
     openWorkspaceFile,
@@ -344,7 +346,7 @@ export function ThreadDetailView() {
     selectFileSearchResult,
     updateBrowserTab,
   } = useThreadFileTabs({
-    apps: threadAppsQuery.data,
+    apps: appsQuery.data,
     threadId,
     environmentId: thread?.environmentId,
     threadType: thread?.type,
@@ -370,24 +372,6 @@ export function ThreadDetailView() {
     onSelectPath: openStorageFile,
     selectedPath: activeStorageFilePath,
   });
-  const togglePersistedSecondaryPanel = useCallback(() => {
-    if (fixedPanelTabsState.secondary.isOpen) {
-      setThreadSecondaryPanel(null);
-      return;
-    }
-    if (isManagerThread && activeFixedSecondaryTab === null) {
-      openApp(STATUS_APP_ID);
-      return;
-    }
-    toggleDefaultPersistedSecondaryPanel();
-  }, [
-    activeFixedSecondaryTab,
-    fixedPanelTabsState.secondary.isOpen,
-    isManagerThread,
-    openApp,
-    setThreadSecondaryPanel,
-    toggleDefaultPersistedSecondaryPanel,
-  ]);
   const handleUseStandardManagerTimelineChange = useCallback(
     (checked: boolean) => {
       if (!isManagerThread) {
@@ -505,13 +489,13 @@ export function ThreadDetailView() {
     togglePanel: toggleSecondaryPanel,
   } = useThreadSecondaryPanelVisibility({
     closePersistedPanel: closeThreadSecondaryPanel,
-    isPersistedOpen: fixedPanelTabsState.secondary.isOpen,
+    isPersistedOpen: isPersistedSecondaryPanelOpen,
     isCompactViewport: renderSecondaryPanelAsDrawer,
     openPersistedDiffFile,
     openPersistedDiffPanel,
     openPersistedPanel: openPersistedSecondaryPanel,
     threadId,
-    togglePersistedPanel: togglePersistedSecondaryPanel,
+    togglePersistedPanel: toggleDefaultPersistedSecondaryPanel,
   });
   const [storedConversationCollapsed, setStoredConversationCollapsed] = useAtom(
     getThreadConversationCollapsedAtom(threadId),
@@ -581,30 +565,29 @@ export function ThreadDetailView() {
     },
     [openSecondaryPanelDiffFile, openWorkspaceFile],
   );
-  const threadAppsById = useMemo(() => {
+  const appsById = useMemo(() => {
     const entries = new Map(
-      (threadAppsQuery.data ?? []).map((app) => [app.id, app]),
+      (appsQuery.data ?? []).map((app) => [app.applicationId, app]),
     );
     return entries;
-  }, [threadAppsQuery.data]);
+  }, [appsQuery.data]);
   const fileTabs = useMemo<SecondaryPanelFileTab[] | undefined>(() => {
     const filenameOf = (path: string) => path.split("/").at(-1) ?? path;
     const tabs = orderedSecondaryFileTabs.map((tab): SecondaryPanelFileTab => {
       switch (tab.kind) {
         case "app": {
-          const app = threadAppsById.get(tab.appId);
-          const appName = app?.name ?? tab.appId;
+          const app = appsById.get(tab.applicationId);
+          const appName = app?.name ?? tab.applicationId;
           return {
             id: tab.id,
             filename: appName,
-            isActive: tab.appId === activeAppId,
-            isPinned: tab.appId === STATUS_APP_ID,
+            isActive: tab.applicationId === activeAppId,
             leadingVisual: app ? (
               <ResolvedAppIcon icon={app.icon} className="size-3.5" />
             ) : undefined,
             statusLabel: null,
-            onSelect: () => activateAppTab(tab.appId),
-            onClose: () => closeAppTab(tab.appId),
+            onSelect: () => activateAppTab(tab.applicationId),
+            onClose: () => closeAppTab(tab.applicationId),
           };
         }
         case "browser": {
@@ -683,7 +666,7 @@ export function ThreadDetailView() {
     closeWorkspaceFileTab,
     isNewTabActive,
     orderedSecondaryFileTabs,
-    threadAppsById,
+    appsById,
   ]);
   const requestedMergeBaseBranch =
     selectedMergeBaseBranch ?? environmentMergeBaseBranch;
@@ -1222,7 +1205,7 @@ export function ThreadDetailView() {
       onSelect={selectFileSearchResult}
     />
   ) : activeAppId ? (
-    <AppTabContent appId={activeAppId} threadId={thread.id} />
+    <AppTabContent applicationId={activeAppId} threadId={thread.id} />
   ) : activeWorkspaceFilePath ? (
     <WorkspaceFilePreviewTabContent
       activePath={activeWorkspaceFilePath}
@@ -1258,6 +1241,7 @@ export function ThreadDetailView() {
     <BrowserTabDeck
       browserTabs={browserTabs}
       activeBrowserTabId={activeBrowserTab?.id ?? null}
+      environmentId={thread.environmentId}
       isPanelOpen={isSecondaryPanelOpen}
       threadId={thread.id}
       onUpdate={updateBrowserTab}
diff --git a/apps/app/src/views/thread-detail/threadSecondaryPanelSelection.test.tsx b/apps/app/src/views/thread-detail/threadSecondaryPanelSelection.test.tsx
index 10fea47d9..fca6b636a 100644
--- a/apps/app/src/views/thread-detail/threadSecondaryPanelSelection.test.tsx
+++ b/apps/app/src/views/thread-detail/threadSecondaryPanelSelection.test.tsx
@@ -1,10 +1,14 @@
 // @vitest-environment jsdom
 
 import { act, cleanup, renderHook, waitFor } from "@testing-library/react";
-import { Provider as JotaiProvider } from "jotai";
+import { Provider as JotaiProvider, useAtomValue } from "jotai";
 import { useCallback, type ReactNode } from "react";
 import { MemoryRouter, useLocation } from "react-router-dom";
 import { afterEach, describe, expect, it } from "vitest";
+import {
+  getThreadSecondaryPanelOpenAtom,
+  getThreadSecondaryPanelOpenStorageKey,
+} from "@/components/secondary-panel/threadSecondaryPanelAtoms";
 import {
   useFixedPanelTabsSecondaryPanelUrlSync,
   useFixedPanelTabsState,
@@ -53,6 +57,9 @@ function createTestWrapper(args: CreateTestWrapperArgs = {}) {
 
 function useSelectionHarness({ threadId }: SelectionHookProps) {
   const fixedPanelTabsState = useFixedPanelTabsState(threadId);
+  const isSecondaryPanelOpen = useAtomValue(
+    getThreadSecondaryPanelOpenAtom(threadId),
+  );
   const activeFixedSecondaryTab = getActiveFixedSecondaryTab({
     fixedPanelTabsState,
   });
@@ -60,7 +67,7 @@ function useSelectionHarness({ threadId }: SelectionHookProps) {
     activeFixedSecondaryTab,
   });
   const activeSecondaryPanel = getActiveThreadSecondaryPanel({
-    fixedPanelTabsState,
+    isSecondaryPanelOpen,
     selectedSecondaryPanel,
   });
   const setThreadSecondaryPanel = useSetThreadSecondaryPanelSelection(threadId);
@@ -70,6 +77,7 @@ function useSelectionHarness({ threadId }: SelectionHookProps) {
   return {
     activeSecondaryPanel,
     fixedPanelTabsState,
+    isSecondaryPanelOpen,
     selectedSecondaryPanel,
     setThreadSecondaryPanel,
     toggleThreadSecondaryPanel,
@@ -116,6 +124,7 @@ describe("thread secondary panel selection", () => {
 
     expect(result.current.activeSecondaryPanel).toBe("git-diff");
     expect(result.current.selectedSecondaryPanel).toBe("git-diff");
+    expect(result.current.isSecondaryPanelOpen).toBe(true);
     expect(result.current.fixedPanelTabsState.secondary.isOpen).toBe(true);
     expect(result.current.fixedPanelTabsState.secondary.activeTabId).toBe(
       "git-diff",
@@ -130,6 +139,7 @@ describe("thread secondary panel selection", () => {
 
     expect(result.current.activeSecondaryPanel).toBeNull();
     expect(result.current.selectedSecondaryPanel).toBe("git-diff");
+    expect(result.current.isSecondaryPanelOpen).toBe(false);
     expect(result.current.fixedPanelTabsState.secondary.isOpen).toBe(false);
     expect(result.current.fixedPanelTabsState.secondary.activeTabId).toBe(
       "git-diff",
@@ -144,9 +154,81 @@ describe("thread secondary panel selection", () => {
 
     expect(result.current.activeSecondaryPanel).toBe("git-diff");
     expect(result.current.selectedSecondaryPanel).toBe("git-diff");
+    expect(result.current.isSecondaryPanelOpen).toBe(true);
     expect(result.current.fixedPanelTabsState.secondary.isOpen).toBe(true);
   });
 
+  it("restores each thread's remembered panel-open state and hydrates it from storage", () => {
+    const threadA = "thr-panel-open-a";
+    const threadB = "thr-panel-open-b";
+    const { rerender, result, unmount } = renderHook(
+      (props: SelectionHookProps) => useSelectionHarness(props),
+      {
+        initialProps: { threadId: threadA },
+        wrapper: createTestWrapper({
+          initialEntries: [`/projects/proj_test/threads/${threadA}`],
+        }),
+      },
+    );
+
+    act(() => {
+      result.current.setThreadSecondaryPanel("thread-info");
+    });
+
+    expect(result.current.isSecondaryPanelOpen).toBe(true);
+    expect(
+      window.localStorage.getItem(
+        getThreadSecondaryPanelOpenStorageKey({ threadId: threadA }),
+      ),
+    ).toBe("true");
+
+    rerender({ threadId: threadB });
+
+    expect(result.current.isSecondaryPanelOpen).toBe(false);
+    expect(result.current.activeSecondaryPanel).toBeNull();
+    expect(
+      window.localStorage.getItem(
+        getThreadSecondaryPanelOpenStorageKey({ threadId: threadB }),
+      ),
+    ).toBeNull();
+
+    act(() => {
+      result.current.toggleThreadSecondaryPanel();
+    });
+    expect(result.current.isSecondaryPanelOpen).toBe(true);
+
+    act(() => {
+      result.current.toggleThreadSecondaryPanel();
+    });
+
+    expect(result.current.isSecondaryPanelOpen).toBe(false);
+    expect(
+      window.localStorage.getItem(
+        getThreadSecondaryPanelOpenStorageKey({ threadId: threadB }),
+      ),
+    ).toBe("false");
+
+    rerender({ threadId: threadA });
+
+    expect(result.current.isSecondaryPanelOpen).toBe(true);
+    expect(result.current.activeSecondaryPanel).toBe("thread-info");
+
+    unmount();
+
+    const { result: reloadedResult } = renderHook(
+      (props: SelectionHookProps) => useSelectionHarness(props),
+      {
+        initialProps: { threadId: threadA },
+        wrapper: createTestWrapper({
+          initialEntries: [`/projects/proj_test/threads/${threadA}`],
+        }),
+      },
+    );
+
+    expect(reloadedResult.current.isSecondaryPanelOpen).toBe(true);
+    expect(reloadedResult.current.activeSecondaryPanel).toBe("thread-info");
+  });
+
   it("consumes a URL override without rewriting another thread preference", async () => {
     const urlThreadId = "thr-url-source";
     const otherThreadId = "thr-url-other";
diff --git a/apps/app/src/views/thread-detail/threadSecondaryPanelSelection.ts b/apps/app/src/views/thread-detail/threadSecondaryPanelSelection.ts
index 7eeae05c4..2279ef360 100644
--- a/apps/app/src/views/thread-detail/threadSecondaryPanelSelection.ts
+++ b/apps/app/src/views/thread-detail/threadSecondaryPanelSelection.ts
@@ -1,8 +1,10 @@
 import { useCallback } from "react";
+import { useAtomValue, useSetAtom } from "jotai";
+import { getThreadSecondaryPanelOpenAtom } from "@/components/secondary-panel/threadSecondaryPanelAtoms";
 import {
   useCloseFixedSecondaryPanel,
+  useOpenFixedSecondaryPanel,
   useSetFixedSecondaryPanelTab,
-  useToggleFixedSecondaryPanel,
 } from "@/lib/fixed-panel-tabs";
 import type {
   FixedPanelTab,
@@ -25,7 +27,7 @@ interface GetSelectedThreadSecondaryPanelArgs {
 }
 
 interface GetActiveThreadSecondaryPanelArgs {
-  fixedPanelTabsState: FixedPanelTabsState;
+  isSecondaryPanelOpen: boolean;
   selectedSecondaryPanel: ActiveThreadSecondaryPanel;
 }
 
@@ -72,10 +74,10 @@ export function getSelectedThreadSecondaryPanel({
 }
 
 export function getActiveThreadSecondaryPanel({
-  fixedPanelTabsState,
+  isSecondaryPanelOpen,
   selectedSecondaryPanel,
 }: GetActiveThreadSecondaryPanelArgs): ActiveThreadSecondaryPanel {
-  return fixedPanelTabsState.secondary.isOpen ? selectedSecondaryPanel : null;
+  return isSecondaryPanelOpen ? selectedSecondaryPanel : null;
 }
 
 export function useSetThreadSecondaryPanelSelection(
@@ -83,21 +85,52 @@ export function useSetThreadSecondaryPanelSelection(
 ): NullableSecondaryPanelSetter {
   const closeFixedSecondaryPanel = useCloseFixedSecondaryPanel(threadId);
   const setFixedSecondaryPanelTab = useSetFixedSecondaryPanelTab(threadId);
+  const setThreadSecondaryPanelOpen = useSetAtom(
+    getThreadSecondaryPanelOpenAtom(threadId),
+  );
 
   return useCallback<NullableSecondaryPanelSetter>(
     (panel) => {
       if (panel === null) {
+        setThreadSecondaryPanelOpen(false);
         closeFixedSecondaryPanel();
         return;
       }
+      setThreadSecondaryPanelOpen(true);
       setFixedSecondaryPanelTab(panel);
     },
-    [closeFixedSecondaryPanel, setFixedSecondaryPanelTab],
+    [
+      closeFixedSecondaryPanel,
+      setFixedSecondaryPanelTab,
+      setThreadSecondaryPanelOpen,
+    ],
   );
 }
 
 export function useToggleThreadSecondaryPanelSelection(
   threadId: ThreadSecondaryPanelThreadId,
 ): () => void {
-  return useToggleFixedSecondaryPanel(threadId);
+  const closeFixedSecondaryPanel = useCloseFixedSecondaryPanel(threadId);
+  const openFixedSecondaryPanel = useOpenFixedSecondaryPanel(threadId);
+  const isSecondaryPanelOpen = useAtomValue(
+    getThreadSecondaryPanelOpenAtom(threadId),
+  );
+  const setThreadSecondaryPanelOpen = useSetAtom(
+    getThreadSecondaryPanelOpenAtom(threadId),
+  );
+
+  return useCallback(() => {
+    if (isSecondaryPanelOpen) {
+      setThreadSecondaryPanelOpen(false);
+      closeFixedSecondaryPanel();
+      return;
+    }
+    setThreadSecondaryPanelOpen(true);
+    openFixedSecondaryPanel();
+  }, [
+    closeFixedSecondaryPanel,
+    isSecondaryPanelOpen,
+    openFixedSecondaryPanel,
+    setThreadSecondaryPanelOpen,
+  ]);
 }
diff --git a/apps/cli/src/__tests__/command-output.test.ts b/apps/cli/src/__tests__/command-output.test.ts
index 5a0d7b157..9c43449c1 100644
--- a/apps/cli/src/__tests__/command-output.test.ts
+++ b/apps/cli/src/__tests__/command-output.test.ts
@@ -445,9 +445,10 @@ describe("CLI command output contracts", () => {
     const output = collectLogPayloads(vi.mocked(console.log)).join("\n");
     expect(output.trim().length).toBeGreaterThan(0);
     expect(output).toContain("Apps");
-    expect(output).toContain("apps/status/data/state.json");
+    expect(output).toContain("<dataDir>/apps/<applicationId>/");
     expect(output).toContain("window.bb.data");
-    expect(output).toContain("bb app list --self");
+    expect(output).toContain("bb app current --json");
+    expect(output).toContain("Do not start a web server");
   });
 
   it("bb guide unknown chapter lists styling in available chapters", async () => {
@@ -1028,9 +1029,7 @@ describe("CLI command output contracts", () => {
     });
     expect(
       writeErr.mock.calls.map((callArgs) => String(callArgs[0] ?? "")).join(""),
-    ).toContain(
-      "error: unknown option '--permission-mode'",
-    );
+    ).toContain("error: unknown option '--permission-mode'");
   });
 
   it("bb manager list reports when no managers are hired", async () => {
@@ -1151,23 +1150,22 @@ describe("CLI command output contracts", () => {
   });
 
   it("bb app list renders resolved app summaries", async () => {
-    vi.stubEnv("BB_THREAD_ID", "thr_current");
     const apps = [
       {
-        id: "status",
-        name: "Status",
+        applicationId: "status",
+        name: "Project Status",
         entry: { path: "index.html", kind: "html" },
         capabilities: ["data", "message"],
         icon: { kind: "builtin", name: "ListTodo" },
       },
       {
-        id: "demo",
+        applicationId: "demo",
         name: "Demo",
         entry: { path: "readme.md", kind: "md" },
         capabilities: [],
         icon: {
           kind: "logo",
-          url: "/api/v1/threads/thr_current/apps/demo/icon",
+          url: "/api/v1/apps/demo/icon",
         },
       },
     ];
@@ -1176,12 +1174,8 @@ describe("CLI command output contracts", () => {
       asServerClient({
         api: {
           v1: {
-            threads: {
-              ":id": {
-                apps: {
-                  $get: get,
-                },
-              },
+            apps: {
+              $get: get,
             },
           },
         },
@@ -1192,90 +1186,112 @@ describe("CLI command output contracts", () => {
       registerAppCommands(program, () => "http://server"),
     );
 
-    expect(get).toHaveBeenCalledWith({ param: { id: "thr_current" } });
+    expect(get).toHaveBeenCalledWith();
     expect(collectLogPayloads(vi.mocked(console.log))).toEqual([
-      "ID                        Name                      Entry                     Capabilities              Icon\n------------------------  ------------------------  ------------------------  ------------------------  ------------------\nstatus                    Status                    html:index.html           data,message              ListTodo\n------------------------  ------------------------  ------------------------  ------------------------  ------------------\ndemo                      Demo                      md:readme.md              -                         logo",
+      "Application ID                    Name                      Entry                     Capabilities              Icon\n--------------------------------  ------------------------  ------------------------  ------------------------  ------------------\nstatus                            Project Status            html:index.html           data,message              ListTodo\n--------------------------------  ------------------------  ------------------------  ------------------------  ------------------\ndemo                              Demo                      md:readme.md              -                         logo",
     ]);
   });
 
-  it("bb app new targets the current thread and posts the selected template", async () => {
-    vi.stubEnv("BB_THREAD_ID", "thr_current");
+  it("bb app new derives a slug from display name", async () => {
     const created = {
-      id: "demo",
-      name: "Demo",
+      applicationId: "review-board",
+      name: "Review Board",
       entry: { path: "index.html", kind: "html" },
       capabilities: ["data", "message"],
       icon: { kind: "builtin", name: "ListTodo" },
+      appsRootPath: "/tmp/bb-data/apps",
+      appRootPath: "/tmp/bb-data/apps/review-board",
+      appDataPath: "/tmp/bb-data/apps/review-board/data",
     };
     const post = vi.fn(async () => created);
     createClientMock.mockReturnValue(
       asServerClient({
         api: {
           v1: {
-            threads: {
-              ":id": {
-                apps: {
-                  $post: post,
-                },
-              },
+            apps: {
+              $post: post,
             },
           },
         },
       }),
     );
 
-    await runCommand(
-      ["app", "new", "demo", "--template", "status"],
-      (program) => registerAppCommands(program, () => "http://server"),
+    await runCommand(["app", "new", "--name", "Review Board"], (program) =>
+      registerAppCommands(program, () => "http://server"),
     );
 
     expect(post).toHaveBeenCalledWith({
-      param: { id: "thr_current" },
-      json: { id: "demo", name: "demo", template: "status" },
+      json: { applicationId: "review-board", name: "Review Board" },
     });
     expect(collectLogPayloads(vi.mocked(console.log))).toEqual([
-      "App created: demo",
-      "  Name:         Demo",
-      "  Entry:        html:index.html",
-      "  Capabilities: data,message",
-      "  Icon:         ListTodo",
+      "Application ID: review-board",
+      "  Name:          Review Board",
+      "  Entry:         html:index.html",
+      "  Capabilities:  data,message",
+      "  Icon:          ListTodo",
+      "  App root:      /tmp/bb-data/apps/review-board",
+      "  App data path: /tmp/bb-data/apps/review-board/data",
     ]);
   });
 
-  it("bb app new derives a valid id from a display name", async () => {
-    vi.stubEnv("BB_THREAD_ID", "thr_current");
+  it("bb app new honors an explicit slug", async () => {
     const created = {
-      id: "my-app",
-      name: "My App",
+      applicationId: "status",
+      name: "status",
       entry: { path: "index.html", kind: "html" },
-      capabilities: ["data"],
-      icon: { kind: "builtin", name: "GridView" },
+      capabilities: ["data", "message"],
+      icon: { kind: "builtin", name: "ListTodo" },
+      appsRootPath: "/tmp/bb-data/apps",
+      appRootPath: "/tmp/bb-data/apps/status",
+      appDataPath: "/tmp/bb-data/apps/status/data",
     };
     const post = vi.fn(async () => created);
     createClientMock.mockReturnValue(
       asServerClient({
         api: {
           v1: {
-            threads: {
-              ":id": {
-                apps: {
-                  $post: post,
-                },
-              },
+            apps: {
+              $post: post,
             },
           },
         },
       }),
     );
 
-    await runCommand(["app", "new", "My App"], (program) =>
+    await runCommand(["app", "new", "--slug", "status"], (program) =>
       registerAppCommands(program, () => "http://server"),
     );
 
     expect(post).toHaveBeenCalledWith({
-      param: { id: "thr_current" },
-      json: { id: "my-app", name: "My App", template: "blank" },
+      json: { applicationId: "status" },
     });
+    expect(collectLogPayloads(vi.mocked(console.log))).toEqual([
+      "Application ID: status",
+      "  Name:          status",
+      "  Entry:         html:index.html",
+      "  Capabilities:  data,message",
+      "  Icon:          ListTodo",
+      "  App root:      /tmp/bb-data/apps/status",
+      "  App data path: /tmp/bb-data/apps/status/data",
+    ]);
+  });
+
+  it("bb app current renders runtime app paths", async () => {
+    vi.stubEnv("BB_APP_ID", "current");
+    vi.stubEnv("BB_APP_ROOT", "/tmp/bb-data/apps/current");
+    vi.stubEnv("BB_APP_DATA_PATH", "/tmp/bb-data/apps/current/data");
+    vi.stubEnv("BB_APPS_ROOT", "/tmp/bb-data/apps");
+
+    await runCommand(["app", "current"], (program) =>
+      registerAppCommands(program, () => "http://server"),
+    );
+
+    expect(collectLogPayloads(vi.mocked(console.log))).toEqual([
+      "Application ID: current",
+      "  App root:      /tmp/bb-data/apps/current",
+      "  App data path: /tmp/bb-data/apps/current/data",
+      "  Apps root:     /tmp/bb-data/apps",
+    ]);
   });
 
   it("bb manager status includes managed child threads", async () => {
diff --git a/apps/cli/src/commands/app.ts b/apps/cli/src/commands/app.ts
index 28552c8e8..76d6d9916 100644
--- a/apps/cli/src/commands/app.ts
+++ b/apps/cli/src/commands/app.ts
@@ -1,101 +1,117 @@
+import { Buffer } from "node:buffer";
+import { readFile } from "node:fs/promises";
 import { Command } from "commander";
-import { appIdSchema, type AppId } from "@bb/domain";
+import {
+  applicationIdSchema,
+  deriveApplicationIdFromName,
+  jsonValueSchema,
+} from "@bb/domain";
+import type { ApplicationId, JsonValue } from "@bb/domain";
 import type {
+  AppDataEntry,
+  AppDataListResponse,
   AppDetail,
   AppIcon,
   AppSummary,
-  AppTemplate,
-  CreateThreadAppRequest,
+  CreateAppRequest,
 } from "@bb/server-contract";
-import { appTemplateSchema } from "@bb/server-contract";
 import { action } from "../action.js";
 import { createClient, unwrap } from "../client.js";
 import { renderBorderlessTable } from "../table.js";
-import {
-  confirmDestructiveAction,
-  outputJson,
-  printContextLabel,
-  requireThreadIdWithLabelOrSelf,
-} from "./helpers.js";
+import { confirmDestructiveAction, outputJson } from "./helpers.js";
 
 type ResolveServerUrl = () => string;
 
-interface AppThreadCommandOptions {
+interface AppJsonOptions {
   json?: boolean;
-  self?: boolean;
 }
 
-interface AppNewCommandOptions extends AppThreadCommandOptions {
+interface AppNewCommandOptions extends AppJsonOptions {
   id?: string;
-  template?: string;
+  name?: string;
+  slug?: string;
 }
 
-interface AppRemoveCommandOptions extends AppThreadCommandOptions {
+interface AppDeleteCommandOptions extends AppJsonOptions {
   yes?: boolean;
 }
 
-interface ResolveAppCommandThreadArgs {
-  options: AppThreadCommandOptions;
-  threadId: string | undefined;
-}
+interface AppDataListCommandOptions extends AppJsonOptions {}
 
-interface AppOpenPayload {
-  app: AppDetail;
-  threadId: string;
-  url: string;
+interface AppDataWriteCommandOptions {
+  file?: string;
+  stdin?: boolean;
 }
 
-interface ResolveNewAppIdArgs {
-  id: string | undefined;
-  name: string;
+interface AppMessageCommandOptions {
+  json: string;
+  targetThread: string;
 }
 
-function parseAppTemplate(value: string | undefined): AppTemplate {
-  const parsed = appTemplateSchema.safeParse(value ?? "blank");
-  if (!parsed.success) {
-    throw new Error("Invalid app template. Expected 'blank' or 'status'.");
-  }
-  return parsed.data;
+interface CurrentAppRuntimeContext {
+  applicationId: ApplicationId;
+  appRootPath: string;
+  appDataPath: string;
+  appsRootPath: string;
 }
 
-function resolveAppCommandThread(args: ResolveAppCommandThreadArgs): string {
-  const resolved = requireThreadIdWithLabelOrSelf(
-    args.threadId,
-    args.options,
+function parseApplicationId(value: string): ApplicationId {
+  const parsed = applicationIdSchema.safeParse(value);
+  if (parsed.success) {
+    return parsed.data;
+  }
+  throw new Error(
+    "Invalid applicationId. Expected a lowercase slug like status or review-board.",
   );
-  printContextLabel(resolved, "Thread", "BB_THREAD_ID", args.options);
-  return resolved.id;
 }
 
-function slugifyAppName(name: string): string {
-  return name
-    .trim()
-    .toLowerCase()
-    .replace(/[^a-z0-9_-]+/gu, "-")
-    .replace(/-+/gu, "-")
-    .replace(/^-|-$/gu, "");
+function deriveApplicationIdFromNameForCli(name: string): ApplicationId {
+  try {
+    return deriveApplicationIdFromName(name);
+  } catch {
+    throw new Error("App name cannot be converted to a valid applicationId.");
+  }
 }
 
-function resolveNewAppId(args: ResolveNewAppIdArgs): AppId {
-  const candidate = args.id ?? slugifyAppName(args.name);
-  const parsed = appIdSchema.safeParse(candidate);
-  if (parsed.success) {
-    return parsed.data;
+function resolveNewApplicationId(opts: AppNewCommandOptions): ApplicationId {
+  if (
+    opts.id !== undefined &&
+    opts.slug !== undefined &&
+    opts.id !== opts.slug
+  ) {
+    throw new Error("Use either --id or --slug, not both.");
   }
-  if (args.id !== undefined) {
-    throw new Error(
-      "Invalid app id. Use letters, numbers, underscores, or hyphens.",
-    );
+  const explicitApplicationId = opts.id ?? opts.slug;
+  if (explicitApplicationId !== undefined) {
+    return parseApplicationId(explicitApplicationId);
   }
-  throw new Error(
-    `Could not derive a valid app id from "${args.name}". Pass --id with letters, numbers, underscores, or hyphens.`,
-  );
+  if (opts.name !== undefined) {
+    return deriveApplicationIdFromNameForCli(opts.name);
+  }
+  throw new Error("Provide --id <slug>, --slug <slug>, or --name <name>.");
+}
+
+function buildCreateAppRequest(opts: AppNewCommandOptions): CreateAppRequest {
+  const applicationId = resolveNewApplicationId(opts);
+  const request: CreateAppRequest = { applicationId };
+  if (opts.name !== undefined) {
+    request.name = opts.name;
+  }
+  return request;
 }
 
-function appUrl(baseUrl: string, threadId: string, appId: string): string {
-  return `${baseUrl.replace(/\/$/u, "")}/api/v1/threads/${encodeURIComponent(
-    threadId,
-  )}/apps/${encodeURIComponent(appId)}/`;
+function encodePathSegments(value: string): string {
+  return value.split("/").map(encodeURIComponent).join("/");
+}
+
+function appDataUrl(
+  baseUrl: string,
+  applicationId: ApplicationId,
+  dataPath: string,
+): string {
+  return `${baseUrl.replace(/\/$/u, "")}/api/v1/apps/${encodeURIComponent(
+    applicationId,
+  )}/data/${encodePathSegments(dataPath)}`;
 }
 
 function formatIcon(icon: AppIcon): string {
@@ -110,12 +126,12 @@ function printAppsTable(apps: AppSummary[]): void {
   console.log(
     renderBorderlessTable(
       {
-        head: ["ID", "Name", "Entry", "Capabilities", "Icon"],
-        colWidths: [24, 24, 24, 24, 18],
+        head: ["Application ID", "Name", "Entry", "Capabilities", "Icon"],
+        colWidths: [32, 24, 24, 24, 18],
         trimTrailingWhitespace: true,
       },
       apps.map((app) => [
-        app.id,
+        app.applicationId,
         app.name,
         `${app.entry.kind}:${app.entry.path}`,
         app.capabilities.join(",") || "-",
@@ -126,157 +142,300 @@ function printAppsTable(apps: AppSummary[]): void {
 }
 
 function printAppDetail(app: AppDetail): void {
-  console.log(`App created: ${app.id}`);
-  console.log(`  Name:         ${app.name}`);
-  console.log(`  Entry:        ${app.entry.kind}:${app.entry.path}`);
-  console.log(`  Capabilities: ${app.capabilities.join(",") || "-"}`);
-  console.log(`  Icon:         ${formatIcon(app.icon)}`);
+  console.log(`Application ID: ${app.applicationId}`);
+  console.log(`  Name:          ${app.name}`);
+  console.log(`  Entry:         ${app.entry.kind}:${app.entry.path}`);
+  console.log(`  Capabilities:  ${app.capabilities.join(",") || "-"}`);
+  console.log(`  Icon:          ${formatIcon(app.icon)}`);
+  console.log(`  App root:      ${app.appRootPath}`);
+  console.log(`  App data path: ${app.appDataPath}`);
+}
+
+function printDataEntries(entries: AppDataEntry[]): void {
+  if (entries.length === 0) {
+    console.log("No app data");
+    return;
+  }
+  console.log(
+    renderBorderlessTable(
+      {
+        head: ["Path", "Size", "Version"],
+        colWidths: [36, 10, 64],
+        trimTrailingWhitespace: true,
+      },
+      entries.map((entry) => [
+        entry.path,
+        String(entry.sizeBytes),
+        entry.version,
+      ]),
+    ),
+  );
+}
+
+function parseJsonValueInput(value: string): JsonValue {
+  return jsonValueSchema.parse(JSON.parse(value));
+}
+
+async function readStdin(): Promise<string> {
+  const chunks: Buffer[] = [];
+  for await (const chunk of process.stdin) {
+    chunks.push(Buffer.isBuffer(chunk) ? chunk : Buffer.from(chunk));
+  }
+  return Buffer.concat(chunks).toString("utf8");
+}
+
+async function readWriteValue(
+  opts: AppDataWriteCommandOptions,
+): Promise<JsonValue> {
+  if (opts.file && opts.stdin) {
+    throw new Error("Use either --file or --stdin, not both.");
+  }
+  if (!opts.file && !opts.stdin) {
+    throw new Error("Provide --file <localPath> or --stdin.");
+  }
+  const content =
+    opts.file !== undefined
+      ? await readFile(opts.file, "utf8")
+      : await readStdin();
+  return parseJsonValueInput(content);
+}
+
+function readCurrentAppRuntimeContext(): CurrentAppRuntimeContext {
+  const applicationId = process.env.BB_APP_ID;
+  const appRootPath = process.env.BB_APP_ROOT;
+  const appDataPath = process.env.BB_APP_DATA_PATH;
+  const appsRootPath = process.env.BB_APPS_ROOT;
+  if (!applicationId || !appRootPath || !appDataPath || !appsRootPath) {
+    throw new Error("current_app_unavailable");
+  }
+  return {
+    applicationId: parseApplicationId(applicationId),
+    appRootPath,
+    appDataPath,
+    appsRootPath,
+  };
 }
 
 export function registerAppCommands(
   program: Command,
   getUrl: ResolveServerUrl,
 ): void {
-  const app = program.command("app").description("Manage thread apps");
+  const app = program.command("app").description("Manage global apps");
+
+  app
+    .command("list")
+    .description("List global apps")
+    .option("--json", "Print machine-readable JSON output")
+    .action(
+      action(async (opts: AppJsonOptions) => {
+        const client = createClient(getUrl());
+        const apps = await unwrap<AppSummary[]>(client.api.v1.apps.$get());
+        if (outputJson(opts, apps)) return;
+        printAppsTable(apps);
+      }),
+    );
+
+  app
+    .command("new")
+    .description("Create a global app")
+    .option("--id <slug>", "Application slug id")
+    .option("--slug <slug>", "Alias for --id")
+    .option(
+      "--name <name>",
+      "Human display name; derives slug when id is omitted",
+    )
+    .option("--json", "Print machine-readable JSON output")
+    .action(
+      action(async (opts: AppNewCommandOptions) => {
+        const client = createClient(getUrl());
+        const created = await unwrap<AppDetail>(
+          client.api.v1.apps.$post({
+            json: buildCreateAppRequest(opts),
+          }),
+        );
+        if (outputJson(opts, created)) return;
+        printAppDetail(created);
+      }),
+    );
 
   app
-    .command("new <name> [threadId]")
-    .description("Create a new app in a thread")
-    .option("--id <appId>", "App id. Defaults to a slug derived from name.")
-    .option("--template <template>", "App template: blank or status", "blank")
-    .option("--self", "Target BB_THREAD_ID explicitly")
+    .command("current")
+    .description("Show current app runtime context")
+    .option("--json", "Print machine-readable JSON output")
+    .action(
+      action(async (opts: AppJsonOptions) => {
+        const current = readCurrentAppRuntimeContext();
+        if (outputJson(opts, current)) return;
+        console.log(`Application ID: ${current.applicationId}`);
+        console.log(`  App root:      ${current.appRootPath}`);
+        console.log(`  App data path: ${current.appDataPath}`);
+        console.log(`  Apps root:     ${current.appsRootPath}`);
+      }),
+    );
+
+  app
+    .command("show <applicationId>")
+    .description("Show a global app")
+    .option("--json", "Print machine-readable JSON output")
+    .action(
+      action(async (rawApplicationId: string, opts: AppJsonOptions) => {
+        const applicationId = parseApplicationId(rawApplicationId);
+        const client = createClient(getUrl());
+        const detail = await unwrap<AppDetail>(
+          client.api.v1.apps[":applicationId"].$get({
+            param: { applicationId },
+          }),
+        );
+        if (outputJson(opts, detail)) return;
+        printAppDetail(detail);
+      }),
+    );
+
+  app
+    .command("delete <applicationId>")
+    .description("Delete a global app")
+    .option("--yes", "Skip the confirmation prompt")
     .option("--json", "Print machine-readable JSON output")
     .action(
       action(
-        async (
-          name: string,
-          threadIdArg: string | undefined,
-          opts: AppNewCommandOptions,
-        ) => {
-          const threadId = resolveAppCommandThread({
-            threadId: threadIdArg,
-            options: opts,
-          });
-          const template = parseAppTemplate(opts.template);
+        async (rawApplicationId: string, opts: AppDeleteCommandOptions) => {
+          const applicationId = parseApplicationId(rawApplicationId);
           const client = createClient(getUrl());
-          const request: CreateThreadAppRequest = {
-            id: resolveNewAppId({ id: opts.id, name }),
-            name,
-            template,
-          };
-          const created = await unwrap<AppDetail>(
-            client.api.v1.threads[":id"].apps.$post({
-              param: { id: threadId },
-              json: request,
+          const appDetail = await unwrap<AppDetail>(
+            client.api.v1.apps[":applicationId"].$get({
+              param: { applicationId },
             }),
           );
-          if (outputJson(opts, created)) return;
-          printAppDetail(created);
+          if (!opts.yes) {
+            const confirmed = await confirmDestructiveAction(
+              `Delete app "${appDetail.name}" (${applicationId})? This cannot be undone.`,
+            );
+            if (!confirmed) {
+              console.log(`App ${applicationId} deletion cancelled`);
+              return;
+            }
+          }
+          await unwrap<{ ok: true }>(
+            client.api.v1.apps[":applicationId"].$delete({
+              param: { applicationId },
+            }),
+          );
+          const payload = { ok: true, applicationId };
+          if (outputJson(opts, payload)) return;
+          console.log(`App ${applicationId} deleted`);
         },
       ),
     );
 
-  app
-    .command("list [threadId]")
-    .description("List apps in a thread")
-    .option("--self", "Target BB_THREAD_ID explicitly")
+  const data = app.command("data").description("Manage global app data");
+
+  data
+    .command("list <applicationId> [path]")
+    .description("List app data entries")
     .option("--json", "Print machine-readable JSON output")
     .action(
       action(
         async (
-          threadIdArg: string | undefined,
-          opts: AppThreadCommandOptions,
+          rawApplicationId: string,
+          prefix: string | undefined,
+          opts: AppDataListCommandOptions,
         ) => {
-          const threadId = resolveAppCommandThread({
-            threadId: threadIdArg,
-            options: opts,
-          });
+          const applicationId = parseApplicationId(rawApplicationId);
           const client = createClient(getUrl());
-          const apps = await unwrap<AppSummary[]>(
-            client.api.v1.threads[":id"].apps.$get({
-              param: { id: threadId },
+          const response = await unwrap<AppDataListResponse>(
+            client.api.v1.apps[":applicationId"].data.$get({
+              param: { applicationId },
+              query: prefix ? { prefix } : {},
             }),
           );
-          if (outputJson(opts, apps)) return;
-          printAppsTable(apps);
+          if (outputJson(opts, response.entries)) return;
+          printDataEntries(response.entries);
         },
       ),
     );
 
-  app
-    .command("open <name> [threadId]")
-    .description("Print an app URL")
-    .option("--self", "Target BB_THREAD_ID explicitly")
-    .option("--json", "Print machine-readable JSON output")
+  data
+    .command("read <applicationId> <path>")
+    .description("Read an app data JSON value")
+    .action(
+      action(async (rawApplicationId: string, dataPath: string) => {
+        const applicationId = parseApplicationId(rawApplicationId);
+        const response = await unwrap<AppDataEntry>(
+          fetch(appDataUrl(getUrl(), applicationId, dataPath), {
+            method: "GET",
+            headers: { Accept: "application/json" },
+          }),
+        );
+        console.log(JSON.stringify(response.value, null, 2));
+      }),
+    );
+
+  data
+    .command("write <applicationId> <path>")
+    .description("Write an app data JSON value")
+    .option("--file <localPath>", "Read JSON value from a local file")
+    .option("--stdin", "Read JSON value from stdin")
     .action(
       action(
         async (
-          name: string,
-          threadIdArg: string | undefined,
-          opts: AppThreadCommandOptions,
+          rawApplicationId: string,
+          dataPath: string,
+          opts: AppDataWriteCommandOptions,
         ) => {
-          const threadId = resolveAppCommandThread({
-            threadId: threadIdArg,
-            options: opts,
-          });
-          const baseUrl = getUrl();
-          const client = createClient(baseUrl);
-          const appDetail = await unwrap<AppDetail>(
-            client.api.v1.threads[":id"].apps[":appId"].$get({
-              param: { id: threadId, appId: name },
+          const applicationId = parseApplicationId(rawApplicationId);
+          const value = await readWriteValue(opts);
+          await unwrap<AppDataEntry>(
+            fetch(appDataUrl(getUrl(), applicationId, dataPath), {
+              method: "PUT",
+              headers: {
+                Accept: "application/json",
+                "Content-Type": "application/json",
+              },
+              body: JSON.stringify({ value }),
             }),
           );
-          const payload: AppOpenPayload = {
-            threadId,
-            app: appDetail,
-            url: appUrl(baseUrl, threadId, appDetail.id),
-          };
-          if (outputJson(opts, payload)) return;
-          console.log(payload.url);
+          console.log(`Wrote ${dataPath}`);
         },
       ),
     );
 
+  data
+    .command("delete <applicationId> <path>")
+    .description("Delete an app data value")
+    .action(
+      action(async (rawApplicationId: string, dataPath: string) => {
+        const applicationId = parseApplicationId(rawApplicationId);
+        await unwrap<{ ok: true }>(
+          fetch(appDataUrl(getUrl(), applicationId, dataPath), {
+            method: "DELETE",
+            headers: { Accept: "application/json" },
+          }),
+        );
+        console.log(`Deleted ${dataPath}`);
+      }),
+    );
+
   app
-    .command("rm <name> [threadId]")
-    .description("Remove an app from a thread")
-    .option("--yes", "Skip the confirmation prompt")
-    .option("--self", "Target BB_THREAD_ID explicitly")
-    .option("--json", "Print machine-readable JSON output")
+    .command("message <applicationId>")
+    .description("Send an app message to a target thread")
+    .requiredOption("--target-thread <threadId>", "Target thread")
+    .requiredOption("--json <payload>", "JSON payload to send")
     .action(
       action(
-        async (
-          name: string,
-          threadIdArg: string | undefined,
-          opts: AppRemoveCommandOptions,
-        ) => {
-          const threadId = resolveAppCommandThread({
-            threadId: threadIdArg,
-            options: opts,
-          });
+        async (rawApplicationId: string, opts: AppMessageCommandOptions) => {
+          const applicationId = parseApplicationId(rawApplicationId);
+          const payload = parseJsonValueInput(opts.json);
           const client = createClient(getUrl());
-          const appDetail = await unwrap<AppDetail>(
-            client.api.v1.threads[":id"].apps[":appId"].$get({
-              param: { id: threadId, appId: name },
+          await unwrap(
+            client.api.v1.apps[":applicationId"].message.$post({
+              param: { applicationId },
+              json: {
+                payload,
+                targetThreadId: opts.targetThread,
+              },
             }),
           );
-          if (!opts.yes) {
-            const confirmed = await confirmDestructiveAction(
-              `Remove app "${appDetail.name}" from thread ${threadId}? This cannot be undone.`,
-            );
-            if (!confirmed) {
-              console.log(`App ${name} removal cancelled`);
-              return;
-            }
-          }
-          await unwrap<{ ok: true }>(
-            client.api.v1.threads[":id"].apps[":appId"].$delete({
-              param: { id: threadId, appId: name },
-            }),
-          );
-          const payload = { ok: true, threadId, appId: name };
-          if (outputJson(opts, payload)) return;
-          console.log(`App ${name} removed`);
+          console.log(`Message sent to ${opts.targetThread}`);
         },
       ),
     );
diff --git a/apps/desktop/src/desktop-browser-view.ts b/apps/desktop/src/desktop-browser-view.ts
index 5ec844ded..303fdf0a0 100644
--- a/apps/desktop/src/desktop-browser-view.ts
+++ b/apps/desktop/src/desktop-browser-view.ts
@@ -7,11 +7,13 @@ import {
 import {
   BB_DESKTOP_BROWSER_MAX_TITLE_LENGTH,
   BB_DESKTOP_BROWSER_MAX_URL_LENGTH,
+  clampBbDesktopBrowserViewBounds,
   type BbDesktopBrowserAttachRequest,
   type BbDesktopBrowserNavigateRequest,
   type BbDesktopBrowserSetBoundsRequest,
   type BbDesktopBrowserSetVisibleRequest,
   type BbDesktopBrowserState,
+  type BbDesktopBrowserViewBounds,
 } from "@bb/server-contract";
 import {
   BB_DESKTOP_BROWSER_OPEN_TAB_CHANNEL,
@@ -65,6 +67,17 @@ interface HostScopedTabArgs {
   tabId: string;
 }
 
+interface ClampBoundsToHostWindowArgs {
+  bounds: BbDesktopBrowserViewBounds;
+  hostWindow: BrowserWindow;
+}
+
+interface SetEntryBoundsArgs {
+  bounds: BbDesktopBrowserViewBounds;
+  entry: BrowserViewEntry;
+  hostWindow: BrowserWindow;
+}
+
 export interface DesktopBrowserViewManager {
   attach(args: HostScopedRequestArgs<BbDesktopBrowserAttachRequest>): void;
   detach(args: HostScopedTabArgs): void;
@@ -99,6 +112,28 @@ function send(hostWindow: BrowserWindow, channel: string, payload: unknown): voi
   hostWindow.webContents.send(channel, payload);
 }
 
+function clampBoundsToHostWindow(
+  args: ClampBoundsToHostWindowArgs,
+): BbDesktopBrowserViewBounds {
+  const contentBounds = args.hostWindow.getContentBounds();
+  return clampBbDesktopBrowserViewBounds({
+    bounds: args.bounds,
+    viewport: {
+      width: contentBounds.width,
+      height: contentBounds.height,
+    },
+  });
+}
+
+function setEntryBounds(args: SetEntryBoundsArgs): void {
+  args.entry.view.setBounds(
+    clampBoundsToHostWindow({
+      bounds: args.bounds,
+      hostWindow: args.hostWindow,
+    }),
+  );
+}
+
 function buildBrowserState(
   tabId: string,
   entry: BrowserViewEntry,
@@ -304,7 +339,7 @@ export function createDesktopBrowserViewManager(
     attach({ hostWindow, request }) {
       const key = browserViewKey(hostWindow, request.tabId);
       const entry = entries.get(key) ?? createEntry(hostWindow, request.tabId);
-      entry.view.setBounds(request.bounds);
+      setEntryBounds({ hostWindow, entry, bounds: request.bounds });
       entry.view.setVisible(request.visible);
       loadIfNeeded(entry, request.url);
       pushState(hostWindow, request.tabId);
@@ -343,7 +378,7 @@ export function createDesktopBrowserViewManager(
     },
     setBounds({ hostWindow, request }) {
       withEntry({ hostWindow, tabId: request.tabId }, (entry) => {
-        entry.view.setBounds(request.bounds);
+        setEntryBounds({ hostWindow, entry, bounds: request.bounds });
       });
     },
     setVisible({ hostWindow, request }) {
diff --git a/apps/desktop/test/desktop-browser-bounds.test.ts b/apps/desktop/test/desktop-browser-bounds.test.ts
new file mode 100644
index 000000000..3109aff61
--- /dev/null
+++ b/apps/desktop/test/desktop-browser-bounds.test.ts
@@ -0,0 +1,45 @@
+import { describe, expect, it } from "vitest";
+import {
+  clampBbDesktopBrowserViewBounds,
+  type BbDesktopBrowserViewBounds,
+  type BbDesktopBrowserViewportBounds,
+} from "@bb/server-contract";
+
+interface BrowserBoundsClampTestCase {
+  bounds: BbDesktopBrowserViewBounds;
+  expected: BbDesktopBrowserViewBounds;
+  label: string;
+  viewport: BbDesktopBrowserViewportBounds;
+}
+
+const browserBoundsClampTestCases: BrowserBoundsClampTestCase[] = [
+  {
+    label: "anchors the left edge and trims overflow at the right and bottom",
+    bounds: { x: 180, y: 48, width: 400, height: 420 },
+    viewport: { width: 500, height: 360 },
+    expected: { x: 180, y: 48, width: 320, height: 312 },
+  },
+  {
+    label: "clamps negative origins to the host content edge",
+    bounds: { x: -24, y: -10, width: 200, height: 120 },
+    viewport: { width: 500, height: 360 },
+    expected: { x: 0, y: 0, width: 176, height: 110 },
+  },
+  {
+    label: "collapses bounds that start outside the host content area",
+    bounds: { x: 640, y: 400, width: 120, height: 90 },
+    viewport: { width: 500, height: 360 },
+    expected: { x: 500, y: 360, width: 0, height: 0 },
+  },
+];
+
+describe("desktop browser bounds containment", () => {
+  it.each(browserBoundsClampTestCases)("$label", (testCase) => {
+    expect(
+      clampBbDesktopBrowserViewBounds({
+        bounds: testCase.bounds,
+        viewport: testCase.viewport,
+      }),
+    ).toEqual(testCase.expected);
+  });
+});
diff --git a/apps/host-daemon/src/app-data-change-reporter.test.ts b/apps/host-daemon/src/app-data-change-reporter.test.ts
index e97fcbf98..19fa7da61 100644
--- a/apps/host-daemon/src/app-data-change-reporter.test.ts
+++ b/apps/host-daemon/src/app-data-change-reporter.test.ts
@@ -39,13 +39,8 @@ afterEach(async () => {
 describe("AppDataChangeReporter", () => {
   it("posts changed app data values and suppresses duplicate versions", async () => {
     const rootPath = await makeTempDir("bb-app-data-reporter-");
-    const statePath = path.join(
-      rootPath,
-      "apps",
-      "status",
-      "data",
-      "state.json",
-    );
+    const appDataPath = path.join(rootPath, "apps", "status", "data");
+    const statePath = path.join(appDataPath, "state.json");
     const posted: HostDaemonAppDataChangePayload[] = [];
     const reporter = new AppDataChangeReporter({
       logger: createLogger(),
@@ -55,24 +50,24 @@ describe("AppDataChangeReporter", () => {
       postAppDataResync: async () => undefined,
     });
 
+    await reporter.replaceTrackedApplications({
+      targets: [{ applicationId: "status", appDataPath }],
+    });
     await writeJsonFile(statePath, { workers: [] });
     await reporter.observe({
-      appId: "status",
+      applicationId: "status",
+      appDataPath,
       path: "state.json",
-      threadId: "thr_one",
-      threadStoragePath: rootPath,
     });
     await reporter.observe({
-      appId: "status",
+      applicationId: "status",
+      appDataPath,
       path: "state.json",
-      threadId: "thr_one",
-      threadStoragePath: rootPath,
     });
 
     expect(posted).toHaveLength(1);
     expect(posted[0]).toMatchObject({
-      appId: "status",
-      threadId: "thr_one",
+      applicationId: "status",
       path: "state.json",
       deleted: false,
       value: { workers: [] },
@@ -82,13 +77,8 @@ describe("AppDataChangeReporter", () => {
 
   it("posts deleted events after observed files are removed", async () => {
     const rootPath = await makeTempDir("bb-app-data-reporter-delete-");
-    const statePath = path.join(
-      rootPath,
-      "apps",
-      "status",
-      "data",
-      "state.json",
-    );
+    const appDataPath = path.join(rootPath, "apps", "status", "data");
+    const statePath = path.join(appDataPath, "state.json");
     const posted: HostDaemonAppDataChangePayload[] = [];
     const reporter = new AppDataChangeReporter({
       logger: createLogger(),
@@ -99,24 +89,24 @@ describe("AppDataChangeReporter", () => {
     });
 
     await writeJsonFile(statePath, { workers: [] });
+    await reporter.replaceTrackedApplications({
+      targets: [{ applicationId: "status", appDataPath }],
+    });
     await reporter.observe({
-      appId: "status",
+      applicationId: "status",
+      appDataPath,
       path: "state.json",
-      threadId: "thr_one",
-      threadStoragePath: rootPath,
     });
     await fs.rm(statePath);
     await reporter.observe({
-      appId: "status",
+      applicationId: "status",
+      appDataPath,
       path: "state.json",
-      threadId: "thr_one",
-      threadStoragePath: rootPath,
     });
 
-    expect(posted).toHaveLength(2);
-    expect(posted[1]).toEqual({
-      appId: "status",
-      threadId: "thr_one",
+    expect(posted).toHaveLength(1);
+    expect(posted[0]).toEqual({
+      applicationId: "status",
       path: "state.json",
       deleted: true,
       value: null,
@@ -126,15 +116,10 @@ describe("AppDataChangeReporter", () => {
 
   it("re-primes tracked threads and posts resync hints after reconnect", async () => {
     const rootPath = await makeTempDir("bb-app-data-reporter-reprime-");
-    const statePath = path.join(
-      rootPath,
-      "apps",
-      "status",
-      "data",
-      "state.json",
-    );
+    const appDataPath = path.join(rootPath, "apps", "status", "data");
+    const statePath = path.join(appDataPath, "state.json");
     const posted: HostDaemonAppDataChangePayload[] = [];
-    const resyncs: Array<{ appId: string; threadId: string }> = [];
+    const resyncs: Array<{ applicationId: string }> = [];
     const reporter = new AppDataChangeReporter({
       logger: createLogger(),
       postAppDataChange: async (payload) => {
@@ -146,31 +131,28 @@ describe("AppDataChangeReporter", () => {
     });
 
     await writeJsonFile(statePath, { workers: [] });
-    await reporter.replaceTrackedThreads({
-      targets: [{ threadId: "thr_one", threadStoragePath: rootPath }],
+    await reporter.replaceTrackedApplications({
+      targets: [{ applicationId: "status", appDataPath }],
     });
     await reporter.observe({
-      appId: "status",
+      applicationId: "status",
+      appDataPath,
       path: "state.json",
-      threadId: "thr_one",
-      threadStoragePath: rootPath,
     });
 
-    expect(resyncs).toEqual([{ appId: "status", threadId: "thr_one" }]);
+    expect(resyncs).toEqual([{ applicationId: "status" }]);
     expect(posted).toHaveLength(0);
 
     await writeJsonFile(statePath, { workers: [{ id: "worker-1" }] });
     await reporter.observe({
-      appId: "status",
+      applicationId: "status",
+      appDataPath,
       path: "state.json",
-      threadId: "thr_one",
-      threadStoragePath: rootPath,
     });
 
     expect(posted).toHaveLength(1);
     expect(posted[0]).toMatchObject({
-      appId: "status",
-      threadId: "thr_one",
+      applicationId: "status",
       path: "state.json",
       deleted: false,
       value: { workers: [{ id: "worker-1" }] },
@@ -179,14 +161,9 @@ describe("AppDataChangeReporter", () => {
 
   it("posts resync hints for apps whose data disappeared while disconnected", async () => {
     const rootPath = await makeTempDir("bb-app-data-reporter-delete-resync-");
-    const statePath = path.join(
-      rootPath,
-      "apps",
-      "status",
-      "data",
-      "state.json",
-    );
-    const resyncs: Array<{ appId: string; threadId: string }> = [];
+    const appDataPath = path.join(rootPath, "apps", "status", "data");
+    const statePath = path.join(appDataPath, "state.json");
+    const resyncs: Array<{ applicationId: string }> = [];
     const reporter = new AppDataChangeReporter({
       logger: createLogger(),
       postAppDataChange: async () => undefined,
@@ -196,22 +173,22 @@ describe("AppDataChangeReporter", () => {
     });
 
     await writeJsonFile(statePath, { workers: [] });
-    await reporter.replaceTrackedThreads({
-      targets: [{ threadId: "thr_one", threadStoragePath: rootPath }],
+    await reporter.replaceTrackedApplications({
+      targets: [{ applicationId: "status", appDataPath }],
     });
     await fs.rm(statePath);
-    await reporter.replaceTrackedThreads({
-      targets: [{ threadId: "thr_one", threadStoragePath: rootPath }],
+    await reporter.replaceTrackedApplications({
+      targets: [{ applicationId: "status", appDataPath }],
     });
 
     expect(resyncs).toEqual([
-      { appId: "status", threadId: "thr_one" },
-      { appId: "status", threadId: "thr_one" },
+      { applicationId: "status" },
+      { applicationId: "status" },
     ]);
   });
 
   it("posts requested app data resync hints", async () => {
-    const resyncs: Array<{ appId: string; threadId: string }> = [];
+    const resyncs: Array<{ applicationId: string }> = [];
     const reporter = new AppDataChangeReporter({
       logger: createLogger(),
       postAppDataChange: async () => undefined,
@@ -221,10 +198,9 @@ describe("AppDataChangeReporter", () => {
     });
 
     await reporter.requestResync({
-      appId: "status",
-      threadId: "thr_one",
+      applicationId: "status",
     });
 
-    expect(resyncs).toEqual([{ appId: "status", threadId: "thr_one" }]);
+    expect(resyncs).toEqual([{ applicationId: "status" }]);
   });
 });
diff --git a/apps/host-daemon/src/app-data-change-reporter.ts b/apps/host-daemon/src/app-data-change-reporter.ts
index 449d6fd49..dac92e2f0 100644
--- a/apps/host-daemon/src/app-data-change-reporter.ts
+++ b/apps/host-daemon/src/app-data-change-reporter.ts
@@ -1,17 +1,18 @@
 import type { HostDaemonAppDataChangePayload } from "@bb/host-daemon-contract";
 import {
   appDataPathSchema,
-  appIdSchema,
+  applicationIdSchema,
   type AppDataPath,
-  type AppId,
+  type ApplicationId,
 } from "@bb/domain";
 import { CommandDispatchError } from "./command-dispatch-support.js";
 import { runtimeErrorLogFields } from "./error-utils.js";
 import type { HostDaemonLogger } from "./logger.js";
 import {
-  listThreadAppDataFromRoot,
-  readAppDataFromRoot,
-  type ThreadAppDataEntry,
+  listApplicationDataFromTargets,
+  readApplicationDataFromTarget,
+  type ApplicationDataEntry,
+  type ApplicationDataTarget,
 } from "./app-data-files.js";
 
 interface CreateAppDataChangeReporterOptions {
@@ -25,14 +26,12 @@ interface AppDataCacheEntry {
 }
 
 interface AppDataResyncPayload {
-  appId: AppId;
-  threadId: string;
+  applicationId: ApplicationId;
 }
 
 interface AppDataCacheKeyArgs {
-  appId: AppId;
+  applicationId: ApplicationId;
   path: AppDataPath;
-  threadId: string;
 }
 
 interface ReportObservedDeleteArgs extends AppDataCacheKeyArgs {
@@ -48,40 +47,34 @@ interface AppDataReporterGenerationArgs {
   generation: number;
 }
 
-interface TrackedAppDataThread {
-  threadId: string;
-  threadStoragePath: string;
+interface ReplaceTrackedApplicationDataTargetsArgs {
+  targets: readonly ApplicationDataTarget[];
 }
 
-interface ReplaceTrackedAppDataThreadsArgs {
-  targets: readonly TrackedAppDataThread[];
-}
-
-interface ReprimeThreadArgs {
+interface ReprimeApplicationsArgs {
   generation: number;
-  target: TrackedAppDataThread;
+  targets: readonly ApplicationDataTarget[];
 }
 
-interface ApplyThreadSnapshotArgs extends ReprimeThreadArgs {
-  snapshotEntries: readonly ThreadAppDataEntry[];
-  snapshotAppIds: readonly AppId[];
+interface ApplyApplicationSnapshotArgs extends ReprimeApplicationsArgs {
+  snapshotEntries: readonly ApplicationDataEntry[];
+  snapshotApplicationIds: readonly ApplicationId[];
 }
 
 interface CachedAppDataKey {
-  appId: AppId;
+  applicationId: ApplicationId;
   cacheKey: string;
   path: AppDataPath;
 }
 
 export interface ObserveAppDataChangeArgs {
-  appId: AppId;
+  applicationId: ApplicationId;
+  appDataPath: string;
   path: AppDataPath;
-  threadId: string;
-  threadStoragePath: string;
 }
 
 function appDataCacheKey(args: AppDataCacheKeyArgs): string {
-  return `${args.threadId}\0${args.appId}\0${args.path}`;
+  return `${args.applicationId}\0${args.path}`;
 }
 
 function isMissingAppDataEntryError(error: Error): boolean {
@@ -99,38 +92,30 @@ function isNonReportableAppDataReadError(error: Error): boolean {
 
 export class AppDataChangeReporter {
   private readonly cache = new Map<string, AppDataCacheEntry>();
-  private readonly appIdsByThreadId = new Map<string, Set<AppId>>();
   private readonly pendingByCacheKey = new Map<string, Promise<void>>();
-  private readonly trackedThreadIds = new Set<string>();
+  private readonly trackedTargets = new Map<ApplicationId, ApplicationDataTarget>();
   private generation = 0;
 
   constructor(private readonly options: CreateAppDataChangeReporterOptions) {}
 
-  async replaceTrackedThreads(
-    args: ReplaceTrackedAppDataThreadsArgs,
+  async replaceTrackedApplications(
+    args: ReplaceTrackedApplicationDataTargetsArgs,
   ): Promise<void> {
     this.generation += 1;
     const generation = this.generation;
-    const nextThreadIds = new Set(
-      args.targets.map((target) => target.threadId),
-    );
-    this.replaceTrackedThreadIds(nextThreadIds);
+    this.replaceTrackedTargets(args.targets);
     this.pendingByCacheKey.clear();
-    await Promise.all(
-      args.targets.map((target) =>
-        this.reprimeThread({
-          generation,
-          target,
-        }),
-      ),
-    );
+    await this.reprimeApplications({
+      generation,
+      targets: args.targets,
+    });
   }
 
   observe(args: ObserveAppDataChangeArgs): Promise<void> {
-    this.trackApp({
-      appId: args.appId,
-      threadId: args.threadId,
-    });
+    const target = this.trackedTargets.get(args.applicationId);
+    if (!target) {
+      return Promise.resolve();
+    }
     const cacheKey = appDataCacheKey(args);
     const generation = this.generation;
     const previous = this.pendingByCacheKey.get(cacheKey) ?? Promise.resolve();
@@ -138,16 +123,19 @@ export class AppDataChangeReporter {
       .catch(() => undefined)
       .then(() =>
         this.reportObservedChange({
-          change: args,
+          change: {
+            applicationId: args.applicationId,
+            appDataPath: target.appDataPath,
+            path: args.path,
+          },
           generation,
         }),
       )
       .catch((error) => {
         this.options.logger.warn(
           {
-            appId: args.appId,
+            applicationId: args.applicationId,
             path: args.path,
-            threadId: args.threadId,
             ...runtimeErrorLogFields(error),
           },
           "Failed to report observed app data change",
@@ -163,10 +151,6 @@ export class AppDataChangeReporter {
   }
 
   requestResync(args: AppDataResyncPayload): Promise<void> {
-    this.trackApp({
-      appId: args.appId,
-      threadId: args.threadId,
-    });
     return this.postResyncHint(args);
   }
 
@@ -174,81 +158,74 @@ export class AppDataChangeReporter {
     return args.generation === this.generation;
   }
 
-  private replaceTrackedThreadIds(threadIds: ReadonlySet<string>): void {
-    for (const threadId of Array.from(this.trackedThreadIds)) {
-      if (threadIds.has(threadId)) {
+  private replaceTrackedTargets(
+    targets: readonly ApplicationDataTarget[],
+  ): void {
+    const nextApplicationIds = new Set(
+      targets.map((target) => target.applicationId),
+    );
+    for (const applicationId of Array.from(this.trackedTargets.keys())) {
+      if (nextApplicationIds.has(applicationId)) {
         continue;
       }
-      this.trackedThreadIds.delete(threadId);
-      this.appIdsByThreadId.delete(threadId);
-      for (const cached of this.cachedKeysForThread({ threadId })) {
+      this.trackedTargets.delete(applicationId);
+      for (const cached of this.cachedKeysForApplication({ applicationId })) {
         this.cache.delete(cached.cacheKey);
       }
     }
-    for (const threadId of threadIds) {
-      this.trackedThreadIds.add(threadId);
+    for (const target of targets) {
+      this.trackedTargets.set(target.applicationId, target);
     }
   }
 
-  private trackApp(args: AppDataResyncPayload): void {
-    this.trackedThreadIds.add(args.threadId);
-    let appIds = this.appIdsByThreadId.get(args.threadId);
-    if (!appIds) {
-      appIds = new Set<AppId>();
-      this.appIdsByThreadId.set(args.threadId, appIds);
-    }
-    appIds.add(args.appId);
-  }
-
-  private cachedKeysForThread(args: { threadId: string }): CachedAppDataKey[] {
-    const prefix = `${args.threadId}\0`;
+  private cachedKeysForApplication(args: {
+    applicationId: ApplicationId;
+  }): CachedAppDataKey[] {
+    const prefix = `${args.applicationId}\0`;
     return Array.from(this.cache.keys())
       .filter((cacheKey) => cacheKey.startsWith(prefix))
       .map((cacheKey) => {
-        const [, rawAppId, rawDataPath] = cacheKey.split("\0");
+        const [rawApplicationId, rawDataPath] = cacheKey.split("\0");
         return {
-          appId: appIdSchema.parse(rawAppId),
+          applicationId: applicationIdSchema.parse(rawApplicationId),
           path: appDataPathSchema.parse(rawDataPath),
           cacheKey,
         };
       });
   }
 
-  private async reprimeThread(args: ReprimeThreadArgs): Promise<void> {
+  private async reprimeApplications(
+    args: ReprimeApplicationsArgs,
+  ): Promise<void> {
     try {
-      const snapshot = await listThreadAppDataFromRoot({
-        rootPath: args.target.threadStoragePath,
+      const snapshot = await listApplicationDataFromTargets({
+        targets: args.targets,
       });
       if (!this.isCurrentGeneration({ generation: args.generation })) {
         return;
       }
-      const previousAppIds = new Set(
-        this.appIdsByThreadId.get(args.target.threadId) ?? [],
-      );
-      await this.applyThreadSnapshot({
+      const previousApplicationIds = new Set(this.trackedTargets.keys());
+      await this.applyApplicationSnapshot({
         ...args,
         snapshotEntries: snapshot.entries,
-        snapshotAppIds: snapshot.appIds,
+        snapshotApplicationIds: snapshot.applicationIds,
       });
-      const resyncAppIds = new Set<AppId>([
-        ...previousAppIds,
-        ...snapshot.appIds,
+      const resyncApplicationIds = new Set<ApplicationId>([
+        ...previousApplicationIds,
+        ...snapshot.applicationIds,
       ]);
       await Promise.all(
-        Array.from(resyncAppIds)
+        Array.from(resyncApplicationIds)
           .sort((left, right) => left.localeCompare(right))
-          .map((appId) =>
+          .map((applicationId) =>
             this.postResyncHint({
-              appId,
-              threadId: args.target.threadId,
+              applicationId,
             }),
           ),
       );
     } catch (error) {
       this.options.logger.warn(
         {
-          threadId: args.target.threadId,
-          threadStoragePath: args.target.threadStoragePath,
           ...runtimeErrorLogFields(error),
         },
         "Failed to reprime app data change cache",
@@ -256,30 +233,26 @@ export class AppDataChangeReporter {
     }
   }
 
-  private async applyThreadSnapshot(
-    args: ApplyThreadSnapshotArgs,
+  private async applyApplicationSnapshot(
+    args: ApplyApplicationSnapshotArgs,
   ): Promise<void> {
     const seenCacheKeys = new Set<string>();
-    const appIds = new Set<AppId>(args.snapshotAppIds);
     for (const snapshotEntry of args.snapshotEntries) {
       if (!this.isCurrentGeneration({ generation: args.generation })) {
         return;
       }
-      appIds.add(snapshotEntry.appId);
       const cacheKey = appDataCacheKey({
-        appId: snapshotEntry.appId,
+        applicationId: snapshotEntry.applicationId,
         path: snapshotEntry.entry.path,
-        threadId: args.target.threadId,
       });
       seenCacheKeys.add(cacheKey);
       this.cache.set(cacheKey, { version: snapshotEntry.entry.version });
     }
-    this.appIdsByThreadId.set(args.target.threadId, appIds);
-    for (const cached of this.cachedKeysForThread({
-      threadId: args.target.threadId,
-    })) {
-      if (!seenCacheKeys.has(cached.cacheKey)) {
-        this.cache.delete(cached.cacheKey);
+    for (const applicationId of args.snapshotApplicationIds) {
+      for (const cached of this.cachedKeysForApplication({ applicationId })) {
+        if (!seenCacheKeys.has(cached.cacheKey)) {
+          this.cache.delete(cached.cacheKey);
+        }
       }
     }
   }
@@ -290,8 +263,7 @@ export class AppDataChangeReporter {
     } catch (error) {
       this.options.logger.warn(
         {
-          appId: args.appId,
-          threadId: args.threadId,
+          applicationId: args.applicationId,
           ...runtimeErrorLogFields(error),
         },
         "Failed to report app data resync hint",
@@ -305,14 +277,17 @@ export class AppDataChangeReporter {
     if (!this.isCurrentGeneration({ generation: args.generation })) {
       return;
     }
+    const target = this.trackedTargets.get(args.change.applicationId);
+    if (!target) {
+      return;
+    }
     const cacheKey = appDataCacheKey(args.change);
     const previous = this.cache.get(cacheKey);
 
     try {
-      const entry = await readAppDataFromRoot({
-        appId: args.change.appId,
+      const entry = await readApplicationDataFromTarget({
         path: args.change.path,
-        rootPath: args.change.threadStoragePath,
+        target,
       });
       if (!this.isCurrentGeneration({ generation: args.generation })) {
         return;
@@ -321,8 +296,7 @@ export class AppDataChangeReporter {
         return;
       }
       await this.options.postAppDataChange({
-        appId: args.change.appId,
-        threadId: args.change.threadId,
+        applicationId: args.change.applicationId,
         path: entry.path,
         deleted: false,
         value: entry.value,
@@ -331,27 +305,21 @@ export class AppDataChangeReporter {
       if (!this.isCurrentGeneration({ generation: args.generation })) {
         return;
       }
-      this.trackApp({
-        appId: args.change.appId,
-        threadId: args.change.threadId,
-      });
       this.cache.set(cacheKey, { version: entry.version });
     } catch (error) {
       if (error instanceof Error && isMissingAppDataEntryError(error)) {
         await this.reportObservedDelete({
-          appId: args.change.appId,
+          applicationId: args.change.applicationId,
           generation: args.generation,
           path: args.change.path,
-          threadId: args.change.threadId,
         });
         return;
       }
       if (error instanceof Error && isNonReportableAppDataReadError(error)) {
         this.options.logger.warn(
           {
-            appId: args.change.appId,
+            applicationId: args.change.applicationId,
             path: args.change.path,
-            threadId: args.change.threadId,
             ...runtimeErrorLogFields(error),
           },
           "Ignoring unreadable observed app data file",
@@ -368,9 +336,12 @@ export class AppDataChangeReporter {
     if (!this.isCurrentGeneration({ generation: args.generation })) {
       return;
     }
+    const cacheKey = appDataCacheKey(args);
+    if (!this.cache.has(cacheKey)) {
+      return;
+    }
     await this.options.postAppDataChange({
-      appId: args.appId,
-      threadId: args.threadId,
+      applicationId: args.applicationId,
       path: args.path,
       deleted: true,
       value: null,
@@ -379,10 +350,6 @@ export class AppDataChangeReporter {
     if (!this.isCurrentGeneration({ generation: args.generation })) {
       return;
     }
-    this.trackApp({
-      appId: args.appId,
-      threadId: args.threadId,
-    });
-    this.cache.delete(appDataCacheKey(args));
+    this.cache.delete(cacheKey);
   }
 }
diff --git a/apps/host-daemon/src/app-data-files.test.ts b/apps/host-daemon/src/app-data-files.test.ts
index cab6c6dc0..d126d352c 100644
--- a/apps/host-daemon/src/app-data-files.test.ts
+++ b/apps/host-daemon/src/app-data-files.test.ts
@@ -1,20 +1,76 @@
 import { randomUUID } from "node:crypto";
+import fs from "node:fs/promises";
 import os from "node:os";
 import path from "node:path";
-import { describe, expect, it } from "vitest";
-import { listThreadAppDataFromRoot } from "./app-data-files.js";
+import { afterEach, describe, expect, it } from "vitest";
+import { listApplicationDataTargetsFromRoot } from "./app-data-files.js";
+
+const tempDirs: string[] = [];
+
+async function makeTempDir(prefix: string): Promise<string> {
+  const dir = await fs.mkdtemp(path.join(os.tmpdir(), prefix));
+  tempDirs.push(dir);
+  return dir;
+}
+
+afterEach(async () => {
+  await Promise.all(
+    tempDirs
+      .splice(0)
+      .map((dir) => fs.rm(dir, { recursive: true, force: true })),
+  );
+});
 
 describe("app data files", () => {
-  it("treats a missing thread storage root as an empty snapshot", async () => {
+  it("treats a missing apps root as an empty target list", async () => {
     const missingRoot = path.join(
       os.tmpdir(),
-      `bb-missing-thread-storage-${randomUUID()}`,
+      `bb-missing-apps-${randomUUID()}`,
     );
 
     await expect(
-      listThreadAppDataFromRoot({
-        rootPath: missingRoot,
+      listApplicationDataTargetsFromRoot({
+        appsRootPath: missingRoot,
+      }),
+    ).resolves.toEqual([]);
+  });
+
+  it("lists valid global application data targets", async () => {
+    const dataDir = await makeTempDir("bb-app-data-files-");
+    const appsRootPath = path.join(dataDir, "apps");
+    const applicationPath = path.join(appsRootPath, "valid");
+    await fs.mkdir(path.join(applicationPath, "data"), { recursive: true });
+    await fs.writeFile(
+      path.join(applicationPath, "manifest.json"),
+      JSON.stringify({
+        manifestVersion: 1,
+        id: "valid",
+        name: "Valid App",
+        entry: "index.html",
+      }),
+      "utf8",
+    );
+    await fs.mkdir(path.join(appsRootPath, "broken"), {
+      recursive: true,
+    });
+    await fs.writeFile(
+      path.join(appsRootPath, "broken", "manifest.json"),
+      JSON.stringify({
+        manifestVersion: 1,
+        id: "other",
+        name: "Broken App",
       }),
-    ).resolves.toEqual({ appIds: [], entries: [] });
+      "utf8",
+    );
+
+    const resolvedApplicationPath = await fs.realpath(applicationPath);
+    await expect(
+      listApplicationDataTargetsFromRoot({ appsRootPath }),
+    ).resolves.toEqual([
+      {
+        applicationId: "valid",
+        appDataPath: path.join(resolvedApplicationPath, "data"),
+      },
+    ]);
   });
 });
diff --git a/apps/host-daemon/src/app-data-files.ts b/apps/host-daemon/src/app-data-files.ts
index 2e1d5fb86..532ff6900 100644
--- a/apps/host-daemon/src/app-data-files.ts
+++ b/apps/host-daemon/src/app-data-files.ts
@@ -2,12 +2,17 @@ import { createHash } from "node:crypto";
 import type { Stats } from "node:fs";
 import fs from "node:fs/promises";
 import path from "node:path";
+import {
+  resolveApplicationDataPath,
+  resolveApplicationManifestPath,
+  resolveAppsRootPath,
+} from "@bb/config/app-storage-paths";
 import {
   appDataPathSchema,
-  appIdSchema,
+  applicationIdSchema,
   jsonValueSchema,
   type AppDataPath,
-  type AppId,
+  type ApplicationId,
   type JsonValue,
 } from "@bb/domain";
 import {
@@ -26,25 +31,24 @@ export interface AppDataEntry {
   version: string;
 }
 
-export interface ThreadAppDataEntry {
-  appId: AppId;
+export interface ApplicationDataEntry {
+  applicationId: ApplicationId;
   entry: AppDataEntry;
 }
 
-export interface ThreadAppDataSnapshot {
-  appIds: AppId[];
-  entries: ThreadAppDataEntry[];
+export interface ApplicationDataSnapshot {
+  applicationIds: ApplicationId[];
+  entries: ApplicationDataEntry[];
 }
 
-interface AppDataTargetArgs {
-  appId: AppId;
-  path: AppDataPath;
-  rootPath: string;
+export interface ApplicationDataTarget {
+  applicationId: ApplicationId;
+  appDataPath: string;
 }
 
-interface ResolveAppDataRootArgs {
-  appId: AppId;
-  rootPath: string;
+interface AppDataTargetArgs {
+  path: AppDataPath;
+  target: ApplicationDataTarget;
 }
 
 interface ReadAppDataJsonArgs {
@@ -57,8 +61,12 @@ interface ListAppDataFilesArgs {
   currentDirectory: string;
 }
 
-interface ListThreadAppDataArgs {
-  rootPath: string;
+interface ListApplicationDataArgs {
+  targets: readonly ApplicationDataTarget[];
+}
+
+interface ListApplicationDataTargetsFromRootArgs {
+  appsRootPath: string;
 }
 
 function sha256(bytes: Buffer): string {
@@ -91,41 +99,68 @@ function parseJsonValue(args: ReadAppDataJsonArgs): JsonValue {
   }
 }
 
+function isIgnoredApplicationStorageEntry(entryName: string): boolean {
+  return (
+    entryName.startsWith(".tmp-app_") || entryName.startsWith(".delete-app_")
+  );
+}
+
+async function isValidApplicationManifest(
+  appsRootPath: string,
+  applicationId: ApplicationId,
+): Promise<boolean> {
+  const dataDir = path.dirname(appsRootPath);
+  try {
+    const rawManifest = JSON.parse(
+      await fs.readFile(
+        resolveApplicationManifestPath(dataDir, applicationId),
+        "utf8",
+      ),
+    );
+    return (
+      rawManifest !== null &&
+      typeof rawManifest === "object" &&
+      "id" in rawManifest &&
+      rawManifest.id === applicationId &&
+      "name" in rawManifest &&
+      typeof rawManifest.name === "string" &&
+      rawManifest.name.trim().length > 0
+    );
+  } catch {
+    return false;
+  }
+}
+
 async function resolveAppDataRoot(
-  args: ResolveAppDataRootArgs,
+  target: ApplicationDataTarget,
 ): Promise<string> {
-  const appId = appIdSchema.parse(args.appId);
-  if (!path.isAbsolute(args.rootPath)) {
-    throw new CommandDispatchError("invalid_path", "rootPath must be absolute");
+  if (!path.isAbsolute(target.appDataPath)) {
+    throw new CommandDispatchError(
+      "invalid_path",
+      "appDataPath must be absolute",
+    );
   }
-  const threadStoragePath = await resolveNonSymlinkDirectoryPath({
-    description: "Thread storage root",
-    path: args.rootPath,
-  });
-  const appDataPath = path.join(threadStoragePath, "apps", appId, "data");
   const resolvedAppDataPath = await resolveNonSymlinkDirectoryPath({
     description: "App data directory",
-    path: appDataPath,
+    path: target.appDataPath,
   });
-  if (!isPathWithinRoot(resolvedAppDataPath, threadStoragePath)) {
+  const appRootPath = path.dirname(resolvedAppDataPath);
+  if (!isPathWithinRoot(resolvedAppDataPath, appRootPath)) {
     throw new CommandDispatchError(
       "invalid_path",
-      "App data path escapes thread storage root",
+      "App data path escapes app root",
     );
   }
   return resolvedAppDataPath;
 }
 
-export async function readAppDataFromRoot(
+export async function readApplicationDataFromTarget(
   args: AppDataTargetArgs,
 ): Promise<AppDataEntry> {
   const appDataPath = appDataPathSchema.parse(args.path);
   let appDataRoot: string;
   try {
-    appDataRoot = await resolveAppDataRoot({
-      appId: args.appId,
-      rootPath: args.rootPath,
-    });
+    appDataRoot = await resolveAppDataRoot(args.target);
   } catch (error) {
     if (isFsErrorWithCode(error, "ENOENT")) {
       throw new ExpectedCommandDispatchError(
@@ -204,56 +239,58 @@ async function listAppDataFilePaths(
   return paths.sort((left, right) => left.localeCompare(right));
 }
 
-export async function listThreadAppDataFromRoot(
-  args: ListThreadAppDataArgs,
-): Promise<ThreadAppDataSnapshot> {
-  if (!path.isAbsolute(args.rootPath)) {
-    throw new CommandDispatchError("invalid_path", "rootPath must be absolute");
-  }
-  let threadStoragePath: string;
+export async function listApplicationDataTargetsFromRoot(
+  args: ListApplicationDataTargetsFromRootArgs,
+): Promise<ApplicationDataTarget[]> {
+  let appsRootPath;
   try {
-    threadStoragePath = await resolveNonSymlinkDirectoryPath({
-      description: "Thread storage root",
-      path: args.rootPath,
+    appsRootPath = await resolveNonSymlinkDirectoryPath({
+      description: "Apps root",
+      path: args.appsRootPath,
     });
   } catch (error) {
     if (isFsErrorWithCode(error, "ENOENT")) {
-      // Archived/deleted thread storage can be cleaned up while the daemon is
-      // still reconciling tracked targets. A missing root is an empty snapshot.
-      return { appIds: [], entries: [] };
+      return [];
     }
     throw error;
   }
-  const appsRoot = path.join(threadStoragePath, "apps");
-  let appDirectories;
-  try {
-    appDirectories = await fs.readdir(appsRoot, { withFileTypes: true });
-  } catch (error) {
-    if (isFsErrorWithCode(error, "ENOENT")) {
-      return { appIds: [], entries: [] };
+  const entries = await fs.readdir(appsRootPath, { withFileTypes: true });
+  const dataDir = path.dirname(appsRootPath);
+  const targets: ApplicationDataTarget[] = [];
+  for (const entry of entries) {
+    if (
+      !entry.isDirectory() ||
+      isIgnoredApplicationStorageEntry(entry.name)
+    ) {
+      continue;
     }
-    throw error;
-  }
-
-  const appIds: AppId[] = [];
-  const snapshotEntries: ThreadAppDataEntry[] = [];
-  for (const directory of appDirectories) {
-    if (!directory.isDirectory()) {
+    const parsed = applicationIdSchema.safeParse(entry.name);
+    if (!parsed.success) {
       continue;
     }
-    const parsedAppId = appIdSchema.safeParse(directory.name);
-    if (!parsedAppId.success) {
+    if (!(await isValidApplicationManifest(appsRootPath, parsed.data))) {
       continue;
     }
-    const appId = parsedAppId.data;
-    appIds.push(appId);
-    const appDataRoot = path.join(appsRoot, appId, "data");
+    targets.push({
+      applicationId: parsed.data,
+      appDataPath: resolveApplicationDataPath(dataDir, parsed.data),
+    });
+  }
+  return targets.sort((left, right) =>
+    left.applicationId.localeCompare(right.applicationId),
+  );
+}
+
+export async function listApplicationDataFromTargets(
+  args: ListApplicationDataArgs,
+): Promise<ApplicationDataSnapshot> {
+  const applicationIds: ApplicationId[] = [];
+  const snapshotEntries: ApplicationDataEntry[] = [];
+  for (const target of args.targets) {
+    applicationIds.push(target.applicationId);
     let resolvedAppDataRoot;
     try {
-      resolvedAppDataRoot = await resolveNonSymlinkDirectoryPath({
-        description: "App data directory",
-        path: appDataRoot,
-      });
+      resolvedAppDataRoot = await resolveAppDataRoot(target);
     } catch (error) {
       if (isFsErrorWithCode(error, "ENOENT")) {
         continue;
@@ -266,25 +303,30 @@ export async function listThreadAppDataFromRoot(
     });
     for (const dataPath of dataPaths) {
       snapshotEntries.push({
-        appId,
-        entry: await readAppDataFromRoot({
-          appId,
+        applicationId: target.applicationId,
+        entry: await readApplicationDataFromTarget({
           path: dataPath,
-          rootPath: threadStoragePath,
+          target,
         }),
       });
     }
   }
 
-  appIds.sort((left, right) => left.localeCompare(right));
+  applicationIds.sort((left, right) => left.localeCompare(right));
   snapshotEntries.sort((left, right) => {
-    const appOrder = left.appId.localeCompare(right.appId);
+    const appOrder = left.applicationId.localeCompare(right.applicationId);
     return appOrder === 0
       ? left.entry.path.localeCompare(right.entry.path)
       : appOrder;
   });
   return {
-    appIds,
+    applicationIds,
     entries: snapshotEntries,
   };
 }
+
+export async function ensureAppsRootPath(dataDir: string): Promise<string> {
+  const appsRootPath = resolveAppsRootPath(dataDir);
+  await fs.mkdir(appsRootPath, { recursive: true });
+  return appsRootPath;
+}
diff --git a/apps/host-daemon/src/app.test.ts b/apps/host-daemon/src/app.test.ts
index cd5b87545..04a210909 100644
--- a/apps/host-daemon/src/app.test.ts
+++ b/apps/host-daemon/src/app.test.ts
@@ -134,6 +134,7 @@ function createFetchRecorder(
           heartbeatIntervalMs: 30000,
           leaseTimeoutMs: 90000,
           trackedThreadTargets: [],
+          trackedApplicationDataTargets: [],
           retiredEnvironmentIds: args.retiredEnvironmentIds ?? [],
         },
         { status: 201 },
@@ -573,6 +574,7 @@ describe("createHostDaemonApp", () => {
             heartbeatIntervalMs: 30000,
             leaseTimeoutMs: 90000,
             trackedThreadTargets: [],
+            trackedApplicationDataTargets: [],
             retiredEnvironmentIds: [],
           },
           { status: 201 },
@@ -651,6 +653,7 @@ describe("createHostDaemonApp", () => {
       shutdown: vi.fn(async () => undefined),
     } satisfies AgentRuntime;
     const hostWatcher = {
+      watchApplicationStorageRoot: vi.fn(() => () => undefined),
       watchWorkspace: vi.fn(() => stopWatchingStatus),
       watchThreadStorageRoot: vi.fn(() => () => undefined),
     } satisfies HostWatcher;
diff --git a/apps/host-daemon/src/app.ts b/apps/host-daemon/src/app.ts
index 378f99482..68aebeb95 100644
--- a/apps/host-daemon/src/app.ts
+++ b/apps/host-daemon/src/app.ts
@@ -1,4 +1,3 @@
-import path from "node:path";
 import { CommandRouter } from "./command-router.js";
 import { createDaemon, type HostDaemon } from "./daemon.js";
 import {
@@ -34,6 +33,12 @@ import {
 import { createReplayCaptureService } from "@bb/replay-capture/writer";
 import { createServerClient } from "./server-client.js";
 import { AppDataChangeReporter } from "./app-data-change-reporter.js";
+import { resolveDataDirSkillsRootPath } from "@bb/config/app-storage-paths";
+import {
+  ensureAppsRootPath,
+  listApplicationDataTargetsFromRoot,
+} from "./app-data-files.js";
+import { cleanupInjectedSkillStagingDirs } from "./injected-skills.js";
 import {
   ServerConnection,
   type CreateReconnectingWebSocket,
@@ -325,6 +330,13 @@ export async function createHostDaemonApp(
       ? { env: { BB_THREAD_STORAGE: options.threadStorageRootPath } }
       : {},
   );
+  const appsRootPath = await ensureAppsRootPath(options.dataDir);
+  const dataDirSkillsRootPath = resolveDataDirSkillsRootPath(options.dataDir);
+  await cleanupInjectedSkillStagingDirs({
+    dataDir: options.dataDir,
+    keepCatalogHashes: [],
+    logger: options.logger,
+  });
   const sessionState: SessionState = {
     value: null,
   };
@@ -371,6 +383,12 @@ export async function createHostDaemonApp(
     postAppDataResync: (payload) => serverClient.postAppDataResync(payload),
   });
 
+  async function refreshTrackedApplicationDataTargets(): Promise<void> {
+    const targets = await listApplicationDataTargetsFromRoot({ appsRootPath });
+    runtimeManager.replaceTrackedApplicationDataTargets(targets);
+    await appDataChangeReporter.replaceTrackedApplications({ targets });
+  }
+
   function buildInteractiveInterruptKey(
     request: PendingInteractiveInterruptRequest,
   ): string {
@@ -493,8 +511,12 @@ export async function createHostDaemonApp(
   runtimeManager = new RuntimeManager({
     bridgeBundleDir: options.bridgeBundleDir,
     createRuntime: options.createRuntime,
+    dataDir: options.dataDir,
+    dataDirSkillsRootPath,
     hostWatcher: options.hostWatcher,
+    logger: options.logger,
     shellEnv: options.runtimeShellEnv,
+    appsRootPath,
     onCapture: (entry) => {
       replayCapture?.recordRuntimeCaptureEntry(entry);
     },
@@ -531,12 +553,57 @@ export async function createHostDaemonApp(
         change: "thread-storage-changed",
       });
     },
-    onThreadAppDataChanged: (change) => {
+    onApplicationStorageTargetsChanged: () => {
+      void refreshTrackedApplicationDataTargets()
+        .then(() => {
+          sendServerMessage({
+            type: "application-storage-changed",
+          });
+        })
+        .catch((error) => {
+          options.logger.warn(
+            {
+              appsRootPath,
+              ...runtimeErrorLogFields(error),
+            },
+            "Failed to refresh tracked app data targets",
+          );
+        });
+    },
+    onApplicationDataChanged: (change) => {
       void appDataChangeReporter.observe(change);
     },
-    onThreadAppDataResync: (change) => {
+    onApplicationDataResync: (change) => {
       void appDataChangeReporter.requestResync(change);
     },
+    onInjectedSkillsChanged: (change) => {
+      options.logger.debug(
+        {
+          applicationId: change.applicationId,
+          changedPaths: change.changedPaths,
+          sourceType: change.sourceType,
+        },
+        "Injected skills changed; future runtime launches will rescan",
+      );
+    },
+    onApplicationStorageWatchError: ({ error }) => {
+      options.logger.warn(
+        {
+          rootPath: error.rootPath,
+          watchError: error.message,
+        },
+        "Application storage watch unavailable; retrying in background",
+      );
+    },
+    onDataDirSkillsWatchError: ({ error }) => {
+      options.logger.warn(
+        {
+          rootPath: error.rootPath,
+          watchError: error.message,
+        },
+        "Data-dir skills watch unavailable; retrying in background",
+      );
+    },
     onThreadStorageWatchError: ({ error }) => {
       options.logger.warn(
         {
@@ -742,11 +809,11 @@ export async function createHostDaemonApp(
       runtimeManager.replaceTrackedThreadStorageTargets(
         session.trackedThreadTargets,
       );
-      void appDataChangeReporter.replaceTrackedThreads({
-        targets: session.trackedThreadTargets.map((target) => ({
-          threadId: target.threadId,
-          threadStoragePath: path.join(threadStorageRootPath, target.threadId),
-        })),
+      runtimeManager.replaceTrackedApplicationDataTargets(
+        session.trackedApplicationDataTargets,
+      );
+      void appDataChangeReporter.replaceTrackedApplications({
+        targets: session.trackedApplicationDataTargets,
       });
       void eventBuffer.flush().catch((error) => {
         options.logger.warn(
diff --git a/apps/host-daemon/src/command-dispatch-support.ts b/apps/host-daemon/src/command-dispatch-support.ts
index 4c874f1f1..b019fdce7 100644
--- a/apps/host-daemon/src/command-dispatch-support.ts
+++ b/apps/host-daemon/src/command-dispatch-support.ts
@@ -8,6 +8,7 @@ import type { AvailableModel, ProviderInfo } from "@bb/domain";
 import type { BufferedEventInput } from "./event-buffer.js";
 import type {
   HostDaemonCommand,
+  HostDaemonInjectedSkillSource,
   HostDaemonOnlineRpcCommand,
   WorkspaceContext,
 } from "@bb/host-daemon-contract";
@@ -214,6 +215,7 @@ export async function requireWorkspaceEnvironment(
   args: {
     dataDir?: string;
     environmentId: string;
+    injectedSkillSources?: readonly HostDaemonInjectedSkillSource[];
     workspaceContext: WorkspaceContext;
   },
   runtimeManager: RuntimeManager,
@@ -227,11 +229,13 @@ export async function requireWorkspaceEnvironment(
         `Loaded environment ${args.environmentId} is bound to ${existing.path}, not ${args.workspaceContext.workspacePath}`,
       );
     }
-    return existing;
   }
 
   return runtimeManager.ensureEnvironment({
     environmentId: args.environmentId,
+    ...(args.injectedSkillSources !== undefined
+      ? { injectedSkillSources: args.injectedSkillSources }
+      : {}),
     ...(args.dataDir
       ? { personalWorkspaceRoot: getPersonalWorkspaceRoot(args.dataDir) }
       : {}),
diff --git a/apps/host-daemon/src/command-handlers/host-files.test.ts b/apps/host-daemon/src/command-handlers/host-files.test.ts
index 7e3d356b1..d189004af 100644
--- a/apps/host-daemon/src/command-handlers/host-files.test.ts
+++ b/apps/host-daemon/src/command-handlers/host-files.test.ts
@@ -249,19 +249,19 @@ describe("writeHostRelativeFile and deleteHostRelativeFile", () => {
     const result = await writeHostRelativeFile({
       type: "host.write_file_relative",
       rootPath,
-      path: "apps/status/data/state.json",
+      path: "data/state.json",
       dotfiles: "deny",
       content,
       contentEncoding: "utf8",
     });
 
     expect(result).toMatchObject({
-      path: "apps/status/data/state.json",
+      path: "data/state.json",
       hash: createHash("sha256").update(content).digest("hex"),
       sizeBytes: Buffer.byteLength(content),
     });
     await expect(
-      fs.readFile(path.join(rootPath, "apps/status/data/state.json"), "utf8"),
+      fs.readFile(path.join(rootPath, "data/state.json"), "utf8"),
     ).resolves.toBe(content);
   });
 
diff --git a/apps/host-daemon/src/command-handlers/thread.ts b/apps/host-daemon/src/command-handlers/thread.ts
index 7c35779cf..af7d1f3cb 100644
--- a/apps/host-daemon/src/command-handlers/thread.ts
+++ b/apps/host-daemon/src/command-handlers/thread.ts
@@ -70,6 +70,7 @@ export async function startThread(
     const entry = await requireResolvedWorkspaceForCommand({
       dataDir: options.dataDir,
       environmentId: command.environmentId,
+      injectedSkillSources: command.injectedSkillSources,
       runtimeManager: options.runtimeManager,
       workspaceContext: command.workspaceContext,
     });
@@ -107,6 +108,7 @@ export async function ensureThreadRuntime(
   const entry = await requireResolvedWorkspaceForCommand({
     dataDir: options.dataDir,
     environmentId: command.environmentId,
+    injectedSkillSources: resumeContext.injectedSkillSources,
     runtimeManager: options.runtimeManager,
     workspaceContext: resumeContext.workspaceContext,
   });
diff --git a/apps/host-daemon/src/injected-skills.test.ts b/apps/host-daemon/src/injected-skills.test.ts
new file mode 100644
index 000000000..9baf60bb1
--- /dev/null
+++ b/apps/host-daemon/src/injected-skills.test.ts
@@ -0,0 +1,246 @@
+import { mkdir, mkdtemp, readFile, rm, symlink, writeFile } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import path from "node:path";
+import { afterEach, describe, expect, it } from "vitest";
+import type {
+  AgentRuntimeClaudeCodeSkillRoot,
+  AgentRuntimeCodexSkillRoot,
+  AgentRuntimeSkillRoot,
+} from "@bb/agent-runtime";
+import type { HostDaemonInjectedSkillSource } from "@bb/host-daemon-contract";
+import { stageInjectedSkillSources } from "./injected-skills.js";
+
+interface WriteSkillArgs {
+  body?: string;
+  name: string;
+  rootPath: string;
+}
+
+interface StageSourceArgs {
+  dataDir: string;
+  skillRootPath: string;
+  skillName: string;
+}
+
+interface CapturedWarning {
+  context: object;
+  message: string;
+}
+
+const tempDirs: string[] = [];
+
+async function makeTempDir(): Promise<string> {
+  const dir = await mkdtemp(path.join(tmpdir(), "bb-host-skills-"));
+  tempDirs.push(dir);
+  return dir;
+}
+
+afterEach(async () => {
+  await Promise.all(
+    tempDirs
+      .splice(0)
+      .map((dir) => rm(dir, { recursive: true, force: true })),
+  );
+});
+
+function isCodexSkillRoot(
+  root: AgentRuntimeSkillRoot,
+): root is AgentRuntimeCodexSkillRoot {
+  return root.providerId === "codex";
+}
+
+function isClaudeCodeSkillRoot(
+  root: AgentRuntimeSkillRoot,
+): root is AgentRuntimeClaudeCodeSkillRoot {
+  return root.providerId === "claude-code";
+}
+
+async function writeSkill(args: WriteSkillArgs): Promise<string> {
+  const skillRootPath = path.join(args.rootPath, args.name);
+  await mkdir(path.join(skillRootPath, "references"), { recursive: true });
+  await writeFile(
+    path.join(skillRootPath, "SKILL.md"),
+    [
+      "---",
+      `name: ${args.name}`,
+      `description: Use ${args.name} when host staging tests run.`,
+      "---",
+      "",
+      args.body ?? "# Skill",
+      "",
+    ].join("\n"),
+    "utf8",
+  );
+  await writeFile(
+    path.join(skillRootPath, "references", "notes.md"),
+    "supporting notes\n",
+    "utf8",
+  );
+  return skillRootPath;
+}
+
+function createDataDirSource(args: StageSourceArgs): HostDaemonInjectedSkillSource {
+  return {
+    sourceType: "data-dir",
+    applicationId: null,
+    name: args.skillName,
+    description: `Use ${args.skillName} when host staging tests run.`,
+    sourceRootPath: args.skillRootPath,
+    skillFilePath: path.join(args.skillRootPath, "SKILL.md"),
+  };
+}
+
+describe("injected skill staging", () => {
+  it("creates a shared staged snapshot for Codex and Claude Code", async () => {
+    const dataDir = await makeTempDir();
+    const skillRootPath = await writeSkill({
+      rootPath: path.join(dataDir, "source-skills"),
+      name: "release-notes",
+    });
+
+    const staged = await stageInjectedSkillSources({
+      dataDir,
+      injectedSkillSources: [
+        createDataDirSource({
+          dataDir,
+          skillName: "release-notes",
+          skillRootPath,
+        }),
+      ],
+    });
+
+    const codexRoot = staged.skillRoots.find(isCodexSkillRoot);
+    const claudeRoot = staged.skillRoots.find(isClaudeCodeSkillRoot);
+    expect(codexRoot).toEqual({
+      id: `global-skills:${staged.catalogHash}:codex`,
+      providerId: "codex",
+      skillDirectoryRootPath: path.join(
+        dataDir,
+        "runtime",
+        "global-skills",
+        staged.catalogHash,
+        "skills",
+      ),
+    });
+    expect(claudeRoot).toEqual({
+      id: `global-skills:${staged.catalogHash}:claude-code`,
+      providerId: "claude-code",
+      localPluginPath: path.join(
+        dataDir,
+        "runtime",
+        "global-skills",
+        staged.catalogHash,
+      ),
+      skillNames: ["release-notes"],
+    });
+
+    if (!claudeRoot) {
+      throw new Error("Expected Claude Code skill root");
+    }
+    await expect(
+      readFile(
+        path.join(claudeRoot.localPluginPath, "skills", "release-notes", "SKILL.md"),
+        "utf8",
+      ),
+    ).resolves.toContain("name: release-notes");
+    await expect(
+      readFile(
+        path.join(
+          claudeRoot.localPluginPath,
+          "skills",
+          "release-notes",
+          "references",
+          "notes.md",
+        ),
+        "utf8",
+      ),
+    ).resolves.toBe("supporting notes\n");
+    await expect(
+      readFile(
+        path.join(claudeRoot.localPluginPath, ".claude-plugin", "plugin.json"),
+        "utf8",
+      ).then((content) => JSON.parse(content)),
+    ).resolves.toMatchObject({
+      name: "bb-global-skills",
+      skills: ["./skills/release-notes"],
+    });
+  });
+
+  it("changes the catalog hash when skill content changes", async () => {
+    const dataDir = await makeTempDir();
+    const sourceRootPath = path.join(dataDir, "source-skills");
+    const skillRootPath = await writeSkill({
+      body: "first body",
+      rootPath: sourceRootPath,
+      name: "release-notes",
+    });
+    const source = createDataDirSource({
+      dataDir,
+      skillName: "release-notes",
+      skillRootPath,
+    });
+    const first = await stageInjectedSkillSources({
+      dataDir,
+      injectedSkillSources: [source],
+    });
+
+    await writeFile(
+      path.join(skillRootPath, "SKILL.md"),
+      [
+        "---",
+        "name: release-notes",
+        "description: Use release-notes when host staging tests run.",
+        "---",
+        "",
+        "second body",
+        "",
+      ].join("\n"),
+      "utf8",
+    );
+    const second = await stageInjectedSkillSources({
+      dataDir,
+      injectedSkillSources: [source],
+    });
+
+    expect(second.catalogHash).not.toBe(first.catalogHash);
+  });
+
+  it("skips symlinked files during staging", async () => {
+    const dataDir = await makeTempDir();
+    const outsideDir = await makeTempDir();
+    const skillRootPath = await writeSkill({
+      rootPath: path.join(dataDir, "source-skills"),
+      name: "release-notes",
+    });
+    await writeFile(path.join(outsideDir, "escape.md"), "escape\n", "utf8");
+    await symlink(
+      path.join(outsideDir, "escape.md"),
+      path.join(skillRootPath, "references", "escape.md"),
+    );
+    const warnings: CapturedWarning[] = [];
+
+    const staged = await stageInjectedSkillSources({
+      dataDir,
+      injectedSkillSources: [
+        createDataDirSource({
+          dataDir,
+          skillName: "release-notes",
+          skillRootPath,
+        }),
+      ],
+      logger: {
+        debug: () => undefined,
+        warn: (context, message) => {
+          warnings.push({ context, message });
+        },
+      },
+    });
+
+    expect(staged.skillRoots).toEqual([]);
+    expect(warnings).toEqual([
+      expect.objectContaining({
+        message: "Skipping injected skill during staging",
+      }),
+    ]);
+  });
+});
diff --git a/apps/host-daemon/src/injected-skills.ts b/apps/host-daemon/src/injected-skills.ts
new file mode 100644
index 000000000..cee671f6d
--- /dev/null
+++ b/apps/host-daemon/src/injected-skills.ts
@@ -0,0 +1,563 @@
+import { createHash } from "node:crypto";
+import type { Dirent } from "node:fs";
+import fs from "node:fs/promises";
+import path from "node:path";
+import { resolveDataDirSkillsRootPath } from "@bb/config/app-storage-paths";
+import type { AgentRuntimeSkillRoot } from "@bb/agent-runtime";
+import type { HostDaemonInjectedSkillSource } from "@bb/host-daemon-contract";
+
+const STAGING_ROOT_SEGMENTS = ["runtime", "global-skills"] as const;
+const SKILL_FILE_NAME = "SKILL.md";
+const SKILL_NAME_PATTERN =
+  /^(?!.*--)[a-z0-9](?:[a-z0-9-]{0,62}[a-z0-9])?$/u;
+const MAX_STAGED_SKILL_FILES = 1_000;
+const MAX_STAGED_SKILL_BYTES = 10 * 1024 * 1024;
+const MAX_STAGED_SKILL_DEPTH = 24;
+export const EMPTY_SKILL_CATALOG_HASH = createHash("sha256")
+  .update("bb-global-skills-v1-empty")
+  .digest("hex");
+
+export interface InjectedSkillsLogger {
+  debug(context: object, message: string): void;
+  warn(context: object, message: string): void;
+}
+
+export interface StageInjectedSkillSourcesArgs {
+  dataDir: string;
+  injectedSkillSources: readonly HostDaemonInjectedSkillSource[];
+  logger?: InjectedSkillsLogger;
+}
+
+export interface CleanupInjectedSkillStagingDirsArgs {
+  dataDir: string;
+  keepCatalogHashes: readonly string[];
+  logger?: InjectedSkillsLogger;
+}
+
+export interface StagedInjectedSkills {
+  catalogHash: string;
+  skillRoots: readonly AgentRuntimeSkillRoot[];
+}
+
+interface CollectedSkillFile {
+  bytes: Buffer;
+  relativePath: string;
+}
+
+interface CollectedSkillDirectory {
+  relativePath: string;
+}
+
+interface CollectedSkillTree {
+  directories: CollectedSkillDirectory[];
+  files: CollectedSkillFile[];
+  source: HostDaemonInjectedSkillSource;
+  totalBytes: number;
+}
+
+interface CollectSkillTreeArgs {
+  source: HostDaemonInjectedSkillSource;
+}
+
+interface WalkSkillTreeArgs {
+  currentPath: string;
+  depth: number;
+  rootPath: string;
+  state: SkillTreeCollectionState;
+}
+
+interface SkillTreeCollectionState {
+  directories: CollectedSkillDirectory[];
+  files: CollectedSkillFile[];
+  totalBytes: number;
+}
+
+interface StageTreeArgs {
+  skillDirectoryPath: string;
+  tree: CollectedSkillTree;
+}
+
+interface WriteStageRootArgs {
+  catalogHash: string;
+  dataDir: string;
+  trees: readonly CollectedSkillTree[];
+}
+
+interface BuildSkillRootsArgs {
+  catalogHash: string;
+  skillNames: readonly string[];
+  stageRootPath: string;
+}
+
+interface PluginManifestAuthor {
+  name: string;
+}
+
+interface ClaudePluginManifest {
+  $schema: string;
+  name: string;
+  version: string;
+  description: string;
+  author: PluginManifestAuthor;
+  skills: string[];
+}
+
+interface CatalogSkillEntry {
+  applicationId: string | null;
+  description: string;
+  name: string;
+  sourceRootPath: string;
+  sourceType: HostDaemonInjectedSkillSource["sourceType"];
+}
+
+interface CatalogFile {
+  catalogHash: string;
+  generatedAt: string;
+  skills: CatalogSkillEntry[];
+}
+
+interface CreateCatalogFileArgs {
+  catalogHash: string;
+  trees: readonly CollectedSkillTree[];
+}
+
+export interface InjectedSkillRootsDiagnostics {
+  dataDirSkillsRootPath: string;
+  stagingRootPath: string;
+}
+
+function createNoopLogger(): InjectedSkillsLogger {
+  return {
+    debug: () => undefined,
+    warn: () => undefined,
+  };
+}
+
+function isFsErrorWithCode(error: Error, code: string): boolean {
+  return "code" in error && error.code === code;
+}
+
+function resolveStagingRootPath(dataDir: string): string {
+  return path.join(dataDir, ...STAGING_ROOT_SEGMENTS);
+}
+
+function resolveStageRootPath(dataDir: string, catalogHash: string): string {
+  return path.join(resolveStagingRootPath(dataDir), catalogHash);
+}
+
+function normalizeRelativePath(relativePath: string): string {
+  return relativePath.split(path.sep).join("/");
+}
+
+function isPathWithinRoot(rootPath: string, candidatePath: string): boolean {
+  const relativePath = path.relative(rootPath, candidatePath);
+  return (
+    relativePath.length === 0 ||
+    (!relativePath.startsWith("..") && !path.isAbsolute(relativePath))
+  );
+}
+
+function sortDirentsByName(left: Dirent, right: Dirent): number {
+  return left.name.localeCompare(right.name);
+}
+
+function sortTreesByName(
+  left: CollectedSkillTree,
+  right: CollectedSkillTree,
+): number {
+  return left.source.name.localeCompare(right.source.name);
+}
+
+function assertUsableSource(source: HostDaemonInjectedSkillSource): void {
+  if (!SKILL_NAME_PATTERN.test(source.name)) {
+    throw new Error(`Invalid injected skill name: ${source.name}`);
+  }
+  if (!path.isAbsolute(source.sourceRootPath)) {
+    throw new Error(
+      `Injected skill source root must be absolute: ${source.sourceRootPath}`,
+    );
+  }
+  if (!path.isAbsolute(source.skillFilePath)) {
+    throw new Error(
+      `Injected skill file path must be absolute: ${source.skillFilePath}`,
+    );
+  }
+  if (!isPathWithinRoot(source.sourceRootPath, source.skillFilePath)) {
+    throw new Error(
+      `Injected skill file path escapes source root: ${source.skillFilePath}`,
+    );
+  }
+  if (path.basename(source.skillFilePath) !== SKILL_FILE_NAME) {
+    throw new Error(
+      `Injected skill file path must end with ${SKILL_FILE_NAME}: ${source.skillFilePath}`,
+    );
+  }
+}
+
+async function walkSkillTree(args: WalkSkillTreeArgs): Promise<void> {
+  if (args.depth > MAX_STAGED_SKILL_DEPTH) {
+    throw new Error(
+      `Skill tree exceeds max depth ${MAX_STAGED_SKILL_DEPTH}: ${args.rootPath}`,
+    );
+  }
+
+  const entries = (await fs.readdir(args.currentPath, {
+    withFileTypes: true,
+  })).sort(sortDirentsByName);
+
+  for (const entry of entries) {
+    const sourcePath = path.join(args.currentPath, entry.name);
+    if (!isPathWithinRoot(args.rootPath, sourcePath)) {
+      throw new Error(`Skill tree entry escapes source root: ${sourcePath}`);
+    }
+    const relativePath = normalizeRelativePath(
+      path.relative(args.rootPath, sourcePath),
+    );
+    const entryStat = await fs.lstat(sourcePath);
+    if (entryStat.isSymbolicLink()) {
+      throw new Error(`Skill tree contains a symlink: ${sourcePath}`);
+    }
+    if (entryStat.isDirectory()) {
+      args.state.directories.push({ relativePath });
+      await walkSkillTree({
+        currentPath: sourcePath,
+        depth: args.depth + 1,
+        rootPath: args.rootPath,
+        state: args.state,
+      });
+      continue;
+    }
+    if (!entryStat.isFile()) {
+      throw new Error(`Skill tree entry is not a regular file: ${sourcePath}`);
+    }
+    if (args.state.files.length + 1 > MAX_STAGED_SKILL_FILES) {
+      throw new Error(
+        `Skill tree exceeds max file count ${MAX_STAGED_SKILL_FILES}: ${args.rootPath}`,
+      );
+    }
+    if (args.state.totalBytes + entryStat.size > MAX_STAGED_SKILL_BYTES) {
+      throw new Error(
+        `Skill tree exceeds max byte count ${MAX_STAGED_SKILL_BYTES}: ${args.rootPath}`,
+      );
+    }
+    const bytes = await fs.readFile(sourcePath);
+    args.state.files.push({
+      bytes,
+      relativePath,
+    });
+    args.state.totalBytes += entryStat.size;
+  }
+}
+
+async function collectSkillTree(
+  args: CollectSkillTreeArgs,
+): Promise<CollectedSkillTree> {
+  assertUsableSource(args.source);
+  const rootStat = await fs.lstat(args.source.sourceRootPath);
+  if (rootStat.isSymbolicLink()) {
+    throw new Error(
+      `Injected skill source root is a symlink: ${args.source.sourceRootPath}`,
+    );
+  }
+  if (!rootStat.isDirectory()) {
+    throw new Error(
+      `Injected skill source root is not a directory: ${args.source.sourceRootPath}`,
+    );
+  }
+  const skillFileStat = await fs.lstat(args.source.skillFilePath);
+  if (skillFileStat.isSymbolicLink()) {
+    throw new Error(
+      `Injected skill file is a symlink: ${args.source.skillFilePath}`,
+    );
+  }
+  if (!skillFileStat.isFile()) {
+    throw new Error(
+      `Injected skill file is not a regular file: ${args.source.skillFilePath}`,
+    );
+  }
+
+  const state: SkillTreeCollectionState = {
+    directories: [],
+    files: [],
+    totalBytes: 0,
+  };
+  await walkSkillTree({
+    currentPath: args.source.sourceRootPath,
+    depth: 0,
+    rootPath: args.source.sourceRootPath,
+    state,
+  });
+
+  return {
+    directories: state.directories,
+    files: state.files,
+    source: args.source,
+    totalBytes: state.totalBytes,
+  };
+}
+
+function hashCollectedTrees(trees: readonly CollectedSkillTree[]): string {
+  const hash = createHash("sha256");
+  hash.update("bb-global-skills-v1");
+  for (const tree of trees) {
+    hash.update("\0skill\0");
+    hash.update(tree.source.name);
+    hash.update("\0");
+    hash.update(tree.source.description);
+    hash.update("\0");
+    hash.update(tree.source.sourceType);
+    hash.update("\0");
+    hash.update(tree.source.applicationId ?? "");
+    hash.update("\0");
+    hash.update(tree.source.sourceRootPath);
+    for (const file of tree.files) {
+      hash.update("\0file\0");
+      hash.update(file.relativePath);
+      hash.update("\0");
+      hash.update(createHash("sha256").update(file.bytes).digest("hex"));
+    }
+  }
+  return hash.digest("hex");
+}
+
+async function copyCollectedTree(args: StageTreeArgs): Promise<void> {
+  await fs.mkdir(args.skillDirectoryPath, { recursive: true });
+  for (const directory of args.tree.directories) {
+    await fs.mkdir(path.join(args.skillDirectoryPath, directory.relativePath), {
+      recursive: true,
+    });
+  }
+  for (const file of args.tree.files) {
+    const destinationPath = path.join(
+      args.skillDirectoryPath,
+      file.relativePath,
+    );
+    await fs.mkdir(path.dirname(destinationPath), { recursive: true });
+    await fs.writeFile(destinationPath, file.bytes);
+  }
+}
+
+function createClaudePluginManifest(
+  skillNames: readonly string[],
+): ClaudePluginManifest {
+  return {
+    $schema: "https://anthropic.com/claude-code/plugin.schema.json",
+    name: "bb-global-skills",
+    version: "0.1.0",
+    description: "Global skills staged by bb.",
+    author: {
+      name: "bb",
+    },
+    skills: skillNames.map((skillName) => `./skills/${skillName}`),
+  };
+}
+
+function createCatalogFile(args: CreateCatalogFileArgs): CatalogFile {
+  return {
+    catalogHash: args.catalogHash,
+    generatedAt: new Date().toISOString(),
+    skills: args.trees.map((tree) => ({
+      applicationId: tree.source.applicationId,
+      description: tree.source.description,
+      name: tree.source.name,
+      sourceRootPath: tree.source.sourceRootPath,
+      sourceType: tree.source.sourceType,
+    })),
+  };
+}
+
+async function writeStageRoot(args: WriteStageRootArgs): Promise<string> {
+  const stagingRootPath = resolveStagingRootPath(args.dataDir);
+  const stageRootPath = resolveStageRootPath(args.dataDir, args.catalogHash);
+  try {
+    await fs.access(path.join(stageRootPath, "catalog.json"));
+    return stageRootPath;
+  } catch (error) {
+    if (!(error instanceof Error) || !isFsErrorWithCode(error, "ENOENT")) {
+      throw error;
+    }
+  }
+
+  await fs.mkdir(stagingRootPath, { recursive: true });
+  const tempRootPath = path.join(
+    stagingRootPath,
+    `.tmp-${args.catalogHash}-${process.pid}-${Date.now()}`,
+  );
+  await fs.rm(tempRootPath, { recursive: true, force: true });
+  await fs.mkdir(path.join(tempRootPath, "skills"), { recursive: true });
+  await fs.mkdir(path.join(tempRootPath, ".claude-plugin"), {
+    recursive: true,
+  });
+
+  try {
+    const skillNames = args.trees.map((tree) => tree.source.name);
+    for (const tree of args.trees) {
+      await copyCollectedTree({
+        skillDirectoryPath: path.join(tempRootPath, "skills", tree.source.name),
+        tree,
+      });
+    }
+    await fs.writeFile(
+      path.join(tempRootPath, ".claude-plugin", "plugin.json"),
+      `${JSON.stringify(createClaudePluginManifest(skillNames), null, 2)}\n`,
+      "utf8",
+    );
+    await fs.writeFile(
+      path.join(tempRootPath, "catalog.json"),
+      `${JSON.stringify(
+        createCatalogFile({
+          catalogHash: args.catalogHash,
+          trees: args.trees,
+        }),
+        null,
+        2,
+      )}\n`,
+      "utf8",
+    );
+    await fs.rename(tempRootPath, stageRootPath);
+  } catch (error) {
+    if (
+      error instanceof Error &&
+      (isFsErrorWithCode(error, "EEXIST") ||
+        isFsErrorWithCode(error, "ENOTEMPTY"))
+    ) {
+      await fs.rm(tempRootPath, { recursive: true, force: true });
+      return stageRootPath;
+    }
+    await fs.rm(tempRootPath, { recursive: true, force: true });
+    throw error;
+  }
+
+  return stageRootPath;
+}
+
+function buildSkillRoots(args: BuildSkillRootsArgs): AgentRuntimeSkillRoot[] {
+  if (args.skillNames.length === 0) {
+    return [];
+  }
+  return [
+    {
+      id: `global-skills:${args.catalogHash}:codex`,
+      providerId: "codex",
+      skillDirectoryRootPath: path.join(args.stageRootPath, "skills"),
+    },
+    {
+      id: `global-skills:${args.catalogHash}:claude-code`,
+      providerId: "claude-code",
+      localPluginPath: args.stageRootPath,
+      skillNames: [...args.skillNames],
+    },
+  ];
+}
+
+export async function stageInjectedSkillSources(
+  args: StageInjectedSkillSourcesArgs,
+): Promise<StagedInjectedSkills> {
+  if (args.injectedSkillSources.length === 0) {
+    return {
+      catalogHash: EMPTY_SKILL_CATALOG_HASH,
+      skillRoots: [],
+    };
+  }
+
+  const logger = args.logger ?? createNoopLogger();
+  const trees: CollectedSkillTree[] = [];
+  const sortedSources = [...args.injectedSkillSources].sort((left, right) =>
+    left.name.localeCompare(right.name),
+  );
+  for (const source of sortedSources) {
+    try {
+      trees.push(await collectSkillTree({ source }));
+    } catch (error) {
+      logger.warn(
+        {
+          applicationId: source.applicationId,
+          name: source.name,
+          sourceRootPath: source.sourceRootPath,
+          sourceType: source.sourceType,
+          reason:
+            error instanceof Error && error.message.trim().length > 0
+              ? error.message
+              : "Unable to stage injected skill",
+        },
+        "Skipping injected skill during staging",
+      );
+    }
+  }
+
+  const sortedTrees = trees.sort(sortTreesByName);
+  if (sortedTrees.length === 0) {
+    return {
+      catalogHash: EMPTY_SKILL_CATALOG_HASH,
+      skillRoots: [],
+    };
+  }
+
+  const catalogHash = hashCollectedTrees(sortedTrees);
+  const stageRootPath = await writeStageRoot({
+    catalogHash,
+    dataDir: args.dataDir,
+    trees: sortedTrees,
+  });
+  const skillNames = sortedTrees.map((tree) => tree.source.name);
+  return {
+    catalogHash,
+    skillRoots: buildSkillRoots({
+      catalogHash,
+      skillNames,
+      stageRootPath,
+    }),
+  };
+}
+
+export async function cleanupInjectedSkillStagingDirs(
+  args: CleanupInjectedSkillStagingDirsArgs,
+): Promise<void> {
+  const stagingRootPath = resolveStagingRootPath(args.dataDir);
+  const keep = new Set(args.keepCatalogHashes);
+  let entries: Dirent[];
+  try {
+    entries = await fs.readdir(stagingRootPath, { withFileTypes: true });
+  } catch (error) {
+    if (error instanceof Error && isFsErrorWithCode(error, "ENOENT")) {
+      return;
+    }
+    throw error;
+  }
+
+  const logger = args.logger ?? createNoopLogger();
+  await Promise.all(
+    entries.map(async (entry) => {
+      if (!entry.isDirectory() || entry.name.startsWith(".tmp-")) {
+        await fs.rm(path.join(stagingRootPath, entry.name), {
+          recursive: true,
+          force: true,
+        });
+        return;
+      }
+      if (keep.has(entry.name)) {
+        return;
+      }
+      logger.debug(
+        {
+          catalogHash: entry.name,
+          stagingRootPath,
+        },
+        "Removing unused injected skill staging directory",
+      );
+      await fs.rm(path.join(stagingRootPath, entry.name), {
+        recursive: true,
+        force: true,
+      });
+    }),
+  );
+}
+
+export function resolveInjectedSkillRootsForDiagnostics(
+  dataDir: string,
+): InjectedSkillRootsDiagnostics {
+  return {
+    dataDirSkillsRootPath: resolveDataDirSkillsRootPath(dataDir),
+    stagingRootPath: resolveStagingRootPath(dataDir),
+  };
+}
diff --git a/apps/host-daemon/src/runtime-manager.test.ts b/apps/host-daemon/src/runtime-manager.test.ts
index 97b639501..4b8a55c8a 100644
--- a/apps/host-daemon/src/runtime-manager.test.ts
+++ b/apps/host-daemon/src/runtime-manager.test.ts
@@ -6,8 +6,10 @@ import { promisify } from "node:util";
 import type { AgentRuntime, AgentRuntimeOptions } from "@bb/agent-runtime";
 import type { ThreadEvent } from "@bb/domain";
 import { threadScope, turnScope } from "@bb/domain";
+import type { HostDaemonInjectedSkillSource } from "@bb/host-daemon-contract";
 import type {
   HostWatcher,
+  WatchApplicationStorageRootArgs,
   ThreadStorageWatchError,
   WatchThreadStorageRootArgs,
   WatchWorkspaceArgs,
@@ -53,10 +55,19 @@ type WatchWorkspaceImplementation = (
 type WatchThreadStorageRootImplementation = (
   args: WatchThreadStorageRootArgs,
 ) => StopWatchingPathChanges;
+type WatchApplicationStorageRootImplementation = (
+  args: WatchApplicationStorageRootArgs,
+) => StopWatchingPathChanges;
 interface RunGitOptions {
   cwd: string;
 }
 
+interface WriteInjectedSkillSourceArgs {
+  dataDir: string;
+  name: string;
+  token: string;
+}
+
 interface RuntimeOptionsRef {
   current: AgentRuntimeOptions | null;
 }
@@ -91,6 +102,34 @@ async function initRepo(): Promise<string> {
   return repoPath;
 }
 
+async function writeInjectedSkillSource(
+  args: WriteInjectedSkillSourceArgs,
+): Promise<HostDaemonInjectedSkillSource> {
+  const sourceRootPath = path.join(args.dataDir, "skills", args.name);
+  await fs.mkdir(sourceRootPath, { recursive: true });
+  await fs.writeFile(
+    path.join(sourceRootPath, "SKILL.md"),
+    [
+      "---",
+      `name: ${args.name}`,
+      `description: Use ${args.name} when runtime manager tests run.`,
+      "---",
+      "",
+      args.token,
+      "",
+    ].join("\n"),
+    "utf8",
+  );
+  return {
+    sourceType: "data-dir",
+    applicationId: null,
+    name: args.name,
+    description: `Use ${args.name} when runtime manager tests run.`,
+    sourceRootPath,
+    skillFilePath: path.join(sourceRootPath, "SKILL.md"),
+  };
+}
+
 afterEach(async () => {
   await Promise.all(
     tempDirs
@@ -202,6 +241,7 @@ function createFakeWorkspace(path: string) {
 
 function createFakeHostWatcher(
   args: {
+    watchApplicationStorageRootImplementation?: WatchApplicationStorageRootImplementation;
     watchThreadStorageRootImplementation?: WatchThreadStorageRootImplementation;
     watchWorkspaceImplementation?: WatchWorkspaceImplementation;
   } = {},
@@ -212,13 +252,20 @@ function createFakeHostWatcher(
   const watchThreadStorageRoot = vi.fn<WatchThreadStorageRootImplementation>(
     args.watchThreadStorageRootImplementation ?? ((_args) => () => undefined),
   );
+  const watchApplicationStorageRoot =
+    vi.fn<WatchApplicationStorageRootImplementation>(
+      args.watchApplicationStorageRootImplementation ??
+        ((_args) => () => undefined),
+    );
   const hostWatcher = {
+    watchApplicationStorageRoot,
     watchWorkspace,
     watchThreadStorageRoot,
   } satisfies HostWatcher;
 
   return {
     hostWatcher,
+    watchApplicationStorageRoot,
     watchThreadStorageRoot,
     watchWorkspace,
   };
@@ -275,6 +322,109 @@ describe("RuntimeManager", () => {
     expect(entry.path).toBe("/tmp/env-1");
   });
 
+  it("passes staged injected skill roots to created runtimes", async () => {
+    const dataDir = await makeTempDir("bb-runtime-manager-skills-");
+    const source = await writeInjectedSkillSource({
+      dataDir,
+      name: "release-notes",
+      token: "first-token",
+    });
+    const provisionWorkspace = createProvisionWorkspaceMock("/tmp/env-1");
+    const runtimeOptions: RuntimeOptionsRef = { current: null };
+    const manager = new RuntimeManager({
+      dataDir,
+      provisionWorkspace,
+      createRuntime: (options) => {
+        runtimeOptions.current = options;
+        return createFakeRuntime();
+      },
+    });
+
+    const entry = await manager.ensureEnvironment({
+      environmentId: "env-skills",
+      injectedSkillSources: [source],
+      workspacePath: "/tmp/env-1",
+    });
+
+    expect(entry.skillCatalogHash).toMatch(/^[a-f0-9]{64}$/u);
+    expect(runtimeOptions.current?.skillRoots).toEqual([
+      {
+        id: `global-skills:${entry.skillCatalogHash}:codex`,
+        providerId: "codex",
+        skillDirectoryRootPath: path.join(
+          dataDir,
+          "runtime",
+          "global-skills",
+          entry.skillCatalogHash ?? "",
+          "skills",
+        ),
+      },
+      {
+        id: `global-skills:${entry.skillCatalogHash}:claude-code`,
+        providerId: "claude-code",
+        localPluginPath: path.join(
+          dataDir,
+          "runtime",
+          "global-skills",
+          entry.skillCatalogHash ?? "",
+        ),
+        skillNames: ["release-notes"],
+      },
+    ]);
+  });
+
+  it("does not reuse an idle runtime with a stale skill catalog hash", async () => {
+    const dataDir = await makeTempDir("bb-runtime-manager-skills-stale-");
+    const source = await writeInjectedSkillSource({
+      dataDir,
+      name: "release-notes",
+      token: "first-token",
+    });
+    const provisionWorkspace = createProvisionWorkspaceMock("/tmp/env-1");
+    const runtimes = [createFakeRuntime(), createFakeRuntime()];
+    const createRuntime = vi.fn(() => {
+      const runtime = runtimes.shift();
+      if (!runtime) {
+        throw new Error("Unexpected runtime creation");
+      }
+      return runtime;
+    });
+    const manager = new RuntimeManager({
+      dataDir,
+      provisionWorkspace,
+      createRuntime,
+    });
+
+    const firstEntry = await manager.ensureEnvironment({
+      environmentId: "env-skills",
+      injectedSkillSources: [source],
+      workspacePath: "/tmp/env-1",
+    });
+    await fs.writeFile(
+      source.skillFilePath,
+      [
+        "---",
+        "name: release-notes",
+        "description: Use release-notes when runtime manager tests run.",
+        "---",
+        "",
+        "second-token",
+        "",
+      ].join("\n"),
+      "utf8",
+    );
+    const secondEntry = await manager.ensureEnvironment({
+      environmentId: "env-skills",
+      injectedSkillSources: [source],
+      workspacePath: "/tmp/env-1",
+    });
+
+    expect(secondEntry).not.toBe(firstEntry);
+    expect(secondEntry.skillCatalogHash).not.toBe(firstEntry.skillCatalogHash);
+    expect(createRuntime).toHaveBeenCalledTimes(2);
+    expect(firstEntry.runtime.shutdown).toHaveBeenCalledTimes(1);
+  });
+
   it("applies unmanaged checkout provisioning to existing runtime entries", async () => {
     const provisionWorkspace = createProvisionWorkspaceMock("/tmp/env-1");
     const createRuntime = vi.fn(() => createFakeRuntime());
@@ -1086,15 +1236,11 @@ describe("RuntimeManager", () => {
       },
     });
     const onThreadStorageChanged = vi.fn();
-    const onThreadAppDataChanged = vi.fn();
-    const onThreadAppDataResync = vi.fn();
     const manager = new RuntimeManager({
       hostWatcher,
       provisionWorkspace: createProvisionWorkspaceMock("/tmp/env-storage"),
       createRuntime: vi.fn(() => createFakeRuntime()),
       onThreadStorageChanged,
-      onThreadAppDataChanged,
-      onThreadAppDataResync,
       threadStorageRootPath: "/tmp/bb-data/thread-storage",
     });
 
@@ -1115,20 +1261,6 @@ describe("RuntimeManager", () => {
       environmentId: "env-storage",
       threadId: "thread-2",
     });
-    watchThreadStorageRootArgs?.onChange({
-      kind: "thread-app-data-changed",
-      appId: "status",
-      environmentId: "env-storage",
-      path: "state.json",
-      threadId: "thread-1",
-    });
-    watchThreadStorageRootArgs?.onChange({
-      kind: "thread-app-data-resync",
-      appId: "status",
-      environmentId: "env-storage",
-      threadId: "thread-1",
-    });
-
     expect(watchThreadStorageRoot).toHaveBeenCalledTimes(1);
     expect(watchThreadStorageRoot).toHaveBeenCalledWith(
       expect.objectContaining({
@@ -1144,22 +1276,82 @@ describe("RuntimeManager", () => {
       threadId: "thread-2",
     });
     expect(onThreadStorageChanged).toHaveBeenCalledTimes(2);
-    expect(onThreadAppDataChanged).toHaveBeenCalledWith({
-      appId: "status",
-      environmentId: "env-storage",
+    expect(stopWatchingPathChanges).not.toHaveBeenCalled();
+
+    await manager.destroyEnvironment("env-storage");
+
+    expect(stopWatchingPathChanges).toHaveBeenCalledTimes(1);
+  });
+
+  it("installs one shared application storage root watcher for app data", async () => {
+    const stopWatchingPathChanges = vi.fn(() => undefined);
+    let watchApplicationStorageRootArgs:
+      | WatchApplicationStorageRootArgs
+      | undefined;
+    const { hostWatcher, watchApplicationStorageRoot } = createFakeHostWatcher({
+      watchApplicationStorageRootImplementation: (args) => {
+        watchApplicationStorageRootArgs = args;
+        return stopWatchingPathChanges;
+      },
+    });
+    const onApplicationStorageTargetsChanged = vi.fn();
+    const onApplicationDataChanged = vi.fn();
+    const onApplicationDataResync = vi.fn();
+    const manager = new RuntimeManager({
+      appsRootPath: "/tmp/bb-data/apps",
+      hostWatcher,
+      provisionWorkspace: createProvisionWorkspaceMock("/tmp/env-storage"),
+      createRuntime: vi.fn(() => createFakeRuntime()),
+      onApplicationStorageTargetsChanged,
+      onApplicationDataChanged,
+      onApplicationDataResync,
+    });
+
+    manager.replaceTrackedApplicationDataTargets([
+      {
+        applicationId: "status",
+        appDataPath: "/tmp/bb-data/apps/status/data",
+      },
+    ]);
+
+    expect(watchApplicationStorageRoot).toHaveBeenCalledTimes(1);
+    expect(watchApplicationStorageRoot).toHaveBeenCalledWith(
+      expect.objectContaining({
+        appsRootPath: "/tmp/bb-data/apps",
+      }),
+    );
+    expect(
+      watchApplicationStorageRootArgs?.resolveApplicationTarget("status"),
+    ).toEqual({
+      applicationId: "status",
+      appDataPath: "/tmp/bb-data/apps/status/data",
+    });
+
+    watchApplicationStorageRootArgs?.onChange({
+      kind: "application-storage-targets-changed",
+    });
+    watchApplicationStorageRootArgs?.onChange({
+      kind: "application-data-changed",
+      applicationId: "status",
+      appDataPath: "/tmp/bb-data/apps/status/data",
       path: "state.json",
-      threadId: "thread-1",
-      threadStoragePath: "/tmp/bb-data/thread-storage/thread-1",
     });
-    expect(onThreadAppDataResync).toHaveBeenCalledWith({
-      appId: "status",
-      environmentId: "env-storage",
-      threadId: "thread-1",
-      threadStoragePath: "/tmp/bb-data/thread-storage/thread-1",
+    watchApplicationStorageRootArgs?.onChange({
+      kind: "application-data-resync",
+      applicationId: "status",
     });
-    expect(stopWatchingPathChanges).not.toHaveBeenCalled();
 
-    await manager.destroyEnvironment("env-storage");
+    expect(onApplicationStorageTargetsChanged).toHaveBeenCalledTimes(1);
+    expect(onApplicationDataChanged).toHaveBeenCalledWith({
+      applicationId: "status",
+      appDataPath: "/tmp/bb-data/apps/status/data",
+      path: "state.json",
+    });
+    expect(onApplicationDataResync).toHaveBeenCalledWith({
+      applicationId: "status",
+    });
+
+    await manager.shutdownAll();
 
     expect(stopWatchingPathChanges).toHaveBeenCalledTimes(1);
   });
diff --git a/apps/host-daemon/src/runtime-manager.ts b/apps/host-daemon/src/runtime-manager.ts
index aea4290fa..1e31d1480 100644
--- a/apps/host-daemon/src/runtime-manager.ts
+++ b/apps/host-daemon/src/runtime-manager.ts
@@ -4,11 +4,13 @@ import {
   createAgentRuntime,
   type AgentRuntime,
   type AgentRuntimeOptions,
+  type AgentRuntimeSkillRoot,
   type AgentRuntimeProcessExitInfo,
 } from "@bb/agent-runtime";
+import type { Logger } from "@bb/logger";
 import type {
   AppDataPath,
-  AppId,
+  ApplicationId,
   PendingInteractionCreate,
   PendingInteractionResolution,
   ThreadEvent,
@@ -23,10 +25,16 @@ import type {
   HostDaemonActiveThread,
   HostDaemonEnvironmentChange,
   HostDaemonLoadedEnvironment,
+  HostDaemonTrackedApplicationDataTarget,
   HostDaemonTrackedThreadTarget,
+  HostDaemonInjectedSkillSource,
 } from "@bb/host-daemon-contract";
 import type {
+  ApplicationDataWatchTarget,
+  ApplicationStorageWatchError,
+  DataDirSkillsWatchError,
   HostWatcher,
+  InjectedSkillsObservedChange,
   ThreadStorageWatchError,
   WorkspaceWatchError,
   WorkspaceStatusWatchChangeKind,
@@ -36,6 +44,12 @@ import {
   type HostWorkspace,
   type ProvisionWorkspaceArgs,
 } from "@bb/host-workspace";
+import {
+  cleanupInjectedSkillStagingDirs,
+  EMPTY_SKILL_CATALOG_HASH,
+  stageInjectedSkillSources,
+  type InjectedSkillsLogger,
+} from "./injected-skills.js";
 
 type StopWatching = () => void | Promise<void>;
 
@@ -56,6 +70,11 @@ interface ThreadStorageTarget {
   threadId: string;
 }
 
+interface ApplicationDataTarget {
+  applicationId: ApplicationId;
+  appDataPath: string;
+}
+
 interface WorkspaceWatchState {
   lastLocalFingerprint: string | null;
   lastSharedRefsFingerprint: string | null;
@@ -69,6 +88,30 @@ interface BuildUnexpectedProviderExitEventsArgs {
   threads: Map<string, RuntimeThreadState>;
 }
 
+interface RuntimeSkillConfig {
+  catalogHash: string;
+  skillRoots: readonly AgentRuntimeSkillRoot[];
+}
+
+interface CreateEntryArgs extends EnsureEnvironmentArgs {
+  skillConfig: RuntimeSkillConfig | null;
+}
+
+interface ApplyExistingEnvironmentProvisionArgs {
+  entry: RuntimeEntry;
+  provision: ProvisionWorkspaceArgs | undefined;
+}
+
+interface EnsureCompatibleEntryArgs {
+  entry: RuntimeEntry;
+  skillConfig: RuntimeSkillConfig | null;
+}
+
+interface ReplaceEntryForSkillCatalogArgs {
+  entry: RuntimeEntry;
+  skillConfig: RuntimeSkillConfig;
+}
+
 function lazyProvisionOpts(
   environmentId: string,
   workspacePath: string,
@@ -98,11 +141,10 @@ function lazyProvisionOpts(
   }
 }
 
-function toErrorMessage(error: unknown): string {
-  if (error instanceof Error && error.message.trim().length > 0) {
-    return error.message;
-  }
-  return "Unknown workspace watch error";
+function toErrorMessage(error: Error): string {
+  return error.message.trim().length > 0
+    ? error.message
+    : "Unknown workspace watch error";
 }
 
 function formatProviderProcessExitStatus(
@@ -149,6 +191,7 @@ function workspaceWatchKindsIncludeSharedRefs(
 export interface RuntimeEntry {
   environmentId: string;
   runtime: AgentRuntime;
+  skillCatalogHash: string | null;
   stopWatchingStatus: StopWatching;
   workspace: HostWorkspace;
   path: string;
@@ -156,38 +199,38 @@ export interface RuntimeEntry {
   threads: Map<string, RuntimeThreadState>;
 }
 
-export interface ThreadAppDataChangedNotification {
-  appId: AppId;
-  environmentId: string;
+export interface ApplicationDataChangedNotification {
+  applicationId: ApplicationId;
+  appDataPath: string;
   path: AppDataPath;
-  threadId: string;
-  threadStoragePath: string;
 }
 
-export interface ThreadAppDataResyncNotification {
-  appId: AppId;
-  environmentId: string;
-  threadId: string;
-  threadStoragePath: string;
+export interface ApplicationDataResyncNotification {
+  applicationId: ApplicationId;
+}
+
+export interface InjectedSkillsChangedNotification {
+  applicationId: ApplicationId | null;
+  changedPaths: string[];
+  sourceType: InjectedSkillsObservedChange["sourceType"];
 }
 
 export interface EnsureEnvironmentArgs {
   environmentId: string;
+  injectedSkillSources?: readonly HostDaemonInjectedSkillSource[];
   personalWorkspaceRoot?: string;
   workspacePath?: string;
   workspaceProvisionType?: WorkspaceProvisionType;
   provision?: ProvisionWorkspaceArgs;
 }
 
-interface ApplyExistingEnvironmentProvisionArgs {
-  entry: RuntimeEntry;
-  provision: ProvisionWorkspaceArgs | undefined;
-}
-
 export interface RuntimeManagerOptions {
   bridgeBundleDir?: AgentRuntimeOptions["bridgeBundleDir"];
   createRuntime?: (options: AgentRuntimeOptions) => AgentRuntime;
+  dataDir?: string;
+  dataDirSkillsRootPath?: string | null;
   hostWatcher?: HostWatcher;
+  logger?: Pick<Logger, "debug" | "warn">;
   provisionWorkspace?: (
     options: ProvisionWorkspaceArgs,
   ) => Promise<HostWorkspace>;
@@ -199,8 +242,17 @@ export interface RuntimeManagerOptions {
     environmentId: string;
     threadId: string;
   }) => void;
-  onThreadAppDataChanged?: (args: ThreadAppDataChangedNotification) => void;
-  onThreadAppDataResync?: (args: ThreadAppDataResyncNotification) => void;
+  appsRootPath?: string | null;
+  onInjectedSkillsChanged?: (args: InjectedSkillsChangedNotification) => void;
+  onApplicationStorageTargetsChanged?: () => void;
+  onApplicationDataChanged?: (args: ApplicationDataChangedNotification) => void;
+  onApplicationDataResync?: (args: ApplicationDataResyncNotification) => void;
+  onApplicationStorageWatchError?: (args: {
+    error: ApplicationStorageWatchError;
+  }) => void;
+  onDataDirSkillsWatchError?: (args: {
+    error: DataDirSkillsWatchError;
+  }) => void;
   onThreadStorageWatchError?: (args: {
     error: ThreadStorageWatchError;
   }) => void;
@@ -218,6 +270,7 @@ export interface RuntimeManagerOptions {
 }
 
 interface RuntimeWorkspaceWriteRootsArgs {
+  appsRootPath: string | null | undefined;
   threadStorageRootPath: string | null | undefined;
   workspaceRoots: readonly string[];
 }
@@ -233,10 +286,16 @@ export class RuntimeManager {
     string,
     ThreadStorageTarget
   >();
+  private readonly trackedApplicationDataTargets = new Map<
+    ApplicationId,
+    ApplicationDataTarget
+  >();
   private providerMaintenanceRuntime: AgentRuntime | null = null;
   private pendingProviderMaintenanceRuntime: Promise<AgentRuntime> | null =
     null;
   private managedShellEnv: NonNullable<AgentRuntimeOptions["shellEnv"]> = {};
+  private stopWatchingApplicationStorageRoot: StopWatching = STOP_WATCHING;
+  private stopWatchingDataDirSkillsRoot: StopWatching = STOP_WATCHING;
   private stopWatchingThreadStorageRoot: StopWatching = STOP_WATCHING;
 
   constructor(private readonly options: RuntimeManagerOptions = {}) {
@@ -244,12 +303,17 @@ export class RuntimeManager {
     this.hostWatcher = options.hostWatcher;
     this.provisionWorkspace = options.provisionWorkspace ?? provisionWorkspace;
     this.baseShellEnv = { ...(options.shellEnv ?? {}) };
+    this.ensureApplicationStorageWatcher();
+    this.ensureDataDirSkillsWatcher();
   }
 
   private runtimeWorkspaceWriteRoots(
     args: RuntimeWorkspaceWriteRootsArgs,
   ): string[] {
     const roots = [...args.workspaceRoots];
+    if (args.appsRootPath) {
+      roots.push(args.appsRootPath);
+    }
     if (args.threadStorageRootPath) {
       // Provider runtimes are environment-scoped and may host multiple threads.
       // BB_THREAD_STORAGE still points agents at their own thread subdirectory;
@@ -363,7 +427,10 @@ export class RuntimeManager {
         error: {
           environmentId: args.environmentId,
           kind: "workspace-watch-error",
-          message: toErrorMessage(error),
+          message:
+            error instanceof Error
+              ? toErrorMessage(error)
+              : "Unknown workspace watch error",
           rootPath: args.workspacePath,
         },
       });
@@ -492,6 +559,107 @@ export class RuntimeManager {
     };
   }
 
+  private getInjectedSkillsLogger(): InjectedSkillsLogger | undefined {
+    return this.options.logger;
+  }
+
+  private async resolveRuntimeSkillConfig(
+    args: EnsureEnvironmentArgs,
+  ): Promise<RuntimeSkillConfig | null> {
+    if (args.injectedSkillSources === undefined) {
+      return null;
+    }
+    if (args.injectedSkillSources.length === 0) {
+      return {
+        catalogHash: EMPTY_SKILL_CATALOG_HASH,
+        skillRoots: [],
+      };
+    }
+    if (!this.options.dataDir) {
+      throw new Error("Runtime skill staging requires a host dataDir");
+    }
+    return stageInjectedSkillSources({
+      dataDir: this.options.dataDir,
+      injectedSkillSources: args.injectedSkillSources,
+      logger: this.getInjectedSkillsLogger(),
+    });
+  }
+
+  private entryHasActiveRuntimeWork(entry: RuntimeEntry): boolean {
+    if (entry.terminals.size > 0) {
+      return true;
+    }
+    for (const thread of entry.threads.values()) {
+      if (thread.status === "active") {
+        return true;
+      }
+    }
+    return false;
+  }
+
+  private async cleanupUnusedInjectedSkillStagingDirs(): Promise<void> {
+    if (!this.options.dataDir) {
+      return;
+    }
+    try {
+      await cleanupInjectedSkillStagingDirs({
+        dataDir: this.options.dataDir,
+        keepCatalogHashes: [...this.entries.values()].flatMap((entry) =>
+          entry.skillCatalogHash === null ? [] : [entry.skillCatalogHash],
+        ),
+        logger: this.getInjectedSkillsLogger(),
+      });
+    } catch (error) {
+      this.options.logger?.warn(
+        {
+          reason:
+            error instanceof Error && error.message.trim().length > 0
+              ? error.message
+              : "Unable to clean injected skill staging directories",
+        },
+        "Failed to clean injected skill staging directories",
+      );
+    }
+  }
+
+  private async replaceEntryForSkillCatalog(
+    args: ReplaceEntryForSkillCatalogArgs,
+  ): Promise<void> {
+    if (this.entryHasActiveRuntimeWork(args.entry)) {
+      throw new Error(
+        `Environment ${args.entry.environmentId} already has an active runtime with injected skill catalog ${args.entry.skillCatalogHash ?? "none"}; requested ${args.skillConfig.catalogHash}`,
+      );
+    }
+
+    this.entries.delete(args.entry.environmentId);
+    this.removeTrackedThreadStorageTargetsForEnvironment(
+      args.entry.environmentId,
+    );
+    this.stopWatchingThreadStorageIfNoTrackedThreads();
+    await this.stopWatchingStatus(args.entry);
+    await args.entry.runtime.shutdown();
+    await this.cleanupUnusedInjectedSkillStagingDirs();
+  }
+
+  private async ensureCompatibleEntry(
+    args: EnsureCompatibleEntryArgs,
+  ): Promise<RuntimeEntry | null> {
+    if (
+      args.skillConfig === null ||
+      args.entry.skillCatalogHash === args.skillConfig.catalogHash ||
+      (args.entry.skillCatalogHash === null &&
+        args.skillConfig.skillRoots.length === 0)
+    ) {
+      return args.entry;
+    }
+
+    await this.replaceEntryForSkillCatalog({
+      entry: args.entry,
+      skillConfig: args.skillConfig,
+    });
+    return null;
+  }
+
   replaceManagedShellEnv(
     shellEnv: NonNullable<AgentRuntimeOptions["shellEnv"]>,
   ): void {
@@ -515,6 +683,19 @@ export class RuntimeManager {
     this.stopWatchingThreadStorageIfNoTrackedThreads();
   }
 
+  replaceTrackedApplicationDataTargets(
+    targets: readonly HostDaemonTrackedApplicationDataTarget[],
+  ): void {
+    this.trackedApplicationDataTargets.clear();
+    for (const target of targets) {
+      this.trackedApplicationDataTargets.set(target.applicationId, {
+        applicationId: target.applicationId,
+        appDataPath: target.appDataPath,
+      });
+    }
+    this.ensureApplicationStorageWatcher();
+  }
+
   async openWorkspace(path: string): Promise<HostWorkspace> {
     return this.provisionWorkspace({
       workspaceProvisionType: "unmanaged",
@@ -545,28 +726,48 @@ export class RuntimeManager {
   }
 
   async ensureEnvironment(args: EnsureEnvironmentArgs): Promise<RuntimeEntry> {
+    const skillConfig = await this.resolveRuntimeSkillConfig(args);
     const existing = this.entries.get(args.environmentId);
     if (existing) {
       await this.applyExistingEnvironmentProvision({
         entry: existing,
         provision: args.provision,
       });
-      return existing;
+      const compatible = await this.ensureCompatibleEntry({
+        entry: existing,
+        skillConfig,
+      });
+      if (compatible) {
+        return compatible;
+      }
     }
 
     const pending = this.pendingEntries.get(args.environmentId);
     if (pending) {
-      return pending;
+      const entry = await pending;
+      const compatible = await this.ensureCompatibleEntry({
+        entry,
+        skillConfig,
+      });
+      if (compatible) {
+        return compatible;
+      }
     }
 
-    const creation = this.createEntry(args).finally(() => {
-      this.pendingEntries.delete(args.environmentId);
-    });
+    const creation = this.createEntry({
+      ...args,
+      skillConfig,
+    })
+      .then((entry) => {
+        this.entries.set(args.environmentId, entry);
+        return entry;
+      })
+      .finally(() => {
+        this.pendingEntries.delete(args.environmentId);
+      });
     this.pendingEntries.set(args.environmentId, creation);
 
-    const entry = await creation;
-    this.entries.set(args.environmentId, entry);
-    return entry;
+    return creation;
   }
 
   private async applyExistingEnvironmentProvision(
@@ -606,6 +807,7 @@ export class RuntimeManager {
     this.stopWatchingThreadStorageIfNoTrackedThreads();
     await entry.runtime.shutdown();
     await entry.workspace.destroy();
+    await this.cleanupUnusedInjectedSkillStagingDirs();
   }
 
   async forgetEnvironment(environmentId: string): Promise<void> {
@@ -630,6 +832,7 @@ export class RuntimeManager {
     this.entries.delete(environmentId);
     await this.stopWatchingStatus(entry);
     await entry.runtime.shutdown();
+    await this.cleanupUnusedInjectedSkillStagingDirs();
   }
 
   async evictIdleEnvironments(): Promise<string[]> {
@@ -665,6 +868,7 @@ export class RuntimeManager {
       throw firstRejected.reason;
     }
 
+    await this.cleanupUnusedInjectedSkillStagingDirs();
     return shutdownResults.flatMap((result) =>
       result.status === "fulfilled" ? [result.value] : [],
     );
@@ -682,6 +886,7 @@ export class RuntimeManager {
     this.entries.clear();
     this.pendingEntries.clear();
     this.trackedThreadStorageTargets.clear();
+    this.trackedApplicationDataTargets.clear();
 
     for (const entry of entries) {
       await this.stopWatchingStatus(entry);
@@ -702,6 +907,11 @@ export class RuntimeManager {
     }
     await this.stopWatchingThreadStorageRoot();
     this.stopWatchingThreadStorageRoot = STOP_WATCHING;
+    await this.stopWatchingApplicationStorageRoot();
+    this.stopWatchingApplicationStorageRoot = STOP_WATCHING;
+    await this.stopWatchingDataDirSkillsRoot();
+    this.stopWatchingDataDirSkillsRoot = STOP_WATCHING;
+    await this.cleanupUnusedInjectedSkillStagingDirs();
   }
 
   private buildUnexpectedProviderExitEvents(
@@ -756,7 +966,9 @@ export class RuntimeManager {
     let runtime: AgentRuntime | null = null;
     runtime = this.createRuntime({
       workspacePath,
-      additionalWorkspaceWriteRoots: [],
+      additionalWorkspaceWriteRoots: this.options.appsRootPath
+        ? [this.options.appsRootPath]
+        : [],
       shellEnv: this.getShellEnv(),
       threadStorageRootPath: this.options.threadStorageRootPath ?? undefined,
       bridgeBundleDir: this.options.bridgeBundleDir,
@@ -789,9 +1001,7 @@ export class RuntimeManager {
     return runtime;
   }
 
-  private async createEntry(
-    args: EnsureEnvironmentArgs,
-  ): Promise<RuntimeEntry> {
+  private async createEntry(args: CreateEntryArgs): Promise<RuntimeEntry> {
     const provision =
       args.provision ??
       (args.workspacePath
@@ -815,6 +1025,7 @@ export class RuntimeManager {
       workspace.getAdditionalWorkspaceWriteRoots(),
     ]);
     const additionalWorkspaceWriteRoots = this.runtimeWorkspaceWriteRoots({
+      appsRootPath: this.options.appsRootPath,
       threadStorageRootPath: this.options.threadStorageRootPath,
       workspaceRoots: workspaceWriteRoots,
     });
@@ -844,6 +1055,9 @@ export class RuntimeManager {
       runtime = this.createRuntime({
         workspacePath: workspace.path,
         additionalWorkspaceWriteRoots,
+        ...(args.skillConfig
+          ? { skillRoots: args.skillConfig.skillRoots }
+          : {}),
         shellEnv: this.getShellEnv(),
         threadStorageRootPath: this.options.threadStorageRootPath ?? undefined,
         bridgeBundleDir: this.options.bridgeBundleDir,
@@ -917,6 +1131,7 @@ export class RuntimeManager {
     return {
       environmentId: args.environmentId,
       runtime,
+      skillCatalogHash: args.skillConfig?.catalogHash ?? null,
       stopWatchingStatus,
       terminals: new Set<string>(),
       workspace,
@@ -956,32 +1171,90 @@ export class RuntimeManager {
               threadId: event.threadId,
             });
           }
-          if (event.kind === "thread-app-data-changed") {
-            this.options.onThreadAppDataChanged?.({
-              appId: event.appId,
-              environmentId: event.environmentId,
+        },
+        onWatchError: (error) => {
+          this.options.onThreadStorageWatchError?.({
+            error,
+          });
+        },
+      });
+  }
+
+  private ensureApplicationStorageWatcher(): void {
+    if (
+      !this.hostWatcher ||
+      this.stopWatchingApplicationStorageRoot !== STOP_WATCHING
+    ) {
+      return;
+    }
+
+    const appsRootPath = this.options.appsRootPath;
+    if (!appsRootPath) {
+      return;
+    }
+
+    this.stopWatchingApplicationStorageRoot =
+      this.hostWatcher.watchApplicationStorageRoot({
+        appsRootPath,
+        resolveApplicationTarget: (applicationId) =>
+          this.findTrackedApplicationDataTarget(applicationId),
+        onChange: (event) => {
+          if (event.kind === "application-storage-targets-changed") {
+            this.options.onApplicationStorageTargetsChanged?.();
+          }
+          if (event.kind === "application-data-changed") {
+            this.options.onApplicationDataChanged?.({
+              applicationId: event.applicationId,
+              appDataPath: event.appDataPath,
               path: event.path,
-              threadId: event.threadId,
-              threadStoragePath: path.join(
-                threadStorageRootPath,
-                event.threadId,
-              ),
             });
           }
-          if (event.kind === "thread-app-data-resync") {
-            this.options.onThreadAppDataResync?.({
-              appId: event.appId,
-              environmentId: event.environmentId,
-              threadId: event.threadId,
-              threadStoragePath: path.join(
-                threadStorageRootPath,
-                event.threadId,
-              ),
+          if (event.kind === "application-data-resync") {
+            this.options.onApplicationDataResync?.({
+              applicationId: event.applicationId,
+            });
+          }
+          if (event.kind === "injected-skills-changed") {
+            this.options.onInjectedSkillsChanged?.({
+              applicationId: event.applicationId,
+              changedPaths: event.changedPaths,
+              sourceType: event.sourceType,
             });
           }
         },
         onWatchError: (error) => {
-          this.options.onThreadStorageWatchError?.({
+          this.options.onApplicationStorageWatchError?.({
+            error,
+          });
+        },
+      });
+  }
+
+  private ensureDataDirSkillsWatcher(): void {
+    if (
+      !this.hostWatcher?.watchDataDirSkillsRoot ||
+      this.stopWatchingDataDirSkillsRoot !== STOP_WATCHING
+    ) {
+      return;
+    }
+
+    const dataDirSkillsRootPath = this.options.dataDirSkillsRootPath;
+    if (!dataDirSkillsRootPath) {
+      return;
+    }
+
+    this.stopWatchingDataDirSkillsRoot =
+      this.hostWatcher.watchDataDirSkillsRoot({
+        dataDirSkillsRootPath,
+        onChange: (event) => {
+          this.options.onInjectedSkillsChanged?.({
+            applicationId: event.applicationId,
+            changedPaths: event.changedPaths,
+            sourceType: event.sourceType,
+          });
+        },
+        onWatchError: (error) => {
+          this.options.onDataDirSkillsWatchError?.({
             error,
           });
         },
@@ -994,6 +1267,12 @@ export class RuntimeManager {
     return this.trackedThreadStorageTargets.get(threadId) ?? null;
   }
 
+  private findTrackedApplicationDataTarget(
+    applicationId: ApplicationId,
+  ): ApplicationDataWatchTarget | null {
+    return this.trackedApplicationDataTargets.get(applicationId) ?? null;
+  }
+
   private removeTrackedThreadStorageTargetsForEnvironment(
     environmentId: string,
   ): void {
diff --git a/apps/host-daemon/src/runtime-shell-env.test.ts b/apps/host-daemon/src/runtime-shell-env.test.ts
index c9a90bd08..1dd25dbd5 100644
--- a/apps/host-daemon/src/runtime-shell-env.test.ts
+++ b/apps/host-daemon/src/runtime-shell-env.test.ts
@@ -142,6 +142,7 @@ describe("prepareRuntimeShellEnv", () => {
   it("prepends the configured bb executable directory to PATH", () => {
     expect(
       prepareRuntimeShellEnv({
+        appsRootPath: "/tmp/bb-data/apps",
         bbExecutableDirectory: "/tmp/bb-bin",
         hostDaemonPort: 3002,
         inheritedPath: "/usr/bin",
@@ -149,6 +150,7 @@ describe("prepareRuntimeShellEnv", () => {
       }),
     ).toEqual({
       PATH: `/tmp/bb-bin${delimiter}/usr/bin`,
+      BB_APPS_ROOT: "/tmp/bb-data/apps",
       BB_SERVER_URL: "http://127.0.0.1:3334",
       BB_HOST_DAEMON_PORT: "3002",
     });
@@ -159,12 +161,14 @@ describe("prepareRuntimeShellEnv", () => {
 
     expect(
       prepareRuntimeShellEnv({
+        appsRootPath: "/tmp/bb-data/apps",
         bbExecutableDirectory: "/tmp/bb-bin",
         hostDaemonPort: 3002,
         serverUrl: "http://127.0.0.1:3334",
       }),
     ).toEqual({
       PATH: `/tmp/bb-bin${delimiter}/usr/local/bin:/usr/bin`,
+      BB_APPS_ROOT: "/tmp/bb-data/apps",
       BB_SERVER_URL: "http://127.0.0.1:3334",
       BB_HOST_DAEMON_PORT: "3002",
     });
@@ -173,12 +177,14 @@ describe("prepareRuntimeShellEnv", () => {
   it("omits the host daemon port when the local API is disabled", () => {
     expect(
       prepareRuntimeShellEnv({
+        appsRootPath: "/tmp/bb-data/apps",
         bbExecutableDirectory: "/tmp/bb-bin",
         inheritedPath: "/usr/bin",
         serverUrl: "http://127.0.0.1:3334",
       }),
     ).toEqual({
       PATH: `/tmp/bb-bin${delimiter}/usr/bin`,
+      BB_APPS_ROOT: "/tmp/bb-data/apps",
       BB_SERVER_URL: "http://127.0.0.1:3334",
     });
   });
diff --git a/apps/host-daemon/src/runtime-shell-env.ts b/apps/host-daemon/src/runtime-shell-env.ts
index 17b017d7d..b53c6dd49 100644
--- a/apps/host-daemon/src/runtime-shell-env.ts
+++ b/apps/host-daemon/src/runtime-shell-env.ts
@@ -10,6 +10,7 @@ export interface ResolveLocalBbExecutableDirectoryOptions {
 }
 
 export interface PrepareRuntimeShellEnvOptions {
+  appsRootPath: string;
   bbExecutableDirectory: string;
   hostDaemonPort?: number;
   serverUrl: string;
@@ -97,6 +98,7 @@ export function prepareRuntimeShellEnv(
       options.bbExecutableDirectory,
       options.inheritedPath ?? process.env.PATH,
     ),
+    BB_APPS_ROOT: options.appsRootPath,
     BB_SERVER_URL: options.serverUrl,
   };
   assignIfDefined({
diff --git a/apps/host-daemon/src/server-connection.ts b/apps/host-daemon/src/server-connection.ts
index fe4575926..6fb1541b2 100644
--- a/apps/host-daemon/src/server-connection.ts
+++ b/apps/host-daemon/src/server-connection.ts
@@ -51,6 +51,10 @@ type HostDaemonEnvironmentChangeMessage = Extract<
   { type: "environment-change" }
 >;
 
+const APPLICATION_STORAGE_CHANGED_MESSAGE = {
+  type: "application-storage-changed",
+} satisfies HostDaemonDaemonWsMessage;
+
 function environmentChangeMessageKey(
   message: HostDaemonEnvironmentChangeMessage,
 ): string {
@@ -96,6 +100,7 @@ export class ServerConnection {
     string,
     HostDaemonEnvironmentChangeMessage
   >();
+  private pendingApplicationStorageChanged = false;
 
   constructor(private readonly options: ServerConnectionOptions) {
     this.sessionCloseHandler = options.onSessionClose;
@@ -133,6 +138,7 @@ export class ServerConnection {
   async shutdown(): Promise<void> {
     this.stopped = true;
     this.pendingEnvironmentChanges.clear();
+    this.pendingApplicationStorageChanged = false;
     this.stopPollingFallback();
     this.clearHeartbeat();
     this.clearSession();
@@ -157,6 +163,9 @@ export class ServerConnection {
     if (payload.type === "environment-change") {
       this.pendingEnvironmentChanges.delete(environmentChangeMessageKey(payload));
     }
+    if (payload.type === "application-storage-changed") {
+      this.pendingApplicationStorageChanged = false;
+    }
     return true;
   }
 
@@ -281,7 +290,7 @@ export class ServerConnection {
             "Connected to server",
           );
           await this.options.onSessionOpened?.(session);
-          this.flushPendingEnvironmentChanges();
+          this.flushPendingRecoverableMessages();
           if (!settled) {
             settled = true;
             resolve(session);
@@ -344,21 +353,26 @@ export class ServerConnection {
   private bufferMessageIfRecoverable(
     message: HostDaemonDaemonWsMessage,
   ): void {
-    if (message.type !== "environment-change") {
-      return;
+    if (message.type === "environment-change") {
+      this.pendingEnvironmentChanges.set(
+        environmentChangeMessageKey(message),
+        message,
+      );
+    }
+    if (message.type === "application-storage-changed") {
+      this.pendingApplicationStorageChanged = true;
     }
-    this.pendingEnvironmentChanges.set(
-      environmentChangeMessageKey(message),
-      message,
-    );
   }
 
-  private flushPendingEnvironmentChanges(): void {
+  private flushPendingRecoverableMessages(): void {
     for (const message of Array.from(this.pendingEnvironmentChanges.values())) {
       if (!this.sendMessage(message)) {
         return;
       }
     }
+    if (this.pendingApplicationStorageChanged) {
+      this.sendMessage(APPLICATION_STORAGE_CHANGED_MESSAGE);
+    }
   }
 
   private handleWebSocketMessage(data: unknown): void {
diff --git a/apps/host-daemon/src/start-host-daemon.ts b/apps/host-daemon/src/start-host-daemon.ts
index d6790e116..a74feabe7 100644
--- a/apps/host-daemon/src/start-host-daemon.ts
+++ b/apps/host-daemon/src/start-host-daemon.ts
@@ -3,6 +3,7 @@ import {
   loadHostDaemonStartConfig,
   type HostDaemonConnectionConfig,
 } from "@bb/config/host-daemon";
+import { resolveAppsRootPath } from "@bb/config/app-storage-paths";
 import type { HostType, ToolCallRequest, ToolCallResponse } from "@bb/domain";
 import { createHostWatcher, type HostWatcher } from "@bb/host-watcher";
 import { createLogger } from "@bb/logger";
@@ -158,6 +159,7 @@ export async function startHostDaemon(
         hostType,
       }));
     const runtimeShellEnv = prepareRuntimeShellEnv({
+      appsRootPath: resolveAppsRootPath(dataDir),
       bbExecutableDirectory,
       hostDaemonPort: localApiConfig?.port,
       serverUrl,
diff --git a/apps/host-daemon/src/workspace-resolution.ts b/apps/host-daemon/src/workspace-resolution.ts
index 402793cbc..40f52c950 100644
--- a/apps/host-daemon/src/workspace-resolution.ts
+++ b/apps/host-daemon/src/workspace-resolution.ts
@@ -1,4 +1,5 @@
 import type {
+  HostDaemonInjectedSkillSource,
   WorkspaceContext,
   WorkspaceResolutionFailure,
   WorkspaceResolutionFailureCode,
@@ -29,6 +30,7 @@ interface WorkspaceResolutionFailureFromErrorArgs {
 interface ResolveWorkspaceForCommandArgs {
   dataDir?: string;
   environmentId: string;
+  injectedSkillSources?: readonly HostDaemonInjectedSkillSource[];
   requireGit?: boolean;
   requireManagedWorktree?: boolean;
   runtimeManager: RuntimeManager;
@@ -126,6 +128,9 @@ export async function resolveWorkspaceForCommand(
       {
         dataDir: args.dataDir,
         environmentId: args.environmentId,
+        ...(args.injectedSkillSources !== undefined
+          ? { injectedSkillSources: args.injectedSkillSources }
+          : {}),
         workspaceContext: args.workspaceContext,
       },
       args.runtimeManager,
diff --git a/apps/host-daemon/test/command/command-router.test.ts b/apps/host-daemon/test/command/command-router.test.ts
index c9d2a7608..d88c2883c 100644
--- a/apps/host-daemon/test/command/command-router.test.ts
+++ b/apps/host-daemon/test/command/command-router.test.ts
@@ -266,6 +266,7 @@ function createStandardRuntimeCommandContext(args: {
     },
     instructions: "Be a helpful coding agent.",
     dynamicTools: [],
+    injectedSkillSources: [],
     instructionMode: "append" as const,
   };
 }
@@ -1417,6 +1418,7 @@ describe("CommandRouter", () => {
             providerThreadId: "provider-a",
             instructions: "Be a helpful coding agent.",
             dynamicTools: [],
+            injectedSkillSources: [],
             instructionMode: "append" as const,
           },
           target: { mode: "start" },
@@ -1449,6 +1451,7 @@ describe("CommandRouter", () => {
             providerThreadId: "provider-b",
             instructions: "Be a helpful coding agent.",
             dynamicTools: [],
+            injectedSkillSources: [],
             instructionMode: "append" as const,
           },
           target: { mode: "start" },
diff --git a/apps/host-daemon/test/command/thread-dispatch.test.ts b/apps/host-daemon/test/command/thread-dispatch.test.ts
index 38e1712ad..7ddd1ce34 100644
--- a/apps/host-daemon/test/command/thread-dispatch.test.ts
+++ b/apps/host-daemon/test/command/thread-dispatch.test.ts
@@ -67,6 +67,7 @@ describe("thread command dispatch", () => {
       },
       instructions: "Be a helpful coding agent.",
       dynamicTools: [],
+      injectedSkillSources: [],
       instructionMode: "append",
     };
 
@@ -126,6 +127,7 @@ describe("thread command dispatch", () => {
             providerThreadId: "provider-thread-stale-turn",
             instructions: "Be a helpful coding agent.",
             dynamicTools: [],
+            injectedSkillSources: [],
             instructionMode: "append",
           },
         },
@@ -183,6 +185,7 @@ describe("thread command dispatch", () => {
         },
         instructions: "Be a helpful coding agent.",
         dynamicTools: [],
+        injectedSkillSources: [],
         instructionMode: "append",
       },
       {
@@ -291,6 +294,7 @@ describe("thread command dispatch", () => {
           providerThreadId: "provider-submit-attachments",
           instructions: "Be a helpful coding agent.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         },
         target: { mode: "start" },
@@ -356,6 +360,7 @@ describe("thread command dispatch", () => {
         },
         instructions: "Be a helpful coding agent.",
         dynamicTools: [],
+        injectedSkillSources: [],
         instructionMode: "append",
       },
       {
@@ -413,6 +418,7 @@ describe("thread command dispatch", () => {
         },
         instructions: "Be a helpful coding agent.",
         dynamicTools: [],
+        injectedSkillSources: [],
         instructionMode: "append",
       },
       {
@@ -471,6 +477,7 @@ describe("thread command dispatch", () => {
           },
           instructions: "Be a helpful coding agent.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         },
         {
@@ -538,6 +545,7 @@ describe("thread command dispatch", () => {
           },
           instructions: "Be a helpful coding agent.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         },
         {
@@ -595,6 +603,7 @@ describe("thread command dispatch", () => {
           },
           instructions: "Be a helpful coding agent.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         },
         {
@@ -653,6 +662,7 @@ describe("thread command dispatch", () => {
             providerThreadId: "provider-runtime-failed-turn-attachments",
             instructions: "Be a helpful coding agent.",
             dynamicTools: [],
+            injectedSkillSources: [],
             instructionMode: "append",
           },
           target: { mode: "start" },
@@ -700,6 +710,7 @@ describe("thread command dispatch", () => {
         },
         instructions: "Be a helpful coding agent.",
         dynamicTools: [],
+        injectedSkillSources: [],
         instructionMode: "append",
       },
       harness.dispatchOptions(),
@@ -827,6 +838,7 @@ describe("thread command dispatch", () => {
         },
         instructions: "Be a helpful coding agent.",
         dynamicTools: [],
+        injectedSkillSources: [],
         instructionMode: "append",
       },
       harness.dispatchOptions(),
@@ -877,6 +889,7 @@ describe("thread command dispatch", () => {
           providerThreadId: "provider-thread-resume-after-archive",
           instructions: "Be a helpful coding agent.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         },
         target: { mode: "start" },
@@ -957,6 +970,7 @@ describe("thread command dispatch", () => {
           providerThreadId: "provider-1",
           instructions: "Be a helpful coding agent.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         },
         target: { mode: "start" },
@@ -987,6 +1001,7 @@ describe("thread command dispatch", () => {
           providerThreadId: "provider-1",
           instructions: "Be a helpful coding agent.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         },
         target: { mode: "auto", expectedTurnId: "turn-1" },
@@ -1063,6 +1078,7 @@ describe("thread command dispatch", () => {
           providerThreadId: "provider-1",
           instructions: "Be a helpful coding agent.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         },
         target: { mode: "start" },
@@ -1096,6 +1112,7 @@ describe("thread command dispatch", () => {
           providerThreadId: "provider-1",
           instructions: "Be a helpful coding agent.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         },
         target: { mode: "start" },
@@ -1146,6 +1163,7 @@ describe("thread command dispatch", () => {
           providerThreadId: "provider-1",
           instructions: "Be a helpful coding agent.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         },
         target: { mode: "auto", expectedTurnId: "turn-1" },
@@ -1203,6 +1221,7 @@ describe("thread command dispatch", () => {
           providerThreadId: "provider-1",
           instructions: "Be a helpful coding agent.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         },
         target: { mode: "auto", expectedTurnId: "turn-old" },
@@ -1254,6 +1273,7 @@ describe("thread command dispatch", () => {
           providerThreadId: "provider-1",
           instructions: "Be a helpful coding agent.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         },
         target: { mode: "steer", expectedTurnId: "turn-old" },
@@ -1299,6 +1319,7 @@ describe("thread command dispatch", () => {
           providerThreadId: "provider-1",
           instructions: "Be a helpful coding agent.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         },
         target: { mode: "steer", expectedTurnId: null },
@@ -1339,6 +1360,7 @@ describe("thread command dispatch", () => {
           providerThreadId: "provider-1",
           instructions: "Be a helpful coding agent.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         },
         target: { mode: "start" },
@@ -1410,6 +1432,7 @@ describe("thread command dispatch", () => {
           providerThreadId: "provider-1",
           instructions: "Be a helpful coding agent.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         },
         target: { mode: "start" },
@@ -1578,6 +1601,7 @@ describe("thread command dispatch", () => {
             },
           },
         ],
+        injectedSkillSources: [],
         instructionMode: "replace",
       },
       harness.dispatchOptions(),
@@ -1616,6 +1640,7 @@ describe("thread command dispatch", () => {
         },
         instructions: "test",
         dynamicTools: [],
+        injectedSkillSources: [],
         instructionMode: "append",
         threadStoragePath: storagePath,
       },
@@ -1651,6 +1676,7 @@ describe("thread command dispatch", () => {
         },
         instructions: "test",
         dynamicTools: [],
+        injectedSkillSources: [],
         instructionMode: "append",
       },
       harness.dispatchOptions(),
@@ -1760,6 +1786,7 @@ describe("thread command dispatch", () => {
           },
           instructions: "test",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
           threadStoragePath: "/tmp/evil-escape",
         },
diff --git a/apps/host-daemon/test/connection/server-connection.test.ts b/apps/host-daemon/test/connection/server-connection.test.ts
index e0fc4e245..e1e7f55c1 100644
--- a/apps/host-daemon/test/connection/server-connection.test.ts
+++ b/apps/host-daemon/test/connection/server-connection.test.ts
@@ -174,6 +174,7 @@ describe("ServerConnection", () => {
           providerThreadId: "provider-1",
           instructions: "Be a helpful coding agent.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         },
         target: { mode: "start" },
@@ -582,6 +583,33 @@ describe("ServerConnection", () => {
     await connection.shutdown();
   });
 
+  it("sends application storage change hints over the daemon websocket", async () => {
+    testServer = await createTestServer();
+    const server = testServer;
+    const { connection } = createConnection(server);
+
+    await connection.start();
+    expect(
+      connection.sendMessage({
+        type: "application-storage-changed",
+      }),
+    ).toBe(true);
+
+    await waitFor(() =>
+      server.heartbeats.some(
+        (entry) => entry.message.type === "application-storage-changed",
+      ),
+    );
+    expect(server.heartbeats).toContainEqual({
+      sessionId: "session-1",
+      message: {
+        type: "application-storage-changed",
+      },
+    });
+
+    await connection.shutdown();
+  });
+
   it("buffers deduplicated environment change hints while disconnected and flushes after reconnect", async () => {
     testServer = await createTestServer();
     const server = testServer;
@@ -643,6 +671,46 @@ describe("ServerConnection", () => {
     await connection.shutdown();
   });
 
+  it("buffers one application storage change hint while disconnected and flushes after reconnect", async () => {
+    testServer = await createTestServer();
+    const server = testServer;
+    const { connection } = createConnection(server);
+
+    expect(
+      connection.sendMessage({
+        type: "application-storage-changed",
+      }),
+    ).toBe(false);
+    expect(
+      connection.sendMessage({
+        type: "application-storage-changed",
+      }),
+    ).toBe(false);
+    expect(server.heartbeats).toEqual([]);
+
+    await connection.start();
+    await waitFor(
+      () =>
+        server.heartbeats.filter(
+          (entry) => entry.message.type === "application-storage-changed",
+        ).length === 1,
+    );
+    expect(
+      server.heartbeats.filter(
+        (entry) => entry.message.type === "application-storage-changed",
+      ),
+    ).toEqual([
+      {
+        sessionId: "session-1",
+        message: {
+          type: "application-storage-changed",
+        },
+      },
+    ]);
+
+    await connection.shutdown();
+  });
+
   it("includes active threads when opening the session", async () => {
     testServer = await createTestServer();
     const activeThreads: HostDaemonActiveThread[] = [
diff --git a/apps/host-daemon/test/helpers/test-server.ts b/apps/host-daemon/test/helpers/test-server.ts
index 47138ab09..30396c702 100644
--- a/apps/host-daemon/test/helpers/test-server.ts
+++ b/apps/host-daemon/test/helpers/test-server.ts
@@ -266,6 +266,7 @@ export async function createTestServer(
         heartbeatIntervalMs: options.heartbeatIntervalMs ?? 25,
         leaseTimeoutMs: options.leaseTimeoutMs ?? 1_000,
         trackedThreadTargets: options.trackedThreadTargets ?? [],
+        trackedApplicationDataTargets: [],
         retiredEnvironmentIds: [],
       },
       201,
diff --git a/apps/host-daemon/test/integration/daemon.integration.test.ts b/apps/host-daemon/test/integration/daemon.integration.test.ts
index 9bd85ef2b..49efd7e72 100644
--- a/apps/host-daemon/test/integration/daemon.integration.test.ts
+++ b/apps/host-daemon/test/integration/daemon.integration.test.ts
@@ -496,6 +496,7 @@ function createStandardThreadStartCommand(args: {
     },
     instructions: "Be a helpful coding agent.",
     dynamicTools: [],
+    injectedSkillSources: [],
     instructionMode: "append" as const,
   };
 }
@@ -533,6 +534,7 @@ function createTurnSubmitCommand(args: {
       providerThreadId: args.providerThreadId,
       instructions: "Be a helpful coding agent.",
       dynamicTools: [],
+      injectedSkillSources: [],
       instructionMode: "append" as const,
     },
     target: { mode: "start" as const },
diff --git a/apps/server/package.json b/apps/server/package.json
index 9ad631528..83e6eb8d5 100644
--- a/apps/server/package.json
+++ b/apps/server/package.json
@@ -4,7 +4,7 @@
   "type": "module",
   "private": true,
   "scripts": {
-    "build": "node ../../scripts/build-node-entry.mjs src/index.ts dist/index.js --clean-dist --templates --external ./start-server.js --copy-dir ../../packages/db/drizzle dist/drizzle --copy-dir src/services/threads/default-template dist/default-template && node ../../scripts/build-node-entry.mjs src/start-server.ts dist/start-server.js",
+    "build": "node ../../scripts/build-node-entry.mjs src/index.ts dist/index.js --clean-dist --templates --external ./start-server.js --copy-dir ../../packages/db/drizzle dist/drizzle && node ../../scripts/build-node-entry.mjs src/start-server.ts dist/start-server.js",
     "bench": "vitest bench --config vitest.config.ts",
     "start": "node dist/index.js",
     "start:prod": "cross-env NODE_ENV=production node dist/index.js",
diff --git a/apps/server/src/internal/app-data-changes.ts b/apps/server/src/internal/app-data-changes.ts
index 13a70484c..e8db5f3f4 100644
--- a/apps/server/src/internal/app-data-changes.ts
+++ b/apps/server/src/internal/app-data-changes.ts
@@ -7,46 +7,10 @@ import {
 import type { Hono } from "hono";
 import type { AppDeps } from "../types.js";
 import { ApiError } from "../errors.js";
-import {
-  requireEnvironment,
-  requirePublicThread,
-} from "../services/lib/entity-lookup.js";
 import {
   requireAuthenticatedDaemonSession,
-  type RequireAuthenticatedDaemonSessionArgs,
 } from "./session-state.js";
 
-interface RequireSessionOwnedThreadArgs {
-  context: RequireAuthenticatedDaemonSessionArgs["context"];
-  deps: AppDeps;
-  sessionId: string;
-  threadId: string;
-}
-
-function requireSessionOwnedThread(args: RequireSessionOwnedThreadArgs): void {
-  const session = requireAuthenticatedDaemonSession({
-    context: args.context,
-    db: args.deps.db,
-    sessionId: args.sessionId,
-  });
-  const thread = requirePublicThread(args.deps.db, args.threadId);
-  if (!thread.environmentId) {
-    throw new ApiError(
-      403,
-      "invalid_request",
-      "Thread does not belong to an environment",
-    );
-  }
-  const environment = requireEnvironment(args.deps.db, thread.environmentId);
-  if (environment.hostId !== session.hostId) {
-    throw new ApiError(
-      403,
-      "invalid_request",
-      "Thread does not belong to the session host",
-    );
-  }
-}
-
 export function registerInternalAppDataChangeRoutes(
   app: Hono,
   deps: AppDeps,
@@ -59,17 +23,15 @@ export function registerInternalAppDataChangeRoutes(
     "/session/app-data-change",
     hostDaemonAppDataChangeRequestSchema,
     async (context, payload) => {
-      requireSessionOwnedThread({
+      requireAuthenticatedDaemonSession({
         context,
-        deps,
+        db: deps.db,
         sessionId: payload.sessionId,
-        threadId: payload.threadId,
       });
 
-      deps.hub.notifyThreadAppData({
+      deps.hub.notifyAppData({
         type: "app-data.changed",
-        threadId: payload.threadId,
-        appId: payload.appId,
+        applicationId: payload.applicationId,
         path: payload.path,
         value: payload.value,
         deleted: payload.deleted,
@@ -83,17 +45,15 @@ export function registerInternalAppDataChangeRoutes(
     "/session/app-data-resync",
     hostDaemonAppDataResyncRequestSchema,
     async (context, payload) => {
-      requireSessionOwnedThread({
+      requireAuthenticatedDaemonSession({
         context,
-        deps,
+        db: deps.db,
         sessionId: payload.sessionId,
-        threadId: payload.threadId,
       });
 
-      deps.hub.notifyThreadAppData({
+      deps.hub.notifyAppData({
         type: "app-data.resync",
-        threadId: payload.threadId,
-        appId: payload.appId,
+        applicationId: payload.applicationId,
       });
       return context.json({ ok: true });
     },
diff --git a/apps/server/src/internal/session.ts b/apps/server/src/internal/session.ts
index 61a17fb98..f8f6f9dc7 100644
--- a/apps/server/src/internal/session.ts
+++ b/apps/server/src/internal/session.ts
@@ -24,6 +24,7 @@ import {
 import { requireAuthenticatedDaemonSession } from "./session-state.js";
 import { readAttachment } from "../services/projects/attachments.js";
 import { handleHostSessionOpened } from "./session-owner-side-effects.js";
+import { listTrackedApplicationDataTargets } from "../services/apps/tracked-application-data-targets.js";
 
 export function registerInternalSessionRoutes(app: Hono, deps: AppDeps): void {
   const { get, post } = typedRoutes<HostDaemonInternalSchema>(app, {
@@ -73,6 +74,11 @@ export function registerInternalSessionRoutes(app: Hono, deps: AppDeps): void {
         leaseTimeoutMs: LEASE_TIMEOUT_MS,
       });
 
+      const trackedApplicationDataTargets =
+        await listTrackedApplicationDataTargets({
+          dataDir: session.dataDir,
+        });
+
       await handleHostSessionOpened(deps, {
         activeThreads: payload.activeThreads,
         hostId: daemon.hostId,
@@ -103,6 +109,7 @@ export function registerInternalSessionRoutes(app: Hono, deps: AppDeps): void {
           heartbeatIntervalMs: HEARTBEAT_INTERVAL_MS,
           leaseTimeoutMs: LEASE_TIMEOUT_MS,
           trackedThreadTargets,
+          trackedApplicationDataTargets,
           retiredEnvironmentIds,
         },
         201,
diff --git a/apps/server/src/routes/apps.ts b/apps/server/src/routes/apps.ts
new file mode 100644
index 000000000..085e8d47e
--- /dev/null
+++ b/apps/server/src/routes/apps.ts
@@ -0,0 +1,1587 @@
+import { Buffer } from "node:buffer";
+import { createHash, randomUUID } from "node:crypto";
+import {
+  mkdir,
+  readdir,
+  readFile,
+  rename,
+  rm,
+  stat,
+  writeFile,
+} from "node:fs/promises";
+import type { Dirent, Stats } from "node:fs";
+import path from "node:path";
+import mimeTypes from "mime-types";
+import type { Hono } from "hono";
+import type { ZodIssue } from "zod";
+import {
+  resolveApplicationDataPath,
+  resolveApplicationManifestPath,
+  resolveApplicationPath,
+  resolveApplicationPublicPath,
+  resolveAppsRootPath,
+} from "@bb/config/app-storage-paths";
+import {
+  appDataPathSchema,
+  applicationIdSchema,
+  deriveApplicationIdFromName,
+  jsonValueSchema,
+} from "@bb/domain";
+import type { AppDataPath, ApplicationId, JsonValue } from "@bb/domain";
+import {
+  appDataListQuerySchema,
+  appDataWriteRequestSchema,
+  appManifestSchema,
+  appMessageRequestSchema,
+  createAppRequestSchema,
+  typedRoutes,
+  type AppCapability,
+  type AppDataEntry,
+  type AppDetail,
+  type AppEntry,
+  type AppIcon,
+  type AppManifest,
+  type AppSummary,
+  type CreateAppRequest,
+  type PublicApiSchema,
+} from "@bb/server-contract";
+import type { AppDeps, LoggedWorkSessionDeps } from "../types.js";
+import { ApiError } from "../errors.js";
+import { requirePublicThread } from "../services/lib/entity-lookup.js";
+import { requireThreadCommandEnvironment } from "../services/threads/thread-command-environment.js";
+import { sendThreadMessage } from "../services/threads/thread-send.js";
+import { injectAppClientScript } from "../services/threads/app-client-script.js";
+import { buildBlankAppIndexHtml } from "../services/threads/blank-app-scaffold.js";
+import {
+  extractRoutePath,
+  parseSafeRelativeRoutePath,
+  type SafeRelativeRoutePath,
+} from "./relative-route-path.js";
+
+interface InvalidAppManifestErrorArgs extends ApplicationManifestReadArgs {
+  issues: AppManifestValidationIssues;
+  manifestPath: string;
+}
+
+interface LogInvalidAppManifestArgs {
+  error: InvalidAppManifestError;
+  message: string;
+}
+
+interface ApplicationManifestReadArgs {
+  applicationId: ApplicationId;
+  dataDir: string;
+}
+
+interface ApplicationSummaryArgs extends ApplicationManifestReadArgs {
+  manifest: AppManifest;
+}
+
+interface ApplicationDetailArgs extends ApplicationManifestReadArgs {}
+
+interface ReadApplicationRelativeFileArgs {
+  applicationId: ApplicationId;
+  dataDir: string;
+  dotfiles: "allow" | "deny";
+  path: string;
+  rootKind: "app" | "data" | "public";
+}
+
+interface ApplicationRootForKindArgs {
+  applicationId: ApplicationId;
+  dataDir: string;
+  rootKind: "app" | "data" | "public";
+}
+
+interface ReadApplicationDataEntryArgs {
+  applicationId: ApplicationId;
+  dataDir: string;
+  dataPath: AppDataPath;
+}
+
+interface ListApplicationDataEntriesArgs {
+  applicationId: ApplicationId;
+  dataDir: string;
+  dataPath: AppDataPath | "";
+}
+
+interface WriteApplicationDataEntryArgs extends ReadApplicationDataEntryArgs {
+  value: JsonValue;
+}
+
+interface DeleteApplicationDataEntryArgs extends ReadApplicationDataEntryArgs {}
+
+interface CreateInjectedAppHtmlResponseArgs {
+  appSessionToken: AppSessionToken | null;
+  capabilities: AppCapability[];
+  html: string;
+  applicationId: ApplicationId;
+  requestUrl: string;
+  targetThreadId: string | null;
+}
+
+interface ApplicationRouteSegmentArgs {
+  applicationId: string;
+}
+
+interface ServeApplicationStaticFileArgs {
+  deps: AppDeps;
+  rawApplicationId: string;
+  rawPath: string;
+}
+
+interface ApplicationStaticFile {
+  bytes: Buffer;
+  path: string;
+}
+
+interface ReadApplicationStaticFileArgs {
+  applicationId: ApplicationId;
+  staticPath: ApplicationStaticPath;
+  dataDir: string;
+}
+
+interface LogoResolution {
+  extension: string;
+}
+
+interface CreateGlobalApplicationArgs {
+  applicationId: ApplicationId;
+  dataDir: string;
+  name: string;
+}
+
+interface CreateApplicationTempRootArgs {
+  appsRootPath: string;
+  applicationId: ApplicationId;
+}
+
+interface PublishApplicationTempRootArgs {
+  applicationPath: string;
+  tempRootPath: string;
+}
+
+interface AppSession {
+  applicationId: ApplicationId;
+  projectId: string;
+  threadId: string;
+}
+
+interface ResolveAppMessageTargetArgs {
+  applicationId: ApplicationId;
+  payload: {
+    appSessionToken?: string;
+    targetThreadId?: string;
+  };
+  sessions: AppSessionStore;
+}
+
+interface CreateAppSessionArgs {
+  applicationId: ApplicationId;
+  projectId: string;
+  threadId: string;
+}
+
+interface AppSessionStore {
+  create(args: CreateAppSessionArgs): AppSessionToken;
+  get(token: string): AppSession | null;
+}
+
+type ApplicationStaticPath = SafeRelativeRoutePath;
+type AppManifestValidationIssues = readonly ZodIssue[];
+type AppManifestValidationLoggerDeps = Pick<AppDeps, "logger">;
+type GlobalAppListDeps = Pick<AppDeps, "config" | "hub" | "logger">;
+type AppSessionToken = string;
+type LogoExtension = "svg" | "png" | "jpg" | "jpeg";
+
+const DATA_DIRECTORY_NAME = "data";
+const MANIFEST_FILE_NAME = "manifest.json";
+const PUBLIC_DIRECTORY_NAME = "public";
+const HTML_CONTENT_TYPE = "text/html; charset=utf-8";
+const NO_STORE_CACHE_CONTROL = "no-store";
+const CONTENT_TYPE_OPTIONS = "nosniff";
+const HTML_ENTRY_MAX_BYTES = 5 * 1024 * 1024;
+const LOGO_MAX_BYTES = 1024 * 1024;
+const LOGO_EXTENSIONS: readonly LogoExtension[] = ["svg", "png", "jpg", "jpeg"];
+const APP_SESSION_TOKEN_PREFIX = "appsess_";
+const INVALID_APP_MANIFEST_MESSAGE =
+  "App manifest failed validation. Inspect manifest.json or rebuild the app.";
+const globalAppListSignatureByDataDir = new Map<string, string>();
+
+class InvalidAppManifestError extends ApiError {
+  readonly applicationId: ApplicationId;
+  readonly manifestPath: string;
+  readonly issues: AppManifestValidationIssues;
+
+  constructor(args: InvalidAppManifestErrorArgs) {
+    super(422, "invalid_manifest", INVALID_APP_MANIFEST_MESSAGE);
+    this.name = "InvalidAppManifestError";
+    this.applicationId = args.applicationId;
+    this.manifestPath = args.manifestPath;
+    this.issues = args.issues;
+  }
+}
+
+function sha256(bytes: Buffer): string {
+  return createHash("sha256").update(bytes).digest("hex");
+}
+
+function canonicalizeJson(value: JsonValue | AppManifest): string {
+  return `${JSON.stringify(value, null, 2)}\n`;
+}
+
+function isFsErrorWithCode(error: Error, code: string): boolean {
+  return "code" in error && error.code === code;
+}
+
+function parseApplicationId(rawApplicationId: string): ApplicationId {
+  const parsed = applicationIdSchema.safeParse(rawApplicationId);
+  if (!parsed.success) {
+    throw new ApiError(400, "invalid_request", "Invalid applicationId");
+  }
+  return parsed.data;
+}
+
+function parseAppDataPath(rawPath: string): AppDataPath {
+  const parsed = appDataPathSchema.safeParse(rawPath);
+  if (!parsed.success) {
+    throw new ApiError(400, "invalid_request", "Invalid app data path");
+  }
+  return parsed.data;
+}
+
+function applicationRouteSegment(args: ApplicationRouteSegmentArgs): string {
+  return `/apps/${encodeURIComponent(args.applicationId)}/`;
+}
+
+function applicationDataRouteSegment(
+  args: ApplicationRouteSegmentArgs,
+): string {
+  return `/apps/${encodeURIComponent(args.applicationId)}/data/`;
+}
+
+function parseAppDataRoutePath(rawPath: string): AppDataPath {
+  return parseAppDataPath(
+    parseSafeRelativeRoutePath({
+      rawPath,
+      dotfileSegmentPolicy: "allow",
+      invalidPathMessage: "Invalid app data path",
+    }).relativePath,
+  );
+}
+
+function parseOptionalAppDataPrefix(
+  rawPrefix: string | undefined,
+): AppDataPath | "" {
+  if (rawPrefix === undefined || rawPrefix === "") {
+    return "";
+  }
+  return parseAppDataPath(rawPrefix);
+}
+
+function applicationRootForKind(args: ApplicationRootForKindArgs): string {
+  if (args.rootKind === "app") {
+    return resolveApplicationPath(args.dataDir, args.applicationId);
+  }
+  if (args.rootKind === "public") {
+    return resolveApplicationPublicPath(args.dataDir, args.applicationId);
+  }
+  return resolveApplicationDataPath(args.dataDir, args.applicationId);
+}
+
+function parseApplicationStaticPath(rawPath: string): ApplicationStaticPath {
+  return parseSafeRelativeRoutePath({
+    rawPath,
+    directoryIndexPath: "index.html",
+    dotfileSegmentPolicy: "not-found",
+    invalidPathMessage: "Invalid app static path",
+  });
+}
+
+function summarizeAppManifestValidationIssues(
+  issues: AppManifestValidationIssues,
+): string {
+  return issues
+    .map((issue) => {
+      const issuePath = issue.path.map(String).join(".");
+      return `${issuePath || "<root>"}: ${issue.message}`;
+    })
+    .join("; ");
+}
+
+function logInvalidAppManifest(
+  deps: AppManifestValidationLoggerDeps,
+  args: LogInvalidAppManifestArgs,
+): void {
+  deps.logger.warn(
+    {
+      applicationId: args.error.applicationId,
+      manifestPath: args.error.manifestPath,
+      issueSummary: summarizeAppManifestValidationIssues(args.error.issues),
+      issues: args.error.issues,
+    },
+    args.message,
+  );
+}
+
+async function readApplicationRelativeFile(
+  args: ReadApplicationRelativeFileArgs,
+): Promise<Buffer> {
+  const rootPath = applicationRootForKind(args);
+  const filePath = path.join(rootPath, args.path);
+  if (
+    args.dotfiles === "deny" &&
+    args.path.split("/").some((segment) => segment.startsWith("."))
+  ) {
+    throw new ApiError(404, "ENOENT", "App file not found");
+  }
+  const relativePath = path.relative(rootPath, filePath);
+  if (relativePath.startsWith("..") || path.isAbsolute(relativePath)) {
+    throw new ApiError(400, "invalid_request", "Invalid app file path");
+  }
+  try {
+    return await readFile(filePath);
+  } catch (error) {
+    if (error instanceof Error && isFsErrorWithCode(error, "ENOENT")) {
+      throw new ApiError(404, "ENOENT", "App file not found");
+    }
+    throw error;
+  }
+}
+
+async function statApplicationRelativeFile(
+  args: ReadApplicationRelativeFileArgs,
+): Promise<Stats> {
+  const rootPath = applicationRootForKind(args);
+  const filePath = path.join(rootPath, args.path);
+  const relativePath = path.relative(rootPath, filePath);
+  if (relativePath.startsWith("..") || path.isAbsolute(relativePath)) {
+    throw new ApiError(400, "invalid_request", "Invalid app file path");
+  }
+  try {
+    return await stat(filePath);
+  } catch (error) {
+    if (error instanceof Error && isFsErrorWithCode(error, "ENOENT")) {
+      throw new ApiError(404, "ENOENT", "App file not found");
+    }
+    throw error;
+  }
+}
+
+async function ensureApplicationFolderExists(
+  args: ApplicationManifestReadArgs,
+): Promise<void> {
+  try {
+    const applicationStats = await stat(
+      resolveApplicationPath(args.dataDir, args.applicationId),
+    );
+    if (!applicationStats.isDirectory()) {
+      throw new InvalidAppManifestError({
+        ...args,
+        manifestPath: resolveApplicationManifestPath(
+          args.dataDir,
+          args.applicationId,
+        ),
+        issues: [],
+      });
+    }
+  } catch (error) {
+    if (error instanceof Error && isFsErrorWithCode(error, "ENOENT")) {
+      throw new ApiError(404, "app_missing", "App not found");
+    }
+    throw error;
+  }
+}
+
+async function readApplicationManifest(
+  args: ApplicationManifestReadArgs,
+): Promise<AppManifest> {
+  await ensureApplicationFolderExists(args);
+  const manifestPath = resolveApplicationManifestPath(
+    args.dataDir,
+    args.applicationId,
+  );
+  let manifestContent: string;
+  try {
+    manifestContent = await readFile(manifestPath, "utf8");
+  } catch (error) {
+    if (error instanceof Error && isFsErrorWithCode(error, "ENOENT")) {
+      throw new InvalidAppManifestError({
+        ...args,
+        manifestPath,
+        issues: [],
+      });
+    }
+    throw error;
+  }
+
+  let parsedJson;
+  try {
+    parsedJson = JSON.parse(manifestContent);
+  } catch {
+    throw new ApiError(
+      422,
+      "invalid_manifest",
+      "App manifest is not valid JSON",
+    );
+  }
+  const manifest = appManifestSchema.safeParse(parsedJson);
+  if (!manifest.success) {
+    throw new InvalidAppManifestError({
+      ...args,
+      manifestPath,
+      issues: manifest.error.issues,
+    });
+  }
+  if (manifest.data.id !== args.applicationId) {
+    throw new ApiError(
+      422,
+      "invalid_manifest",
+      "App manifest id must match its directory name",
+    );
+  }
+  return manifest.data;
+}
+
+async function readApplicationManifestForRequest(
+  deps: AppDeps,
+  args: ApplicationManifestReadArgs,
+): Promise<AppManifest> {
+  try {
+    return await readApplicationManifest(args);
+  } catch (error) {
+    if (error instanceof InvalidAppManifestError) {
+      logInvalidAppManifest(deps, {
+        error,
+        message: "Rejected invalid global app manifest",
+      });
+    }
+    throw error;
+  }
+}
+
+function entryKindForPath(entryPath: string): AppEntry["kind"] {
+  const normalized = entryPath.toLowerCase();
+  if (normalized.endsWith(".html")) {
+    return "html";
+  }
+  if (normalized.endsWith(".md")) {
+    return "md";
+  }
+  throw new ApiError(
+    422,
+    "invalid_manifest",
+    "App entry must end in .html or .md",
+  );
+}
+
+async function resolveApplicationEntry(
+  args: ApplicationManifestReadArgs & { manifest: AppManifest },
+): Promise<AppEntry> {
+  if (args.manifest.entry !== undefined) {
+    return {
+      path: args.manifest.entry,
+      kind: entryKindForPath(args.manifest.entry),
+    };
+  }
+
+  for (const candidate of ["index.html", "index.md"]) {
+    try {
+      await statApplicationRelativeFile({
+        ...args,
+        path: candidate,
+        rootKind: "public",
+        dotfiles: "deny",
+      });
+      return {
+        path: candidate,
+        kind: entryKindForPath(candidate),
+      };
+    } catch (error) {
+      if (error instanceof ApiError && error.body.code === "ENOENT") {
+        continue;
+      }
+      throw error;
+    }
+  }
+
+  throw new ApiError(
+    404,
+    "ENOENT",
+    "App entry not found: index.html or index.md",
+  );
+}
+
+async function tryResolveLogo(
+  args: ApplicationManifestReadArgs,
+): Promise<LogoResolution | null> {
+  let entries: Dirent[];
+  try {
+    entries = await readdir(
+      resolveApplicationPath(args.dataDir, args.applicationId),
+      {
+        withFileTypes: true,
+      },
+    );
+  } catch (error) {
+    if (error instanceof Error && isFsErrorWithCode(error, "ENOENT")) {
+      return null;
+    }
+    throw error;
+  }
+  const topLevelFiles = new Set(
+    entries.filter((entry) => entry.isFile()).map((entry) => entry.name),
+  );
+  for (const extension of LOGO_EXTENSIONS) {
+    if (topLevelFiles.has(`logo.${extension}`)) {
+      return { extension };
+    }
+  }
+  return null;
+}
+
+async function resolveApplicationIcon(
+  args: ApplicationSummaryArgs,
+): Promise<AppIcon> {
+  if (args.manifest.icon !== undefined) {
+    return { kind: "builtin", name: args.manifest.icon };
+  }
+  const logo = await tryResolveLogo(args);
+  if (logo) {
+    return {
+      kind: "logo",
+      url: `/api/v1/apps/${encodeURIComponent(args.applicationId)}/icon`,
+    };
+  }
+  return { kind: "builtin", name: "GridView" };
+}
+
+async function buildApplicationSummary(
+  args: ApplicationSummaryArgs,
+): Promise<AppSummary> {
+  const [entry, icon] = await Promise.all([
+    resolveApplicationEntry(args),
+    resolveApplicationIcon(args),
+  ]);
+  return {
+    applicationId: args.manifest.id,
+    name: args.manifest.name,
+    entry,
+    capabilities: args.manifest.capabilities,
+    icon,
+  };
+}
+
+async function buildApplicationDetail(
+  deps: AppDeps,
+  args: ApplicationDetailArgs,
+): Promise<AppDetail> {
+  const manifest = await readApplicationManifestForRequest(deps, args);
+  return {
+    ...(await buildApplicationSummary({
+      ...args,
+      manifest,
+    })),
+    appsRootPath: resolveAppsRootPath(args.dataDir),
+    appRootPath: resolveApplicationPath(args.dataDir, args.applicationId),
+    appDataPath: resolveApplicationDataPath(args.dataDir, args.applicationId),
+  };
+}
+
+function assertAppCapability(
+  manifest: AppManifest,
+  capability: AppCapability,
+): void {
+  if (!manifest.capabilities.includes(capability)) {
+    throw new ApiError(
+      403,
+      "invalid_request",
+      `App does not have the ${capability} capability`,
+    );
+  }
+}
+
+function isIgnoredApplicationStorageEntry(entryName: string): boolean {
+  return entryName.startsWith(".tmp-") || entryName.startsWith(".delete-");
+}
+
+async function listGlobalApplications(
+  deps: GlobalAppListDeps,
+): Promise<AppSummary[]> {
+  const appsRootPath = resolveAppsRootPath(deps.config.dataDir);
+  let entries: Dirent[];
+  try {
+    entries = await readdir(appsRootPath, { withFileTypes: true });
+  } catch (error) {
+    if (error instanceof Error && isFsErrorWithCode(error, "ENOENT")) {
+      return [];
+    }
+    throw error;
+  }
+
+  const applicationIds = entries
+    .filter(
+      (entry) =>
+        entry.isDirectory() && !isIgnoredApplicationStorageEntry(entry.name),
+    )
+    .map((entry) => applicationIdSchema.safeParse(entry.name))
+    .filter((entry) => entry.success)
+    .map((entry) => entry.data)
+    .sort((left, right) => left.localeCompare(right));
+
+  const summaries: AppSummary[] = [];
+  for (const applicationId of applicationIds) {
+    try {
+      const manifest = await readApplicationManifest({
+        dataDir: deps.config.dataDir,
+        applicationId,
+      });
+      summaries.push(
+        await buildApplicationSummary({
+          dataDir: deps.config.dataDir,
+          applicationId,
+          manifest,
+        }),
+      );
+    } catch (error) {
+      if (error instanceof InvalidAppManifestError) {
+        logInvalidAppManifest(deps, {
+          error,
+          message: "Skipping invalid global app manifest",
+        });
+        continue;
+      }
+      if (error instanceof ApiError && error.body.code === "invalid_manifest") {
+        deps.logger.warn(
+          {
+            applicationId,
+            appRootPath: resolveApplicationPath(
+              deps.config.dataDir,
+              applicationId,
+            ),
+            message: error.body.message,
+          },
+          "Skipping invalid global app manifest",
+        );
+        continue;
+      }
+      throw error;
+    }
+  }
+  return summaries;
+}
+
+function globalAppListSignature(apps: readonly AppSummary[]): string {
+  return JSON.stringify(apps);
+}
+
+function rememberGlobalAppListSignature(
+  deps: Pick<GlobalAppListDeps, "config">,
+  apps: readonly AppSummary[],
+): void {
+  globalAppListSignatureByDataDir.set(
+    deps.config.dataDir,
+    globalAppListSignature(apps),
+  );
+}
+
+export async function refreshGlobalAppListSignature(
+  deps: GlobalAppListDeps,
+): Promise<AppSummary[]> {
+  const apps = await listGlobalApplications(deps);
+  rememberGlobalAppListSignature(deps, apps);
+  return apps;
+}
+
+export async function notifyGlobalAppsChanged(
+  deps: GlobalAppListDeps,
+): Promise<void> {
+  await refreshGlobalAppListSignature(deps);
+  deps.hub.notifySystem(["apps-changed"]);
+}
+
+export async function notifyGlobalAppsChangedIfListChanged(
+  deps: GlobalAppListDeps,
+): Promise<void> {
+  const apps = await listGlobalApplications(deps);
+  const nextSignature = globalAppListSignature(apps);
+  const previousSignature = globalAppListSignatureByDataDir.get(
+    deps.config.dataDir,
+  );
+  globalAppListSignatureByDataDir.set(deps.config.dataDir, nextSignature);
+  if (previousSignature !== nextSignature) {
+    deps.hub.notifySystem(["apps-changed"]);
+  }
+}
+
+function createHtmlResponse(html: string): Response {
+  return new Response(html, {
+    status: 200,
+    headers: {
+      "cache-control": NO_STORE_CACHE_CONTROL,
+      "content-type": HTML_CONTENT_TYPE,
+      "x-content-type-options": CONTENT_TYPE_OPTIONS,
+    },
+  });
+}
+
+function buildAppWebSocketUrl(
+  deps: LoggedWorkSessionDeps,
+  requestUrl: string,
+): string {
+  if (deps.config.isDevelopment) {
+    return `ws://localhost:${deps.config.serverPort}/ws`;
+  }
+  const url = new URL(requestUrl);
+  url.protocol = url.protocol === "https:" ? "wss:" : "ws:";
+  url.pathname = "/ws";
+  url.search = "";
+  url.hash = "";
+  return url.toString();
+}
+
+function createInjectedAppHtmlResponse(
+  deps: LoggedWorkSessionDeps,
+  args: CreateInjectedAppHtmlResponseArgs,
+): Response {
+  return createHtmlResponse(
+    injectAppClientScript(args.html, {
+      appId: args.applicationId,
+      applicationId: args.applicationId,
+      appSessionToken: args.appSessionToken,
+      capabilities: args.capabilities,
+      targetThreadId: args.targetThreadId,
+      dataUrl: `/api/v1/apps/${encodeURIComponent(args.applicationId)}/data`,
+      messageUrl: `/api/v1/apps/${encodeURIComponent(
+        args.applicationId,
+      )}/message`,
+      wsUrl: buildAppWebSocketUrl(deps, args.requestUrl),
+    }),
+  );
+}
+
+function createAppSessionStore(): AppSessionStore {
+  const sessions = new Map<AppSessionToken, AppSession>();
+  return {
+    create(args) {
+      const token = `${APP_SESSION_TOKEN_PREFIX}${randomUUID().replaceAll(
+        "-",
+        "",
+      )}`;
+      sessions.set(token, args);
+      return token;
+    },
+    get(token) {
+      return sessions.get(token) ?? null;
+    },
+  };
+}
+
+function maybeCreateAppSession(
+  deps: AppDeps,
+  sessions: AppSessionStore,
+  applicationId: ApplicationId,
+  rawTargetThreadId: string | undefined,
+): AppSessionToken | null {
+  if (rawTargetThreadId === undefined || rawTargetThreadId.trim() === "") {
+    return null;
+  }
+  const thread = requirePublicThread(deps.db, rawTargetThreadId);
+  return sessions.create({
+    applicationId,
+    projectId: thread.projectId,
+    threadId: thread.id,
+  });
+}
+
+async function serveApplicationEntry(
+  deps: AppDeps,
+  sessions: AppSessionStore,
+  rawApplicationId: string,
+  requestUrl: string,
+  rawTargetThreadId: string | undefined,
+): Promise<Response> {
+  const applicationId = parseApplicationId(rawApplicationId);
+  const manifest = await readApplicationManifestForRequest(deps, {
+    dataDir: deps.config.dataDir,
+    applicationId,
+  });
+  const entry = await resolveApplicationEntry({
+    dataDir: deps.config.dataDir,
+    applicationId,
+    manifest,
+  });
+  if (entry.kind !== "html") {
+    throw new ApiError(404, "invalid_request", "App entry is not HTML");
+  }
+  const metadata = await statApplicationRelativeFile({
+    dataDir: deps.config.dataDir,
+    applicationId,
+    rootKind: "public",
+    path: entry.path,
+    dotfiles: "deny",
+  });
+  if (metadata.size > HTML_ENTRY_MAX_BYTES) {
+    throw new ApiError(
+      413,
+      "file_too_large",
+      "App HTML entry exceeds the 5 MB limit",
+      false,
+    );
+  }
+  const result = await readApplicationRelativeFile({
+    dataDir: deps.config.dataDir,
+    applicationId,
+    rootKind: "public",
+    path: entry.path,
+    dotfiles: "deny",
+  });
+  const token = maybeCreateAppSession(
+    deps,
+    sessions,
+    applicationId,
+    rawTargetThreadId,
+  );
+  return createInjectedAppHtmlResponse(deps, {
+    applicationId,
+    requestUrl,
+    targetThreadId: rawTargetThreadId ?? null,
+    appSessionToken: token,
+    html: result.toString("utf8"),
+    capabilities: manifest.capabilities,
+  });
+}
+
+function isPrivateApplicationStaticPath(
+  staticPath: ApplicationStaticPath,
+): boolean {
+  const [topLevelSegment] = staticPath.relativePath.split("/");
+  return (
+    topLevelSegment === MANIFEST_FILE_NAME ||
+    topLevelSegment === DATA_DIRECTORY_NAME
+  );
+}
+
+async function readApplicationStaticFile(
+  args: ReadApplicationStaticFileArgs,
+): Promise<ApplicationStaticFile> {
+  if (isPrivateApplicationStaticPath(args.staticPath)) {
+    throw new ApiError(404, "ENOENT", "App file not found");
+  }
+
+  return {
+    path: args.staticPath.relativePath,
+    bytes: await readApplicationRelativeFile({
+      dataDir: args.dataDir,
+      applicationId: args.applicationId,
+      rootKind: "public",
+      path: args.staticPath.relativePath,
+      dotfiles: "deny",
+    }),
+  };
+}
+
+async function serveApplicationStaticFile(
+  args: ServeApplicationStaticFileArgs,
+): Promise<Response> {
+  const applicationId = parseApplicationId(args.rawApplicationId);
+  const staticPath = parseApplicationStaticPath(args.rawPath);
+  await readApplicationManifestForRequest(args.deps, {
+    dataDir: args.deps.config.dataDir,
+    applicationId,
+  });
+  const result = await readApplicationStaticFile({
+    dataDir: args.deps.config.dataDir,
+    applicationId,
+    staticPath,
+  });
+  const contentType =
+    mimeTypes.lookup(result.path) || "application/octet-stream";
+  return new Response(new Uint8Array(result.bytes), {
+    status: 200,
+    headers: {
+      "cache-control": NO_STORE_CACHE_CONTROL,
+      "content-type": contentType,
+      "x-content-type-options": CONTENT_TYPE_OPTIONS,
+    },
+  });
+}
+
+async function serveApplicationIcon(
+  deps: AppDeps,
+  rawApplicationId: string,
+): Promise<Response> {
+  const applicationId = parseApplicationId(rawApplicationId);
+  const manifest = await readApplicationManifestForRequest(deps, {
+    dataDir: deps.config.dataDir,
+    applicationId,
+  });
+  if (manifest.icon !== undefined) {
+    throw new ApiError(404, "ENOENT", "App uses a built-in icon");
+  }
+  const logo = await tryResolveLogo({
+    dataDir: deps.config.dataDir,
+    applicationId,
+  });
+  if (!logo) {
+    throw new ApiError(404, "ENOENT", "App logo not found");
+  }
+  const logoPath = `logo.${logo.extension}`;
+  const metadata = await statApplicationRelativeFile({
+    dataDir: deps.config.dataDir,
+    applicationId,
+    rootKind: "app",
+    path: logoPath,
+    dotfiles: "deny",
+  });
+  if (metadata.size > LOGO_MAX_BYTES) {
+    throw new ApiError(
+      413,
+      "file_too_large",
+      "App logo exceeds the 1 MB limit",
+      false,
+    );
+  }
+  const result = await readApplicationRelativeFile({
+    dataDir: deps.config.dataDir,
+    applicationId,
+    rootKind: "app",
+    path: logoPath,
+    dotfiles: "deny",
+  });
+  const contentType = mimeTypes.lookup(logoPath) || "application/octet-stream";
+  return new Response(new Uint8Array(result), {
+    status: 200,
+    headers: {
+      "cache-control": NO_STORE_CACHE_CONTROL,
+      "content-type": contentType,
+      "x-content-type-options": CONTENT_TYPE_OPTIONS,
+    },
+  });
+}
+
+async function readApplicationDataEntry(
+  args: ReadApplicationDataEntryArgs,
+): Promise<AppDataEntry> {
+  const filePath = path.join(
+    resolveApplicationDataPath(args.dataDir, args.applicationId),
+    ...args.dataPath.split("/"),
+  );
+  let bytes: Buffer;
+  let metadata: Stats;
+  try {
+    [bytes, metadata] = await Promise.all([readFile(filePath), stat(filePath)]);
+  } catch (error) {
+    if (error instanceof Error && isFsErrorWithCode(error, "ENOENT")) {
+      throw new ApiError(404, "ENOENT", `App data not found: ${args.dataPath}`);
+    }
+    throw error;
+  }
+  let value: JsonValue;
+  try {
+    value = jsonValueSchema.parse(JSON.parse(bytes.toString("utf8")));
+  } catch {
+    throw new ApiError(
+      422,
+      "invalid_json",
+      `App data path ${args.dataPath} does not contain valid JSON`,
+    );
+  }
+  return {
+    path: args.dataPath,
+    value,
+    version: sha256(bytes),
+    sizeBytes: metadata.size,
+    modifiedAtMs: metadata.mtimeMs,
+  };
+}
+
+async function listAppDataFilePaths(
+  appDataRoot: string,
+  currentDirectory: string,
+): Promise<AppDataPath[]> {
+  const entries = await readdir(currentDirectory, { withFileTypes: true });
+  const paths: AppDataPath[] = [];
+  for (const entry of entries) {
+    if (entry.name.startsWith(".")) {
+      continue;
+    }
+    const entryPath = path.join(currentDirectory, entry.name);
+    if (entry.isDirectory()) {
+      paths.push(...(await listAppDataFilePaths(appDataRoot, entryPath)));
+      continue;
+    }
+    if (!entry.isFile()) {
+      continue;
+    }
+    const relativePath = path
+      .relative(appDataRoot, entryPath)
+      .split(path.sep)
+      .join("/");
+    const parsed = appDataPathSchema.safeParse(relativePath);
+    if (parsed.success) {
+      paths.push(parsed.data);
+    }
+  }
+  return paths.sort((left, right) => left.localeCompare(right));
+}
+
+function shouldListAppDataPrefixAfterReadError(error: Error): boolean {
+  return error instanceof ApiError && error.body.code === "ENOENT";
+}
+
+async function listApplicationDataEntries(
+  args: ListApplicationDataEntriesArgs,
+): Promise<AppDataEntry[]> {
+  if (args.dataPath !== "") {
+    try {
+      return [
+        await readApplicationDataEntry({
+          applicationId: args.applicationId,
+          dataPath: args.dataPath,
+          dataDir: args.dataDir,
+        }),
+      ];
+    } catch (error) {
+      if (
+        !(error instanceof Error) ||
+        !shouldListAppDataPrefixAfterReadError(error)
+      ) {
+        throw error;
+      }
+    }
+  }
+
+  const appDataRoot = resolveApplicationDataPath(
+    args.dataDir,
+    args.applicationId,
+  );
+  const listRoot = args.dataPath
+    ? path.join(appDataRoot, args.dataPath)
+    : appDataRoot;
+  let dataPaths: AppDataPath[];
+  try {
+    dataPaths = await listAppDataFilePaths(appDataRoot, listRoot);
+  } catch (error) {
+    if (error instanceof Error && isFsErrorWithCode(error, "ENOENT")) {
+      return [];
+    }
+    throw error;
+  }
+
+  return Promise.all(
+    dataPaths.map((dataPath) =>
+      readApplicationDataEntry({
+        applicationId: args.applicationId,
+        dataDir: args.dataDir,
+        dataPath,
+      }),
+    ),
+  );
+}
+
+async function writeApplicationDataEntry(
+  args: WriteApplicationDataEntryArgs,
+): Promise<AppDataEntry> {
+  const content = canonicalizeJson(args.value);
+  const appDataRoot = resolveApplicationDataPath(
+    args.dataDir,
+    args.applicationId,
+  );
+  const filePath = path.join(appDataRoot, ...args.dataPath.split("/"));
+  const relativePath = path.relative(appDataRoot, filePath);
+  if (relativePath.startsWith("..") || path.isAbsolute(relativePath)) {
+    throw new ApiError(400, "invalid_request", "Invalid app data path");
+  }
+  await mkdir(path.dirname(filePath), { recursive: true });
+  await writeFile(filePath, content, "utf8");
+  return readApplicationDataEntry(args);
+}
+
+async function deleteApplicationDataEntry(
+  args: DeleteApplicationDataEntryArgs,
+): Promise<void> {
+  const appDataRoot = resolveApplicationDataPath(
+    args.dataDir,
+    args.applicationId,
+  );
+  const filePath = path.join(appDataRoot, ...args.dataPath.split("/"));
+  const relativePath = path.relative(appDataRoot, filePath);
+  if (relativePath.startsWith("..") || path.isAbsolute(relativePath)) {
+    throw new ApiError(400, "invalid_request", "Invalid app data path");
+  }
+  try {
+    await rm(filePath);
+  } catch (error) {
+    if (error instanceof Error && isFsErrorWithCode(error, "ENOENT")) {
+      throw new ApiError(404, "ENOENT", `App data not found: ${args.dataPath}`);
+    }
+    throw error;
+  }
+}
+
+function createTempNonce(): string {
+  return randomUUID().replaceAll("-", "").slice(0, 16);
+}
+
+function deriveCreateApplicationId(payload: CreateAppRequest): ApplicationId {
+  if (payload.applicationId !== undefined) {
+    return payload.applicationId;
+  }
+  if (payload.name !== undefined) {
+    try {
+      return deriveApplicationIdFromName(payload.name);
+    } catch {
+      throw new ApiError(
+        400,
+        "invalid_request",
+        "App name cannot be converted to a valid applicationId",
+      );
+    }
+  }
+  throw new ApiError(400, "invalid_request", "Provide applicationId or name");
+}
+
+function resolveCreateApplicationName(
+  payload: CreateAppRequest,
+  applicationId: ApplicationId,
+): string {
+  return payload.name === undefined || payload.name.trim().length === 0
+    ? applicationId
+    : payload.name;
+}
+
+async function createApplicationTempRoot(
+  args: CreateApplicationTempRootArgs,
+): Promise<string> {
+  const tempRootPath = path.join(
+    args.appsRootPath,
+    `.tmp-${args.applicationId}-${createTempNonce()}`,
+  );
+  await mkdir(tempRootPath, { recursive: false });
+  return tempRootPath;
+}
+
+async function writeInitialApplicationFiles(
+  tempRootPath: string,
+  applicationId: ApplicationId,
+  name: string,
+): Promise<void> {
+  const manifest: AppManifest = {
+    manifestVersion: 1,
+    id: applicationId,
+    name,
+    entry: "index.html",
+    capabilities: ["data", "message"],
+  };
+  await mkdir(path.join(tempRootPath, PUBLIC_DIRECTORY_NAME), {
+    recursive: true,
+  });
+  await mkdir(path.join(tempRootPath, DATA_DIRECTORY_NAME), {
+    recursive: true,
+  });
+  await writeFile(
+    path.join(tempRootPath, MANIFEST_FILE_NAME),
+    canonicalizeJson(manifest),
+    "utf8",
+  );
+  await writeFile(
+    path.join(tempRootPath, PUBLIC_DIRECTORY_NAME, "index.html"),
+    buildBlankAppIndexHtml({ name }),
+    "utf8",
+  );
+  await writeFile(
+    path.join(tempRootPath, DATA_DIRECTORY_NAME, "state.json"),
+    canonicalizeJson({}),
+    "utf8",
+  );
+  appManifestSchema.parse(
+    JSON.parse(
+      await readFile(path.join(tempRootPath, MANIFEST_FILE_NAME), "utf8"),
+    ),
+  );
+}
+
+async function publishApplicationTempRoot(
+  args: PublishApplicationTempRootArgs,
+): Promise<"published" | "collision"> {
+  try {
+    await stat(args.applicationPath);
+    return "collision";
+  } catch (error) {
+    if (!(error instanceof Error) || !isFsErrorWithCode(error, "ENOENT")) {
+      throw error;
+    }
+  }
+  try {
+    await rename(args.tempRootPath, args.applicationPath);
+    return "published";
+  } catch (error) {
+    if (
+      error instanceof Error &&
+      (isFsErrorWithCode(error, "EEXIST") ||
+        isFsErrorWithCode(error, "ENOTEMPTY"))
+    ) {
+      return "collision";
+    }
+    throw error;
+  }
+}
+
+export async function createGlobalApplication(
+  args: CreateGlobalApplicationArgs,
+): Promise<ApplicationId> {
+  const appsRootPath = resolveAppsRootPath(args.dataDir);
+  await mkdir(appsRootPath, { recursive: true });
+
+  const applicationPath = resolveApplicationPath(
+    args.dataDir,
+    args.applicationId,
+  );
+  let tempRootPath: string | null = null;
+  try {
+    tempRootPath = await createApplicationTempRoot({
+      appsRootPath,
+      applicationId: args.applicationId,
+    });
+    await writeInitialApplicationFiles(
+      tempRootPath,
+      args.applicationId,
+      args.name,
+    );
+    const result = await publishApplicationTempRoot({
+      applicationPath,
+      tempRootPath,
+    });
+    if (result === "collision") {
+      await rm(tempRootPath, { recursive: true, force: true });
+      tempRootPath = null;
+      throw new ApiError(
+        409,
+        "app_exists",
+        `an app with id "${args.applicationId}" already exists`,
+      );
+    }
+    return args.applicationId;
+  } catch (error) {
+    if (tempRootPath !== null) {
+      await rm(tempRootPath, { recursive: true, force: true }).catch(
+        () => undefined,
+      );
+    }
+    if (error instanceof ApiError) {
+      throw error;
+    }
+    throw new ApiError(
+      500,
+      "scaffold_failed",
+      error instanceof Error ? error.message : "Failed to scaffold app",
+    );
+  }
+}
+
+async function deleteGlobalApplication(
+  dataDir: string,
+  applicationId: ApplicationId,
+): Promise<"deleted" | "partial"> {
+  const applicationPath = resolveApplicationPath(dataDir, applicationId);
+  try {
+    await stat(applicationPath);
+  } catch (error) {
+    if (error instanceof Error && isFsErrorWithCode(error, "ENOENT")) {
+      throw new ApiError(404, "app_missing", "App not found");
+    }
+    throw error;
+  }
+  const tombstonePath = path.join(
+    resolveAppsRootPath(dataDir),
+    `.delete-${applicationId}-${createTempNonce()}`,
+  );
+  try {
+    await rename(applicationPath, tombstonePath);
+  } catch (error) {
+    throw new ApiError(
+      500,
+      "delete_failed",
+      error instanceof Error ? error.message : "Failed to delete app",
+    );
+  }
+  try {
+    await rm(tombstonePath, { recursive: true, force: true });
+    return "deleted";
+  } catch {
+    return "partial";
+  }
+}
+
+function formatAppMessagePayload(payload: JsonValue): string {
+  return typeof payload === "string"
+    ? payload
+    : JSON.stringify(payload, null, 2);
+}
+
+function resolveAppMessageTarget(
+  deps: AppDeps,
+  args: ResolveAppMessageTargetArgs,
+): AppSession {
+  const token =
+    args.payload.appSessionToken === undefined
+      ? null
+      : args.sessions.get(args.payload.appSessionToken);
+  if (args.payload.appSessionToken !== undefined && token === null) {
+    throw new ApiError(403, "forbidden", "Invalid app session token");
+  }
+  if (token !== null && token.applicationId !== args.applicationId) {
+    throw new ApiError(
+      403,
+      "forbidden",
+      "App session token does not match app",
+    );
+  }
+  if (args.payload.targetThreadId !== undefined) {
+    const thread = requirePublicThread(deps.db, args.payload.targetThreadId);
+    if (token !== null && token.threadId !== thread.id) {
+      throw new ApiError(403, "forbidden", "App message target mismatch");
+    }
+    return {
+      applicationId: args.applicationId,
+      threadId: thread.id,
+      projectId: thread.projectId,
+    };
+  }
+  if (token !== null) {
+    return token;
+  }
+  throw new ApiError(
+    400,
+    "message_target_required",
+    "App message requires an app session token or targetThreadId",
+  );
+}
+
+export function registerGlobalAppRoutes(app: Hono, deps: AppDeps): void {
+  const { get, post, put, del } = typedRoutes<PublicApiSchema>(app, {
+    onValidationError: (msg) => new ApiError(400, "invalid_request", msg),
+  });
+  const appSessions = createAppSessionStore();
+
+  get("/apps", async (context) =>
+    context.json(await refreshGlobalAppListSignature(deps)),
+  );
+
+  post("/apps", createAppRequestSchema, async (context, payload) => {
+    const applicationId = deriveCreateApplicationId(payload);
+    const createdApplicationId = await createGlobalApplication({
+      applicationId,
+      dataDir: deps.config.dataDir,
+      name: resolveCreateApplicationName(payload, applicationId),
+    });
+    const detail = await buildApplicationDetail(deps, {
+      dataDir: deps.config.dataDir,
+      applicationId: createdApplicationId,
+    });
+    await notifyGlobalAppsChanged(deps);
+    return context.json(detail, 201);
+  });
+
+  get("/apps/:applicationId", async (context) => {
+    const applicationId = parseApplicationId(
+      context.req.param("applicationId"),
+    );
+    return context.json(
+      await buildApplicationDetail(deps, {
+        dataDir: deps.config.dataDir,
+        applicationId,
+      }),
+    );
+  });
+
+  del("/apps/:applicationId", async (context) => {
+    const applicationId = parseApplicationId(
+      context.req.param("applicationId"),
+    );
+    const result = await deleteGlobalApplication(
+      deps.config.dataDir,
+      applicationId,
+    );
+    await notifyGlobalAppsChanged(deps);
+    if (result === "partial") {
+      throw new ApiError(
+        500,
+        "delete_partial",
+        "App was removed from normal lists, but tombstone cleanup failed",
+      );
+    }
+    return context.json({ ok: true });
+  });
+
+  get(
+    "/apps/:applicationId/data",
+    appDataListQuerySchema,
+    async (context, query) => {
+      const applicationId = parseApplicationId(
+        context.req.param("applicationId"),
+      );
+      const manifest = await readApplicationManifestForRequest(deps, {
+        dataDir: deps.config.dataDir,
+        applicationId,
+      });
+      assertAppCapability(manifest, "data");
+      const dataPath = parseOptionalAppDataPrefix(query.prefix);
+      return context.json({
+        entries: await listApplicationDataEntries({
+          dataDir: deps.config.dataDir,
+          applicationId,
+          dataPath,
+        }),
+      });
+    },
+  );
+
+  post(
+    "/apps/:applicationId/message",
+    appMessageRequestSchema,
+    async (context, payload) => {
+      const applicationId = parseApplicationId(
+        context.req.param("applicationId"),
+      );
+      const manifest = await readApplicationManifestForRequest(deps, {
+        dataDir: deps.config.dataDir,
+        applicationId,
+      });
+      assertAppCapability(manifest, "message");
+      const target = resolveAppMessageTarget(deps, {
+        applicationId,
+        payload,
+        sessions: appSessions,
+      });
+      const thread = requirePublicThread(deps.db, target.threadId);
+      const environment = await requireThreadCommandEnvironment(deps, {
+        thread,
+      });
+      await sendThreadMessage(deps, {
+        environment,
+        thread,
+        trigger: "user",
+        payload: {
+          input: [
+            {
+              type: "text",
+              text: formatAppMessagePayload(payload.payload),
+            },
+          ],
+          mode: "auto",
+        },
+      });
+      return context.json({ ok: true }, 202);
+    },
+  );
+
+  app.get("/apps/:applicationId/", async (context) =>
+    serveApplicationEntry(
+      deps,
+      appSessions,
+      context.req.param("applicationId"),
+      context.req.url,
+      context.req.query("targetThreadId"),
+    ),
+  );
+
+  app.get("/apps/:applicationId/icon", async (context) =>
+    serveApplicationIcon(deps, context.req.param("applicationId")),
+  );
+
+  get("/apps/:applicationId/data/*", async (context) => {
+    const applicationId = parseApplicationId(
+      context.req.param("applicationId"),
+    );
+    const manifest = await readApplicationManifestForRequest(deps, {
+      dataDir: deps.config.dataDir,
+      applicationId,
+    });
+    assertAppCapability(manifest, "data");
+    const dataPath = parseAppDataRoutePath(
+      extractRoutePath({
+        requestUrl: context.req.url,
+        routeSegment: applicationDataRouteSegment({ applicationId }),
+      }),
+    );
+    const entry = await readApplicationDataEntry({
+      dataDir: deps.config.dataDir,
+      applicationId,
+      dataPath,
+    });
+    const response = context.json(entry);
+    response.headers.set("cache-control", NO_STORE_CACHE_CONTROL);
+    response.headers.set("etag", `"${entry.version}"`);
+    return response;
+  });
+
+  put(
+    "/apps/:applicationId/data/*",
+    appDataWriteRequestSchema,
+    async (context, payload) => {
+      const applicationId = parseApplicationId(
+        context.req.param("applicationId"),
+      );
+      const manifest = await readApplicationManifestForRequest(deps, {
+        dataDir: deps.config.dataDir,
+        applicationId,
+      });
+      assertAppCapability(manifest, "data");
+      const dataPath = parseAppDataRoutePath(
+        extractRoutePath({
+          requestUrl: context.req.url,
+          routeSegment: applicationDataRouteSegment({ applicationId }),
+        }),
+      );
+      const entry = await writeApplicationDataEntry({
+        dataDir: deps.config.dataDir,
+        applicationId,
+        dataPath,
+        value: payload.value,
+      });
+      const response = context.json(entry);
+      response.headers.set("cache-control", NO_STORE_CACHE_CONTROL);
+      response.headers.set("etag", `"${entry.version}"`);
+      return response;
+    },
+  );
+
+  del("/apps/:applicationId/data/*", async (context) => {
+    const applicationId = parseApplicationId(
+      context.req.param("applicationId"),
+    );
+    const manifest = await readApplicationManifestForRequest(deps, {
+      dataDir: deps.config.dataDir,
+      applicationId,
+    });
+    assertAppCapability(manifest, "data");
+    const dataPath = parseAppDataRoutePath(
+      extractRoutePath({
+        requestUrl: context.req.url,
+        routeSegment: applicationDataRouteSegment({ applicationId }),
+      }),
+    );
+    await deleteApplicationDataEntry({
+      dataDir: deps.config.dataDir,
+      applicationId,
+      dataPath,
+    });
+    const response = context.json({ ok: true });
+    response.headers.set("cache-control", NO_STORE_CACHE_CONTROL);
+    return response;
+  });
+
+  app.get("/apps/:applicationId/*", async (context) => {
+    const applicationId = context.req.param("applicationId");
+    return serveApplicationStaticFile({
+      deps,
+      rawApplicationId: applicationId,
+      rawPath: extractRoutePath({
+        requestUrl: context.req.url,
+        routeSegment: applicationRouteSegment({ applicationId }),
+      }),
+    });
+  });
+}
diff --git a/apps/server/src/routes/threads/apps.ts b/apps/server/src/routes/threads/apps.ts
deleted file mode 100644
index a884b8ee1..000000000
--- a/apps/server/src/routes/threads/apps.ts
+++ /dev/null
@@ -1,1320 +0,0 @@
-import { Buffer } from "node:buffer";
-import { createHash } from "node:crypto";
-import path from "node:path";
-import mimeTypes from "mime-types";
-import type { Hono } from "hono";
-import type { ZodIssue } from "zod";
-import {
-  FILE_LIST_LIMIT_MAX,
-  type HostDaemonCommand,
-  type HostDaemonCommandResult,
-  type HostDaemonDurableCommandType,
-  type HostDaemonOnlineRpcResult,
-  type HostDaemonRetryableOnlineRpcCommand,
-  type HostDaemonRetryableOnlineRpcCommandType,
-  type HostDaemonRetryableOnlineRpcResult,
-} from "@bb/host-daemon-contract";
-import {
-  appDataPathSchema,
-  appIdSchema,
-  jsonValueSchema,
-} from "@bb/domain";
-import type { AppDataPath, AppId, JsonValue } from "@bb/domain";
-import {
-  appDataListQuerySchema,
-  appDataWriteRequestSchema,
-  appManifestSchema,
-  appMessageRequestSchema,
-  createThreadAppRequestSchema,
-  typedRoutes,
-  type AppCapability,
-  type AppDataEntry,
-  type AppDetail,
-  type AppEntry,
-  type AppIcon,
-  type AppManifest,
-  type AppSummary,
-  type AppTemplate,
-  type CreateThreadAppRequest,
-  type PublicApiSchema,
-} from "@bb/server-contract";
-import type { AppDeps, LoggedWorkSessionDeps } from "../../types.js";
-import { COMMAND_TIMEOUT_MS } from "../../constants.js";
-import { ApiError } from "../../errors.js";
-import { queueCommandAndWait } from "../../services/hosts/command-wait.js";
-import { callHostRetryableOnlineRpc } from "../../services/hosts/online-rpc.js";
-import {
-  createDaemonFileContentResponse,
-  decodeDaemonFileContent,
-  type DaemonFileReadResult,
-  remapDaemonFileRouteError,
-} from "../../services/hosts/daemon-file-response.js";
-import { requirePublicThread } from "../../services/lib/entity-lookup.js";
-import { requireThreadCommandEnvironment } from "../../services/threads/thread-command-environment.js";
-import { sendThreadMessage } from "../../services/threads/thread-send.js";
-import { injectAppClientScript } from "../../services/threads/app-client-script.js";
-import { buildBlankAppIndexHtml } from "../../services/threads/blank-app-scaffold.js";
-import {
-  extractRoutePath,
-  parseSafeRelativeRoutePath,
-  type SafeRelativeRoutePath,
-} from "../relative-route-path.js";
-import { requireThreadStorageTarget } from "./data.js";
-
-interface ThreadAppsTarget {
-  hostId: string;
-  storagePath: string;
-}
-
-interface AppManifestReadArgs {
-  appId: AppId;
-  target: ThreadAppsTarget;
-}
-
-interface InvalidAppManifestErrorArgs extends AppManifestReadArgs {
-  issues: AppManifestValidationIssues;
-}
-
-interface LogInvalidAppManifestArgs {
-  error: InvalidAppManifestError;
-  message: string;
-}
-
-interface AppSummaryArgs extends AppManifestReadArgs {
-  manifest: AppManifest;
-  requestThreadId: string;
-}
-
-interface AppDetailArgs extends AppManifestReadArgs {
-  requestThreadId: string;
-}
-
-interface AppRootArgs {
-  appId: AppId;
-  target: ThreadAppsTarget;
-}
-
-interface AppDataRootArgs extends AppRootArgs {}
-
-interface ReadAppRelativeFileArgs {
-  appId: AppId;
-  dotfiles: "allow" | "deny";
-  path: string;
-  rootKind: "app" | "assets" | "data";
-  target: ThreadAppsTarget;
-}
-
-interface ReadAppFileMetadataArgs {
-  appId: AppId;
-  path: string;
-  rootKind: "app" | "assets" | "data";
-  target: ThreadAppsTarget;
-}
-
-interface AppRootForKindArgs {
-  appId: AppId;
-  rootKind: "app" | "assets" | "data";
-  target: ThreadAppsTarget;
-}
-
-interface ReadAppDataEntryArgs {
-  appId: AppId;
-  dataPath: AppDataPath;
-  target: ThreadAppsTarget;
-}
-
-interface ListAppDataEntriesArgs {
-  appId: AppId;
-  dataPath: AppDataPath | "";
-  target: ThreadAppsTarget;
-}
-
-interface WriteAppDataEntryArgs extends ReadAppDataEntryArgs {
-  value: JsonValue;
-}
-
-interface DeleteAppDataEntryArgs extends ReadAppDataEntryArgs {}
-
-interface CreateInjectedAppHtmlResponseArgs {
-  appId: AppId;
-  capabilities: AppCapability[];
-  html: string;
-  requestUrl: string;
-  threadId: string;
-}
-
-interface AppAssetRouteSegmentArgs {
-  appId: string;
-  threadId: string;
-}
-
-type AppAssetPath = SafeRelativeRoutePath;
-
-interface LogoResolution {
-  extension: string;
-}
-
-interface TemplateFile {
-  content: string;
-  path: string;
-}
-
-interface ScaffoldAppArgs {
-  request: CreateThreadAppRequest;
-  target: ThreadAppsTarget;
-  threadId: string;
-}
-
-type AppManifestValidationIssues = readonly ZodIssue[];
-type AppManifestValidationLoggerDeps = Pick<AppDeps, "logger">;
-
-interface ReadHostCommandArgs<
-  TType extends HostDaemonRetryableOnlineRpcCommandType,
-> {
-  command: Extract<HostDaemonRetryableOnlineRpcCommand, { type: TType }>;
-  hostId: string;
-}
-
-interface QueueHostCommandArgs<TType extends HostDaemonDurableCommandType> {
-  command: Extract<HostDaemonCommand, { type: TType }>;
-  hostId: string;
-}
-
-const APPS_DIRECTORY_NAME = "apps";
-const ASSETS_DIRECTORY_NAME = "assets";
-const DATA_DIRECTORY_NAME = "data";
-const MANIFEST_FILE_NAME = "manifest.json";
-const HTML_CONTENT_TYPE = "text/html; charset=utf-8";
-const NO_STORE_CACHE_CONTROL = "no-store";
-const CONTENT_TYPE_OPTIONS = "nosniff";
-const HTML_ENTRY_MAX_BYTES = 5 * 1024 * 1024;
-const LOGO_MAX_BYTES = 1024 * 1024;
-const LOGO_EXTENSIONS = ["svg", "png", "jpg", "jpeg"] as const;
-const APP_ROUTE_DATA_SEGMENT = "/data/";
-const INVALID_APP_MANIFEST_MESSAGE =
-  "App manifest failed validation. Inspect manifest.json or rebuild the app.";
-
-class InvalidAppManifestError extends ApiError {
-  readonly appId: AppId;
-  readonly manifestPath: string;
-  readonly issues: AppManifestValidationIssues;
-
-  constructor(args: InvalidAppManifestErrorArgs) {
-    super(422, "invalid_manifest", INVALID_APP_MANIFEST_MESSAGE);
-    this.name = "InvalidAppManifestError";
-    this.appId = args.appId;
-    this.manifestPath = path.join(appRootPath(args), MANIFEST_FILE_NAME);
-    this.issues = args.issues;
-  }
-}
-
-function sha256(bytes: Buffer): string {
-  return createHash("sha256").update(bytes).digest("hex");
-}
-
-function canonicalizeJson(value: JsonValue): string {
-  return `${JSON.stringify(value, null, 2)}\n`;
-}
-
-function parseAppId(rawAppId: string): AppId {
-  const parsed = appIdSchema.safeParse(rawAppId);
-  if (!parsed.success) {
-    throw new ApiError(400, "invalid_request", "Invalid app id");
-  }
-  return parsed.data;
-}
-
-function parseAppDataPath(rawPath: string): AppDataPath {
-  const parsed = appDataPathSchema.safeParse(rawPath);
-  if (!parsed.success) {
-    throw new ApiError(400, "invalid_request", "Invalid app data path");
-  }
-  return parsed.data;
-}
-
-function parseAppDataRoutePath(rawPath: string): AppDataPath {
-  return parseAppDataPath(
-    parseSafeRelativeRoutePath({
-      rawPath,
-      dotfileSegmentPolicy: "allow",
-      invalidPathMessage: "Invalid app data path",
-    }).relativePath,
-  );
-}
-
-function appAssetRouteSegment(args: AppAssetRouteSegmentArgs): string {
-  return `/threads/${encodeURIComponent(args.threadId)}/apps/${encodeURIComponent(args.appId)}/`;
-}
-
-function parseOptionalAppDataPrefix(
-  rawPrefix: string | undefined,
-): AppDataPath | "" {
-  if (rawPrefix === undefined || rawPrefix === "") {
-    return "";
-  }
-  return parseAppDataPath(rawPrefix);
-}
-
-function appRootPath(args: AppRootArgs): string {
-  return path.join(args.target.storagePath, APPS_DIRECTORY_NAME, args.appId);
-}
-
-function appAssetsRootPath(args: AppRootArgs): string {
-  return path.join(appRootPath(args), ASSETS_DIRECTORY_NAME);
-}
-
-function appDataRootPath(args: AppDataRootArgs): string {
-  return path.join(appRootPath(args), DATA_DIRECTORY_NAME);
-}
-
-function appRootForKind(args: AppRootForKindArgs): string {
-  if (args.rootKind === "app") {
-    return appRootPath(args);
-  }
-  if (args.rootKind === "assets") {
-    return appAssetsRootPath(args);
-  }
-  return appDataRootPath(args);
-}
-
-function parseAppAssetPath(rawPath: string): AppAssetPath {
-  return parseSafeRelativeRoutePath({
-    rawPath,
-    directoryIndexPath: "index.html",
-    dotfileSegmentPolicy: "not-found",
-    invalidPathMessage: "Invalid app asset path",
-  });
-}
-
-function decodeDaemonTextFile(result: DaemonFileReadResult): string {
-  return Buffer.from(decodeDaemonFileContent(result)).toString("utf8");
-}
-
-function summarizeAppManifestValidationIssues(
-  issues: AppManifestValidationIssues,
-): string {
-  return issues
-    .map((issue) => {
-      const issuePath = issue.path.map(String).join(".");
-      return `${issuePath || "<root>"}: ${issue.message}`;
-    })
-    .join("; ");
-}
-
-function logInvalidAppManifest(
-  deps: AppManifestValidationLoggerDeps,
-  args: LogInvalidAppManifestArgs,
-): void {
-  deps.logger.warn(
-    {
-      appId: args.error.appId,
-      manifestPath: args.error.manifestPath,
-      issueSummary: summarizeAppManifestValidationIssues(args.error.issues),
-      issues: args.error.issues,
-    },
-    args.message,
-  );
-}
-
-function remapAppCommandError(error: unknown): never {
-  if (!(error instanceof ApiError)) {
-    throw error;
-  }
-  if (error.body.code === "ENOENT") {
-    throw new ApiError(
-      404,
-      error.body.code,
-      error.body.message,
-      error.body.retryable,
-    );
-  }
-  if (error.body.code === "invalid_path") {
-    throw new ApiError(
-      400,
-      error.body.code,
-      error.body.message,
-      error.body.retryable,
-    );
-  }
-  if (error.body.code === "invalid_json") {
-    throw new ApiError(
-      422,
-      error.body.code,
-      error.body.message,
-      error.body.retryable,
-    );
-  }
-  throw error;
-}
-
-async function readHostCommand<
-  TType extends HostDaemonRetryableOnlineRpcCommandType,
->(
-  deps: AppDeps,
-  args: ReadHostCommandArgs<TType>,
-): Promise<HostDaemonRetryableOnlineRpcResult<TType>> {
-  try {
-    return await callHostRetryableOnlineRpc(deps, {
-      hostId: args.hostId,
-      timeoutMs: COMMAND_TIMEOUT_MS,
-      command: args.command,
-    });
-  } catch (error) {
-    remapAppCommandError(error);
-  }
-}
-
-async function queueHostCommand<TType extends HostDaemonDurableCommandType>(
-  deps: AppDeps,
-  args: QueueHostCommandArgs<TType>,
-): Promise<HostDaemonCommandResult<TType>> {
-  try {
-    return await queueCommandAndWait(deps, {
-      hostId: args.hostId,
-      timeoutMs: COMMAND_TIMEOUT_MS,
-      command: args.command,
-    });
-  } catch (error) {
-    remapAppCommandError(error);
-  }
-}
-
-async function requireThreadAppsTarget(
-  deps: LoggedWorkSessionDeps,
-  threadId: string,
-): Promise<ThreadAppsTarget> {
-  const target = await requireThreadStorageTarget(deps, { threadId });
-  return {
-    hostId: target.hostId,
-    storagePath: target.storagePath,
-  };
-}
-
-async function readAppRelativeFile(
-  deps: AppDeps,
-  args: ReadAppRelativeFileArgs,
-): Promise<DaemonFileReadResult> {
-  return readHostCommand(deps, {
-    hostId: args.target.hostId,
-    command: {
-      type: "host.read_file_relative",
-      rootPath: appRootForKind(args),
-      path: args.path,
-      dotfiles: args.dotfiles,
-    },
-  });
-}
-
-async function readAppFileMetadata(
-  deps: AppDeps,
-  args: ReadAppFileMetadataArgs,
-): Promise<HostDaemonOnlineRpcResult<"host.file_metadata">> {
-  return readHostCommand(deps, {
-    hostId: args.target.hostId,
-    command: {
-      type: "host.file_metadata",
-      path: path.join(appRootForKind(args), args.path),
-      rootPath: appRootForKind(args),
-    },
-  });
-}
-
-async function readAppManifest(
-  deps: AppDeps,
-  args: AppManifestReadArgs,
-): Promise<AppManifest> {
-  const result = await readAppRelativeFile(deps, {
-    appId: args.appId,
-    target: args.target,
-    rootKind: "app",
-    path: MANIFEST_FILE_NAME,
-    dotfiles: "deny",
-  });
-  let parsedJson: unknown;
-  try {
-    parsedJson = JSON.parse(decodeDaemonTextFile(result));
-  } catch {
-    throw new ApiError(422, "invalid_json", "App manifest is not valid JSON");
-  }
-  const manifest = appManifestSchema.safeParse(parsedJson);
-  if (!manifest.success) {
-    throw new InvalidAppManifestError({
-      appId: args.appId,
-      target: args.target,
-      issues: manifest.error.issues,
-    });
-  }
-  if (manifest.data.id !== args.appId) {
-    throw new ApiError(
-      422,
-      "invalid_request",
-      "App manifest id must match its directory name",
-    );
-  }
-  return manifest.data;
-}
-
-async function readAppManifestForRequest(
-  deps: AppDeps,
-  args: AppManifestReadArgs,
-): Promise<AppManifest> {
-  try {
-    return await readAppManifest(deps, args);
-  } catch (error) {
-    if (error instanceof InvalidAppManifestError) {
-      logInvalidAppManifest(deps, {
-        error,
-        message: "Rejected invalid thread app manifest",
-      });
-    }
-    throw error;
-  }
-}
-
-function entryKindForPath(entryPath: string): AppEntry["kind"] {
-  const normalized = entryPath.toLowerCase();
-  if (normalized.endsWith(".html")) {
-    return "html";
-  }
-  if (normalized.endsWith(".md")) {
-    return "md";
-  }
-  throw new ApiError(
-    422,
-    "invalid_request",
-    "App entry must end in .html or .md",
-  );
-}
-
-async function resolveAppEntry(
-  deps: AppDeps,
-  args: AppManifestReadArgs & { manifest: AppManifest },
-): Promise<AppEntry> {
-  if (args.manifest.entry !== undefined) {
-    return {
-      path: args.manifest.entry,
-      kind: entryKindForPath(args.manifest.entry),
-    };
-  }
-
-  for (const candidate of ["index.html", "index.md"]) {
-    try {
-      await readAppFileMetadata(deps, {
-        appId: args.appId,
-        target: args.target,
-        path: candidate,
-        rootKind: "assets",
-      });
-      return {
-        path: candidate,
-        kind: entryKindForPath(candidate),
-      };
-    } catch (error) {
-      if (error instanceof ApiError && error.body.code === "ENOENT") {
-        continue;
-      }
-      throw error;
-    }
-  }
-
-  throw new ApiError(
-    404,
-    "ENOENT",
-    "App entry not found: index.html or index.md",
-  );
-}
-
-async function tryResolveLogo(
-  deps: AppDeps,
-  args: AppManifestReadArgs,
-): Promise<LogoResolution | null> {
-  let listResult: HostDaemonOnlineRpcResult<"host.list_paths">;
-  try {
-    listResult = await readHostCommand(deps, {
-      hostId: args.target.hostId,
-      command: {
-        type: "host.list_paths",
-        path: appRootPath(args),
-        limit: LOGO_EXTENSIONS.length,
-        includeFiles: true,
-        includeDirectories: false,
-      },
-    });
-  } catch (error) {
-    if (error instanceof ApiError && error.body.code === "ENOENT") {
-      return null;
-    }
-    throw error;
-  }
-
-  const topLevelFiles = new Set(
-    listResult.paths
-      .filter((entry) => entry.kind === "file" && !entry.path.includes("/"))
-      .map((entry) => entry.path),
-  );
-  for (const extension of LOGO_EXTENSIONS) {
-    if (topLevelFiles.has(`logo.${extension}`)) {
-      return { extension };
-    }
-  }
-  return null;
-}
-
-async function resolveAppIcon(
-  deps: AppDeps,
-  args: AppSummaryArgs,
-): Promise<AppIcon> {
-  if (args.manifest.icon !== undefined) {
-    return { kind: "builtin", name: args.manifest.icon };
-  }
-  const logo = await tryResolveLogo(deps, args);
-  if (logo) {
-    return {
-      kind: "logo",
-      url: `/api/v1/threads/${encodeURIComponent(
-        args.requestThreadId,
-      )}/apps/${encodeURIComponent(args.appId)}/icon`,
-    };
-  }
-  return { kind: "builtin", name: "GridView" };
-}
-
-async function buildAppSummary(
-  deps: AppDeps,
-  args: AppSummaryArgs,
-): Promise<AppSummary> {
-  const [entry, icon] = await Promise.all([
-    resolveAppEntry(deps, args),
-    resolveAppIcon(deps, args),
-  ]);
-  return {
-    id: args.manifest.id,
-    name: args.manifest.name,
-    entry,
-    capabilities: args.manifest.capabilities,
-    icon,
-  };
-}
-
-async function buildAppDetail(
-  deps: AppDeps,
-  args: AppDetailArgs,
-): Promise<AppDetail> {
-  let manifest: AppManifest;
-  try {
-    manifest = await readAppManifestForRequest(deps, args);
-  } catch (error) {
-    if (
-      error instanceof ApiError &&
-      error.status === 404 &&
-      error.body.code === "ENOENT" &&
-      error.body.message.includes(MANIFEST_FILE_NAME)
-    ) {
-      throw new ApiError(
-        404,
-        "app_not_provisioned",
-        `App "${args.appId}" is not provisioned yet; missing ${MANIFEST_FILE_NAME}. Restart bb from a current build if this manager was created before app seeding was available.`,
-      );
-    }
-    throw error;
-  }
-  return buildAppSummary(deps, {
-    ...args,
-    manifest,
-  });
-}
-
-function assertAppCapability(
-  manifest: AppManifest,
-  capability: AppCapability,
-): void {
-  if (!manifest.capabilities.includes(capability)) {
-    throw new ApiError(
-      403,
-      "invalid_request",
-      `App does not have the ${capability} capability`,
-    );
-  }
-}
-
-async function listThreadApps(
-  deps: AppDeps,
-  threadId: string,
-): Promise<AppSummary[]> {
-  const target = await requireThreadAppsTarget(deps, threadId);
-  let listResult: HostDaemonOnlineRpcResult<"host.list_paths">;
-  try {
-    listResult = await readHostCommand(deps, {
-      hostId: target.hostId,
-      command: {
-        type: "host.list_paths",
-        path: path.join(target.storagePath, APPS_DIRECTORY_NAME),
-        limit: FILE_LIST_LIMIT_MAX,
-        includeFiles: false,
-        includeDirectories: true,
-      },
-    });
-  } catch (error) {
-    if (error instanceof ApiError && error.body.code === "ENOENT") {
-      return [];
-    }
-    throw error;
-  }
-
-  const appIds = listResult.paths
-    .filter((entry) => entry.kind === "directory" && !entry.path.includes("/"))
-    .map((entry) => appIdSchema.safeParse(entry.path))
-    .filter((entry) => entry.success)
-    .map((entry) => entry.data)
-    .sort((left, right) => left.localeCompare(right));
-
-  const summaries: AppSummary[] = [];
-  for (const appId of appIds) {
-    try {
-      const manifest = await readAppManifest(deps, { appId, target });
-      summaries.push(
-        await buildAppSummary(deps, {
-          appId,
-          target,
-          manifest,
-          requestThreadId: threadId,
-        }),
-      );
-    } catch (error) {
-      if (error instanceof InvalidAppManifestError) {
-        logInvalidAppManifest(deps, {
-          error,
-          message: "Skipping invalid thread app manifest",
-        });
-        continue;
-      }
-      throw error;
-    }
-  }
-  return summaries;
-}
-
-async function validateAppManifestForServe(
-  deps: AppDeps,
-  args: AppManifestReadArgs,
-): Promise<void> {
-  await readAppManifestForRequest(deps, args);
-}
-
-function createHtmlResponse(html: string): Response {
-  return new Response(html, {
-    status: 200,
-    headers: {
-      "cache-control": NO_STORE_CACHE_CONTROL,
-      "content-type": HTML_CONTENT_TYPE,
-      "x-content-type-options": CONTENT_TYPE_OPTIONS,
-    },
-  });
-}
-
-function buildAppWebSocketUrl(
-  deps: LoggedWorkSessionDeps,
-  requestUrl: string,
-): string {
-  if (deps.config.isDevelopment) {
-    return `ws://localhost:${deps.config.serverPort}/ws`;
-  }
-  const url = new URL(requestUrl);
-  url.protocol = url.protocol === "https:" ? "wss:" : "ws:";
-  url.pathname = "/ws";
-  url.search = "";
-  url.hash = "";
-  return url.toString();
-}
-
-function createInjectedAppHtmlResponse(
-  deps: LoggedWorkSessionDeps,
-  args: CreateInjectedAppHtmlResponseArgs,
-): Response {
-  // Phase 1 app capabilities are advisory because app HTML is still served from
-  // bb's same origin. We gate the injected bridge and app-owned routes by the
-  // manifest-declared list, but real isolation waits for the third-party
-  // extensions phase: sandboxed/opaque-origin iframes with a postMessage bridge.
-  return createHtmlResponse(
-    injectAppClientScript(args.html, {
-      appId: args.appId,
-      capabilities: args.capabilities,
-      threadId: args.threadId,
-      dataUrl: `/api/v1/threads/${encodeURIComponent(
-        args.threadId,
-      )}/apps/${encodeURIComponent(args.appId)}/data`,
-      messageUrl: `/api/v1/threads/${encodeURIComponent(
-        args.threadId,
-      )}/apps/${encodeURIComponent(args.appId)}/message`,
-      wsUrl: buildAppWebSocketUrl(deps, args.requestUrl),
-    }),
-  );
-}
-
-async function serveAppEntry(
-  deps: AppDeps,
-  threadId: string,
-  rawAppId: string,
-  requestUrl: string,
-): Promise<Response> {
-  const appId = parseAppId(rawAppId);
-  const target = await requireThreadAppsTarget(deps, threadId);
-  const manifest = await readAppManifestForRequest(deps, { appId, target });
-  const entry = await resolveAppEntry(deps, { appId, target, manifest });
-  if (entry.kind !== "html") {
-    throw new ApiError(404, "invalid_request", "App entry is not HTML");
-  }
-  const metadata = await readAppFileMetadata(deps, {
-    appId,
-    target,
-    rootKind: "assets",
-    path: entry.path,
-  });
-  if (metadata.sizeBytes > HTML_ENTRY_MAX_BYTES) {
-    throw new ApiError(
-      413,
-      "file_too_large",
-      "App HTML entry exceeds the 5 MB limit",
-      false,
-    );
-  }
-  const result = await readAppRelativeFile(deps, {
-    appId,
-    target,
-    rootKind: "assets",
-    path: entry.path,
-    dotfiles: "deny",
-  });
-  return createInjectedAppHtmlResponse(deps, {
-    appId,
-    requestUrl,
-    threadId,
-    html: decodeDaemonTextFile(result),
-    capabilities: manifest.capabilities,
-  });
-}
-
-async function serveAppAsset(
-  deps: AppDeps,
-  threadId: string,
-  rawAppId: string,
-  rawPath: string,
-): Promise<Response> {
-  const appId = parseAppId(rawAppId);
-  const assetPath = parseAppAssetPath(rawPath);
-  const target = await requireThreadAppsTarget(deps, threadId);
-  await validateAppManifestForServe(deps, { appId, target });
-  try {
-    const result = await readAppRelativeFile(deps, {
-      appId,
-      target,
-      rootKind: "assets",
-      path: assetPath.relativePath,
-      dotfiles: "deny",
-    });
-    return createDaemonFileContentResponse(result, {
-      headers: {
-        "cache-control": NO_STORE_CACHE_CONTROL,
-        "x-content-type-options": CONTENT_TYPE_OPTIONS,
-      },
-    });
-  } catch (error) {
-    return remapDaemonFileRouteError(error);
-  }
-}
-
-async function serveAppIcon(
-  deps: AppDeps,
-  threadId: string,
-  rawAppId: string,
-): Promise<Response> {
-  const appId = parseAppId(rawAppId);
-  const target = await requireThreadAppsTarget(deps, threadId);
-  const manifest = await readAppManifestForRequest(deps, { appId, target });
-  if (manifest.icon !== undefined) {
-    throw new ApiError(404, "ENOENT", "App uses a built-in icon");
-  }
-  const logo = await tryResolveLogo(deps, { appId, target });
-  if (!logo) {
-    throw new ApiError(404, "ENOENT", "App logo not found");
-  }
-  const logoPath = `logo.${logo.extension}`;
-  const metadata = await readAppFileMetadata(deps, {
-    appId,
-    target,
-    rootKind: "app",
-    path: logoPath,
-  });
-  if (metadata.sizeBytes > LOGO_MAX_BYTES) {
-    throw new ApiError(
-      413,
-      "file_too_large",
-      "App logo exceeds the 1 MB limit",
-      false,
-    );
-  }
-  const result = await readAppRelativeFile(deps, {
-    appId,
-    target,
-    rootKind: "app",
-    path: logoPath,
-    dotfiles: "deny",
-  });
-  const contentType = mimeTypes.lookup(logoPath) || "application/octet-stream";
-  return new Response(decodeDaemonFileContent(result), {
-    status: 200,
-    headers: {
-      "cache-control": NO_STORE_CACHE_CONTROL,
-      "content-type": contentType,
-      "x-content-type-options": CONTENT_TYPE_OPTIONS,
-    },
-  });
-}
-
-async function readAppDataEntry(
-  deps: AppDeps,
-  args: ReadAppDataEntryArgs,
-): Promise<AppDataEntry> {
-  const file = await readAppRelativeFile(deps, {
-    appId: args.appId,
-    target: args.target,
-    rootKind: "data",
-    path: args.dataPath,
-    dotfiles: "deny",
-  });
-  let value: JsonValue;
-  const bytes = Buffer.from(decodeDaemonFileContent(file));
-  try {
-    value = jsonValueSchema.parse(JSON.parse(bytes.toString("utf8")));
-  } catch {
-    throw new ApiError(
-      422,
-      "invalid_json",
-      `App data path ${args.dataPath} does not contain valid JSON`,
-    );
-  }
-  const modifiedAtMs =
-    file.modifiedAtMs ??
-    (
-      await readAppFileMetadata(deps, {
-        appId: args.appId,
-        target: args.target,
-        rootKind: "data",
-        path: args.dataPath,
-      })
-    ).modifiedAtMs;
-  return {
-    path: args.dataPath,
-    value,
-    version: sha256(bytes),
-    sizeBytes: file.sizeBytes,
-    modifiedAtMs,
-  };
-}
-
-function shouldListAppDataPrefixAfterReadError(error: Error): boolean {
-  return (
-    error instanceof ApiError &&
-    (error.body.code === "ENOENT" ||
-      (error.body.code === "invalid_path" &&
-        error.body.message.includes("Path is a directory")))
-  );
-}
-
-async function listAppDataEntries(
-  deps: AppDeps,
-  args: ListAppDataEntriesArgs,
-): Promise<AppDataEntry[]> {
-  if (args.dataPath !== "") {
-    try {
-      return [
-        await readAppDataEntry(deps, {
-          appId: args.appId,
-          dataPath: args.dataPath,
-          target: args.target,
-        }),
-      ];
-    } catch (error) {
-      if (
-        !(error instanceof Error) ||
-        !shouldListAppDataPrefixAfterReadError(error)
-      ) {
-        throw error;
-      }
-    }
-  }
-
-  const listRoot = args.dataPath
-    ? path.join(appDataRootPath(args), args.dataPath)
-    : appDataRootPath(args);
-  let listResult: HostDaemonOnlineRpcResult<"host.list_paths">;
-  try {
-    listResult = await readHostCommand(deps, {
-      hostId: args.target.hostId,
-      command: {
-        type: "host.list_paths",
-        path: listRoot,
-        limit: FILE_LIST_LIMIT_MAX,
-        includeFiles: true,
-        includeDirectories: false,
-      },
-    });
-  } catch (error) {
-    if (error instanceof ApiError && error.body.code === "ENOENT") {
-      return [];
-    }
-    throw error;
-  }
-
-  const dataPaths = listResult.paths
-    .filter((entry) => entry.kind === "file")
-    .map((entry) =>
-      args.dataPath ? `${args.dataPath}/${entry.path}` : entry.path,
-    )
-    .map((entryPath) => appDataPathSchema.safeParse(entryPath))
-    .filter((entryPath) => entryPath.success)
-    .map((entryPath) => entryPath.data)
-    .sort((left, right) => left.localeCompare(right));
-
-  return Promise.all(
-    dataPaths.map((dataPath) =>
-      readAppDataEntry(deps, {
-        appId: args.appId,
-        dataPath,
-        target: args.target,
-      }),
-    ),
-  );
-}
-
-async function writeAppDataEntry(
-  deps: AppDeps,
-  args: WriteAppDataEntryArgs,
-): Promise<AppDataEntry> {
-  const content = canonicalizeJson(args.value);
-  const result = await queueHostCommand(deps, {
-    hostId: args.target.hostId,
-    command: {
-      type: "host.write_file_relative",
-      rootPath: appDataRootPath(args),
-      path: args.dataPath,
-      dotfiles: "deny",
-      content,
-      contentEncoding: "utf8",
-    },
-  });
-  return {
-    path: args.dataPath,
-    value: args.value,
-    version: result.hash,
-    sizeBytes: result.sizeBytes,
-    modifiedAtMs: result.modifiedAtMs,
-  };
-}
-
-async function deleteAppDataEntry(
-  deps: AppDeps,
-  args: DeleteAppDataEntryArgs,
-): Promise<void> {
-  await queueHostCommand(deps, {
-    hostId: args.target.hostId,
-    command: {
-      type: "host.delete_file_relative",
-      rootPath: appDataRootPath(args),
-      path: args.dataPath,
-      dotfiles: "deny",
-    },
-  });
-}
-
-function createTemplateManifest(
-  request: CreateThreadAppRequest,
-  template: AppTemplate,
-): AppManifest {
-  const manifest: AppManifest = {
-    manifestVersion: 1,
-    id: request.id,
-    name: request.name,
-    entry: "index.html",
-    contributions: ["thread.app"],
-    capabilities: ["data", "message"],
-  };
-  if (template === "status") {
-    manifest.icon = "ListTodo";
-  }
-  return manifest;
-}
-
-function templateFilesForRequest(
-  request: CreateThreadAppRequest,
-): TemplateFile[] {
-  const manifest = createTemplateManifest(request, request.template);
-  return [
-    {
-      path: MANIFEST_FILE_NAME,
-      content: canonicalizeJson(manifest),
-    },
-    {
-      path: "assets/index.html",
-      content: buildBlankAppIndexHtml({ name: request.name }),
-    },
-    {
-      path: "data/state.json",
-      content: canonicalizeJson({}),
-    },
-  ];
-}
-
-async function scaffoldApp(
-  deps: AppDeps,
-  args: ScaffoldAppArgs,
-): Promise<AppDetail> {
-  try {
-    await readAppManifestForRequest(deps, {
-      appId: args.request.id,
-      target: args.target,
-    });
-    throw new ApiError(409, "invalid_request", "App already exists");
-  } catch (error) {
-    if (!(error instanceof ApiError) || error.status !== 404) {
-      throw error;
-    }
-  }
-
-  const files = templateFilesForRequest(args.request);
-  for (const file of files) {
-    await queueHostCommand(deps, {
-      hostId: args.target.hostId,
-      command: {
-        type: "host.write_file_relative",
-        rootPath: appRootPath({
-          appId: args.request.id,
-          target: args.target,
-        }),
-        path: file.path,
-        dotfiles: "deny",
-        content: file.content,
-        contentEncoding: "utf8",
-      },
-    });
-  }
-  return buildAppDetail(deps, {
-    appId: args.request.id,
-    target: args.target,
-    requestThreadId: args.threadId,
-  });
-}
-
-export function registerThreadAppRoutes(app: Hono, deps: AppDeps): void {
-  const { get, post, put, del } = typedRoutes<PublicApiSchema>(app, {
-    onValidationError: (msg) => new ApiError(400, "invalid_request", msg),
-  });
-
-  get("/threads/:id/apps", async (context) =>
-    context.json(await listThreadApps(deps, context.req.param("id"))),
-  );
-
-  post(
-    "/threads/:id/apps",
-    createThreadAppRequestSchema,
-    async (context, payload) => {
-      const threadId = context.req.param("id");
-      const target = await requireThreadAppsTarget(deps, threadId);
-      const detail = await scaffoldApp(deps, {
-        target,
-        request: payload,
-        threadId,
-      });
-      return context.json(detail, 201);
-    },
-  );
-
-  get("/threads/:id/apps/:appId", async (context) => {
-    const threadId = context.req.param("id");
-    const appId = parseAppId(context.req.param("appId"));
-    const target = await requireThreadAppsTarget(deps, threadId);
-    return context.json(
-      await buildAppDetail(deps, {
-        appId,
-        target,
-        requestThreadId: threadId,
-      }),
-    );
-  });
-
-  del("/threads/:id/apps/:appId", async (context) => {
-    const threadId = context.req.param("id");
-    const appId = parseAppId(context.req.param("appId"));
-    const target = await requireThreadAppsTarget(deps, threadId);
-    const result = await queueHostCommand(deps, {
-      hostId: target.hostId,
-      command: {
-        type: "host.delete_path_relative",
-        rootPath: path.join(target.storagePath, APPS_DIRECTORY_NAME),
-        path: appId,
-        dotfiles: "deny",
-      },
-    });
-    if (!result.deleted) {
-      throw new ApiError(404, "ENOENT", `App not found: ${appId}`);
-    }
-    return context.json({ ok: true });
-  });
-
-  get(
-    "/threads/:id/apps/:appId/data",
-    appDataListQuerySchema,
-    async (context, query) => {
-      const target = await requireThreadAppsTarget(
-        deps,
-        context.req.param("id"),
-      );
-      const appId = parseAppId(context.req.param("appId"));
-      assertAppCapability(
-        await readAppManifestForRequest(deps, { appId, target }),
-        "data",
-      );
-      const dataPath = parseOptionalAppDataPrefix(query.prefix);
-      return context.json({
-        entries: await listAppDataEntries(deps, {
-          appId,
-          target,
-          dataPath,
-        }),
-      });
-    },
-  );
-
-  post(
-    "/threads/:id/apps/:appId/message",
-    appMessageRequestSchema,
-    async (context, payload) => {
-      const thread = requirePublicThread(deps.db, context.req.param("id"));
-      const manifest = await readAppManifestForRequest(deps, {
-        appId: parseAppId(context.req.param("appId")),
-        target: await requireThreadAppsTarget(deps, thread.id),
-      });
-      assertAppCapability(manifest, "message");
-      const environment = await requireThreadCommandEnvironment(deps, {
-        thread,
-      });
-      await sendThreadMessage(deps, {
-        environment,
-        thread,
-        trigger: "user",
-        payload: {
-          input: [{ type: "text", text: payload.text }],
-          mode: "auto",
-        },
-      });
-      return context.json({ ok: true });
-    },
-  );
-
-  app.get("/threads/:id/apps/:appId/", async (context) =>
-    serveAppEntry(
-      deps,
-      context.req.param("id"),
-      context.req.param("appId"),
-      context.req.url,
-    ),
-  );
-
-  app.get("/threads/:id/apps/:appId/icon", async (context) =>
-    serveAppIcon(deps, context.req.param("id"), context.req.param("appId")),
-  );
-
-  get("/threads/:id/apps/:appId/data/*", async (context) => {
-    const target = await requireThreadAppsTarget(deps, context.req.param("id"));
-    const appId = parseAppId(context.req.param("appId"));
-    assertAppCapability(
-      await readAppManifestForRequest(deps, { appId, target }),
-      "data",
-    );
-    const dataPath = parseAppDataRoutePath(
-      extractRoutePath({
-        requestUrl: context.req.url,
-        routeSegment: APP_ROUTE_DATA_SEGMENT,
-      }),
-    );
-    const entry = await readAppDataEntry(deps, {
-      appId,
-      target,
-      dataPath,
-    });
-    const response = context.json(entry);
-    response.headers.set("cache-control", NO_STORE_CACHE_CONTROL);
-    response.headers.set("etag", `"${entry.version}"`);
-    return response;
-  });
-
-  put(
-    "/threads/:id/apps/:appId/data/*",
-    appDataWriteRequestSchema,
-    async (context, payload) => {
-      const target = await requireThreadAppsTarget(
-        deps,
-        context.req.param("id"),
-      );
-      const appId = parseAppId(context.req.param("appId"));
-      const manifest = await readAppManifestForRequest(deps, {
-        appId,
-        target,
-      });
-      assertAppCapability(manifest, "data");
-      const dataPath = parseAppDataRoutePath(
-        extractRoutePath({
-          requestUrl: context.req.url,
-          routeSegment: APP_ROUTE_DATA_SEGMENT,
-        }),
-      );
-      const entry = await writeAppDataEntry(deps, {
-        appId,
-        target,
-        dataPath,
-        value: payload.value,
-      });
-      const response = context.json(entry);
-      response.headers.set("cache-control", NO_STORE_CACHE_CONTROL);
-      response.headers.set("etag", `"${entry.version}"`);
-      return response;
-    },
-  );
-
-  del("/threads/:id/apps/:appId/data/*", async (context) => {
-    const target = await requireThreadAppsTarget(deps, context.req.param("id"));
-    const appId = parseAppId(context.req.param("appId"));
-    const manifest = await readAppManifestForRequest(deps, { appId, target });
-    assertAppCapability(manifest, "data");
-    const dataPath = parseAppDataRoutePath(
-      extractRoutePath({
-        requestUrl: context.req.url,
-        routeSegment: APP_ROUTE_DATA_SEGMENT,
-      }),
-    );
-    await deleteAppDataEntry(deps, {
-      appId,
-      target,
-      dataPath,
-    });
-    const response = context.json({ ok: true });
-    response.headers.set("cache-control", NO_STORE_CACHE_CONTROL);
-    return response;
-  });
-
-  // Keep this flat asset wildcard last among GET app routes so typed app
-  // endpoints such as /data/* and /icon keep their route ownership.
-  app.get("/threads/:id/apps/:appId/*", async (context) => {
-    const threadId = context.req.param("id");
-    const appId = context.req.param("appId");
-    return serveAppAsset(
-      deps,
-      threadId,
-      appId,
-      extractRoutePath({
-        requestUrl: context.req.url,
-        routeSegment: appAssetRouteSegment({ threadId, appId }),
-      }),
-    );
-  });
-}
diff --git a/apps/server/src/routes/threads/index.ts b/apps/server/src/routes/threads/index.ts
index 73f8159de..d5c0519a0 100644
--- a/apps/server/src/routes/threads/index.ts
+++ b/apps/server/src/routes/threads/index.ts
@@ -1,7 +1,6 @@
 import type { Hono } from "hono";
 import type { AppDeps } from "../../types.js";
 import { registerThreadActionRoutes } from "./actions.js";
-import { registerThreadAppRoutes } from "./apps.js";
 import { registerThreadBaseRoutes } from "./base.js";
 import { registerThreadDataRoutes } from "./data.js";
 import { registerThreadInteractionRoutes } from "./interactions.js";
@@ -13,7 +12,6 @@ export function registerThreadRoutes(app: Hono, deps: AppDeps): void {
   if (deps.config.featureFlags.terminals) {
     registerThreadTerminalRoutes(app, deps);
   }
-  registerThreadAppRoutes(app, deps);
   registerThreadDataRoutes(app, deps);
   registerThreadInteractionRoutes(app, deps);
 }
diff --git a/apps/server/src/server.ts b/apps/server/src/server.ts
index 888ee7d66..38d4c6eb0 100644
--- a/apps/server/src/server.ts
+++ b/apps/server/src/server.ts
@@ -11,6 +11,7 @@ import {
 import type { AppDeps, ServerAppDeps } from "./types.js";
 import { ApiError, errorToResponse } from "./errors.js";
 import { registerAutomationRoutes } from "./routes/automations.js";
+import { registerGlobalAppRoutes } from "./routes/apps.js";
 import { registerEnvironmentRoutes } from "./routes/environments.js";
 import { registerFileRoutes } from "./routes/files.js";
 import { registerHostRoutes } from "./routes/hosts.js";
@@ -244,6 +245,7 @@ export function createApp(
     return next();
   });
   const publicApi = new Hono();
+  registerGlobalAppRoutes(publicApi, deps);
   registerProjectRoutes(publicApi, deps);
   registerAutomationRoutes(publicApi, deps);
   registerFileRoutes(publicApi, deps);
diff --git a/apps/server/src/services/apps/tracked-application-data-targets.ts b/apps/server/src/services/apps/tracked-application-data-targets.ts
new file mode 100644
index 000000000..97f7ad53c
--- /dev/null
+++ b/apps/server/src/services/apps/tracked-application-data-targets.ts
@@ -0,0 +1,79 @@
+import { readdir, readFile } from "node:fs/promises";
+import {
+  resolveApplicationDataPath,
+  resolveApplicationManifestPath,
+  resolveAppsRootPath,
+} from "@bb/config/app-storage-paths";
+import { applicationIdSchema, type ApplicationId } from "@bb/domain";
+import { appManifestSchema } from "@bb/server-contract";
+
+export interface TrackedApplicationDataTarget {
+  applicationId: ApplicationId;
+  appDataPath: string;
+}
+
+interface ListTrackedApplicationDataTargetsArgs {
+  dataDir: string;
+}
+
+function isIgnoredApplicationStorageEntry(entryName: string): boolean {
+  return (
+    entryName.startsWith(".tmp-app_") || entryName.startsWith(".delete-app_")
+  );
+}
+
+async function isValidApplicationManifest(
+  dataDir: string,
+  applicationId: ApplicationId,
+): Promise<boolean> {
+  try {
+    const manifest = appManifestSchema.parse(
+      JSON.parse(
+        await readFile(
+          resolveApplicationManifestPath(dataDir, applicationId),
+          "utf8",
+        ),
+      ),
+    );
+    return manifest.id === applicationId;
+  } catch {
+    return false;
+  }
+}
+
+export async function listTrackedApplicationDataTargets(
+  args: ListTrackedApplicationDataTargetsArgs,
+): Promise<TrackedApplicationDataTarget[]> {
+  let entries;
+  try {
+    entries = await readdir(resolveAppsRootPath(args.dataDir), {
+      withFileTypes: true,
+    });
+  } catch {
+    return [];
+  }
+
+  const targets: TrackedApplicationDataTarget[] = [];
+  for (const entry of entries) {
+    if (
+      !entry.isDirectory() ||
+      isIgnoredApplicationStorageEntry(entry.name)
+    ) {
+      continue;
+    }
+    const parsed = applicationIdSchema.safeParse(entry.name);
+    if (!parsed.success) {
+      continue;
+    }
+    if (!(await isValidApplicationManifest(args.dataDir, parsed.data))) {
+      continue;
+    }
+    targets.push({
+      applicationId: parsed.data,
+      appDataPath: resolveApplicationDataPath(args.dataDir, parsed.data),
+    });
+  }
+  return targets.sort((left, right) =>
+    left.applicationId.localeCompare(right.applicationId),
+  );
+}
diff --git a/apps/server/src/services/skills/injected-skills.ts b/apps/server/src/services/skills/injected-skills.ts
new file mode 100644
index 000000000..db0739ab6
--- /dev/null
+++ b/apps/server/src/services/skills/injected-skills.ts
@@ -0,0 +1,467 @@
+import type { Dirent } from "node:fs";
+import fs from "node:fs";
+import path from "node:path";
+import matter from "gray-matter";
+import {
+  resolveApplicationManifestPath,
+  resolveApplicationPath,
+  resolveAppsRootPath,
+  resolveDataDirSkillsRootPath,
+} from "@bb/config/app-storage-paths";
+import { applicationIdSchema, type ApplicationId } from "@bb/domain";
+import type { HostDaemonInjectedSkillSource } from "@bb/host-daemon-contract";
+import { appManifestSchema } from "@bb/server-contract";
+import { z } from "zod";
+import type { ServerLogger } from "../../types.js";
+
+const SKILL_FILE_NAME = "SKILL.md";
+const SKILL_NAME_PATTERN =
+  /^(?!.*--)[a-z0-9](?:[a-z0-9-]{0,62}[a-z0-9])?$/u;
+const SKILL_FRONTMATTER_DELIMITER = "---";
+
+const skillFrontmatterSchema = z
+  .object({
+    name: z
+      .string()
+      .max(64)
+      .regex(
+        SKILL_NAME_PATTERN,
+        "Skill name must use lowercase letters, numbers, and single hyphens",
+      ),
+    description: z
+      .string()
+      .max(1024)
+      .refine((value) => value.trim().length > 0, {
+        message: "Skill description must be non-empty",
+      }),
+  })
+  .passthrough();
+
+export interface ResolveInjectedSkillSourcesArgs {
+  dataDir: string;
+}
+
+interface SkillCandidateSource {
+  applicationId: ApplicationId | null;
+  sourceType: HostDaemonInjectedSkillSource["sourceType"];
+}
+
+interface SkillRootScanArgs extends SkillCandidateSource {
+  logger: ServerLogger;
+  skillsRootPath: string;
+}
+
+interface SkillCandidateArgs extends SkillCandidateSource {
+  candidatePath: string;
+  directoryName: string;
+  logger: ServerLogger;
+}
+
+interface InvalidSkillLogArgs extends SkillCandidateSource {
+  candidatePath: string;
+  logger: ServerLogger;
+  reason: string;
+}
+
+interface SkillCollisionLogArgs {
+  colliding: readonly HostDaemonInjectedSkillSource[];
+  logger: ServerLogger;
+  name: string;
+}
+
+interface ReadValidApplicationIdsArgs {
+  appsRootPath: string;
+  dataDir: string;
+  logger: ServerLogger;
+}
+
+interface ApplicationManifestReadArgs {
+  applicationId: ApplicationId;
+  dataDir: string;
+  logger: ServerLogger;
+}
+
+function isFsErrorWithCode(error: Error, code: string): boolean {
+  return "code" in error && error.code === code;
+}
+
+function compactZodIssues(issues: z.ZodIssue[]): string {
+  return issues
+    .map((issue) => `${issue.path.join(".") || "root"}: ${issue.message}`)
+    .join("; ");
+}
+
+function hasSupportedFrontmatterDelimiter(content: string): boolean {
+  const trimmed = content.trimStart();
+  return (
+    trimmed.startsWith(`${SKILL_FRONTMATTER_DELIMITER}\n`) ||
+    trimmed.startsWith(`${SKILL_FRONTMATTER_DELIMITER}\r\n`)
+  );
+}
+
+function logInvalidSkill(args: InvalidSkillLogArgs): void {
+  args.logger.warn(
+    {
+      applicationId: args.applicationId,
+      candidatePath: args.candidatePath,
+      reason: args.reason,
+      sourceType: args.sourceType,
+    },
+    "Skipping invalid injected skill",
+  );
+}
+
+function logSkillCollision(args: SkillCollisionLogArgs): void {
+  for (const source of args.colliding) {
+    args.logger.warn(
+      {
+        applicationId: source.applicationId,
+        name: args.name,
+        sourceRootPath: source.sourceRootPath,
+        sourceType: source.sourceType,
+      },
+      "Skipping colliding injected skill",
+    );
+  }
+}
+
+function sortDirentsByName(left: Dirent, right: Dirent): number {
+  return left.name.localeCompare(right.name);
+}
+
+function toSkillFilePath(candidatePath: string): string {
+  return path.join(candidatePath, SKILL_FILE_NAME);
+}
+
+function readSkillCandidate(
+  args: SkillCandidateArgs,
+): HostDaemonInjectedSkillSource | null {
+  const skillFilePath = toSkillFilePath(args.candidatePath);
+  let skillFileStat;
+  try {
+    skillFileStat = fs.lstatSync(skillFilePath);
+  } catch (error) {
+    if (error instanceof Error && isFsErrorWithCode(error, "ENOENT")) {
+      logInvalidSkill({
+        ...args,
+        reason: "Missing SKILL.md",
+      });
+      return null;
+    }
+    throw error;
+  }
+
+  if (skillFileStat.isSymbolicLink()) {
+    logInvalidSkill({
+      ...args,
+      reason: "SKILL.md is a symlink",
+    });
+    return null;
+  }
+  if (!skillFileStat.isFile()) {
+    logInvalidSkill({
+      ...args,
+      reason: "SKILL.md is not a regular file",
+    });
+    return null;
+  }
+
+  const content = fs.readFileSync(skillFilePath, "utf8");
+  if (!hasSupportedFrontmatterDelimiter(content)) {
+    logInvalidSkill({
+      ...args,
+      reason: "SKILL.md frontmatter must start with a plain --- delimiter",
+    });
+    return null;
+  }
+
+  let parsed;
+  try {
+    parsed = matter(content);
+  } catch (error) {
+    logInvalidSkill({
+      ...args,
+      reason:
+        error instanceof Error && error.message.trim().length > 0
+          ? error.message
+          : "Invalid SKILL.md frontmatter",
+    });
+    return null;
+  }
+
+  const frontmatter = skillFrontmatterSchema.safeParse(parsed.data);
+  if (!frontmatter.success) {
+    logInvalidSkill({
+      ...args,
+      reason: compactZodIssues(frontmatter.error.issues),
+    });
+    return null;
+  }
+
+  if (frontmatter.data.name !== args.directoryName) {
+    logInvalidSkill({
+      ...args,
+      reason: "Frontmatter name must match the skill directory name",
+    });
+    return null;
+  }
+
+  if (args.sourceType === "data-dir") {
+    return {
+      sourceType: "data-dir",
+      applicationId: null,
+      name: frontmatter.data.name,
+      description: frontmatter.data.description,
+      sourceRootPath: args.candidatePath,
+      skillFilePath,
+    };
+  }
+
+  if (args.applicationId === null) {
+    throw new Error("Global app skill source requires an applicationId");
+  }
+  return {
+    sourceType: "global-app",
+    applicationId: args.applicationId,
+    name: frontmatter.data.name,
+    description: frontmatter.data.description,
+    sourceRootPath: args.candidatePath,
+    skillFilePath,
+  };
+}
+
+function readSkillsRoot(
+  args: SkillRootScanArgs,
+): HostDaemonInjectedSkillSource[] {
+  let rootStat;
+  try {
+    rootStat = fs.lstatSync(args.skillsRootPath);
+  } catch (error) {
+    if (error instanceof Error && isFsErrorWithCode(error, "ENOENT")) {
+      return [];
+    }
+    throw error;
+  }
+
+  if (rootStat.isSymbolicLink()) {
+    args.logger.warn(
+      {
+        applicationId: args.applicationId,
+        skillsRootPath: args.skillsRootPath,
+        sourceType: args.sourceType,
+      },
+      "Skipping symlinked injected skills root",
+    );
+    return [];
+  }
+  if (!rootStat.isDirectory()) {
+    args.logger.warn(
+      {
+        applicationId: args.applicationId,
+        skillsRootPath: args.skillsRootPath,
+        sourceType: args.sourceType,
+      },
+      "Skipping non-directory injected skills root",
+    );
+    return [];
+  }
+
+  const entries = fs.readdirSync(args.skillsRootPath, {
+    withFileTypes: true,
+  }).sort(sortDirentsByName);
+  const sources: HostDaemonInjectedSkillSource[] = [];
+
+  for (const entry of entries) {
+    const candidatePath = path.join(args.skillsRootPath, entry.name);
+    if (entry.isSymbolicLink()) {
+      logInvalidSkill({
+        ...args,
+        candidatePath,
+        reason: "Skill directory is a symlink",
+      });
+      continue;
+    }
+    if (!entry.isDirectory()) {
+      logInvalidSkill({
+        ...args,
+        candidatePath,
+        reason: "Skill candidate is not a directory",
+      });
+      continue;
+    }
+    const source = readSkillCandidate({
+      applicationId: args.applicationId,
+      candidatePath,
+      directoryName: entry.name,
+      logger: args.logger,
+      sourceType: args.sourceType,
+    });
+    if (source) {
+      sources.push(source);
+    }
+  }
+
+  return sources;
+}
+
+function hasValidApplicationManifest(
+  args: ApplicationManifestReadArgs,
+): boolean {
+  let parsedJson;
+  try {
+    parsedJson = JSON.parse(
+      fs.readFileSync(
+        resolveApplicationManifestPath(args.dataDir, args.applicationId),
+        "utf8",
+      ),
+    );
+  } catch (error) {
+    args.logger.warn(
+      {
+        applicationId: args.applicationId,
+        manifestPath: resolveApplicationManifestPath(
+          args.dataDir,
+          args.applicationId,
+        ),
+        reason:
+          error instanceof Error && error.message.trim().length > 0
+            ? error.message
+            : "Invalid app manifest",
+      },
+      "Skipping invalid global app manifest for injected skills",
+    );
+    return false;
+  }
+
+  const manifest = appManifestSchema.safeParse(parsedJson);
+  if (!manifest.success) {
+    args.logger.warn(
+      {
+        applicationId: args.applicationId,
+        issues: compactZodIssues(manifest.error.issues),
+        manifestPath: resolveApplicationManifestPath(
+          args.dataDir,
+          args.applicationId,
+        ),
+      },
+      "Skipping invalid global app manifest for injected skills",
+    );
+    return false;
+  }
+
+  if (manifest.data.id !== args.applicationId) {
+    args.logger.warn(
+      {
+        applicationId: args.applicationId,
+        manifestId: manifest.data.id,
+        manifestPath: resolveApplicationManifestPath(
+          args.dataDir,
+          args.applicationId,
+        ),
+      },
+      "Skipping global app skills because manifest id does not match directory",
+    );
+    return false;
+  }
+
+  return true;
+}
+
+function readValidApplicationIds(
+  args: ReadValidApplicationIdsArgs,
+): ApplicationId[] {
+  let entries: Dirent[];
+  try {
+    entries = fs.readdirSync(args.appsRootPath, { withFileTypes: true });
+  } catch (error) {
+    if (error instanceof Error && isFsErrorWithCode(error, "ENOENT")) {
+      return [];
+    }
+    throw error;
+  }
+
+  const applicationIds: ApplicationId[] = [];
+  for (const entry of entries.sort(sortDirentsByName)) {
+    if (!entry.isDirectory()) {
+      continue;
+    }
+    const parsed = applicationIdSchema.safeParse(entry.name);
+    if (!parsed.success) {
+      continue;
+    }
+    const isValid = hasValidApplicationManifest({
+      applicationId: parsed.data,
+      dataDir: args.dataDir,
+      logger: args.logger,
+    });
+    if (isValid) {
+      applicationIds.push(parsed.data);
+    }
+  }
+  return applicationIds;
+}
+
+function excludeCollisions(
+  logger: ServerLogger,
+  sources: readonly HostDaemonInjectedSkillSource[],
+): HostDaemonInjectedSkillSource[] {
+  const byName = new Map<string, HostDaemonInjectedSkillSource[]>();
+  for (const source of sources) {
+    const existing = byName.get(source.name) ?? [];
+    existing.push(source);
+    byName.set(source.name, existing);
+  }
+
+  const resolved: HostDaemonInjectedSkillSource[] = [];
+  for (const [name, entries] of byName) {
+    if (entries.length === 1) {
+      const source = entries[0];
+      if (source) {
+        resolved.push(source);
+      }
+      continue;
+    }
+    logSkillCollision({
+      colliding: entries,
+      logger,
+      name,
+    });
+  }
+
+  return resolved.sort((left, right) => left.name.localeCompare(right.name));
+}
+
+export function resolveInjectedSkillSources(
+  logger: ServerLogger,
+  args: ResolveInjectedSkillSourcesArgs,
+): HostDaemonInjectedSkillSource[] {
+  const dataDirSources = readSkillsRoot({
+    applicationId: null,
+    logger,
+    skillsRootPath: resolveDataDirSkillsRootPath(args.dataDir),
+    sourceType: "data-dir",
+  });
+
+  const appSources: HostDaemonInjectedSkillSource[] = [];
+  const appsRootPath = resolveAppsRootPath(args.dataDir);
+  const applicationIds = readValidApplicationIds({
+    appsRootPath,
+    dataDir: args.dataDir,
+    logger,
+  });
+  for (const applicationId of applicationIds) {
+    appSources.push(
+      ...readSkillsRoot({
+        applicationId,
+        logger,
+        skillsRootPath: path.join(
+          resolveApplicationPath(args.dataDir, applicationId),
+          "skills",
+        ),
+        sourceType: "global-app",
+      }),
+    );
+  }
+
+  return excludeCollisions(logger, [...dataDirSources, ...appSources]);
+}
diff --git a/apps/server/src/services/threads/app-client-script.ts b/apps/server/src/services/threads/app-client-script.ts
index 262e3708d..90e315d63 100644
--- a/apps/server/src/services/threads/app-client-script.ts
+++ b/apps/server/src/services/threads/app-client-script.ts
@@ -1,12 +1,14 @@
-import type { AppId } from "@bb/domain";
+import type { ApplicationId } from "@bb/domain";
 import type { AppCapability } from "@bb/server-contract";
 
 export interface AppClientBootstrap {
-  appId: AppId;
+  appId: ApplicationId;
+  applicationId: ApplicationId;
+  appSessionToken: string | null;
   capabilities: AppCapability[];
   dataUrl: string;
   messageUrl: string;
-  threadId: string;
+  targetThreadId: string | null;
   wsUrl: string;
 }
 
@@ -241,7 +243,7 @@ function buildAppClientJavascript(bootstrapJson: string): string {
   var socketSubscribed = false;
   var subscriptionReady = null;
   var resolveSubscriptionReady = null;
-  var subscriptionEntityId = bootstrap.threadId + ":app:" + bootstrap.appId + ":data";
+  var subscriptionEntityId = bootstrap.applicationId + ":data";
 
   function pathMatchesPrefix(path, prefix) {
     return prefix === "" || path === prefix || path.indexOf(prefix + "/") === 0;
@@ -274,8 +276,7 @@ function buildAppClientJavascript(bootstrapJson: string): string {
   function handleBroadcast(message) {
     if (
       !message ||
-      message.threadId !== bootstrap.threadId ||
-      message.appId !== bootstrap.appId
+      message.applicationId !== bootstrap.applicationId
     ) {
       return;
     }
@@ -449,8 +450,8 @@ function buildAppClientJavascript(bootstrapJson: string): string {
   }
 
   function message(text) {
-    if (typeof text !== "string") {
-      throw new TypeError("window.bb.message(text) requires a string");
+    if (text === undefined || !isJsonValue(text)) {
+      throw new TypeError("window.bb.message(payload) requires a JSON value");
     }
     return fetch(bootstrap.messageUrl, {
       method: "POST",
@@ -459,14 +460,17 @@ function buildAppClientJavascript(bootstrapJson: string): string {
         "Accept": "application/json",
         "Content-Type": "application/json"
       },
-      body: JSON.stringify({ text: text })
+      body: JSON.stringify({
+        payload: text,
+        appSessionToken: bootstrap.appSessionToken || undefined
+      })
     }).then(function (response) {
       if (response.ok) return undefined;
       return rejectResponse(response);
     });
   }
 
-  var bb = { appId: bootstrap.appId };
+  var bb = { appId: bootstrap.appId, applicationId: bootstrap.applicationId };
   if (hasCapability("data")) {
     bb.data = {
       read: read,
diff --git a/apps/server/src/services/threads/blank-app-scaffold.ts b/apps/server/src/services/threads/blank-app-scaffold.ts
index 489cdd965..c0fa9fad5 100644
--- a/apps/server/src/services/threads/blank-app-scaffold.ts
+++ b/apps/server/src/services/threads/blank-app-scaffold.ts
@@ -159,12 +159,9 @@ const BLANK_APP_SCAFFOLD_EXTRA_STYLES = `<style>
       }
     </style>`;
 
-// Blank-template scaffold rendered into apps/<id>/assets/index.html. Composes
-// the documented bb default styling head with a scaffold-only style block and
-// the task-list visual vocabulary borrowed from the bundled status app, so new
-// apps start out looking bb-native rather than like bare HTML. The same
-// scaffold powers both `bb app new` (any name) and the bundled default status
-// app seeded into every manager thread (name="Status").
+// Blank-template scaffold rendered into an app's public/index.html. Composes
+// the documented bb default styling head with a scaffold-only style block so
+// new apps start out looking bb-native rather than like bare HTML.
 const BLANK_APP_INDEX_HTML_TEMPLATE = `<!doctype html>
 <html lang="en">
   <head>
@@ -183,7 +180,7 @@ const BLANK_APP_INDEX_HTML_TEMPLATE = `<!doctype html>
 
     <main class="panel">
       <p class="placeholder">
-        Customize this static app in assets/index.html. No web server or build step needed.
+        Customize this static app in public/index.html. No web server or build step needed.
       </p>
 
       <section class="section">
@@ -202,8 +199,8 @@ const BLANK_APP_INDEX_HTML_TEMPLATE = `<!doctype html>
     </main>
 
     <script>
-      if (window.bb && window.bb.appId) {
-        document.getElementById("bb-app-id").textContent = window.bb.appId;
+      if (window.bb && window.bb.applicationId) {
+        document.getElementById("bb-app-id").textContent = window.bb.applicationId;
       }
     </script>
   </body>
diff --git a/apps/server/src/services/threads/default-template/apps/status/manifest.json b/apps/server/src/services/threads/default-template/apps/status/manifest.json
deleted file mode 100644
index 8f83d9dc3..000000000
--- a/apps/server/src/services/threads/default-template/apps/status/manifest.json
+++ /dev/null
@@ -1,9 +0,0 @@
-{
-  "manifestVersion": 1,
-  "id": "status",
-  "name": "Status",
-  "icon": "ListTodo",
-  "entry": "index.html",
-  "contributions": ["thread.app"],
-  "capabilities": ["data", "message"]
-}
diff --git a/apps/server/src/services/threads/manager-storage-templates.ts b/apps/server/src/services/threads/manager-storage-templates.ts
index fb7718590..23a148ecf 100644
--- a/apps/server/src/services/threads/manager-storage-templates.ts
+++ b/apps/server/src/services/threads/manager-storage-templates.ts
@@ -1,56 +1,25 @@
-import { constants as fsConstants, readFileSync } from "node:fs";
+import { constants as fsConstants } from "node:fs";
 import type { Dirent } from "node:fs";
-import {
-  copyFile,
-  mkdir,
-  readdir,
-  readFile,
-  writeFile,
-} from "node:fs/promises";
+import { copyFile, mkdir, readdir, readFile } from "node:fs/promises";
 import path from "node:path";
-import { fileURLToPath } from "node:url";
 import {
   managerTemplateNameSchema,
   type ManagerTemplateName,
 } from "@bb/domain";
 import type { LoggedWorkSessionDeps, ServerLogger } from "../../types.js";
 import { ensureHostSessionReadyForWork } from "../hosts/host-lifecycle.js";
-import { buildBlankAppIndexHtml } from "./blank-app-scaffold.js";
 
 export const MANAGER_TEMPLATE_DIR_NAME = "manager-templates";
 export const ACTIVE_MANAGER_TEMPLATE_FILE_NAME = "active";
 export const DEFAULT_MANAGER_TEMPLATE_NAME: ManagerTemplateName = "default";
 
-const BUNDLED_STATUS_APP_NAME = "Status";
-const BUNDLED_STATUS_APP_INDEX_HTML = buildBlankAppIndexHtml({
-  name: BUNDLED_STATUS_APP_NAME,
-});
-const BUNDLED_STATUS_APP_STATE_JSON = "{}\n";
-
-const moduleDir = path.dirname(fileURLToPath(import.meta.url));
-const defaultTemplateAssetDir = path.join(moduleDir, "default-template");
-
-function loadDefaultTemplateAsset(fileName: string): string {
-  return readFileSync(path.join(defaultTemplateAssetDir, fileName), "utf8");
-}
-
 type ManagerTemplateLogger = Pick<ServerLogger, "debug" | "warn">;
 
-interface BuiltInManagerTemplateFile {
-  content: string;
-  fileName: string;
-}
-
 interface TemplateFileToCopy {
   relativePath: string;
   sourcePath: string;
 }
 
-interface BuiltInManagerTemplateSet {
-  files: readonly BuiltInManagerTemplateFile[];
-  name: ManagerTemplateName;
-}
-
 interface ResolveManagerTemplateNameArgs {
   dataDir: string;
   explicitTemplateName: ManagerTemplateName | null;
@@ -72,14 +41,6 @@ interface CopyTemplateFilesArgs {
   threadStoragePath: string;
 }
 
-interface CopyBuiltInTemplateFilesArgs {
-  files: readonly BuiltInManagerTemplateFile[];
-  logger: ManagerTemplateLogger;
-  templateName: ManagerTemplateName;
-  threadId: string;
-  threadStoragePath: string;
-}
-
 interface FsErrorWithCodeArgs {
   code: string;
   error: unknown;
@@ -95,34 +56,6 @@ interface ManagerTemplateSetPathArgs extends ManagerTemplateRootPathArgs {
 
 type CopyTemplateFilesResult = "copied" | "missing";
 
-// Built-in defaults stay in the server bundle. They are always overlaid on top
-// of any user-authored template copy so newly-provisioned threads have a
-// working status surface even if the user's template omits these files.
-// User-authored files win because they are copied first and the overlay uses
-// the `wx` flag, which refuses to overwrite existing destinations.
-//
-// The bundled status app shares its index.html with the `bb app new` blank
-// scaffold (via buildBlankAppIndexHtml) so new users open a bb-styled
-// starting-point dashboard they can ask their agent to customize, rather than
-// inheriting any one workflow-specific UI.
-const BUILT_IN_DEFAULT_MANAGER_TEMPLATE_SET: BuiltInManagerTemplateSet = {
-  name: DEFAULT_MANAGER_TEMPLATE_NAME,
-  files: [
-    {
-      fileName: "apps/status/manifest.json",
-      content: loadDefaultTemplateAsset("apps/status/manifest.json"),
-    },
-    {
-      fileName: "apps/status/assets/index.html",
-      content: BUNDLED_STATUS_APP_INDEX_HTML,
-    },
-    {
-      fileName: "apps/status/data/state.json",
-      content: BUNDLED_STATUS_APP_STATE_JSON,
-    },
-  ],
-};
-
 function isFsErrorWithCode(args: FsErrorWithCodeArgs): boolean {
   return (
     typeof args.error === "object" &&
@@ -277,37 +210,6 @@ async function collectTemplateFiles(
   return files;
 }
 
-async function copyBuiltInTemplateFiles(
-  args: CopyBuiltInTemplateFilesArgs,
-): Promise<void> {
-  await mkdir(args.threadStoragePath, { recursive: true });
-
-  for (const file of args.files) {
-    const destinationPath = path.join(args.threadStoragePath, file.fileName);
-    try {
-      await mkdir(path.dirname(destinationPath), { recursive: true });
-      await writeFile(destinationPath, file.content, {
-        encoding: "utf8",
-        flag: "wx",
-      });
-    } catch (error) {
-      if (isFsErrorWithCode({ error, code: "EEXIST" })) {
-        continue;
-      }
-      throw error;
-    }
-  }
-
-  args.logger.debug(
-    {
-      templateName: args.templateName,
-      threadId: args.threadId,
-      threadStoragePath: args.threadStoragePath,
-    },
-    "Overlaid bundled apps/status seed onto manager storage",
-  );
-}
-
 export async function seedManagerThreadStorage(
   deps: LoggedWorkSessionDeps,
   args: SeedManagerThreadStorageArgs,
@@ -342,15 +244,7 @@ export async function seedManagerThreadStorage(
         templateDirPath,
         threadId: args.threadId,
       },
-      "Manager template directory is missing; overlaying bundled seed only",
+      "Manager template directory is missing; no template files were seeded",
     );
   }
-
-  await copyBuiltInTemplateFiles({
-    files: BUILT_IN_DEFAULT_MANAGER_TEMPLATE_SET.files,
-    logger: deps.logger,
-    templateName,
-    threadId: args.threadId,
-    threadStoragePath: args.threadStoragePath,
-  });
 }
diff --git a/apps/server/src/services/threads/thread-commands.ts b/apps/server/src/services/threads/thread-commands.ts
index 9de7cd578..b0f0e355c 100644
--- a/apps/server/src/services/threads/thread-commands.ts
+++ b/apps/server/src/services/threads/thread-commands.ts
@@ -284,6 +284,7 @@ export async function buildThreadStartCommand(
     options: toRuntimeExecutionOptions(args),
     instructions: runtimeContext.instructions,
     dynamicTools: runtimeContext.dynamicTools,
+    injectedSkillSources: runtimeContext.injectedSkillSources,
     ...(runtimeContext.disallowedTools?.length
       ? { disallowedTools: [...runtimeContext.disallowedTools] }
       : {}),
@@ -312,6 +313,7 @@ function buildPreparedTurnSubmitCommandPayload(
       providerThreadId: args.providerThreadId,
       instructions: args.runtimeContext.instructions,
       dynamicTools: args.runtimeContext.dynamicTools,
+      injectedSkillSources: args.runtimeContext.injectedSkillSources,
       ...(args.runtimeContext.disallowedTools?.length
         ? { disallowedTools: [...args.runtimeContext.disallowedTools] }
         : {}),
diff --git a/apps/server/src/services/threads/thread-lifecycle.ts b/apps/server/src/services/threads/thread-lifecycle.ts
index 3790c5e0e..3608dbcb9 100644
--- a/apps/server/src/services/threads/thread-lifecycle.ts
+++ b/apps/server/src/services/threads/thread-lifecycle.ts
@@ -957,6 +957,21 @@ async function advanceActiveThreadStartIfPresent(
   return true;
 }
 
+function hasQueuedActiveThreadStart(
+  deps: WorkSessionDeps,
+  args: QueueThreadStartCommandArgs,
+): boolean {
+  const operation = getThreadOperation(deps.db, {
+    threadId: args.thread.id,
+    kind: "start",
+  });
+  return (
+    operation !== null &&
+    isActiveLifecycleOperationState(operation.state) &&
+    hasQueuedThreadOperationCommand(deps, operation.commandId)
+  );
+}
+
 /**
  * Makes the provision-to-start durability boundary atomic: after a crash, the
  * thread should have either an active provision op to retry or an active start
@@ -1032,7 +1047,7 @@ async function requestThreadStartOnce(
   const baseCommand = await buildThreadStartCommand(deps, {
     ...args,
   });
-  if (await advanceActiveThreadStartIfPresent(deps, args)) {
+  if (hasQueuedActiveThreadStart(deps, args)) {
     return;
   }
 
diff --git a/apps/server/src/services/threads/thread-runtime-config.ts b/apps/server/src/services/threads/thread-runtime-config.ts
index 36565fc62..7ef6480b7 100644
--- a/apps/server/src/services/threads/thread-runtime-config.ts
+++ b/apps/server/src/services/threads/thread-runtime-config.ts
@@ -12,6 +12,7 @@ import type {
   WorkspaceProvisionType,
   EnvironmentStatus,
 } from "@bb/domain";
+import type { HostDaemonInjectedSkillSource } from "@bb/host-daemon-contract";
 import { renderTemplate } from "@bb/templates";
 import { ApiError } from "../../errors.js";
 import type { AppDeps, LoggedWorkSessionDeps } from "../../types.js";
@@ -21,6 +22,7 @@ import {
   buildExistingThreadExecutionInput,
   resolveExistingThreadExecutionPlan,
 } from "./thread-execution-plan.js";
+import { resolveInjectedSkillSources } from "../skills/injected-skills.js";
 export { getSupportedReasoningLevelsForProvider } from "./thread-reasoning-policy.js";
 
 const STANDARD_AGENT_INSTRUCTIONS = renderTemplate(
@@ -89,6 +91,7 @@ export interface ResolvePermissionEscalationArgs {
 export interface ResolvedThreadRuntimeCommandConfig {
   dynamicTools: DynamicTool[];
   disallowedTools?: readonly string[];
+  injectedSkillSources: HostDaemonInjectedSkillSource[];
   instructionMode: InstructionMode;
   instructions: string;
   projectId: string;
@@ -152,10 +155,14 @@ export async function resolveThreadRuntimeCommandConfig(
   const projectRootPath =
     defaultSource?.type === "local_path" ? defaultSource.path : workspacePath;
   const { workspaceProvisionType } = args.environment;
+  const injectedSkillSources = resolveInjectedSkillSources(deps.logger, {
+    dataDir: deps.config.dataDir,
+  });
 
   if (args.thread.type !== "manager") {
     return {
       dynamicTools: [],
+      injectedSkillSources,
       instructionMode: "append",
       instructions: STANDARD_AGENT_INSTRUCTIONS,
       projectId: args.thread.projectId,
@@ -175,6 +182,7 @@ export async function resolveThreadRuntimeCommandConfig(
   return {
     dynamicTools: MANAGER_DYNAMIC_TOOLS,
     disallowedTools: MANAGER_DISALLOWED_TOOLS,
+    injectedSkillSources,
     instructionMode: "replace",
     instructions: renderTemplate("managerAgentInstructions", {
       hostId: args.environment.hostId,
diff --git a/apps/server/src/services/threads/thread-storage.ts b/apps/server/src/services/threads/thread-storage.ts
index e90ef9293..5db7161c7 100644
--- a/apps/server/src/services/threads/thread-storage.ts
+++ b/apps/server/src/services/threads/thread-storage.ts
@@ -53,6 +53,7 @@ export async function requireThreadStorageContext(
     threadStoragePath: resolveThreadStoragePathFromRoot({
       threadStorageRootPath: resolveThreadStorageRootPath({
         dataDir: session.dataDir,
+        env: {},
       }),
       threadId: args.threadId,
     }),
diff --git a/apps/server/src/ws/daemon-protocol.ts b/apps/server/src/ws/daemon-protocol.ts
index d435074ed..facc709b7 100644
--- a/apps/server/src/ws/daemon-protocol.ts
+++ b/apps/server/src/ws/daemon-protocol.ts
@@ -10,6 +10,7 @@ import { runtimeErrorLogFields } from "../services/lib/error-log-fields.js";
 import { requireAuthorizedActiveSession } from "../internal/session-state.js";
 import { handleDaemonSocketClosed } from "../internal/session-owner-side-effects.js";
 import { notifyDaemonEnvironmentChange } from "../internal/environment-changes.js";
+import { notifyGlobalAppsChangedIfListChanged } from "../routes/apps.js";
 import { decodeSocketPayload } from "./decode-payload.js";
 
 interface DaemonSocket {
@@ -99,7 +100,11 @@ export function onDaemonSocketMessage(
       hostId: args.hostId,
       sessionId: args.sessionId,
     });
-    heartbeatSession(deps.db, session.id, Date.now() + session.leaseTimeoutMs);
+    heartbeatSession(
+      deps.db,
+      session.id,
+      Math.max(Date.now() + session.leaseTimeoutMs, session.leaseExpiresAt + 1),
+    );
     if (result.data.type === "environment-change") {
       notifyDaemonEnvironmentChange(deps, {
         hostId: args.hostId,
@@ -108,6 +113,17 @@ export function onDaemonSocketMessage(
       });
       return;
     }
+    if (result.data.type === "application-storage-changed") {
+      void notifyGlobalAppsChangedIfListChanged(deps).catch((error) => {
+        deps.logger.warn(
+          {
+            ...runtimeErrorLogFields(deps.config, error),
+          },
+          "Failed to refresh global app list after daemon storage change",
+        );
+      });
+      return;
+    }
     if (result.data.type === "host-rpc.response") {
       const disposition = deps.hub.recordHostOnlineRpcResponse({
         message: result.data,
diff --git a/apps/server/src/ws/hub.ts b/apps/server/src/ws/hub.ts
index 435b66282..4850281e5 100644
--- a/apps/server/src/ws/hub.ts
+++ b/apps/server/src/ws/hub.ts
@@ -505,9 +505,9 @@ export class NotificationHub implements DbNotifier {
     }
   }
 
-  notifyThreadAppData(message: AppDataBroadcastMessage): void {
+  notifyAppData(message: AppDataBroadcastMessage): void {
     this.notifyClientsByKey(
-      subKey("thread", `${message.threadId}:app:${message.appId}:data`),
+      subKey("app", `${message.applicationId}:data`),
       JSON.stringify(appDataBroadcastMessageSchema.parse(message)),
     );
   }
diff --git a/apps/server/test/app/hub.test.ts b/apps/server/test/app/hub.test.ts
index eb35ca35f..790151151 100644
--- a/apps/server/test/app/hub.test.ts
+++ b/apps/server/test/app/hub.test.ts
@@ -91,11 +91,10 @@ describe("NotificationHub", () => {
     const hub = new NotificationHub();
     const socket = createMockSocket();
 
-    hub.subscribe(socket, "thread", "thread-1:app:status:data");
-    hub.notifyThreadAppData({
+    hub.subscribe(socket, "app", "status:data");
+    hub.notifyAppData({
       type: "app-data.changed",
-      threadId: "thread-1",
-      appId: "status",
+      applicationId: "status",
       path: "state.json",
       value: { workers: [] },
       deleted: false,
@@ -105,8 +104,7 @@ describe("NotificationHub", () => {
     expect(socket.messages).toHaveLength(1);
     expect(JSON.parse(socket.messages[0])).toEqual({
       type: "app-data.changed",
-      threadId: "thread-1",
-      appId: "status",
+      applicationId: "status",
       path: "state.json",
       value: { workers: [] },
       deleted: false,
@@ -118,18 +116,16 @@ describe("NotificationHub", () => {
     const hub = new NotificationHub();
     const socket = createMockSocket();
 
-    hub.subscribe(socket, "thread", "thread-1:app:status:data");
-    hub.notifyThreadAppData({
+    hub.subscribe(socket, "app", "status:data");
+    hub.notifyAppData({
       type: "app-data.resync",
-      threadId: "thread-1",
-      appId: "status",
+      applicationId: "status",
     });
 
     expect(socket.messages).toHaveLength(1);
     expect(JSON.parse(socket.messages[0])).toEqual({
       type: "app-data.resync",
-      threadId: "thread-1",
-      appId: "status",
+      applicationId: "status",
     });
   });
 
diff --git a/apps/server/test/hosts/expired-commands.test.ts b/apps/server/test/hosts/expired-commands.test.ts
index 4f71b6043..179a27973 100644
--- a/apps/server/test/hosts/expired-commands.test.ts
+++ b/apps/server/test/hosts/expired-commands.test.ts
@@ -145,6 +145,7 @@ describe("expired commands", () => {
         },
         instructions: "instructions",
         dynamicTools: [],
+        injectedSkillSources: [],
         instructionMode: "append" as const,
       }),
     },
@@ -409,6 +410,7 @@ describe("expired commands", () => {
           },
           instructions: "instructions",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         },
       });
@@ -603,6 +605,7 @@ describe("expired commands", () => {
             providerThreadId: "provider-expired-turn-submit",
             instructions: "instructions",
             dynamicTools: [],
+            injectedSkillSources: [],
             instructionMode: "append",
           },
         }),
diff --git a/apps/server/test/internal/internal-app-data-change.test.ts b/apps/server/test/internal/internal-app-data-change.test.ts
index 39b10a2f1..9608d5009 100644
--- a/apps/server/test/internal/internal-app-data-change.test.ts
+++ b/apps/server/test/internal/internal-app-data-change.test.ts
@@ -1,38 +1,16 @@
 import { describe, expect, it, vi } from "vitest";
 import { internalAuthHeaders } from "../helpers/commands.js";
 import { readJson } from "../helpers/json.js";
-import {
-  seedEnvironment,
-  seedHostSession,
-  seedProjectWithSource,
-  seedThread,
-} from "../helpers/seed.js";
+import { seedHostSession } from "../helpers/seed.js";
 import { withTestHarness } from "../helpers/test-app.js";
 
 describe("internal app-data change route", () => {
-  it("broadcasts daemon-reported app data changes for session-owned threads", async () => {
+  it("broadcasts daemon-reported app data changes", async () => {
     await withTestHarness(async (harness) => {
-      const { host, session } = seedHostSession(harness.deps, {
+      const { session } = seedHostSession(harness.deps, {
         id: "host-app-data-change",
       });
-      const { project } = seedProjectWithSource(harness.deps, {
-        hostId: host.id,
-      });
-      const environment = seedEnvironment(harness.deps, {
-        hostId: host.id,
-        projectId: project.id,
-        path: "/tmp/app-data-change",
-        status: "ready",
-      });
-      const thread = seedThread(harness.deps, {
-        projectId: project.id,
-        environmentId: environment.id,
-        type: "manager",
-      });
-      const notifyThreadAppDataSpy = vi.spyOn(
-        harness.hub,
-        "notifyThreadAppData",
-      );
+      const notifyAppDataSpy = vi.spyOn(harness.hub, "notifyAppData");
 
       const response = await harness.app.request(
         "/internal/session/app-data-change",
@@ -41,8 +19,7 @@ describe("internal app-data change route", () => {
           headers: internalAuthHeaders(harness),
           body: JSON.stringify({
             sessionId: session.id,
-            threadId: thread.id,
-            appId: "status",
+            applicationId: "status",
             path: "state.json",
             value: { workers: [] },
             deleted: false,
@@ -52,10 +29,9 @@ describe("internal app-data change route", () => {
       );
 
       expect(response.status).toBe(200);
-      expect(notifyThreadAppDataSpy).toHaveBeenCalledWith({
+      expect(notifyAppDataSpy).toHaveBeenCalledWith({
         type: "app-data.changed",
-        threadId: thread.id,
-        appId: "status",
+        applicationId: "status",
         path: "state.json",
         value: { workers: [] },
         deleted: false,
@@ -64,32 +40,9 @@ describe("internal app-data change route", () => {
     });
   });
 
-  it("rejects daemon-reported app data changes for threads owned by another host", async () => {
+  it("rejects daemon-reported app data changes for unknown sessions", async () => {
     await withTestHarness(async (harness) => {
-      const hostA = seedHostSession(harness.deps, {
-        id: "host-app-data-change-a",
-      });
-      const hostB = seedHostSession(harness.deps, {
-        id: "host-app-data-change-b",
-      });
-      const { project } = seedProjectWithSource(harness.deps, {
-        hostId: hostB.host.id,
-      });
-      const environment = seedEnvironment(harness.deps, {
-        hostId: hostB.host.id,
-        projectId: project.id,
-        path: "/tmp/app-data-change-other",
-        status: "ready",
-      });
-      const thread = seedThread(harness.deps, {
-        projectId: project.id,
-        environmentId: environment.id,
-        type: "manager",
-      });
-      const notifyThreadAppDataSpy = vi.spyOn(
-        harness.hub,
-        "notifyThreadAppData",
-      );
+      const notifyAppDataSpy = vi.spyOn(harness.hub, "notifyAppData");
 
       const response = await harness.app.request(
         "/internal/session/app-data-change",
@@ -97,9 +50,8 @@ describe("internal app-data change route", () => {
           method: "POST",
           headers: internalAuthHeaders(harness),
           body: JSON.stringify({
-            sessionId: hostA.session.id,
-            threadId: thread.id,
-            appId: "status",
+            sessionId: "missing-session",
+            applicationId: "status",
             path: "state.json",
             value: null,
             deleted: true,
@@ -108,37 +60,20 @@ describe("internal app-data change route", () => {
         },
       );
 
-      expect(response.status).toBe(403);
+      expect(response.status).toBe(401);
       await expect(readJson(response)).resolves.toMatchObject({
-        code: "invalid_request",
+        code: "inactive_session",
       });
-      expect(notifyThreadAppDataSpy).not.toHaveBeenCalled();
+      expect(notifyAppDataSpy).not.toHaveBeenCalled();
     });
   });
 
   it("broadcasts daemon-requested app data resync hints", async () => {
     await withTestHarness(async (harness) => {
-      const { host, session } = seedHostSession(harness.deps, {
+      const { session } = seedHostSession(harness.deps, {
         id: "host-app-data-resync",
       });
-      const { project } = seedProjectWithSource(harness.deps, {
-        hostId: host.id,
-      });
-      const environment = seedEnvironment(harness.deps, {
-        hostId: host.id,
-        projectId: project.id,
-        path: "/tmp/app-data-resync",
-        status: "ready",
-      });
-      const thread = seedThread(harness.deps, {
-        projectId: project.id,
-        environmentId: environment.id,
-        type: "manager",
-      });
-      const notifyThreadAppDataSpy = vi.spyOn(
-        harness.hub,
-        "notifyThreadAppData",
-      );
+      const notifyAppDataSpy = vi.spyOn(harness.hub, "notifyAppData");
 
       const response = await harness.app.request(
         "/internal/session/app-data-resync",
@@ -147,17 +82,15 @@ describe("internal app-data change route", () => {
           headers: internalAuthHeaders(harness),
           body: JSON.stringify({
             sessionId: session.id,
-            threadId: thread.id,
-            appId: "status",
+            applicationId: "status",
           }),
         },
       );
 
       expect(response.status).toBe(200);
-      expect(notifyThreadAppDataSpy).toHaveBeenCalledWith({
+      expect(notifyAppDataSpy).toHaveBeenCalledWith({
         type: "app-data.resync",
-        threadId: thread.id,
-        appId: "status",
+        applicationId: "status",
       });
     });
   });
diff --git a/apps/server/test/internal/internal-command-result-idempotency.test.ts b/apps/server/test/internal/internal-command-result-idempotency.test.ts
index 0a7090bd1..ee2b934dd 100644
--- a/apps/server/test/internal/internal-command-result-idempotency.test.ts
+++ b/apps/server/test/internal/internal-command-result-idempotency.test.ts
@@ -334,6 +334,7 @@ describe("internal command result idempotency", () => {
           },
           instructions: "Be a helpful coding agent.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         },
       });
diff --git a/apps/server/test/internal/internal-command-result-thread-failure.test.ts b/apps/server/test/internal/internal-command-result-thread-failure.test.ts
index d460ac203..b03bc0970 100644
--- a/apps/server/test/internal/internal-command-result-thread-failure.test.ts
+++ b/apps/server/test/internal/internal-command-result-thread-failure.test.ts
@@ -192,6 +192,7 @@ async function queueManagedTurnSubmitScenario(
         providerThreadId: args.providerThreadId,
         instructions: "You are a helpful assistant.",
         dynamicTools: [],
+        injectedSkillSources: [],
         instructionMode: "append",
       },
       target: { mode: "steer", expectedTurnId: args.turnId },
@@ -256,6 +257,7 @@ describe("thread command failure side effects", () => {
           },
           instructions: "You are a helpful assistant.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         }),
       });
@@ -340,6 +342,7 @@ describe("thread command failure side effects", () => {
           },
           instructions: "You are a helpful assistant.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         }),
       });
@@ -457,6 +460,7 @@ describe("thread command failure side effects", () => {
           },
           instructions: "You are a helpful assistant.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         }),
       });
@@ -539,6 +543,7 @@ describe("thread command failure side effects", () => {
             providerThreadId: "provider-thread-1",
             instructions: "You are a helpful assistant.",
             dynamicTools: [],
+            injectedSkillSources: [],
             instructionMode: "append",
           },
           target: { mode: "steer", expectedTurnId: "turn-active" },
@@ -642,6 +647,7 @@ describe("thread command failure side effects", () => {
             providerThreadId: "provider-thread-stop-race",
             instructions: "You are a helpful assistant.",
             dynamicTools: [],
+            injectedSkillSources: [],
             instructionMode: "append",
           },
           target: { mode: "steer", expectedTurnId: "turn-stop-race" },
@@ -1021,6 +1027,7 @@ describe("thread command failure side effects", () => {
             providerThreadId: "provider-thread-1",
             instructions: "You are a helpful assistant.",
             dynamicTools: [],
+            injectedSkillSources: [],
             instructionMode: "append",
           },
           target: { mode: "start" },
@@ -1096,6 +1103,7 @@ describe("thread command failure side effects", () => {
           },
           instructions: "You are a helpful assistant.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         }),
       });
diff --git a/apps/server/test/internal/internal-environment-change.test.ts b/apps/server/test/internal/internal-environment-change.test.ts
index 86dab9f8c..e7e8e4c0e 100644
--- a/apps/server/test/internal/internal-environment-change.test.ts
+++ b/apps/server/test/internal/internal-environment-change.test.ts
@@ -1,4 +1,12 @@
+import { mkdir, rm, writeFile } from "node:fs/promises";
+import path from "node:path";
+import {
+  resolveApplicationManifestPath,
+  resolveApplicationPath,
+  resolveApplicationPublicPath,
+} from "@bb/config/app-storage-paths";
 import { getEnvironment } from "@bb/db";
+import type { AppManifest } from "@bb/server-contract";
 import { describe, expect, it, vi } from "vitest";
 import { onDaemonSocketMessage } from "../../src/ws/daemon-protocol.js";
 import {
@@ -20,6 +28,38 @@ function createTestDaemonSocket(): TestDaemonSocket {
   };
 }
 
+async function waitFor(
+  predicate: () => boolean,
+  timeoutMs = 1_000,
+): Promise<void> {
+  const startedAt = Date.now();
+  while (!predicate()) {
+    if (Date.now() - startedAt > timeoutMs) {
+      throw new Error("Timed out waiting for condition");
+    }
+    await new Promise((resolve) => setTimeout(resolve, 10));
+  }
+}
+
+async function writeApplication(
+  dataDir: string,
+  manifest: AppManifest,
+): Promise<void> {
+  await mkdir(resolveApplicationPublicPath(dataDir, manifest.id), {
+    recursive: true,
+  });
+  await writeFile(
+    resolveApplicationManifestPath(dataDir, manifest.id),
+    `${JSON.stringify(manifest, null, 2)}\n`,
+    "utf8",
+  );
+  await writeFile(
+    path.join(resolveApplicationPublicPath(dataDir, manifest.id), "index.html"),
+    "<!doctype html><title>External App</title>",
+    "utf8",
+  );
+}
+
 describe("internal environment change websocket hints", () => {
   it("does not resolve host RPC waiters from a different daemon session", async () => {
     await withTestHarness(async (harness) => {
@@ -220,4 +260,79 @@ describe("internal environment change websocket hints", () => {
       expect(notifyEnvironmentSpy).not.toHaveBeenCalled();
     });
   });
+
+  it("notifies app list clients when a daemon watcher reports an externally added app", async () => {
+    await withTestHarness(async (harness) => {
+      const { host, session } = seedHostSession(harness.deps, {
+        id: "host-app-added",
+      });
+      const notifySystemSpy = vi.spyOn(harness.hub, "notifySystem");
+      const socket = createTestDaemonSocket();
+
+      const initialListResponse = await harness.app.request("/api/v1/apps");
+      expect(initialListResponse.status).toBe(200);
+      await writeApplication(harness.config.dataDir, {
+        manifestVersion: 1,
+        id: "external-added",
+        name: "External Added",
+        entry: "index.html",
+        capabilities: [],
+      });
+
+      onDaemonSocketMessage(harness.deps, {
+        hostId: host.id,
+        sessionId: session.id,
+        socket,
+        raw: JSON.stringify({
+          type: "application-storage-changed",
+        }),
+      });
+
+      await waitFor(() =>
+        notifySystemSpy.mock.calls.some(([changes]) =>
+          changes.includes("apps-changed"),
+        ),
+      );
+      expect(socket.close).not.toHaveBeenCalled();
+    });
+  });
+
+  it("notifies app list clients when a daemon watcher reports an externally removed app", async () => {
+    await withTestHarness(async (harness) => {
+      const { host, session } = seedHostSession(harness.deps, {
+        id: "host-app-removed",
+      });
+      await writeApplication(harness.config.dataDir, {
+        manifestVersion: 1,
+        id: "external-removed",
+        name: "External Removed",
+        entry: "index.html",
+        capabilities: [],
+      });
+      const initialListResponse = await harness.app.request("/api/v1/apps");
+      expect(initialListResponse.status).toBe(200);
+      const notifySystemSpy = vi.spyOn(harness.hub, "notifySystem");
+      const socket = createTestDaemonSocket();
+
+      await rm(
+        resolveApplicationPath(harness.config.dataDir, "external-removed"),
+        { recursive: true, force: true },
+      );
+      onDaemonSocketMessage(harness.deps, {
+        hostId: host.id,
+        sessionId: session.id,
+        socket,
+        raw: JSON.stringify({
+          type: "application-storage-changed",
+        }),
+      });
+
+      await waitFor(() =>
+        notifySystemSpy.mock.calls.some(([changes]) =>
+          changes.includes("apps-changed"),
+        ),
+      );
+      expect(socket.close).not.toHaveBeenCalled();
+    });
+  });
 });
diff --git a/apps/server/test/internal/internal-event-side-effects.test.ts b/apps/server/test/internal/internal-event-side-effects.test.ts
index f9525a000..677081dad 100644
--- a/apps/server/test/internal/internal-event-side-effects.test.ts
+++ b/apps/server/test/internal/internal-event-side-effects.test.ts
@@ -1196,6 +1196,7 @@ describe("internal event side effects", () => {
             providerThreadId: "provider-child-command-event-dedupe",
             instructions: "You are a helpful assistant.",
             dynamicTools: [],
+            injectedSkillSources: [],
             instructionMode: "append",
           },
           target: { mode: "steer", expectedTurnId: turnId },
diff --git a/apps/server/test/public/public-apps.test.ts b/apps/server/test/public/public-apps.test.ts
new file mode 100644
index 000000000..43b6137c1
--- /dev/null
+++ b/apps/server/test/public/public-apps.test.ts
@@ -0,0 +1,579 @@
+import { mkdir, readFile, readdir, writeFile } from "node:fs/promises";
+import path from "node:path";
+import {
+  resolveApplicationDataPath,
+  resolveApplicationManifestPath,
+  resolveApplicationPath,
+  resolveApplicationPublicPath,
+  resolveAppsRootPath,
+} from "@bb/config/app-storage-paths";
+import {
+  appDetailSchema,
+  appSummarySchema,
+  type AppManifest,
+} from "@bb/server-contract";
+import { describe, expect, it, vi } from "vitest";
+import { readJson } from "../helpers/json.js";
+import {
+  seedEnvironment,
+  seedHostSession,
+  seedProjectWithSource,
+  seedThread,
+  seedThreadRuntimeState,
+} from "../helpers/seed.js";
+import { withTestHarness } from "../helpers/test-app.js";
+
+const VALID_APP_ID = "status";
+const VALID_MANIFEST: AppManifest = {
+  manifestVersion: 1,
+  id: VALID_APP_ID,
+  name: "Valid App",
+  icon: "ListTodo",
+  entry: "index.html",
+  capabilities: ["data", "message"],
+};
+
+async function writeApplication(
+  dataDir: string,
+  manifest: AppManifest,
+): Promise<void> {
+  await mkdir(resolveApplicationPublicPath(dataDir, manifest.id), {
+    recursive: true,
+  });
+  await mkdir(resolveApplicationDataPath(dataDir, manifest.id), {
+    recursive: true,
+  });
+  await writeFile(
+    resolveApplicationManifestPath(dataDir, manifest.id),
+    `${JSON.stringify(manifest, null, 2)}\n`,
+    "utf8",
+  );
+  await writeFile(
+    path.join(resolveApplicationPublicPath(dataDir, manifest.id), "index.html"),
+    "<!doctype html><title>Valid App</title>",
+    "utf8",
+  );
+}
+
+async function writeRawApplicationManifest(
+  dataDir: string,
+  applicationId: string,
+  manifestContent: string,
+): Promise<void> {
+  await mkdir(resolveApplicationPublicPath(dataDir, applicationId), {
+    recursive: true,
+  });
+  await writeFile(
+    resolveApplicationManifestPath(dataDir, applicationId),
+    manifestContent,
+    "utf8",
+  );
+  await writeFile(
+    path.join(
+      resolveApplicationPublicPath(dataDir, applicationId),
+      "index.html",
+    ),
+    "<!doctype html><title>Test App</title>",
+    "utf8",
+  );
+}
+
+async function writeApplicationPublicFile(
+  dataDir: string,
+  applicationId: string,
+  relativePath: string,
+  content: string,
+): Promise<void> {
+  const filePath = path.join(
+    resolveApplicationPublicPath(dataDir, applicationId),
+    relativePath,
+  );
+  await mkdir(path.dirname(filePath), { recursive: true });
+  await writeFile(filePath, content, "utf8");
+}
+
+function appRequestPath(resolvedUrl: URL): string {
+  return `${resolvedUrl.pathname}${resolvedUrl.search}${resolvedUrl.hash}`;
+}
+
+describe("public global app routes", () => {
+  it("lists and gets valid global apps by application id", async () => {
+    await withTestHarness(async (harness) => {
+      await writeApplication(harness.config.dataDir, VALID_MANIFEST);
+      await mkdir(
+        resolveApplicationPath(harness.config.dataDir, "invalid-app"),
+        { recursive: true },
+      );
+      await writeFile(
+        resolveApplicationManifestPath(harness.config.dataDir, "invalid-app"),
+        JSON.stringify({
+          ...VALID_MANIFEST,
+          id: "other",
+          name: "Invalid",
+        }),
+        "utf8",
+      );
+
+      const listResponse = await harness.app.request("/api/v1/apps");
+      expect(listResponse.status).toBe(200);
+      const apps = appSummarySchema.array().parse(await readJson(listResponse));
+      expect(apps.map((app) => app.applicationId)).toEqual([VALID_APP_ID]);
+
+      const getResponse = await harness.app.request(
+        `/api/v1/apps/${VALID_APP_ID}`,
+      );
+      expect(getResponse.status).toBe(200);
+      const detail = appDetailSchema.parse(await readJson(getResponse));
+      expect(detail).toMatchObject({
+        applicationId: VALID_APP_ID,
+        name: "Valid App",
+        appRootPath: resolveApplicationPath(
+          harness.config.dataDir,
+          VALID_APP_ID,
+        ),
+        appDataPath: resolveApplicationDataPath(
+          harness.config.dataDir,
+          VALID_APP_ID,
+        ),
+      });
+    });
+  });
+
+  it("uses manifest name for display with a slug fallback", async () => {
+    await withTestHarness(async (harness) => {
+      await writeRawApplicationManifest(
+        harness.config.dataDir,
+        "named-app",
+        JSON.stringify({
+          manifestVersion: 1,
+          id: "named-app",
+          name: "Named App",
+          entry: "index.html",
+        }),
+      );
+      await writeRawApplicationManifest(
+        harness.config.dataDir,
+        "missing-name",
+        JSON.stringify({
+          manifestVersion: 1,
+          id: "missing-name",
+          entry: "index.html",
+        }),
+      );
+      await writeRawApplicationManifest(
+        harness.config.dataDir,
+        "empty-name",
+        JSON.stringify({
+          manifestVersion: 1,
+          id: "empty-name",
+          name: "",
+          entry: "index.html",
+        }),
+      );
+
+      const listResponse = await harness.app.request("/api/v1/apps");
+      expect(listResponse.status).toBe(200);
+      const apps = appSummarySchema.array().parse(await readJson(listResponse));
+      expect(
+        apps.map((app) => ({
+          applicationId: app.applicationId,
+          name: app.name,
+        })),
+      ).toEqual([
+        { applicationId: "empty-name", name: "empty-name" },
+        { applicationId: "missing-name", name: "missing-name" },
+        { applicationId: "named-app", name: "Named App" },
+      ]);
+    });
+  });
+
+  it("returns app_missing and invalid_manifest distinctly", async () => {
+    await withTestHarness(async (harness) => {
+      const missingResponse = await harness.app.request("/api/v1/apps/missing");
+      expect(missingResponse.status).toBe(404);
+      await expect(readJson(missingResponse)).resolves.toMatchObject({
+        code: "app_missing",
+      });
+
+      await mkdir(
+        resolveApplicationPath(harness.config.dataDir, "invalid-app"),
+        { recursive: true },
+      );
+      await writeFile(
+        resolveApplicationManifestPath(harness.config.dataDir, "invalid-app"),
+        JSON.stringify({ ...VALID_MANIFEST, id: "other" }),
+        "utf8",
+      );
+
+      const invalidResponse = await harness.app.request(
+        "/api/v1/apps/invalid-app",
+      );
+      expect(invalidResponse.status).toBe(422);
+      await expect(readJson(invalidResponse)).resolves.toMatchObject({
+        code: "invalid_manifest",
+      });
+    });
+  });
+
+  it("serves public web-root files from the app route", async () => {
+    await withTestHarness(async (harness) => {
+      const applicationId = "vite-spa";
+      await writeApplication(harness.config.dataDir, {
+        manifestVersion: 1,
+        id: applicationId,
+        name: "Vite SPA",
+        entry: "index.html",
+        capabilities: ["data"],
+      });
+      await writeApplicationPublicFile(
+        harness.config.dataDir,
+        applicationId,
+        "index.html",
+        [
+          "<!doctype html>",
+          "<html><head>",
+          '<script type="module" src="./index-flat.js"></script>',
+          '<script type="module" src="./assets/index-relative.js"></script>',
+          '<link rel="stylesheet" href="./assets/index.css">',
+          "</head><body></body></html>",
+        ].join(""),
+      );
+      await writeApplicationPublicFile(
+        harness.config.dataDir,
+        applicationId,
+        "index-flat.js",
+        'import("./chunk.js"); window.flatAsset = true;',
+      );
+      await writeApplicationPublicFile(
+        harness.config.dataDir,
+        applicationId,
+        "chunk.js",
+        "window.dynamicChunk = true;",
+      );
+      await writeApplicationPublicFile(
+        harness.config.dataDir,
+        applicationId,
+        "assets/index-relative.js",
+        "window.relativeAsset = true;",
+      );
+      await writeApplicationPublicFile(
+        harness.config.dataDir,
+        applicationId,
+        "assets/index.css",
+        'body { background-image: url("./logo.svg"); }',
+      );
+      await writeApplicationPublicFile(
+        harness.config.dataDir,
+        applicationId,
+        "assets/logo.svg",
+        "<svg></svg>",
+      );
+
+      const entryResponse = await harness.app.request(
+        `/api/v1/apps/${applicationId}/`,
+      );
+      expect(entryResponse.status).toBe(200);
+      const html = await entryResponse.text();
+      expect(html).not.toContain("<base");
+      expect(html).toContain('src="./index-flat.js"');
+      expect(html).toContain('src="./assets/index-relative.js"');
+      expect(html).toContain('href="./assets/index.css"');
+
+      const pageUrl = new URL(`http://bb.test/api/v1/apps/${applicationId}/`);
+      const flatResponse = await harness.app.request(
+        appRequestPath(new URL("./index-flat.js", pageUrl)),
+      );
+      const relativeResponse = await harness.app.request(
+        appRequestPath(new URL("./assets/index-relative.js", pageUrl)),
+      );
+      const dynamicChunkResponse = await harness.app.request(
+        appRequestPath(new URL("./chunk.js", pageUrl)),
+      );
+      const cssResponse = await harness.app.request(
+        appRequestPath(new URL("./assets/index.css", pageUrl)),
+      );
+      const cssAssetResponse = await harness.app.request(
+        appRequestPath(
+          new URL("./logo.svg", new URL("./assets/index.css", pageUrl)),
+        ),
+      );
+
+      expect(flatResponse.status).toBe(200);
+      await expect(flatResponse.text()).resolves.toBe(
+        'import("./chunk.js"); window.flatAsset = true;',
+      );
+      expect(relativeResponse.status).toBe(200);
+      await expect(relativeResponse.text()).resolves.toBe(
+        "window.relativeAsset = true;",
+      );
+      expect(dynamicChunkResponse.status).toBe(200);
+      await expect(dynamicChunkResponse.text()).resolves.toBe(
+        "window.dynamicChunk = true;",
+      );
+      expect(cssResponse.status).toBe(200);
+      await expect(cssResponse.text()).resolves.toBe(
+        'body { background-image: url("./logo.svg"); }',
+      );
+      expect(cssAssetResponse.status).toBe(200);
+      await expect(cssAssetResponse.text()).resolves.toBe("<svg></svg>");
+    });
+  });
+
+  it("serves markdown entries from the public web root", async () => {
+    await withTestHarness(async (harness) => {
+      const applicationId = "readme";
+      await writeApplication(harness.config.dataDir, {
+        manifestVersion: 1,
+        id: applicationId,
+        name: "Readme",
+        entry: "docs/index.md",
+        capabilities: [],
+      });
+      await writeApplicationPublicFile(
+        harness.config.dataDir,
+        applicationId,
+        "docs/index.md",
+        "# App Notes\n",
+      );
+
+      const detailResponse = await harness.app.request(
+        `/api/v1/apps/${applicationId}`,
+      );
+      expect(detailResponse.status).toBe(200);
+      const detail = appDetailSchema.parse(await readJson(detailResponse));
+      expect(detail.entry).toEqual({
+        kind: "md",
+        path: "docs/index.md",
+      });
+
+      const markdownResponse = await harness.app.request(
+        `/api/v1/apps/${applicationId}/docs/index.md`,
+      );
+      expect(markdownResponse.status).toBe(200);
+      await expect(markdownResponse.text()).resolves.toBe("# App Notes\n");
+    });
+  });
+
+  it("rejects traversal attempts for public static files", async () => {
+    await withTestHarness(async (harness) => {
+      await writeApplication(harness.config.dataDir, VALID_MANIFEST);
+
+      const response = await harness.app.request(
+        `/api/v1/apps/${VALID_APP_ID}/..%2Fmanifest.json`,
+      );
+
+      expect(response.status).toBe(400);
+      await expect(readJson(response)).resolves.toMatchObject({
+        code: "invalid_path",
+      });
+    });
+  });
+
+  it("does not expose manifest or data files through the public static path", async () => {
+    await withTestHarness(async (harness) => {
+      const applicationId = "private-files";
+      await writeApplication(harness.config.dataDir, {
+        manifestVersion: 1,
+        id: applicationId,
+        name: "Private Files",
+        entry: "index.html",
+        capabilities: [],
+      });
+      await writeApplicationPublicFile(
+        harness.config.dataDir,
+        applicationId,
+        "manifest.json",
+        '{"leak":true}\n',
+      );
+      await writeFile(
+        path.join(
+          resolveApplicationDataPath(harness.config.dataDir, applicationId),
+          "state.json",
+        ),
+        '{"secret":true}\n',
+        "utf8",
+      );
+
+      const manifestResponse = await harness.app.request(
+        `/api/v1/apps/${applicationId}/manifest.json`,
+      );
+      expect(manifestResponse.status).toBe(404);
+
+      const dataResponse = await harness.app.request(
+        `/api/v1/apps/${applicationId}/data/state.json`,
+      );
+      expect(dataResponse.status).toBe(403);
+      await expect(readJson(dataResponse)).resolves.toMatchObject({
+        code: "invalid_request",
+      });
+    });
+  });
+
+  it("creates and deletes apps atomically on the filesystem", async () => {
+    await withTestHarness(async (harness) => {
+      const notifySystemSpy = vi.spyOn(harness.hub, "notifySystem");
+      const createResponse = await harness.app.request("/api/v1/apps", {
+        method: "POST",
+        body: JSON.stringify({ name: "Created App" }),
+      });
+      expect(createResponse.status).toBe(201);
+      expect(notifySystemSpy).toHaveBeenCalledWith(["apps-changed"]);
+      const created = appDetailSchema.parse(await readJson(createResponse));
+      expect(created.applicationId).toBe("created-app");
+      expect(created.name).toBe("Created App");
+
+      const manifestText = await readFile(
+        resolveApplicationManifestPath(
+          harness.config.dataDir,
+          created.applicationId,
+        ),
+        "utf8",
+      );
+      expect(JSON.parse(manifestText)).toMatchObject({
+        id: "created-app",
+        name: "Created App",
+      });
+      await expect(
+        readFile(
+          path.join(
+            resolveApplicationPublicPath(
+              harness.config.dataDir,
+              created.applicationId,
+            ),
+            "index.html",
+          ),
+          "utf8",
+        ),
+      ).resolves.toContain("Created App");
+      const appRootEntries = await readdir(
+        resolveAppsRootPath(harness.config.dataDir),
+      );
+      expect(appRootEntries.some((entry) => entry.startsWith(".tmp-"))).toBe(
+        false,
+      );
+
+      notifySystemSpy.mockClear();
+      const deleteResponse = await harness.app.request(
+        `/api/v1/apps/${created.applicationId}`,
+        { method: "DELETE" },
+      );
+      expect(deleteResponse.status).toBe(200);
+      expect(notifySystemSpy).toHaveBeenCalledWith(["apps-changed"]);
+      const deletedGetResponse = await harness.app.request(
+        `/api/v1/apps/${created.applicationId}`,
+      );
+      expect(deletedGetResponse.status).toBe(404);
+    });
+  });
+
+  it("creates explicit slug apps and defaults manifest name to the slug", async () => {
+    await withTestHarness(async (harness) => {
+      const createResponse = await harness.app.request("/api/v1/apps", {
+        method: "POST",
+        body: JSON.stringify({ applicationId: "review-board" }),
+      });
+      expect(createResponse.status).toBe(201);
+      const created = appDetailSchema.parse(await readJson(createResponse));
+      expect(created).toMatchObject({
+        applicationId: "review-board",
+        name: "review-board",
+        appRootPath: resolveApplicationPath(
+          harness.config.dataDir,
+          "review-board",
+        ),
+        appDataPath: resolveApplicationDataPath(
+          harness.config.dataDir,
+          "review-board",
+        ),
+      });
+      const manifestText = await readFile(
+        resolveApplicationManifestPath(harness.config.dataDir, "review-board"),
+        "utf8",
+      );
+      expect(JSON.parse(manifestText)).toMatchObject({
+        id: "review-board",
+        name: "review-board",
+      });
+    });
+  });
+
+  it("rejects duplicate app slugs", async () => {
+    await withTestHarness(async (harness) => {
+      const firstResponse = await harness.app.request("/api/v1/apps", {
+        method: "POST",
+        body: JSON.stringify({ applicationId: "status", name: "Status" }),
+      });
+      expect(firstResponse.status).toBe(201);
+
+      const duplicateResponse = await harness.app.request("/api/v1/apps", {
+        method: "POST",
+        body: JSON.stringify({ applicationId: "status", name: "Status" }),
+      });
+      expect(duplicateResponse.status).toBe(409);
+      await expect(readJson(duplicateResponse)).resolves.toMatchObject({
+        code: "app_exists",
+        message: 'an app with id "status" already exists',
+      });
+    });
+  });
+
+  it("requires an explicit message target outside an iframe session", async () => {
+    await withTestHarness(async (harness) => {
+      await writeApplication(harness.config.dataDir, VALID_MANIFEST);
+
+      const response = await harness.app.request(
+        `/api/v1/apps/${VALID_APP_ID}/message`,
+        {
+          method: "POST",
+          body: JSON.stringify({ payload: "hello" }),
+        },
+      );
+
+      expect(response.status).toBe(400);
+      await expect(readJson(response)).resolves.toMatchObject({
+        code: "message_target_required",
+      });
+    });
+  });
+
+  it("accepts explicit targetThreadId for non-iframe app messages", async () => {
+    await withTestHarness(async (harness) => {
+      await writeApplication(harness.config.dataDir, VALID_MANIFEST);
+      const { host } = seedHostSession(harness.deps, {
+        id: "host-app-message",
+      });
+      const { project } = seedProjectWithSource(harness.deps, {
+        hostId: host.id,
+      });
+      const environment = seedEnvironment(harness.deps, {
+        hostId: host.id,
+        projectId: project.id,
+        path: "/tmp/app-message",
+        status: "ready",
+      });
+      const thread = seedThread(harness.deps, {
+        projectId: project.id,
+        environmentId: environment.id,
+      });
+      seedThreadRuntimeState(harness.deps, {
+        environmentId: environment.id,
+        providerThreadId: "provider-app-message",
+        threadId: thread.id,
+      });
+
+      const response = await harness.app.request(
+        `/api/v1/apps/${VALID_APP_ID}/message`,
+        {
+          method: "POST",
+          headers: { "content-type": "application/json" },
+          body: JSON.stringify({
+            payload: "hello",
+            targetThreadId: thread.id,
+          }),
+        },
+      );
+
+      expect(response.status).toBe(202);
+    });
+  });
+});
diff --git a/apps/server/test/public/public-thread-apps.test.ts b/apps/server/test/public/public-thread-apps.test.ts
deleted file mode 100644
index e47e37014..000000000
--- a/apps/server/test/public/public-thread-apps.test.ts
+++ /dev/null
@@ -1,1375 +0,0 @@
-import { createHash } from "node:crypto";
-import { mkdtemp, rm, writeFile } from "node:fs/promises";
-import { tmpdir } from "node:os";
-import path from "node:path";
-import type { JsonValue } from "@bb/domain";
-import type { HostDaemonCommand } from "@bb/host-daemon-contract";
-import {
-  appDataListResponseSchema,
-  appDataReadResponseSchema,
-  appDetailSchema,
-  appSummarySchema,
-  type AppManifest,
-} from "@bb/server-contract";
-import { describe, expect, it, vi } from "vitest";
-import {
-  reportQueuedCommandError,
-  reportQueuedCommandSuccess,
-  waitForQueuedCommand,
-  waitForQueuedCommandAfter,
-  type QueuedCommand,
-} from "../helpers/commands.js";
-import { readJson } from "../helpers/json.js";
-import { createApp } from "../../src/server.js";
-import type { TestAppHarness } from "../helpers/test-app.js";
-import {
-  seedEnvironment,
-  seedHostSession,
-  seedProjectWithSource,
-  seedThread,
-} from "../helpers/seed.js";
-import { createTestAppHarness, withTestHarness } from "../helpers/test-app.js";
-
-interface ManagerThreadStorageFixture {
-  hostId: string;
-  threadId: string;
-  storageRootPath: string;
-}
-
-interface ReadFileResultArgs {
-  content: string;
-  mimeType?: string;
-  path: string;
-}
-
-interface PathEntryArgs {
-  kind: "directory" | "file";
-  path: string;
-}
-
-interface ManifestReadArgs {
-  appId: string;
-  afterCursor?: number;
-  fixture: ManagerThreadStorageFixture;
-  harness: TestAppHarness;
-  manifest: JsonValue;
-}
-
-type WriteFileRelativeQueuedCommand = QueuedCommand<
-  Extract<HostDaemonCommand, { type: "host.write_file_relative" }>
->;
-
-const STATUS_MANIFEST: AppManifest = {
-  manifestVersion: 1,
-  id: "status",
-  name: "Status",
-  icon: "ListTodo",
-  entry: "index.html",
-  contributions: ["thread.app"],
-  capabilities: ["data", "message"],
-};
-
-function seedManagerThreadStorage(
-  harness: TestAppHarness,
-): ManagerThreadStorageFixture {
-  const { host } = seedHostSession(harness.deps, {
-    id: "host-thread-apps",
-  });
-  const { project } = seedProjectWithSource(harness.deps, {
-    hostId: host.id,
-    path: "/tmp/project-source",
-  });
-  const environment = seedEnvironment(harness.deps, {
-    hostId: host.id,
-    projectId: project.id,
-    path: "/tmp/project-source",
-  });
-  const thread = seedThread(harness.deps, {
-    projectId: project.id,
-    environmentId: environment.id,
-    type: "manager",
-  });
-  return {
-    hostId: host.id,
-    threadId: thread.id,
-    storageRootPath: `/tmp/bb-host-data/${host.id}/thread-storage/${thread.id}`,
-  };
-}
-
-function appRoot(fixture: ManagerThreadStorageFixture, appId: string): string {
-  return `${fixture.storageRootPath}/apps/${appId}`;
-}
-
-function appAssetsRoot(
-  fixture: ManagerThreadStorageFixture,
-  appId: string,
-): string {
-  return `${appRoot(fixture, appId)}/assets`;
-}
-
-function appDataRoot(
-  fixture: ManagerThreadStorageFixture,
-  appId: string,
-): string {
-  return `${appRoot(fixture, appId)}/data`;
-}
-
-function sha256Text(content: string): string {
-  return createHash("sha256").update(content).digest("hex");
-}
-
-function readFileResult(args: ReadFileResultArgs) {
-  return {
-    path: args.path,
-    content: args.content,
-    contentEncoding: "utf8" as const,
-    ...(args.mimeType ? { mimeType: args.mimeType } : {}),
-    sizeBytes: Buffer.byteLength(args.content),
-  };
-}
-
-function pathEntry(args: PathEntryArgs) {
-  return {
-    kind: args.kind,
-    path: args.path,
-    name: args.path.split("/").at(-1) ?? args.path,
-    score: 1,
-    positions: [],
-  };
-}
-
-function requireWriteFileRelativeCommand(
-  queued: QueuedCommand,
-): WriteFileRelativeQueuedCommand {
-  if (queued.command.type === "host.write_file_relative") {
-    return {
-      command: queued.command,
-      row: queued.row,
-    };
-  }
-  throw new Error("Expected host.write_file_relative command");
-}
-
-async function reportManifestRead(
-  args: ManifestReadArgs,
-): Promise<QueuedCommand> {
-  const queued = args.afterCursor
-    ? await waitForQueuedCommandAfter(
-        args.harness,
-        args.afterCursor,
-        ({ command }) =>
-          command.type === "host.read_file_relative" &&
-          command.rootPath === appRoot(args.fixture, args.appId) &&
-          command.path === "manifest.json",
-      )
-    : await waitForQueuedCommand(
-        args.harness,
-        ({ command }) =>
-          command.type === "host.read_file_relative" &&
-          command.rootPath === appRoot(args.fixture, args.appId) &&
-          command.path === "manifest.json",
-      );
-  const content = `${JSON.stringify(args.manifest, null, 2)}\n`;
-  await reportQueuedCommandSuccess(
-    args.harness,
-    queued,
-    readFileResult({
-      path: "manifest.json",
-      content,
-      mimeType: "application/json",
-    }),
-  );
-  return queued;
-}
-
-describe("public thread app routes", () => {
-  it("lists app summaries from daemon-owned manifests", async () => {
-    await withTestHarness(async (harness) => {
-      const fixture = seedManagerThreadStorage(harness);
-      const request = harness.app.request(
-        `/api/v1/threads/${fixture.threadId}/apps`,
-      );
-      const listCommand = await waitForQueuedCommand(
-        harness,
-        ({ command }) =>
-          command.type === "host.list_paths" &&
-          command.path === `${fixture.storageRootPath}/apps`,
-      );
-      await reportQueuedCommandSuccess(harness, listCommand, {
-        paths: [
-          pathEntry({ kind: "directory", path: "demo" }),
-          pathEntry({ kind: "directory", path: "status" }),
-        ],
-        truncated: false,
-      });
-      await reportManifestRead({
-        harness,
-        fixture,
-        appId: "demo",
-        afterCursor: listCommand.row.cursor,
-        manifest: {
-          ...STATUS_MANIFEST,
-          id: "demo",
-          name: "Demo",
-          icon: "GridView",
-        },
-      });
-      await reportManifestRead({
-        harness,
-        fixture,
-        appId: "status",
-        afterCursor: listCommand.row.cursor,
-        manifest: STATUS_MANIFEST,
-      });
-
-      const response = await request;
-      expect(response.status).toBe(200);
-      const apps = appSummarySchema.array().parse(await readJson(response));
-      expect(apps.map((app) => app.id)).toEqual(["demo", "status"]);
-      expect(apps[0]?.icon).toEqual({ kind: "builtin", name: "GridView" });
-      expect(apps[1]?.icon).toEqual({ kind: "builtin", name: "ListTodo" });
-    });
-  });
-
-  it("skips invalid app manifests when listing app summaries", async () => {
-    const harness = await createTestAppHarness();
-    const warn = vi.spyOn(harness.deps.logger, "warn");
-    try {
-      const fixture = seedManagerThreadStorage(harness);
-      const request = harness.app.request(
-        `/api/v1/threads/${fixture.threadId}/apps`,
-      );
-      const listCommand = await waitForQueuedCommand(
-        harness,
-        ({ command }) =>
-          command.type === "host.list_paths" &&
-          command.path === `${fixture.storageRootPath}/apps`,
-      );
-      await reportQueuedCommandSuccess(harness, listCommand, {
-        paths: [
-          pathEntry({ kind: "directory", path: "broken" }),
-          pathEntry({ kind: "directory", path: "status" }),
-        ],
-        truncated: false,
-      });
-      await reportManifestRead({
-        harness,
-        fixture,
-        appId: "broken",
-        afterCursor: listCommand.row.cursor,
-        manifest: {
-          ...STATUS_MANIFEST,
-          id: "broken",
-          name: "Broken",
-          icon: "NotAnIcon",
-        },
-      });
-      await reportManifestRead({
-        harness,
-        fixture,
-        appId: "status",
-        afterCursor: listCommand.row.cursor,
-        manifest: STATUS_MANIFEST,
-      });
-
-      const response = await request;
-      expect(response.status).toBe(200);
-      const apps = appSummarySchema.array().parse(await readJson(response));
-      expect(apps.map((app) => app.id)).toEqual(["status"]);
-      expect(warn).toHaveBeenCalledWith(
-        expect.objectContaining({
-          appId: "broken",
-          manifestPath: `${appRoot(fixture, "broken")}/manifest.json`,
-          issueSummary: expect.stringContaining("icon"),
-          issues: expect.any(Array),
-        }),
-        "Skipping invalid thread app manifest",
-      );
-    } finally {
-      warn.mockRestore();
-      await harness.cleanup();
-    }
-  });
-
-  it("returns a provisioned-app error when app detail is missing manifest.json", async () => {
-    await withTestHarness(async (harness) => {
-      const fixture = seedManagerThreadStorage(harness);
-      const request = harness.app.request(
-        `/api/v1/threads/${fixture.threadId}/apps/status`,
-      );
-      const manifestCommand = await waitForQueuedCommand(
-        harness,
-        ({ command }) =>
-          command.type === "host.read_file_relative" &&
-          command.rootPath === appRoot(fixture, "status") &&
-          command.path === "manifest.json",
-      );
-      await reportQueuedCommandError(harness, manifestCommand, {
-        errorCode: "ENOENT",
-        errorMessage: "Path does not exist: manifest.json",
-      });
-
-      const response = await request;
-      expect(response.status).toBe(404);
-      await expect(readJson(response)).resolves.toMatchObject({
-        code: "app_not_provisioned",
-        message: expect.stringContaining("missing manifest.json"),
-      });
-    });
-  });
-
-  it("returns an invalid-manifest error when app detail manifest validation fails", async () => {
-    await withTestHarness(async (harness) => {
-      const fixture = seedManagerThreadStorage(harness);
-      const request = harness.app.request(
-        `/api/v1/threads/${fixture.threadId}/apps/broken`,
-      );
-      await reportManifestRead({
-        harness,
-        fixture,
-        appId: "broken",
-        manifest: {
-          ...STATUS_MANIFEST,
-          id: "broken",
-          name: "Broken",
-          icon: "NotAnIcon",
-        },
-      });
-
-      const response = await request;
-      expect(response.status).toBe(422);
-      const body = await readJson(response);
-      expect(body).toMatchObject({
-        code: "invalid_manifest",
-        message: expect.stringContaining("failed validation"),
-      });
-      expect(JSON.stringify(body)).not.toContain("NotAnIcon");
-    });
-  });
-
-  it("returns an invalid-manifest error before serving app assets", async () => {
-    await withTestHarness(async (harness) => {
-      const fixture = seedManagerThreadStorage(harness);
-      const request = harness.app.request(
-        `/api/v1/threads/${fixture.threadId}/apps/broken/index.html`,
-      );
-      await reportManifestRead({
-        harness,
-        fixture,
-        appId: "broken",
-        manifest: {
-          ...STATUS_MANIFEST,
-          id: "broken",
-          name: "Broken",
-          icon: "NotAnIcon",
-        },
-      });
-
-      const response = await request;
-      expect(response.status).toBe(422);
-      await expect(readJson(response)).resolves.toMatchObject({
-        code: "invalid_manifest",
-        message: expect.stringContaining("failed validation"),
-      });
-    });
-  });
-
-  it("serves HTML app entries with capability-scoped window.bb injection", async () => {
-    await withTestHarness(async (harness) => {
-      const fixture = seedManagerThreadStorage(harness);
-      const html =
-        "<!doctype html><html><head></head><body>Status</body></html>";
-      const request = harness.app.request(
-        `/api/v1/threads/${fixture.threadId}/apps/status/`,
-      );
-      const manifestCommand = await reportManifestRead({
-        harness,
-        fixture,
-        appId: "status",
-        manifest: STATUS_MANIFEST,
-      });
-      const metadataCommand = await waitForQueuedCommandAfter(
-        harness,
-        manifestCommand.row.cursor,
-        ({ command }) =>
-          command.type === "host.file_metadata" &&
-          command.path === `${appAssetsRoot(fixture, "status")}/index.html`,
-      );
-      await reportQueuedCommandSuccess(harness, metadataCommand, {
-        path: `${appAssetsRoot(fixture, "status")}/index.html`,
-        modifiedAtMs: 1234,
-        sizeBytes: Buffer.byteLength(html),
-      });
-      const entryCommand = await waitForQueuedCommandAfter(
-        harness,
-        metadataCommand.row.cursor,
-        ({ command }) =>
-          command.type === "host.read_file_relative" &&
-          command.rootPath === appAssetsRoot(fixture, "status") &&
-          command.path === "index.html",
-      );
-      await reportQueuedCommandSuccess(
-        harness,
-        entryCommand,
-        readFileResult({
-          path: "index.html",
-          content: html,
-          mimeType: "text/html",
-        }),
-      );
-
-      const response = await request;
-      expect(response.status).toBe(200);
-      expect(response.headers.get("content-type")).toBe(
-        "text/html; charset=utf-8",
-      );
-      const body = await response.text();
-      expect(body).toContain("data-bb-app-client");
-      expect(body).toContain("window.bb");
-      expect(body).toContain('"capabilities":["data","message"]');
-      expect(body).toContain("<body>Status</body>");
-    });
-  });
-
-  it("serves flat app asset URLs from the internal assets directory", async () => {
-    await withTestHarness(async (harness) => {
-      const fixture = seedManagerThreadStorage(harness);
-      const request = harness.app.request(
-        `/api/v1/threads/${fixture.threadId}/apps/status/index-Cd7sCqsN.js`,
-      );
-      const manifestCommand = await reportManifestRead({
-        harness,
-        fixture,
-        appId: "status",
-        manifest: STATUS_MANIFEST,
-      });
-      const assetCommand = await waitForQueuedCommandAfter(
-        harness,
-        manifestCommand.row.cursor,
-        ({ command }) =>
-          command.type === "host.read_file_relative" &&
-          command.rootPath === appAssetsRoot(fixture, "status") &&
-          command.path === "index-Cd7sCqsN.js",
-      );
-      expect(assetCommand.command).toMatchObject({ dotfiles: "deny" });
-      await reportQueuedCommandSuccess(
-        harness,
-        assetCommand,
-        readFileResult({
-          path: "index-Cd7sCqsN.js",
-          content: "console.log('status');",
-          mimeType: "application/javascript",
-        }),
-      );
-
-      const response = await request;
-      expect(response.status).toBe(200);
-      expect(response.headers.get("content-type")).toBe(
-        "application/javascript",
-      );
-      expect(response.headers.get("x-content-type-options")).toBe("nosniff");
-      await expect(response.text()).resolves.toBe("console.log('status');");
-    });
-  });
-
-  it("serves nested flat app asset URLs without collapsing path segments", async () => {
-    await withTestHarness(async (harness) => {
-      const fixture = seedManagerThreadStorage(harness);
-      const request = harness.app.request(
-        `/api/v1/threads/${fixture.threadId}/apps/status/chunks/index-Cd7sCqsN.js`,
-      );
-      const manifestCommand = await reportManifestRead({
-        harness,
-        fixture,
-        appId: "status",
-        manifest: STATUS_MANIFEST,
-      });
-      const assetCommand = await waitForQueuedCommandAfter(
-        harness,
-        manifestCommand.row.cursor,
-        ({ command }) =>
-          command.type === "host.read_file_relative" &&
-          command.rootPath === appAssetsRoot(fixture, "status") &&
-          command.path === "chunks/index-Cd7sCqsN.js",
-      );
-      await reportQueuedCommandSuccess(
-        harness,
-        assetCommand,
-        readFileResult({
-          path: "chunks/index-Cd7sCqsN.js",
-          content: "export const status = true;",
-          mimeType: "application/javascript",
-        }),
-      );
-
-      const response = await request;
-      expect(response.status).toBe(200);
-      expect(response.headers.get("content-type")).toBe(
-        "application/javascript",
-      );
-      await expect(response.text()).resolves.toBe(
-        "export const status = true;",
-      );
-    });
-  });
-
-  it("returns JSON 404 for missing flat app assets instead of the outer SPA shell", async () => {
-    const staticDir = await mkdtemp(path.join(tmpdir(), "bb-apps-static-"));
-    await writeFile(
-      path.join(staticDir, "index.html"),
-      '<!doctype html><html lang="en" class="bb-app-shell-root"><head><title>bb</title></head><body>shell</body></html>',
-      "utf8",
-    );
-    const harness = await createTestAppHarness();
-    const serverApp = createApp(harness.deps, { staticDir });
-    try {
-      const fixture = seedManagerThreadStorage(harness);
-      const request = serverApp.app.request(
-        `/api/v1/threads/${fixture.threadId}/apps/status/missing.js`,
-      );
-      const manifestCommand = await reportManifestRead({
-        harness,
-        fixture,
-        appId: "status",
-        manifest: STATUS_MANIFEST,
-      });
-      const assetCommand = await waitForQueuedCommandAfter(
-        harness,
-        manifestCommand.row.cursor,
-        ({ command }) =>
-          command.type === "host.read_file_relative" &&
-          command.rootPath === appAssetsRoot(fixture, "status") &&
-          command.path === "missing.js",
-      );
-      await reportQueuedCommandError(harness, assetCommand, {
-        errorCode: "ENOENT",
-        errorMessage: "Path does not exist: missing.js",
-      });
-
-      const response = await request;
-      const body = await response.text();
-      expect(response.status).toBe(404);
-      expect(response.headers.get("content-type")).toBe("application/json");
-      expect(body).not.toContain("bb-app-shell-root");
-      expect(JSON.parse(body)).toMatchObject({
-        code: "ENOENT",
-        message: "Path does not exist: missing.js",
-      });
-    } finally {
-      await serverApp.closeWebSockets();
-      await harness.cleanup();
-      await rm(staticDir, { recursive: true, force: true });
-    }
-  });
-
-  it("proxies app data list, read, write, and delete through generic daemon file commands", async () => {
-    await withTestHarness(async (harness) => {
-      const fixture = seedManagerThreadStorage(harness);
-      const stateJson = `${JSON.stringify({ workers: [] }, null, 2)}\n`;
-
-      const listRequest = harness.app.request(
-        `/api/v1/threads/${fixture.threadId}/apps/status/data`,
-      );
-      const listManifest = await reportManifestRead({
-        harness,
-        fixture,
-        appId: "status",
-        manifest: STATUS_MANIFEST,
-      });
-      const listCommand = await waitForQueuedCommandAfter(
-        harness,
-        listManifest.row.cursor,
-        ({ command }) =>
-          command.type === "host.list_paths" &&
-          command.path === appDataRoot(fixture, "status"),
-      );
-      await reportQueuedCommandSuccess(harness, listCommand, {
-        paths: [pathEntry({ kind: "file", path: "state.json" })],
-        truncated: false,
-      });
-      const listRead = await waitForQueuedCommandAfter(
-        harness,
-        listCommand.row.cursor,
-        ({ command }) =>
-          command.type === "host.read_file_relative" &&
-          command.rootPath === appDataRoot(fixture, "status") &&
-          command.path === "state.json",
-      );
-      await reportQueuedCommandSuccess(
-        harness,
-        listRead,
-        readFileResult({
-          path: "state.json",
-          content: stateJson,
-          mimeType: "application/json",
-        }),
-      );
-      const listMetadata = await waitForQueuedCommandAfter(
-        harness,
-        listCommand.row.cursor,
-        ({ command }) =>
-          command.type === "host.file_metadata" &&
-          command.path === `${appDataRoot(fixture, "status")}/state.json`,
-      );
-      await reportQueuedCommandSuccess(harness, listMetadata, {
-        path: `${appDataRoot(fixture, "status")}/state.json`,
-        modifiedAtMs: 1234,
-        sizeBytes: Buffer.byteLength(stateJson),
-      });
-      const listResponse = await listRequest;
-      expect(listResponse.status).toBe(200);
-      expect(
-        appDataListResponseSchema.parse(await readJson(listResponse)),
-      ).toEqual({
-        entries: [
-          {
-            path: "state.json",
-            value: { workers: [] },
-            version: sha256Text(stateJson),
-            sizeBytes: Buffer.byteLength(stateJson),
-            modifiedAtMs: 1234,
-          },
-        ],
-      });
-
-      const readRequest = harness.app.request(
-        `/api/v1/threads/${fixture.threadId}/apps/status/data/state.json`,
-      );
-      const readManifest = await reportManifestRead({
-        harness,
-        fixture,
-        appId: "status",
-        afterCursor: listMetadata.row.cursor,
-        manifest: STATUS_MANIFEST,
-      });
-      const readCommand = await waitForQueuedCommandAfter(
-        harness,
-        readManifest.row.cursor,
-        ({ command }) =>
-          command.type === "host.read_file_relative" &&
-          command.rootPath === appDataRoot(fixture, "status") &&
-          command.path === "state.json",
-      );
-      await reportQueuedCommandSuccess(
-        harness,
-        readCommand,
-        readFileResult({
-          path: "state.json",
-          content: stateJson,
-          mimeType: "application/json",
-        }),
-      );
-      const readMetadata = await waitForQueuedCommandAfter(
-        harness,
-        readManifest.row.cursor,
-        ({ command }) =>
-          command.type === "host.file_metadata" &&
-          command.path === `${appDataRoot(fixture, "status")}/state.json`,
-      );
-      await reportQueuedCommandSuccess(harness, readMetadata, {
-        path: `${appDataRoot(fixture, "status")}/state.json`,
-        modifiedAtMs: 2345,
-        sizeBytes: Buffer.byteLength(stateJson),
-      });
-      const readResponse = await readRequest;
-      expect(readResponse.status).toBe(200);
-      expect(
-        appDataReadResponseSchema.parse(await readJson(readResponse)),
-      ).toEqual({
-        path: "state.json",
-        value: { workers: [] },
-        version: sha256Text(stateJson),
-        sizeBytes: Buffer.byteLength(stateJson),
-        modifiedAtMs: 2345,
-      });
-
-      const nextValue = { workers: [{ id: "worker-1" }] };
-      const nextJson = `${JSON.stringify(nextValue, null, 2)}\n`;
-      const writeRequest = harness.app.request(
-        `/api/v1/threads/${fixture.threadId}/apps/status/data/state.json`,
-        {
-          method: "PUT",
-          headers: { "content-type": "application/json" },
-          body: JSON.stringify({ value: nextValue }),
-        },
-      );
-      const writeManifest = await reportManifestRead({
-        harness,
-        fixture,
-        appId: "status",
-        afterCursor: readMetadata.row.cursor,
-        manifest: STATUS_MANIFEST,
-      });
-      const writeCommand = await waitForQueuedCommandAfter(
-        harness,
-        writeManifest.row.cursor,
-        ({ command }) =>
-          command.type === "host.write_file_relative" &&
-          command.rootPath === appDataRoot(fixture, "status") &&
-          command.path === "state.json",
-      );
-      expect(writeCommand.command).toMatchObject({
-        dotfiles: "deny",
-        content: nextJson,
-        contentEncoding: "utf8",
-      });
-      await reportQueuedCommandSuccess(harness, writeCommand, {
-        path: "state.json",
-        hash: sha256Text(nextJson),
-        modifiedAtMs: 3456,
-        sizeBytes: Buffer.byteLength(nextJson),
-      });
-      const writeResponse = await writeRequest;
-      expect(writeResponse.status).toBe(200);
-      expect(
-        appDataReadResponseSchema.parse(await readJson(writeResponse)),
-      ).toEqual({
-        path: "state.json",
-        value: nextValue,
-        version: sha256Text(nextJson),
-        sizeBytes: Buffer.byteLength(nextJson),
-        modifiedAtMs: 3456,
-      });
-
-      const deleteRequest = harness.app.request(
-        `/api/v1/threads/${fixture.threadId}/apps/status/data/state.json`,
-        { method: "DELETE" },
-      );
-      const deleteManifest = await reportManifestRead({
-        harness,
-        fixture,
-        appId: "status",
-        afterCursor: writeCommand.row.cursor,
-        manifest: STATUS_MANIFEST,
-      });
-      const deleteCommand = await waitForQueuedCommandAfter(
-        harness,
-        deleteManifest.row.cursor,
-        ({ command }) =>
-          command.type === "host.delete_file_relative" &&
-          command.rootPath === appDataRoot(fixture, "status") &&
-          command.path === "state.json",
-      );
-      await reportQueuedCommandSuccess(harness, deleteCommand, {
-        path: "state.json",
-        deleted: true,
-        previousHash: sha256Text(nextJson),
-      });
-      const deleteResponse = await deleteRequest;
-      expect(deleteResponse.status).toBe(200);
-      await expect(readJson(deleteResponse)).resolves.toEqual({ ok: true });
-    });
-  });
-
-  it("lists app data subtree prefixes when the prefix is a directory", async () => {
-    await withTestHarness(async (harness) => {
-      const fixture = seedManagerThreadStorage(harness);
-      const oneJson = `${JSON.stringify({ title: "One" }, null, 2)}\n`;
-      const twoJson = `${JSON.stringify({ title: "Two" }, null, 2)}\n`;
-
-      const request = harness.app.request(
-        `/api/v1/threads/${fixture.threadId}/apps/status/data?prefix=tasks`,
-      );
-      const manifestCommand = await reportManifestRead({
-        harness,
-        fixture,
-        appId: "status",
-        manifest: STATUS_MANIFEST,
-      });
-      const prefixRead = await waitForQueuedCommandAfter(
-        harness,
-        manifestCommand.row.cursor,
-        ({ command }) =>
-          command.type === "host.read_file_relative" &&
-          command.rootPath === appDataRoot(fixture, "status") &&
-          command.path === "tasks",
-      );
-      await reportQueuedCommandError(harness, prefixRead, {
-        errorCode: "invalid_path",
-        errorMessage: "Path is a directory, not a file",
-      });
-      const listCommand = await waitForQueuedCommandAfter(
-        harness,
-        prefixRead.row.cursor,
-        ({ command }) =>
-          command.type === "host.list_paths" &&
-          command.path === `${appDataRoot(fixture, "status")}/tasks`,
-      );
-      await reportQueuedCommandSuccess(harness, listCommand, {
-        paths: [
-          pathEntry({ kind: "file", path: "one.json" }),
-          pathEntry({ kind: "file", path: "nested/two.json" }),
-        ],
-        truncated: false,
-      });
-
-      const oneRead = await waitForQueuedCommandAfter(
-        harness,
-        listCommand.row.cursor,
-        ({ command }) =>
-          command.type === "host.read_file_relative" &&
-          command.rootPath === appDataRoot(fixture, "status") &&
-          command.path === "tasks/one.json",
-      );
-      await reportQueuedCommandSuccess(
-        harness,
-        oneRead,
-        readFileResult({
-          path: "tasks/one.json",
-          content: oneJson,
-          mimeType: "application/json",
-        }),
-      );
-      const twoRead = await waitForQueuedCommandAfter(
-        harness,
-        listCommand.row.cursor,
-        ({ command }) =>
-          command.type === "host.read_file_relative" &&
-          command.rootPath === appDataRoot(fixture, "status") &&
-          command.path === "tasks/nested/two.json",
-      );
-      await reportQueuedCommandSuccess(
-        harness,
-        twoRead,
-        readFileResult({
-          path: "tasks/nested/two.json",
-          content: twoJson,
-          mimeType: "application/json",
-        }),
-      );
-      const oneMetadata = await waitForQueuedCommandAfter(
-        harness,
-        oneRead.row.cursor,
-        ({ command }) =>
-          command.type === "host.file_metadata" &&
-          command.path === `${appDataRoot(fixture, "status")}/tasks/one.json`,
-      );
-      await reportQueuedCommandSuccess(harness, oneMetadata, {
-        path: `${appDataRoot(fixture, "status")}/tasks/one.json`,
-        modifiedAtMs: 1111,
-        sizeBytes: Buffer.byteLength(oneJson),
-      });
-      const twoMetadata = await waitForQueuedCommandAfter(
-        harness,
-        twoRead.row.cursor,
-        ({ command }) =>
-          command.type === "host.file_metadata" &&
-          command.path ===
-            `${appDataRoot(fixture, "status")}/tasks/nested/two.json`,
-      );
-      await reportQueuedCommandSuccess(harness, twoMetadata, {
-        path: `${appDataRoot(fixture, "status")}/tasks/nested/two.json`,
-        modifiedAtMs: 2222,
-        sizeBytes: Buffer.byteLength(twoJson),
-      });
-
-      const response = await request;
-      expect(response.status).toBe(200);
-      expect(appDataListResponseSchema.parse(await readJson(response))).toEqual(
-        {
-          entries: [
-            {
-              path: "tasks/nested/two.json",
-              value: { title: "Two" },
-              version: sha256Text(twoJson),
-              sizeBytes: Buffer.byteLength(twoJson),
-              modifiedAtMs: 2222,
-            },
-            {
-              path: "tasks/one.json",
-              value: { title: "One" },
-              version: sha256Text(oneJson),
-              sizeBytes: Buffer.byteLength(oneJson),
-              modifiedAtMs: 1111,
-            },
-          ],
-        },
-      );
-    });
-  });
-
-  it("serves top-level logo icons and 404s built-in icons", async () => {
-    await withTestHarness(async (harness) => {
-      const fixture = seedManagerThreadStorage(harness);
-      const logoManifest: AppManifest = {
-        manifestVersion: 1,
-        id: "demo",
-        name: "Demo",
-        entry: "index.html",
-        contributions: ["thread.app"],
-        capabilities: ["data", "message"],
-      };
-      const logoSvg = '<svg xmlns="http://www.w3.org/2000/svg"></svg>';
-      const request = harness.app.request(
-        `/api/v1/threads/${fixture.threadId}/apps/demo/icon`,
-      );
-      const manifestCommand = await reportManifestRead({
-        harness,
-        fixture,
-        appId: "demo",
-        manifest: logoManifest,
-      });
-      const logoListCommand = await waitForQueuedCommandAfter(
-        harness,
-        manifestCommand.row.cursor,
-        ({ command }) =>
-          command.type === "host.list_paths" &&
-          command.path === appRoot(fixture, "demo"),
-      );
-      await reportQueuedCommandSuccess(harness, logoListCommand, {
-        paths: [pathEntry({ kind: "file", path: "logo.svg" })],
-        truncated: false,
-      });
-      const metadataCommand = await waitForQueuedCommandAfter(
-        harness,
-        logoListCommand.row.cursor,
-        ({ command }) =>
-          command.type === "host.file_metadata" &&
-          command.path === `${appRoot(fixture, "demo")}/logo.svg`,
-      );
-      await reportQueuedCommandSuccess(harness, metadataCommand, {
-        path: `${appRoot(fixture, "demo")}/logo.svg`,
-        modifiedAtMs: 4567,
-        sizeBytes: Buffer.byteLength(logoSvg),
-      });
-      const readCommand = await waitForQueuedCommandAfter(
-        harness,
-        metadataCommand.row.cursor,
-        ({ command }) =>
-          command.type === "host.read_file_relative" &&
-          command.rootPath === appRoot(fixture, "demo") &&
-          command.path === "logo.svg",
-      );
-      await reportQueuedCommandSuccess(
-        harness,
-        readCommand,
-        readFileResult({
-          path: "logo.svg",
-          content: logoSvg,
-          mimeType: "image/svg+xml",
-        }),
-      );
-      const response = await request;
-      expect(response.status).toBe(200);
-      expect(response.headers.get("content-type")).toBe("image/svg+xml");
-      await expect(response.text()).resolves.toBe(logoSvg);
-
-      const builtInRequest = harness.app.request(
-        `/api/v1/threads/${fixture.threadId}/apps/status/icon`,
-      );
-      await reportManifestRead({
-        harness,
-        fixture,
-        appId: "status",
-        afterCursor: readCommand.row.cursor,
-        manifest: STATUS_MANIFEST,
-      });
-      const builtInResponse = await builtInRequest;
-      expect(builtInResponse.status).toBe(404);
-    });
-  });
-
-  it("does not serve logo symlinks omitted by the daemon path listing", async () => {
-    await withTestHarness(async (harness) => {
-      const fixture = seedManagerThreadStorage(harness);
-      const logoManifest: AppManifest = {
-        manifestVersion: 1,
-        id: "demo",
-        name: "Demo",
-        entry: "index.html",
-        contributions: ["thread.app"],
-        capabilities: ["data", "message"],
-      };
-      const request = harness.app.request(
-        `/api/v1/threads/${fixture.threadId}/apps/demo/icon`,
-      );
-      const manifestCommand = await reportManifestRead({
-        harness,
-        fixture,
-        appId: "demo",
-        manifest: logoManifest,
-      });
-      const logoListCommand = await waitForQueuedCommandAfter(
-        harness,
-        manifestCommand.row.cursor,
-        ({ command }) =>
-          command.type === "host.list_paths" &&
-          command.path === appRoot(fixture, "demo"),
-      );
-      await reportQueuedCommandSuccess(harness, logoListCommand, {
-        paths: [pathEntry({ kind: "file", path: "manifest.json" })],
-        truncated: false,
-      });
-
-      const response = await request;
-      expect(response.status).toBe(404);
-    });
-  });
-
-  it("scaffolds status-template apps through the server lifecycle route", async () => {
-    await withTestHarness(async (harness) => {
-      const fixture = seedManagerThreadStorage(harness);
-      const request = harness.app.request(
-        `/api/v1/threads/${fixture.threadId}/apps`,
-        {
-          method: "POST",
-          headers: { "content-type": "application/json" },
-          body: JSON.stringify({
-            id: "demo",
-            name: "Demo",
-            template: "status",
-          }),
-        },
-      );
-      const existingCommand = await waitForQueuedCommand(
-        harness,
-        ({ command }) =>
-          command.type === "host.read_file_relative" &&
-          command.rootPath === appRoot(fixture, "demo") &&
-          command.path === "manifest.json",
-      );
-      await reportQueuedCommandError(harness, existingCommand, {
-        errorCode: "ENOENT",
-        errorMessage: "Path does not exist: manifest.json",
-      });
-
-      const manifestWrite = await waitForQueuedCommandAfter(
-        harness,
-        existingCommand.row.cursor,
-        ({ command }) =>
-          command.type === "host.write_file_relative" &&
-          command.rootPath === appRoot(fixture, "demo") &&
-          command.path === "manifest.json",
-      );
-      expect(manifestWrite.command).toMatchObject({
-        dotfiles: "deny",
-        contentEncoding: "utf8",
-      });
-      const manifestWriteCommand =
-        requireWriteFileRelativeCommand(manifestWrite);
-      await reportQueuedCommandSuccess(harness, manifestWrite, {
-        path: "manifest.json",
-        hash: sha256Text(manifestWriteCommand.command.content),
-        modifiedAtMs: 1000,
-        sizeBytes: Buffer.byteLength(manifestWriteCommand.command.content),
-      });
-
-      const htmlWrite = await waitForQueuedCommandAfter(
-        harness,
-        manifestWrite.row.cursor,
-        ({ command }) =>
-          command.type === "host.write_file_relative" &&
-          command.rootPath === appRoot(fixture, "demo") &&
-          command.path === "assets/index.html",
-      );
-      const htmlWriteCommand = requireWriteFileRelativeCommand(htmlWrite);
-      await reportQueuedCommandSuccess(harness, htmlWrite, {
-        path: "assets/index.html",
-        hash: sha256Text(htmlWriteCommand.command.content),
-        modifiedAtMs: 1001,
-        sizeBytes: Buffer.byteLength(htmlWriteCommand.command.content),
-      });
-
-      const stateWrite = await waitForQueuedCommandAfter(
-        harness,
-        htmlWrite.row.cursor,
-        ({ command }) =>
-          command.type === "host.write_file_relative" &&
-          command.rootPath === appRoot(fixture, "demo") &&
-          command.path === "data/state.json",
-      );
-      const stateWriteCommand = requireWriteFileRelativeCommand(stateWrite);
-      await reportQueuedCommandSuccess(harness, stateWrite, {
-        path: "data/state.json",
-        hash: sha256Text(stateWriteCommand.command.content),
-        modifiedAtMs: 1002,
-        sizeBytes: Buffer.byteLength(stateWriteCommand.command.content),
-      });
-
-      await reportManifestRead({
-        harness,
-        fixture,
-        appId: "demo",
-        afterCursor: stateWrite.row.cursor,
-        manifest: {
-          manifestVersion: 1,
-          id: "demo",
-          name: "Demo",
-          icon: "ListTodo",
-          entry: "index.html",
-          contributions: ["thread.app"],
-          capabilities: ["data", "message"],
-        },
-      });
-
-      const response = await request;
-      expect(response.status).toBe(201);
-      expect(appDetailSchema.parse(await readJson(response))).toMatchObject({
-        id: "demo",
-        name: "Demo",
-        entry: { kind: "html", path: "index.html" },
-        icon: { kind: "builtin", name: "ListTodo" },
-        capabilities: ["data", "message"],
-      });
-    });
-  });
-
-  it("scaffolds blank-template apps with the bb-styled index.html", async () => {
-    await withTestHarness(async (harness) => {
-      const fixture = seedManagerThreadStorage(harness);
-      const request = harness.app.request(
-        `/api/v1/threads/${fixture.threadId}/apps`,
-        {
-          method: "POST",
-          headers: { "content-type": "application/json" },
-          body: JSON.stringify({
-            id: "blank-demo",
-            name: "Blank Demo",
-            template: "blank",
-          }),
-        },
-      );
-      const existingCommand = await waitForQueuedCommand(
-        harness,
-        ({ command }) =>
-          command.type === "host.read_file_relative" &&
-          command.rootPath === appRoot(fixture, "blank-demo") &&
-          command.path === "manifest.json",
-      );
-      await reportQueuedCommandError(harness, existingCommand, {
-        errorCode: "ENOENT",
-        errorMessage: "Path does not exist: manifest.json",
-      });
-
-      const manifestWrite = await waitForQueuedCommandAfter(
-        harness,
-        existingCommand.row.cursor,
-        ({ command }) =>
-          command.type === "host.write_file_relative" &&
-          command.rootPath === appRoot(fixture, "blank-demo") &&
-          command.path === "manifest.json",
-      );
-      const manifestWriteCommand =
-        requireWriteFileRelativeCommand(manifestWrite);
-      await reportQueuedCommandSuccess(harness, manifestWrite, {
-        path: "manifest.json",
-        hash: sha256Text(manifestWriteCommand.command.content),
-        modifiedAtMs: 1000,
-        sizeBytes: Buffer.byteLength(manifestWriteCommand.command.content),
-      });
-
-      const htmlWrite = await waitForQueuedCommandAfter(
-        harness,
-        manifestWrite.row.cursor,
-        ({ command }) =>
-          command.type === "host.write_file_relative" &&
-          command.rootPath === appRoot(fixture, "blank-demo") &&
-          command.path === "assets/index.html",
-      );
-      const htmlWriteCommand = requireWriteFileRelativeCommand(htmlWrite);
-      const html = htmlWriteCommand.command.content;
-      // bb design tokens come through verbatim from `bb guide styling`.
-      expect(html).toContain('--font-sans: "Inter"');
-      expect(html).toContain("oklch(0.9551 0 0)");
-      expect(html).toContain("@media (prefers-color-scheme: dark)");
-      // Placeholder copy keeps the blank scaffold aligned with app guidance.
-      expect(html).toContain(
-        "No web server or build step needed.",
-      );
-      // Task-list row vocabulary is present so the scaffold looks bb-native.
-      expect(html).toContain('class="row"');
-      expect(html).toContain('class="pill"');
-      // App name is interpolated into the visible title.
-      expect(html).toContain("<title>Blank Demo</title>");
-      await reportQueuedCommandSuccess(harness, htmlWrite, {
-        path: "assets/index.html",
-        hash: sha256Text(html),
-        modifiedAtMs: 1001,
-        sizeBytes: Buffer.byteLength(html),
-      });
-
-      const stateWrite = await waitForQueuedCommandAfter(
-        harness,
-        htmlWrite.row.cursor,
-        ({ command }) =>
-          command.type === "host.write_file_relative" &&
-          command.rootPath === appRoot(fixture, "blank-demo") &&
-          command.path === "data/state.json",
-      );
-      const stateWriteCommand = requireWriteFileRelativeCommand(stateWrite);
-      await reportQueuedCommandSuccess(harness, stateWrite, {
-        path: "data/state.json",
-        hash: sha256Text(stateWriteCommand.command.content),
-        modifiedAtMs: 1002,
-        sizeBytes: Buffer.byteLength(stateWriteCommand.command.content),
-      });
-
-      const manifestRead = await reportManifestRead({
-        harness,
-        fixture,
-        appId: "blank-demo",
-        afterCursor: stateWrite.row.cursor,
-        manifest: {
-          manifestVersion: 1,
-          id: "blank-demo",
-          name: "Blank Demo",
-          entry: "index.html",
-          contributions: ["thread.app"],
-          capabilities: ["data", "message"],
-        },
-      });
-
-      // No icon in manifest -> server probes the app root for a logo file.
-      const logoListCommand = await waitForQueuedCommandAfter(
-        harness,
-        manifestRead.row.cursor,
-        ({ command }) =>
-          command.type === "host.list_paths" &&
-          command.path === appRoot(fixture, "blank-demo"),
-      );
-      await reportQueuedCommandSuccess(harness, logoListCommand, {
-        paths: [],
-        truncated: false,
-      });
-
-      const response = await request;
-      expect(response.status).toBe(201);
-      expect(appDetailSchema.parse(await readJson(response))).toMatchObject({
-        id: "blank-demo",
-        name: "Blank Demo",
-        entry: { kind: "html", path: "index.html" },
-        icon: { kind: "builtin", name: "GridView" },
-        capabilities: ["data", "message"],
-      });
-    });
-  });
-
-  it("HTML-escapes the app name in the blank scaffold to block XSS", async () => {
-    await withTestHarness(async (harness) => {
-      const fixture = seedManagerThreadStorage(harness);
-      const maliciousName = `<script>alert(1)</script> & "q" 'a'`;
-      const request = harness.app.request(
-        `/api/v1/threads/${fixture.threadId}/apps`,
-        {
-          method: "POST",
-          headers: { "content-type": "application/json" },
-          body: JSON.stringify({
-            id: "xss-demo",
-            name: maliciousName,
-            template: "blank",
-          }),
-        },
-      );
-      const existingCommand = await waitForQueuedCommand(
-        harness,
-        ({ command }) =>
-          command.type === "host.read_file_relative" &&
-          command.rootPath === appRoot(fixture, "xss-demo") &&
-          command.path === "manifest.json",
-      );
-      await reportQueuedCommandError(harness, existingCommand, {
-        errorCode: "ENOENT",
-        errorMessage: "Path does not exist: manifest.json",
-      });
-
-      const manifestWrite = await waitForQueuedCommandAfter(
-        harness,
-        existingCommand.row.cursor,
-        ({ command }) =>
-          command.type === "host.write_file_relative" &&
-          command.rootPath === appRoot(fixture, "xss-demo") &&
-          command.path === "manifest.json",
-      );
-      const manifestWriteCommand =
-        requireWriteFileRelativeCommand(manifestWrite);
-      await reportQueuedCommandSuccess(harness, manifestWrite, {
-        path: "manifest.json",
-        hash: sha256Text(manifestWriteCommand.command.content),
-        modifiedAtMs: 2000,
-        sizeBytes: Buffer.byteLength(manifestWriteCommand.command.content),
-      });
-
-      const htmlWrite = await waitForQueuedCommandAfter(
-        harness,
-        manifestWrite.row.cursor,
-        ({ command }) =>
-          command.type === "host.write_file_relative" &&
-          command.rootPath === appRoot(fixture, "xss-demo") &&
-          command.path === "assets/index.html",
-      );
-      const htmlWriteCommand = requireWriteFileRelativeCommand(htmlWrite);
-      const html = htmlWriteCommand.command.content;
-
-      // Raw special characters from the name must never reach the rendered
-      // HTML where they would be interpreted as markup.
-      expect(html).not.toContain("<script>alert(1)</script>");
-      expect(html).not.toContain('name & "q"');
-      expect(html).not.toContain("'a'");
-      // Each special char in the name is replaced with its entity form.
-      expect(html).toContain("&lt;script&gt;alert(1)&lt;/script&gt;");
-      expect(html).toContain("&amp;");
-      expect(html).toContain("&quot;q&quot;");
-      expect(html).toContain("&#39;a&#39;");
-      // The escaped name shows up in both the <title> and the visible header.
-      const escapedName =
-        "&lt;script&gt;alert(1)&lt;/script&gt; &amp; &quot;q&quot; &#39;a&#39;";
-      expect(html).toContain(`<title>${escapedName}</title>`);
-      expect(html).toContain(
-        `<span class="title">${escapedName}</span>`,
-      );
-
-      await reportQueuedCommandSuccess(harness, htmlWrite, {
-        path: "assets/index.html",
-        hash: sha256Text(html),
-        modifiedAtMs: 2001,
-        sizeBytes: Buffer.byteLength(html),
-      });
-
-      const stateWrite = await waitForQueuedCommandAfter(
-        harness,
-        htmlWrite.row.cursor,
-        ({ command }) =>
-          command.type === "host.write_file_relative" &&
-          command.rootPath === appRoot(fixture, "xss-demo") &&
-          command.path === "data/state.json",
-      );
-      const stateWriteCommand = requireWriteFileRelativeCommand(stateWrite);
-      await reportQueuedCommandSuccess(harness, stateWrite, {
-        path: "data/state.json",
-        hash: sha256Text(stateWriteCommand.command.content),
-        modifiedAtMs: 2002,
-        sizeBytes: Buffer.byteLength(stateWriteCommand.command.content),
-      });
-
-      const manifestRead = await reportManifestRead({
-        harness,
-        fixture,
-        appId: "xss-demo",
-        afterCursor: stateWrite.row.cursor,
-        manifest: {
-          manifestVersion: 1,
-          id: "xss-demo",
-          name: maliciousName,
-          entry: "index.html",
-          contributions: ["thread.app"],
-          capabilities: ["data", "message"],
-        },
-      });
-
-      const logoListCommand = await waitForQueuedCommandAfter(
-        harness,
-        manifestRead.row.cursor,
-        ({ command }) =>
-          command.type === "host.list_paths" &&
-          command.path === appRoot(fixture, "xss-demo"),
-      );
-      await reportQueuedCommandSuccess(harness, logoListCommand, {
-        paths: [],
-        truncated: false,
-      });
-
-      const response = await request;
-      expect(response.status).toBe(201);
-    });
-  });
-});
diff --git a/apps/server/test/public/public-threads.manager-and-ownership.test.ts b/apps/server/test/public/public-threads.manager-and-ownership.test.ts
index 05af96067..944c869c7 100644
--- a/apps/server/test/public/public-threads.manager-and-ownership.test.ts
+++ b/apps/server/test/public/public-threads.manager-and-ownership.test.ts
@@ -471,7 +471,7 @@ describe("public thread manager and ownership routes", () => {
         name: "default",
         files: {
           "PREFERENCES.md": "default prefs\n",
-          "apps/status/data/state.json": '{"prs":[]}\n',
+          "notes/state.json": '{"prs":[]}\n',
         },
       });
 
@@ -529,8 +529,11 @@ describe("public thread manager and ownership routes", () => {
         readFile(path.join(storagePath, "PREFERENCES.md"), "utf8"),
       ).resolves.toBe("default prefs\n");
       await expect(
-        readFile(path.join(storagePath, "apps/status/data/state.json"), "utf8"),
+        readFile(path.join(storagePath, "notes/state.json"), "utf8"),
       ).resolves.toBe('{"prs":[]}\n');
+      await expect(
+        stat(path.join(storagePath, "apps", "status", "manifest.json")),
+      ).rejects.toThrow();
     } finally {
       await harness.cleanup();
       await rm(dataDir, { recursive: true, force: true });
@@ -1107,17 +1110,8 @@ describe("public thread manager and ownership routes", () => {
         stat(path.join(storagePath, "PREFERENCES.md")),
       ).rejects.toThrow();
       await expect(
-        readFile(path.join(storagePath, "apps/status/manifest.json"), "utf8"),
-      ).resolves.toContain('"id": "status"');
-      await expect(
-        readFile(
-          path.join(storagePath, "apps/status/assets/index.html"),
-          "utf8",
-        ),
-      ).resolves.toContain("<title>Status</title>");
-      await expect(
-        readFile(path.join(storagePath, "apps/status/data/state.json"), "utf8"),
-      ).resolves.toBe("{}\n");
+        stat(path.join(storagePath, "apps", "status", "manifest.json")),
+      ).rejects.toThrow();
     } finally {
       await harness.cleanup();
       await rm(dataDir, { recursive: true, force: true });
diff --git a/apps/server/test/scheduling/nudge-sweep.test.ts b/apps/server/test/scheduling/nudge-sweep.test.ts
index a74ae42b1..a15fdc8a0 100644
--- a/apps/server/test/scheduling/nudge-sweep.test.ts
+++ b/apps/server/test/scheduling/nudge-sweep.test.ts
@@ -321,6 +321,7 @@ describe("nudge sweep", () => {
               providerThreadId: "provider-manager-thread",
               instructions: "manager instructions",
               dynamicTools: [],
+              injectedSkillSources: [],
               instructionMode: "append",
             },
             target: { mode: "start" },
diff --git a/apps/server/test/services/threads/app-client-script.test.ts b/apps/server/test/services/threads/app-client-script.test.ts
index c2ad6b769..c5a091151 100644
--- a/apps/server/test/services/threads/app-client-script.test.ts
+++ b/apps/server/test/services/threads/app-client-script.test.ts
@@ -13,7 +13,10 @@ type OpenHandler = () => void;
 type CloseHandler = () => void;
 type ErrorHandler = () => void;
 type MessageHandler = (event: SocketMessageEvent) => void;
-type FetchMock = (input: RequestInfo | URL, init?: RequestInit) => Promise<Response>;
+type FetchMock = (
+  input: RequestInfo | URL,
+  init?: RequestInit,
+) => Promise<Response>;
 
 interface SocketMessageEvent {
   data: string;
@@ -35,10 +38,12 @@ interface DeferredResponse {
 
 const bootstrap: AppClientBootstrap = {
   appId: "status",
+  applicationId: "status",
+  appSessionToken: "appsess_test",
   capabilities: ["data", "message"],
-  threadId: "thr_123",
-  dataUrl: "/api/v1/threads/thr_123/apps/status/data",
-  messageUrl: "/api/v1/threads/thr_123/apps/status/message",
+  dataUrl: "/api/v1/apps/status/data",
+  messageUrl: "/api/v1/apps/status/message",
+  targetThreadId: "thr_123",
   wsUrl: "ws://server/ws",
 };
 
@@ -147,10 +152,10 @@ describe("app client script", () => {
     expect(JSON.parse(socket.messages[0] ?? "")).toEqual({
       type: "subscribe",
       entity: "thread",
-      id: "thr_123:app:status:data",
+      id: "status:data",
     });
     expect(fetchMock).toHaveBeenCalledWith(
-      "/api/v1/threads/thr_123/apps/status/data",
+      "/api/v1/apps/status/data",
       expect.objectContaining({ method: "GET" }),
     );
   });
@@ -194,12 +199,12 @@ describe("app client script", () => {
       {
         type: "subscribe",
         entity: "thread",
-        id: "thr_123:app:status:data",
+        id: "status:data",
       },
       {
         type: "unsubscribe",
         entity: "thread",
-        id: "thr_123:app:status:data",
+        id: "status:data",
       },
     ]);
   });
@@ -248,8 +253,7 @@ describe("app client script", () => {
     await flushPromises();
     socket.emit({
       type: "app-data.resync",
-      threadId: "thr_123",
-      appId: "status",
+      applicationId: "status",
     });
     await vi.waitFor(() => {
       expect(callback).toHaveBeenCalledTimes(2);
diff --git a/apps/server/test/skills/injected-skills.test.ts b/apps/server/test/skills/injected-skills.test.ts
new file mode 100644
index 000000000..7780f8506
--- /dev/null
+++ b/apps/server/test/skills/injected-skills.test.ts
@@ -0,0 +1,221 @@
+import { mkdir, mkdtemp, rm, symlink, writeFile } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import path from "node:path";
+import { afterEach, describe, expect, it } from "vitest";
+import { resolveApplicationPath } from "@bb/config/app-storage-paths";
+import { applicationIdSchema, type ApplicationId } from "@bb/domain";
+import { resolveInjectedSkillSources } from "../../src/services/skills/injected-skills.js";
+import type { ServerLogger } from "../../src/types.js";
+
+interface CapturedWarning {
+  context: object;
+  message: string;
+}
+
+interface CapturingLogger {
+  logger: ServerLogger;
+  warnings: CapturedWarning[];
+}
+
+interface WriteSkillArgs {
+  description?: string;
+  name: string;
+  rootPath: string;
+}
+
+interface WriteApplicationArgs {
+  applicationId: ApplicationId;
+  dataDir: string;
+}
+
+const tempDirs: string[] = [];
+
+async function makeTempDir(): Promise<string> {
+  const root = await mkdtemp(path.join(tmpdir(), "bb-injected-skills-"));
+  tempDirs.push(root);
+  return root;
+}
+
+afterEach(async () => {
+  await Promise.all(
+    tempDirs.splice(0).map((dir) => rm(dir, { recursive: true, force: true })),
+  );
+});
+
+function createCapturingLogger(): CapturingLogger {
+  const warnings: CapturedWarning[] = [];
+  function captureWarning(...args: Parameters<ServerLogger["warn"]>): void {
+    const firstArg = args[0];
+    const secondArg = args[1];
+    warnings.push({
+      context:
+        typeof firstArg === "object" && firstArg !== null ? firstArg : {},
+      message:
+        typeof secondArg === "string"
+          ? secondArg
+          : typeof firstArg === "string"
+            ? firstArg
+            : "",
+    });
+  }
+  return {
+    warnings,
+    logger: {
+      debug: () => undefined,
+      error: () => undefined,
+      info: () => undefined,
+      warn: captureWarning,
+    },
+  };
+}
+
+async function writeSkill(args: WriteSkillArgs): Promise<string> {
+  const skillRootPath = path.join(args.rootPath, args.name);
+  await mkdir(skillRootPath, { recursive: true });
+  await writeFile(
+    path.join(skillRootPath, "SKILL.md"),
+    [
+      "---",
+      `name: ${args.name}`,
+      `description: ${args.description ?? `Use ${args.name} when tests need it.`}`,
+      "---",
+      "",
+      `# ${args.name}`,
+      "",
+    ].join("\n"),
+    "utf8",
+  );
+  return skillRootPath;
+}
+
+async function writeApplication(args: WriteApplicationArgs): Promise<string> {
+  const appRootPath = resolveApplicationPath(args.dataDir, args.applicationId);
+  await mkdir(appRootPath, { recursive: true });
+  await writeFile(
+    path.join(appRootPath, "manifest.json"),
+    `${JSON.stringify(
+      {
+        manifestVersion: 1,
+        id: args.applicationId,
+        name: "Skill Test App",
+        capabilities: [],
+      },
+      null,
+      2,
+    )}\n`,
+    "utf8",
+  );
+  return appRootPath;
+}
+
+describe("injected skill source discovery", () => {
+  it("aggregates valid data-dir and global app skills", async () => {
+    const dataDir = await makeTempDir();
+    const applicationId = applicationIdSchema.parse("skillstest");
+    const appRootPath = await writeApplication({ dataDir, applicationId });
+    const dataDirSkillRoot = await writeSkill({
+      rootPath: path.join(dataDir, "skills"),
+      name: "release-notes",
+    });
+    const appSkillRoot = await writeSkill({
+      rootPath: path.join(appRootPath, "skills"),
+      name: "summarize-trades",
+    });
+    const { logger } = createCapturingLogger();
+
+    const sources = await resolveInjectedSkillSources(logger, { dataDir });
+
+    expect(sources).toEqual([
+      {
+        sourceType: "data-dir",
+        applicationId: null,
+        name: "release-notes",
+        description: "Use release-notes when tests need it.",
+        sourceRootPath: dataDirSkillRoot,
+        skillFilePath: path.join(dataDirSkillRoot, "SKILL.md"),
+      },
+      {
+        sourceType: "global-app",
+        applicationId,
+        name: "summarize-trades",
+        description: "Use summarize-trades when tests need it.",
+        sourceRootPath: appSkillRoot,
+        skillFilePath: path.join(appSkillRoot, "SKILL.md"),
+      },
+    ]);
+  });
+
+  it("skips invalid skills and logs the reason", async () => {
+    const dataDir = await makeTempDir();
+    const skillRootPath = path.join(dataDir, "skills", "valid-name");
+    await mkdir(skillRootPath, { recursive: true });
+    await writeFile(
+      path.join(skillRootPath, "SKILL.md"),
+      [
+        "---",
+        "name: other-name",
+        "description: Use when the mismatch test runs.",
+        "---",
+        "",
+      ].join("\n"),
+      "utf8",
+    );
+    const { logger, warnings } = createCapturingLogger();
+
+    expect(resolveInjectedSkillSources(logger, { dataDir })).toEqual([]);
+    expect(warnings).toEqual([
+      expect.objectContaining({
+        message: "Skipping invalid injected skill",
+      }),
+    ]);
+    expect(warnings[0]?.context).toMatchObject({
+      candidatePath: skillRootPath,
+      reason: "Frontmatter name must match the skill directory name",
+      sourceType: "data-dir",
+    });
+  });
+
+  it("rejects symlinked skill directories", async () => {
+    const dataDir = await makeTempDir();
+    const outsideRoot = await makeTempDir();
+    const skillsRootPath = path.join(dataDir, "skills");
+    await mkdir(skillsRootPath, { recursive: true });
+    await writeSkill({
+      rootPath: outsideRoot,
+      name: "outside-skill",
+    });
+    await symlink(
+      path.join(outsideRoot, "outside-skill"),
+      path.join(skillsRootPath, "outside-skill"),
+    );
+    const { logger, warnings } = createCapturingLogger();
+
+    expect(resolveInjectedSkillSources(logger, { dataDir })).toEqual([]);
+    expect(warnings[0]?.context).toMatchObject({
+      reason: "Skill directory is a symlink",
+      sourceType: "data-dir",
+    });
+  });
+
+  it("excludes all sources with colliding names across both roots", async () => {
+    const dataDir = await makeTempDir();
+    const applicationId = applicationIdSchema.parse("collision");
+    const appRootPath = await writeApplication({ dataDir, applicationId });
+    await writeSkill({
+      rootPath: path.join(dataDir, "skills"),
+      name: "shared-skill",
+    });
+    await writeSkill({
+      rootPath: path.join(appRootPath, "skills"),
+      name: "shared-skill",
+    });
+    const { logger, warnings } = createCapturingLogger();
+
+    expect(resolveInjectedSkillSources(logger, { dataDir })).toEqual([]);
+    expect(
+      warnings.filter(
+        (warning) => warning.message === "Skipping colliding injected skill",
+      ),
+    ).toHaveLength(2);
+  });
+});
diff --git a/apps/server/test/threads/manager-storage-templates.test.ts b/apps/server/test/threads/manager-storage-templates.test.ts
index 547d46ffb..573fa68d6 100644
--- a/apps/server/test/threads/manager-storage-templates.test.ts
+++ b/apps/server/test/threads/manager-storage-templates.test.ts
@@ -18,7 +18,6 @@ import {
   managerTemplateRootPath,
   seedManagerThreadStorage,
 } from "../../src/services/threads/manager-storage-templates.js";
-import { buildBlankAppIndexHtml } from "../../src/services/threads/blank-app-scaffold.js";
 import type { TestAppHarness } from "../helpers/test-app.js";
 import { seedHost } from "../helpers/seed.js";
 import { createTestAppHarness, testLogger, withTestHarness } from "../helpers/test-app.js";
@@ -76,42 +75,6 @@ async function createSeedHarness(): Promise<SeedHarness> {
   };
 }
 
-async function readBundledManifestJson(): Promise<string> {
-  return readFile(
-    new URL(
-      "../../src/services/threads/default-template/apps/status/manifest.json",
-      import.meta.url,
-    ),
-    "utf8",
-  );
-}
-
-const BUNDLED_STATUS_INDEX_HTML = buildBlankAppIndexHtml({ name: "Status" });
-const BUNDLED_STATUS_STATE_JSON = "{}\n";
-
-async function expectBundledStatusAppSeeded(
-  threadStoragePath: string,
-): Promise<void> {
-  await expect(
-    readFile(
-      path.join(threadStoragePath, "apps/status/manifest.json"),
-      "utf8",
-    ),
-  ).resolves.toBe(await readBundledManifestJson());
-  await expect(
-    readFile(
-      path.join(threadStoragePath, "apps/status/assets/index.html"),
-      "utf8",
-    ),
-  ).resolves.toBe(BUNDLED_STATUS_INDEX_HTML);
-  await expect(
-    readFile(
-      path.join(threadStoragePath, "apps/status/data/state.json"),
-      "utf8",
-    ),
-  ).resolves.toBe(BUNDLED_STATUS_STATE_JSON);
-}
-
 async function writeManagerTemplateSet(
   args: WriteManagerTemplateSetArgs,
 ): Promise<void> {
@@ -169,7 +132,7 @@ describe("manager storage templates", () => {
     });
   });
 
-  it("seeds the bundled status app when default resolves and no user template directory exists", async () => {
+  it("does not seed hidden default files when no user template directory exists", async () => {
     const { dataDir, harness, hostId } = await createSeedHarness();
     try {
       const threadStoragePath = await seedStorage({
@@ -180,7 +143,7 @@ describe("manager storage templates", () => {
         threadId: "thr-default-fallback",
       });
 
-      await expectBundledStatusAppSeeded(threadStoragePath);
+      await expect(stat(threadStoragePath)).rejects.toThrow();
       await expect(
         stat(managerTemplateRootPath({ dataDir })),
       ).rejects.toThrow();
@@ -190,7 +153,7 @@ describe("manager storage templates", () => {
     }
   });
 
-  it("overlays the bundled status app on top of user-authored default files", async () => {
+  it("copies user-authored default template files", async () => {
     const { dataDir, harness, hostId } = await createSeedHarness();
     try {
       await writeManagerTemplateSet({
@@ -198,6 +161,7 @@ describe("manager storage templates", () => {
         name: DEFAULT_MANAGER_TEMPLATE_NAME,
         files: {
           "USER.md": "user notes\n",
+          "notes/state.json": '{"prs":[]}\n',
         },
       });
 
@@ -212,25 +176,41 @@ describe("manager storage templates", () => {
       await expect(
         readFile(path.join(threadStoragePath, "USER.md"), "utf8"),
       ).resolves.toBe("user notes\n");
-      await expectBundledStatusAppSeeded(threadStoragePath);
+      await expect(
+        readFile(path.join(threadStoragePath, "notes/state.json"), "utf8"),
+      ).resolves.toBe('{"prs":[]}\n');
+      await expect(
+        stat(path.join(threadStoragePath, "apps", "status", "manifest.json")),
+      ).rejects.toThrow();
     } finally {
       await harness.cleanup();
       await rm(dataDir, { recursive: true, force: true });
     }
   });
 
-  it("user-authored files win over the bundled overlay at the same path", async () => {
+  it("does not overwrite files that already exist in thread storage", async () => {
     const { dataDir, harness, hostId } = await createSeedHarness();
     try {
       await writeManagerTemplateSet({
         dataDir,
         name: DEFAULT_MANAGER_TEMPLATE_NAME,
         files: {
-          "apps/status/manifest.json": '{"user":true}\n',
+          "USER.md": "template notes\n",
         },
       });
+      const threadStoragePath = path.join(
+        dataDir,
+        "thread-storage",
+        "thr-user-overrides",
+      );
+      await mkdir(threadStoragePath, { recursive: true });
+      await writeFile(
+        path.join(threadStoragePath, "USER.md"),
+        "existing notes\n",
+        "utf8",
+      );
 
-      const threadStoragePath = await seedStorage({
+      await seedStorage({
         dataDir,
         explicitTemplateName: null,
         harness,
@@ -239,30 +219,15 @@ describe("manager storage templates", () => {
       });
 
       await expect(
-        readFile(
-          path.join(threadStoragePath, "apps/status/manifest.json"),
-          "utf8",
-        ),
-      ).resolves.toBe('{"user":true}\n');
-      await expect(
-        readFile(
-          path.join(threadStoragePath, "apps/status/assets/index.html"),
-          "utf8",
-        ),
-      ).resolves.toBe(BUNDLED_STATUS_INDEX_HTML);
-      await expect(
-        readFile(
-          path.join(threadStoragePath, "apps/status/data/state.json"),
-          "utf8",
-        ),
-      ).resolves.toBe(BUNDLED_STATUS_STATE_JSON);
+        readFile(path.join(threadStoragePath, "USER.md"), "utf8"),
+      ).resolves.toBe("existing notes\n");
     } finally {
       await harness.cleanup();
       await rm(dataDir, { recursive: true, force: true });
     }
   });
 
-  it("overlays the bundled status app even when the default template directory is empty", async () => {
+  it("creates an empty storage directory when the default template directory is empty", async () => {
     const { dataDir, harness, hostId } = await createSeedHarness();
     try {
       await writeManagerTemplateSet({
@@ -279,14 +244,18 @@ describe("manager storage templates", () => {
         threadId: "thr-empty-default",
       });
 
-      await expectBundledStatusAppSeeded(threadStoragePath);
+      const storageStat = await stat(threadStoragePath);
+      expect(storageStat.isDirectory()).toBe(true);
+      await expect(
+        stat(path.join(threadStoragePath, "apps", "status", "manifest.json")),
+      ).rejects.toThrow();
     } finally {
       await harness.cleanup();
       await rm(dataDir, { recursive: true, force: true });
     }
   });
 
-  it("warns and still overlays bundled status when active points to a missing non-default template", async () => {
+  it("warns and seeds nothing when active points to a missing non-default template", async () => {
     const { dataDir, harness, hostId } = await createSeedHarness();
     const logger = {
       ...testLogger,
@@ -308,13 +277,13 @@ describe("manager storage templates", () => {
         threadId: "thr-missing-active",
       });
 
-      await expectBundledStatusAppSeeded(threadStoragePath);
+      await expect(stat(threadStoragePath)).rejects.toThrow();
       expect(logger.warn).toHaveBeenCalledWith(
         expect.objectContaining({
           templateName: MINE_MANAGER_TEMPLATE_NAME,
           threadId: "thr-missing-active",
         }),
-        "Manager template directory is missing; overlaying bundled seed only",
+        "Manager template directory is missing; no template files were seeded",
       );
     } finally {
       await harness.cleanup();
@@ -322,7 +291,7 @@ describe("manager storage templates", () => {
     }
   });
 
-  it("warns and still overlays bundled status when an explicit non-default template is missing", async () => {
+  it("warns and seeds nothing when an explicit non-default template is missing", async () => {
     const { dataDir, harness, hostId } = await createSeedHarness();
     const logger = {
       ...testLogger,
@@ -339,13 +308,13 @@ describe("manager storage templates", () => {
         threadId: "thr-missing-explicit",
       });
 
-      await expectBundledStatusAppSeeded(threadStoragePath);
+      await expect(stat(threadStoragePath)).rejects.toThrow();
       expect(logger.warn).toHaveBeenCalledWith(
         expect.objectContaining({
           templateName: MINE_MANAGER_TEMPLATE_NAME,
           threadId: "thr-missing-explicit",
         }),
-        "Manager template directory is missing; overlaying bundled seed only",
+        "Manager template directory is missing; no template files were seeded",
       );
     } finally {
       await harness.cleanup();
@@ -353,7 +322,7 @@ describe("manager storage templates", () => {
     }
   });
 
-  it("seeds from the active non-default template and overlays bundled status when that directory exists", async () => {
+  it("seeds from the active non-default template when that directory exists", async () => {
     const { dataDir, harness, hostId } = await createSeedHarness();
     try {
       await writeActiveManagerTemplate({
@@ -389,7 +358,9 @@ describe("manager storage templates", () => {
           "utf8",
         ),
       ).resolves.toBe("{}\n");
-      await expectBundledStatusAppSeeded(threadStoragePath);
+      await expect(
+        stat(path.join(threadStoragePath, "apps", "status", "manifest.json")),
+      ).rejects.toThrow();
     } finally {
       await harness.cleanup();
       await rm(dataDir, { recursive: true, force: true });
diff --git a/apps/server/test/threads/thread-runtime-config.test.ts b/apps/server/test/threads/thread-runtime-config.test.ts
index 2e8b8fa6c..5c63e39af 100644
--- a/apps/server/test/threads/thread-runtime-config.test.ts
+++ b/apps/server/test/threads/thread-runtime-config.test.ts
@@ -1,10 +1,14 @@
+import { mkdir, writeFile } from "node:fs/promises";
+import path from "node:path";
 import { describe, expect, it } from "vitest";
 import { markThreadDeleted, setThreadExecutionOverride } from "@bb/db";
+import { encodeClientTurnRequestIdNumber } from "@bb/domain";
 import {
   resolvePermissionEscalation,
   resolveExecutionOptions,
   resolveThreadRuntimeCommandConfig,
 } from "../../src/services/threads/thread-runtime-config.js";
+import { buildThreadStartCommand } from "../../src/services/threads/thread-commands.js";
 import {
   seedEnvironment,
   seedHostSession,
@@ -17,6 +21,30 @@ function resolveLocalTimezone(): string {
   return Intl.DateTimeFormat().resolvedOptions().timeZone || "UTC";
 }
 
+interface WriteRuntimeSkillArgs {
+  dataDir: string;
+  name: string;
+}
+
+async function writeRuntimeSkill(args: WriteRuntimeSkillArgs): Promise<string> {
+  const sourceRootPath = path.join(args.dataDir, "skills", args.name);
+  await mkdir(sourceRootPath, { recursive: true });
+  await writeFile(
+    path.join(sourceRootPath, "SKILL.md"),
+    [
+      "---",
+      `name: ${args.name}`,
+      `description: Use ${args.name} when server runtime tests run.`,
+      "---",
+      "",
+      "# Test Skill",
+      "",
+    ].join("\n"),
+    "utf8",
+  );
+  return sourceRootPath;
+}
+
 describe("thread runtime config", () => {
   it.each([
     {
@@ -263,6 +291,60 @@ describe("thread runtime config", () => {
     });
   });
 
+  it("serializes injected skill sources into new thread start commands", async () => {
+    await withTestHarness(async (harness) => {
+      const sourceRootPath = await writeRuntimeSkill({
+        dataDir: harness.config.dataDir,
+        name: "release-notes",
+      });
+      const { host } = seedHostSession(harness.deps, {
+        id: "host-runtime-injected-skills",
+      });
+      const { project } = seedProjectWithSource(harness.deps, {
+        hostId: host.id,
+      });
+      const environment = seedEnvironment(harness.deps, {
+        hostId: host.id,
+        projectId: project.id,
+      });
+      const thread = seedThread(harness.deps, {
+        projectId: project.id,
+        environmentId: environment.id,
+        providerId: "codex",
+      });
+      const execution = await resolveExecutionOptions(harness.deps, {
+        threadId: thread.id,
+        requestedExecution: {
+          model: "gpt-5",
+          source: "client/turn/requested",
+        },
+      });
+
+      const command = await buildThreadStartCommand(harness.deps, {
+        environment,
+        execution,
+        permissionEscalation: "ask",
+        input: [{ type: "text", text: "hello" }],
+        managerTemplateName: null,
+        projectId: project.id,
+        providerId: "codex",
+        requestId: encodeClientTurnRequestIdNumber({ value: 1 }),
+        thread,
+      });
+
+      expect(command.injectedSkillSources).toEqual([
+        {
+          sourceType: "data-dir",
+          applicationId: null,
+          name: "release-notes",
+          description: "Use release-notes when server runtime tests run.",
+          sourceRootPath,
+          skillFilePath: path.join(sourceRootPath, "SKILL.md"),
+        },
+      ]);
+    });
+  });
+
   it("consumes the sticky thread execution override across turns without a request value", async () => {
     await withTestHarness(async (harness) => {
       const { host } = seedHostSession(harness.deps, {
diff --git a/docs/migrating-status-to-apps.md b/docs/migrating-status-to-apps.md
deleted file mode 100644
index 9ea6c3374..000000000
--- a/docs/migrating-status-to-apps.md
+++ /dev/null
@@ -1,199 +0,0 @@
-# Migrating from STATUS to Apps
-
-The legacy **STATUS** surface (`STATUS.html` / `STATUS.md` / a `STATUS/` folder
-plus the `STATUS-data/` key–value store) has been removed. A thread now exposes
-one or more **apps** instead, and the old single status dashboard becomes a
-regular app with the id `status`.
-
-This guide is for an **existing manager** (or any thread) whose storage still
-contains the old STATUS files and needs to move to the new format. New threads
-already seed a `status` app automatically and need no migration.
-
-For the full feature reference, run `bb guide app`. This doc only covers the
-mechanical migration.
-
----
-
-## What changed
-
-| Legacy STATUS                                                                 | New Apps                                                                                                               |
-| ----------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------- |
-| `STATUS/index.html`, `STATUS.html`, or `STATUS.md` in the thread-storage root | `apps/<id>/assets/<entry>` on disk, served at `/api/v1/threads/<thread-id>/apps/<id>/<entry>`                          |
-| One implicit status surface per thread                                        | Any number of apps; the dashboard is just the app with id `status`                                                     |
-| `STATUS-data/<key>.json` (flat keys, `^[A-Za-z0-9_-]{1,80}$`)                 | `apps/<id>/data/<path>` (nested paths allowed; default: a single `data/state.json`)                                    |
-| `window.bbStatusState` (`get`/`set`/`delete`/`list`/`on`)                     | `window.bb.data` (`read`/`write`/`delete`/`list`/`onChange`)                                                           |
-| `window.bbThreadTell(text)`                                                   | `window.bb.message(text)`                                                                                              |
-| Served at `/api/v1/threads/<id>/status/`                                      | Served at `/api/v1/threads/<id>/apps/<id>/`                                                                            |
-| Globals always injected                                                       | Injected only for **HTML** entries, gated by manifest `capabilities`; **Markdown** entries are static (no `window.bb`) |
-
----
-
-## Target layout
-
-```text
-<thread-storage>/
-  apps/
-    status/
-      manifest.json     # metadata — NOT served
-      assets/           # internal storage for browser files
-        index.html      # (or index.md)
-      data/             # file-based key/value store
-        state.json      # default: keep all state in one blob
-      logo.svg          # optional; otherwise a built-in icon is used
-```
-
-`manifest.json` for the status dashboard:
-
-```json
-{
-  "manifestVersion": 1,
-  "id": "status",
-  "name": "Status",
-  "icon": "ListTodo",
-  "entry": "index.html",
-  "contributions": ["thread.app"],
-  "capabilities": ["data", "message"]
-}
-```
-
-- `id` must match the directory name and `^[A-Za-z0-9_-]+$`.
-- `entry` is resolved relative to `assets/`. Use `index.html` for an
-  interactive dashboard, or `index.md` for a static document (Markdown apps do
-  **not** get `window.bb`).
-- `icon` is a built-in icon name. To use a custom image instead, drop a
-  top-level `logo.svg` / `logo.png` / `logo.jpg` and omit `icon`; with neither,
-  apps fall back to the `GridView` icon.
-- `capabilities`: `data` injects `window.bb.data`, `message` injects
-  `window.bb.message`. List only what the app uses.
-
-Browser files under `assets/` are served from the flat app URL. For example,
-`apps/status/assets/index-Cd7sCqsN.js` is requested as
-`/api/v1/threads/<thread-id>/apps/status/index-Cd7sCqsN.js`; do not include an
-`assets/` segment in HTML references. Apps are served directly from these
-static files, so there is no app-specific web server, npm install, or build
-step requirement.
-
----
-
-## Migration steps
-
-### 1. Create the app directory
-
-```bash
-APP="$BB_THREAD_STORAGE/apps/status"
-mkdir -p "$APP/assets" "$APP/data"
-```
-
-### 2. Move the markup into `assets/`
-
-- `STATUS.html` → `apps/status/assets/index.html`
-- `STATUS/index.html` (+ its CSS/JS/images/fonts) → `apps/status/assets/` (keep the same relative structure; everything under `assets/` is served from the flat app URL)
-- `STATUS.md` → `apps/status/assets/index.md` (set `entry` to `index.md`; remember a Markdown entry is static)
-
-Use flat relative HTML references, such as `<script type="module"
-src="./index-abc.js"></script>` or `<link rel="stylesheet"
-href="./style.css">`. If you are moving existing Vite build output, set
-`build.assetsDir = ""` so emitted CSS/JS/assets sit alongside `index.html`
-inside `assets/`; otherwise keep the app as plain static files.
-
-### 3. Migrate the state
-
-The default convention is a **single `data/state.json` blob**. If your old
-dashboard used a few `STATUS-data/*.json` keys, consolidate them:
-
-```bash
-# Example: fold STATUS-data/prs.json + STATUS-data/workers.json into one blob.
-jq -n \
-  --slurpfile prs     "$BB_THREAD_STORAGE/STATUS-data/prs.json" \
-  --slurpfile workers "$BB_THREAD_STORAGE/STATUS-data/workers.json" \
-  '{ prs: $prs[0], workers: $workers[0] }' \
-  > "$BB_THREAD_STORAGE/apps/status/data/state.json"
-```
-
-Or, if you prefer to keep separate keys, each old `STATUS-data/<key>.json`
-becomes `apps/status/data/<key>.json` (nested paths like `data/tasks/123` are
-also allowed — see `bb guide app` for the path rules).
-
-### 4. Update the in-page JavaScript
-
-Replace the old globals (HTML entries only):
-
-| Old                                    | New                                       |
-| -------------------------------------- | ----------------------------------------- |
-| `window.bbStatusState.get(key)`        | `await window.bb.data.read(path)`         |
-| `window.bbStatusState.set(key, value)` | `await window.bb.data.write(path, value)` |
-| `window.bbStatusState.delete(key)`     | `await window.bb.data.delete(path)`       |
-| `window.bbStatusState.list()`          | `await window.bb.data.list(prefix)`       |
-| `window.bbStatusState.on(key, cb)`     | `window.bb.data.onChange(prefix, cb)`     |
-| `window.bbStatusState.on("*", cb)`     | `window.bb.data.onChange("", cb)`         |
-| `window.bbThreadTell(text)`            | `await window.bb.message(text)`           |
-
-Notes:
-
-- All `window.bb.data` methods are async (return Promises). `read` resolves to
-  the parsed JSON value or `undefined`.
-- `onChange(prefix, cb)` does **subtree** matching: `onChange("tasks")` fires
-  for `tasks` and `tasks/*` but not `tasksfoo`; `onChange("")` watches
-  everything. It **replays** existing matches once on registration, then streams
-  live changes. The callback receives `{ path, value, deleted }`.
-- If you consolidated into a single `state.json`, the common pattern is:
-
-  ```js
-  window.bb.data.read("state.json").then(render);
-  window.bb.data.onChange("state.json", (event) => render(event.value));
-  ```
-
-- Guard the helpers (`window.bb.data?.…`, `window.bb.message?.(…)`) — they are
-  only present when the matching capability is declared.
-
-### 5. Update how the agent / maintainer writes state
-
-Agents (and any maintainer worker) write app data by writing the files
-**directly on disk** — the daemon watches `data/` and broadcasts changes to open
-clients. Use the same atomic temp-file + rename pattern as before, just to the
-new path:
-
-```bash
-DIR="$BB_THREAD_STORAGE/apps/status/data"
-mkdir -p "$DIR"
-tmp=$(mktemp "$DIR/.state.XXXXXX")
-printf '%s\n' "$NEW_STATE_JSON" > "$tmp" && mv "$tmp" "$DIR/state.json"
-```
-
-(The browser side uses `window.bb.data.write(...)`, which routes through the
-daemon to the same file. Both paths converge on the one watched directory.)
-
-If a long-running maintainer worker used to write `STATUS-data/task_*.json`,
-re-point it at `apps/status/data/…` (a single `state.json` is recommended).
-
-### 6. Remove the old STATUS files
-
-Once the app renders correctly:
-
-```bash
-rm -rf "$BB_THREAD_STORAGE"/STATUS.html \
-       "$BB_THREAD_STORAGE"/STATUS.md \
-       "$BB_THREAD_STORAGE"/STATUS \
-       "$BB_THREAD_STORAGE"/STATUS-data
-```
-
-### 7. Verify
-
-```bash
-bb app list <thread-id>          # should show the `status` app
-bb app open status               # prints the served URL to open in the panel
-```
-
-Or open the thread's secondary panel: the pinned `Status` tab (and the `+`
-launcher) should show the app, and writing `data/state.json` should update it
-live with no reload.
-
----
-
-## Quick reference
-
-- Full feature docs: `bb guide app` (manifest, `window.bb`, data paths, icons,
-  entry types, the `bb app` CLI).
-- Styling tokens for app HTML are documented there too (`bb guide styling`
-  redirects to the app guide).
-- `bb app new <name>` scaffolds additional apps; `bb app rm <name>` removes one.
diff --git a/packages/config/package.json b/packages/config/package.json
index 3f53eb5a5..4e9770c48 100644
--- a/packages/config/package.json
+++ b/packages/config/package.json
@@ -97,6 +97,11 @@
       "source": "./src/bb-app-managed-config.ts",
       "types": "./src/bb-app-managed-config.ts",
       "default": "./src/bb-app-managed-config.ts"
+    },
+    "./app-storage-paths": {
+      "source": "./src/app-storage-paths.ts",
+      "types": "./src/app-storage-paths.ts",
+      "default": "./src/app-storage-paths.ts"
     }
   },
   "scripts": {
diff --git a/packages/config/src/app-storage-paths.ts b/packages/config/src/app-storage-paths.ts
new file mode 100644
index 000000000..232b9a5f2
--- /dev/null
+++ b/packages/config/src/app-storage-paths.ts
@@ -0,0 +1,41 @@
+import { join } from "node:path";
+import { applicationIdSchema, type ApplicationId } from "@bb/domain";
+
+export function resolveAppsRootPath(dataDir: string): string {
+  return join(dataDir, "apps");
+}
+
+export function resolveDataDirSkillsRootPath(dataDir: string): string {
+  return join(dataDir, "skills");
+}
+
+export function resolveApplicationPath(
+  dataDir: string,
+  applicationId: ApplicationId,
+): string {
+  return join(
+    resolveAppsRootPath(dataDir),
+    applicationIdSchema.parse(applicationId),
+  );
+}
+
+export function resolveApplicationManifestPath(
+  dataDir: string,
+  applicationId: ApplicationId,
+): string {
+  return join(resolveApplicationPath(dataDir, applicationId), "manifest.json");
+}
+
+export function resolveApplicationPublicPath(
+  dataDir: string,
+  applicationId: ApplicationId,
+): string {
+  return join(resolveApplicationPath(dataDir, applicationId), "public");
+}
+
+export function resolveApplicationDataPath(
+  dataDir: string,
+  applicationId: ApplicationId,
+): string {
+  return join(resolveApplicationPath(dataDir, applicationId), "data");
+}
diff --git a/packages/config/test/app-storage-paths.test.ts b/packages/config/test/app-storage-paths.test.ts
new file mode 100644
index 000000000..afb7b3740
--- /dev/null
+++ b/packages/config/test/app-storage-paths.test.ts
@@ -0,0 +1,24 @@
+import { describe, expect, it } from "vitest";
+import {
+  resolveApplicationDataPath,
+  resolveApplicationPath,
+  resolveApplicationPublicPath,
+} from "../src/app-storage-paths.js";
+
+describe("app storage paths", () => {
+  it("uses validated application ids as path segments", () => {
+    expect(resolveApplicationPath("/tmp/bb-data", "review-board")).toBe(
+      "/tmp/bb-data/apps/review-board",
+    );
+    expect(resolveApplicationDataPath("/tmp/bb-data", "status")).toBe(
+      "/tmp/bb-data/apps/status/data",
+    );
+    expect(resolveApplicationPublicPath("/tmp/bb-data", "status")).toBe(
+      "/tmp/bb-data/apps/status/public",
+    );
+  });
+
+  it("rejects invalid application id path segments", () => {
+    expect(() => resolveApplicationPath("/tmp/bb-data", "a/b")).toThrow();
+  });
+});
diff --git a/packages/config/test/config.test.ts b/packages/config/test/config.test.ts
index f606bcf63..90c8168db 100644
--- a/packages/config/test/config.test.ts
+++ b/packages/config/test/config.test.ts
@@ -23,6 +23,7 @@ import {
 import { loadServerPortConfig } from "../src/server-port.js";
 import { loadServerConfig } from "../src/server.js";
 import { loadViteDevConfig } from "../src/vite-dev.js";
+import { resolveDataDirSkillsRootPath } from "../src/app-storage-paths.js";
 
 async function importConfigModules(): Promise<void> {
   vi.resetModules();
@@ -199,6 +200,12 @@ describe("data-dir helpers", () => {
       "/tmp/bb-data/bb.db",
     );
   });
+
+  it("derives the data-dir-level skills root from a resolved data dir", () => {
+    expect(resolveDataDirSkillsRootPath("/tmp/bb-data")).toBe(
+      "/tmp/bb-data/skills",
+    );
+  });
 });
 
 describe("port helpers", () => {
diff --git a/packages/domain/src/apps.ts b/packages/domain/src/apps.ts
index 5f72ec99a..25dd2b363 100644
--- a/packages/domain/src/apps.ts
+++ b/packages/domain/src/apps.ts
@@ -1,13 +1,36 @@
 import { z } from "zod";
 
+export const APPLICATION_ID_MAX_LENGTH = 64;
+const APPLICATION_ID_PATTERN = /^[a-z0-9][a-z0-9-]*$/u;
+const APPLICATION_NAME_SLUG_SEGMENT_PATTERN = /[a-z0-9]+/gu;
 const APP_DATA_PATH_SEGMENT_PATTERN = /^[A-Za-z0-9._-]{1,80}$/u;
 const APP_DATA_PATH_MAX_DEPTH = 8;
 // Keep these app-data path limits in sync with the injected app client
 // validator in apps/server/src/services/threads/app-client-script.ts.
 const APP_DATA_PATH_MAX_LENGTH = 512;
 
-export const appIdSchema = z.string().regex(/^[A-Za-z0-9_-]+$/u);
-export type AppId = z.infer<typeof appIdSchema>;
+export const applicationIdSchema = z
+  .string()
+  .min(1)
+  .max(APPLICATION_ID_MAX_LENGTH)
+  .regex(
+    APPLICATION_ID_PATTERN,
+    "Application id must be a lowercase slug containing only letters, numbers, and hyphens",
+  );
+export type ApplicationId = z.infer<typeof applicationIdSchema>;
+
+export function deriveApplicationIdFromName(name: string): ApplicationId {
+  const normalizedName = name
+    .normalize("NFKD")
+    .toLowerCase()
+    .replace(/[\u0300-\u036f]/gu, "");
+  const segments = normalizedName.match(APPLICATION_NAME_SLUG_SEGMENT_PATTERN);
+  const slug = (segments ?? [])
+    .join("-")
+    .slice(0, APPLICATION_ID_MAX_LENGTH)
+    .replace(/-+$/u, "");
+  return applicationIdSchema.parse(slug);
+}
 
 export const appDataPathSchema = z.string().superRefine((value, context) => {
   if (
diff --git a/packages/domain/src/change-kinds.ts b/packages/domain/src/change-kinds.ts
index c0e410d1b..bcba9a74e 100644
--- a/packages/domain/src/change-kinds.ts
+++ b/packages/domain/src/change-kinds.ts
@@ -7,6 +7,7 @@ export const REALTIME_ENTITIES = [
   "environment",
   "host",
   "system",
+  "app",
 ] as const;
 export type RealtimeEntity = (typeof REALTIME_ENTITIES)[number];
 export const realtimeEntitySchema = z.enum(REALTIME_ENTITIES);
@@ -58,7 +59,7 @@ export const HOST_CHANGE_KINDS = [
 ] as const;
 export type HostChangeKind = (typeof HOST_CHANGE_KINDS)[number];
 
-export const SYSTEM_CHANGE_KINDS = ["config-changed"] as const;
+export const SYSTEM_CHANGE_KINDS = ["config-changed", "apps-changed"] as const;
 export type SystemChangeKind = (typeof SYSTEM_CHANGE_KINDS)[number];
 
 export const subscribeMessageSchema = z.object({
diff --git a/packages/domain/src/index.ts b/packages/domain/src/index.ts
index 90b402e28..4df4078b2 100644
--- a/packages/domain/src/index.ts
+++ b/packages/domain/src/index.ts
@@ -59,8 +59,13 @@ export type {
 export { managerTemplateNameSchema } from "./manager-templates.js";
 export type { ManagerTemplateName } from "./manager-templates.js";
 
-export { appDataPathSchema, appIdSchema } from "./apps.js";
-export type { AppDataPath, AppId } from "./apps.js";
+export {
+  APPLICATION_ID_MAX_LENGTH,
+  appDataPathSchema,
+  applicationIdSchema,
+  deriveApplicationIdFromName,
+} from "./apps.js";
+export type { AppDataPath, ApplicationId } from "./apps.js";
 
 export { threadDynamicContextFileStatusValues } from "./manager-dynamic-context.js";
 export type { ThreadDynamicContextFileStatus } from "./manager-dynamic-context.js";
@@ -423,9 +428,7 @@ export {
   providerTurnWatchdogReasonSchema,
   providerTurnWatchdogReasonValues,
 } from "./provider-turn-watchdog.js";
-export type {
-  ProviderTurnWatchdogActivityEventType,
-} from "./provider-turn-watchdog.js";
+export type { ProviderTurnWatchdogActivityEventType } from "./provider-turn-watchdog.js";
 
 export {
   buildThreadEvent,
diff --git a/packages/domain/test/apps.test.ts b/packages/domain/test/apps.test.ts
new file mode 100644
index 000000000..4e59c0e44
--- /dev/null
+++ b/packages/domain/test/apps.test.ts
@@ -0,0 +1,22 @@
+import { describe, expect, it } from "vitest";
+import {
+  applicationIdSchema,
+  deriveApplicationIdFromName,
+} from "../src/index.js";
+
+describe("application ids", () => {
+  it("accepts lowercase app slugs", () => {
+    expect(applicationIdSchema.safeParse("status").success).toBe(true);
+    expect(applicationIdSchema.safeParse("review-board").success).toBe(true);
+  });
+
+  it("rejects non-slug application ids", () => {
+    for (const value of ["Bad", "a/b", "..", "a.b", ""]) {
+      expect(applicationIdSchema.safeParse(value).success).toBe(false);
+    }
+  });
+
+  it("derives application ids from display names", () => {
+    expect(deriveApplicationIdFromName("Review Board")).toBe("review-board");
+  });
+});
diff --git a/packages/host-daemon-contract/src/commands.ts b/packages/host-daemon-contract/src/commands.ts
index 5b518c5b1..ecb6e40b0 100644
--- a/packages/host-daemon-contract/src/commands.ts
+++ b/packages/host-daemon-contract/src/commands.ts
@@ -17,6 +17,7 @@ import {
   clientTurnRequestIdSchema,
   gitBranchNameSchema,
   jsonObjectSchema,
+  applicationIdSchema,
 } from "@bb/domain";
 import {
   replayCaptureDaemonListResponseSchema,
@@ -24,12 +25,14 @@ import {
 } from "@bb/replay-capture/schema";
 import { z } from "zod";
 
-export const HOST_DAEMON_PROTOCOL_VERSION = 29 as const;
+export const HOST_DAEMON_PROTOCOL_VERSION = 30 as const;
 
 export const FILE_LIST_QUERY_MAX_LENGTH = 256;
 export const FILE_LIST_LIMIT_MAX = 10_000;
 export const BRANCH_LIST_QUERY_MAX_LENGTH = 256;
 export const BRANCH_LIST_LIMIT_MAX = 1_000;
+const INJECTED_SKILL_NAME_PATTERN =
+  /^(?!.*--)[a-z0-9](?:[a-z0-9-]{0,62}[a-z0-9])?$/u;
 
 export const HOST_DAEMON_DURABLE_COMMAND_TYPES = [
   "thread.start",
@@ -109,6 +112,42 @@ const hostDaemonProviderThreadTargetSchema = z.object({
   threadId: z.string().min(1),
 });
 
+export const hostDaemonInjectedSkillSourceBaseSchema = z
+  .object({
+    name: z.string().max(64).regex(INJECTED_SKILL_NAME_PATTERN),
+    description: z.string().min(1).max(1024),
+    sourceRootPath: z.string().min(1),
+    skillFilePath: z.string().min(1),
+  })
+  .strict();
+
+export const hostDaemonDataDirInjectedSkillSourceSchema =
+  hostDaemonInjectedSkillSourceBaseSchema
+    .extend({
+      sourceType: z.literal("data-dir"),
+      applicationId: z.null(),
+    })
+    .strict();
+
+export const hostDaemonGlobalAppInjectedSkillSourceSchema =
+  hostDaemonInjectedSkillSourceBaseSchema
+    .extend({
+      sourceType: z.literal("global-app"),
+      applicationId: applicationIdSchema,
+    })
+    .strict();
+
+export const hostDaemonInjectedSkillSourceSchema = z.discriminatedUnion(
+  "sourceType",
+  [
+    hostDaemonDataDirInjectedSkillSourceSchema,
+    hostDaemonGlobalAppInjectedSkillSourceSchema,
+  ],
+);
+export type HostDaemonInjectedSkillSource = z.infer<
+  typeof hostDaemonInjectedSkillSourceSchema
+>;
+
 const hostDaemonThreadRuntimeContextSchema = z.object({
   workspaceContext: workspaceContextSchema,
   projectId: z.string().min(1),
@@ -116,6 +155,7 @@ const hostDaemonThreadRuntimeContextSchema = z.object({
   options: hostDaemonExecutionOptionsSchema,
   instructions: z.string().min(1),
   dynamicTools: z.array(dynamicToolSchema),
+  injectedSkillSources: z.array(hostDaemonInjectedSkillSourceSchema),
   disallowedTools: z.array(z.string()).optional(),
   instructionMode: instructionModeSchema,
 });
diff --git a/packages/host-daemon-contract/src/index.ts b/packages/host-daemon-contract/src/index.ts
index e7941f378..499a8d862 100644
--- a/packages/host-daemon-contract/src/index.ts
+++ b/packages/host-daemon-contract/src/index.ts
@@ -96,8 +96,12 @@ export {
   hostDaemonCommandResultReportSchema,
   hostDaemonCommandResultSchemaByType,
   hostDaemonCommandSchema,
+  hostDaemonDataDirInjectedSkillSourceSchema,
   hostDaemonDurableCommandTypeSchema,
   hostDaemonExecutionOptionsSchema,
+  hostDaemonGlobalAppInjectedSkillSourceSchema,
+  hostDaemonInjectedSkillSourceBaseSchema,
+  hostDaemonInjectedSkillSourceSchema,
   hostDaemonOnlineRpcCommandSchema,
   hostDaemonOnlineRpcCommandTypeSchema,
   hostDaemonOnlineRpcResultSchemaByType,
@@ -148,6 +152,7 @@ export type {
   HostDaemonCommandResultReport,
   HostDaemonCommandResultReportWithoutSession,
   HostDaemonDurableCommandType,
+  HostDaemonInjectedSkillSource,
   HostDaemonOnlineRpcCommand,
   HostDaemonOnlineRpcCommandType,
   HostDaemonOnlineRpcResult,
@@ -200,6 +205,7 @@ export {
   hostDaemonSessionCloseReasonSchema,
   hostDaemonSessionOpenRequestSchema,
   hostDaemonSessionOpenResponseSchema,
+  hostDaemonTrackedApplicationDataTargetSchema,
   hostDaemonTerminalOutputChunkSchema,
   hostDaemonTrackedThreadTargetSchema,
   hostDaemonToolCallRequestSchema,
@@ -238,6 +244,7 @@ export type {
   HostDaemonSessionCloseReason,
   HostDaemonSessionOpenRequest,
   HostDaemonSessionOpenResponse,
+  HostDaemonTrackedApplicationDataTarget,
   HostDaemonTrackedThreadTarget,
   HostDaemonToolCallRequest,
   HostDaemonToolCallResponse,
diff --git a/packages/host-daemon-contract/src/session.ts b/packages/host-daemon-contract/src/session.ts
index fb8542878..ecbbf5490 100644
--- a/packages/host-daemon-contract/src/session.ts
+++ b/packages/host-daemon-contract/src/session.ts
@@ -8,7 +8,7 @@ import {
   pendingInteractionCreateSchema,
   pendingInteractionStatusSchema,
   appDataPathSchema,
-  appIdSchema,
+  applicationIdSchema,
   terminalColsSchema,
   terminalDataBase64Schema,
   terminalRowsSchema,
@@ -55,6 +55,14 @@ export type HostDaemonTrackedThreadTarget = z.infer<
   typeof hostDaemonTrackedThreadTargetSchema
 >;
 
+export const hostDaemonTrackedApplicationDataTargetSchema = z.object({
+  applicationId: applicationIdSchema,
+  appDataPath: z.string().min(1),
+});
+export type HostDaemonTrackedApplicationDataTarget = z.infer<
+  typeof hostDaemonTrackedApplicationDataTargetSchema
+>;
+
 export const hostDaemonSessionOpenRequestSchema = z.object({
   hostId: z.string().min(1),
   instanceId: z.string().min(1),
@@ -98,6 +106,9 @@ export const hostDaemonSessionOpenResponseSchema = z
     heartbeatIntervalMs: z.number().int().positive(),
     leaseTimeoutMs: z.number().int().positive(),
     trackedThreadTargets: z.array(hostDaemonTrackedThreadTargetSchema),
+    trackedApplicationDataTargets: z.array(
+      hostDaemonTrackedApplicationDataTargetSchema,
+    ),
     retiredEnvironmentIds: z.array(z.string().min(1)).default([]),
   })
   .strict();
@@ -213,8 +224,7 @@ export type HostDaemonEnvironmentChangePayload = z.infer<
 
 const hostDaemonAppDataChangePayloadBaseSchema = z
   .object({
-    threadId: z.string().min(1),
-    appId: appIdSchema,
+    applicationId: applicationIdSchema,
     path: appDataPathSchema,
     value: jsonValueSchema.nullable(),
     deleted: z.boolean(),
@@ -266,8 +276,7 @@ export type HostDaemonAppDataChangeRequest = z.infer<
 
 export const hostDaemonAppDataResyncPayloadSchema = z
   .object({
-    threadId: z.string().min(1),
-    appId: appIdSchema,
+    applicationId: applicationIdSchema,
   })
   .strict();
 export type HostDaemonAppDataResyncPayload = z.infer<
@@ -517,6 +526,12 @@ const hostDaemonEnvironmentChangeMessageSchema =
     })
     .strict();
 
+const hostDaemonApplicationStorageChangedMessageSchema = z
+  .object({
+    type: z.literal("application-storage-changed"),
+  })
+  .strict();
+
 const hostDaemonTerminalOpenedMessageSchema = z
   .object({
     type: z.literal("terminal.opened"),
@@ -571,6 +586,7 @@ const hostDaemonTerminalErrorMessageSchema = z
 export const hostDaemonDaemonWsMessageSchema = z.union([
   hostDaemonHeartbeatMessageSchema,
   hostDaemonEnvironmentChangeMessageSchema,
+  hostDaemonApplicationStorageChangedMessageSchema,
   hostDaemonTerminalOpenedMessageSchema,
   hostDaemonTerminalOutputMessageSchema,
   hostDaemonTerminalReplayMessageSchema,
diff --git a/packages/host-daemon-contract/test/contract.test.ts b/packages/host-daemon-contract/test/contract.test.ts
index 2231f010f..09f6d2d27 100644
--- a/packages/host-daemon-contract/test/contract.test.ts
+++ b/packages/host-daemon-contract/test/contract.test.ts
@@ -371,10 +371,9 @@ function expectHostRpcResponseRoundTrip(
     hostDaemonOnlineRpcResponseMessageSchema.parse(jsonRoundTripped),
     name,
   ).toEqual(message);
-  expect(
-    hostDaemonDaemonWsMessageSchema.parse(jsonRoundTripped),
-    name,
-  ).toEqual(message);
+  expect(hostDaemonDaemonWsMessageSchema.parse(jsonRoundTripped), name).toEqual(
+    message,
+  );
 }
 
 function terminalDataBase64(byteLength: number): string {
@@ -796,13 +795,13 @@ describe("host-daemon command schemas", () => {
     expect(
       hostDaemonOnlineRpcCommandSchema.parse({
         type: "host.read_file_relative",
-        rootPath: "/tmp/bb-data/thread-storage/thread-123/apps/status/assets",
+        rootPath: "/tmp/bb-data/apps/demo/assets",
         path: "logo.png",
         dotfiles: "deny",
       }),
     ).toMatchObject({
       type: "host.read_file_relative",
-      rootPath: "/tmp/bb-data/thread-storage/thread-123/apps/status/assets",
+      rootPath: "/tmp/bb-data/apps/demo/assets",
       path: "logo.png",
       dotfiles: "deny",
     });
@@ -810,7 +809,7 @@ describe("host-daemon command schemas", () => {
     expect(
       hostDaemonCommandSchema.parse({
         type: "host.write_file_relative",
-        rootPath: "/tmp/bb-data/thread-storage/thread-123/apps/status/data",
+        rootPath: "/tmp/bb-data/apps/demo/data",
         path: "state.json",
         dotfiles: "deny",
         content: "[1,2,3]\n",
@@ -824,7 +823,7 @@ describe("host-daemon command schemas", () => {
     expect(
       hostDaemonCommandSchema.parse({
         type: "host.delete_file_relative",
-        rootPath: "/tmp/bb-data/thread-storage/thread-123/apps/status/data",
+        rootPath: "/tmp/bb-data/apps/demo/data",
         path: "state.json",
         dotfiles: "deny",
       }),
@@ -1088,7 +1087,7 @@ describe("host-daemon command schemas", () => {
     expect(() =>
       hostDaemonOnlineRpcCommandSchema.parse({
         type: "host.read_file_relative",
-        rootPath: "/tmp/bb-data/thread-storage/thread-123/apps/status/assets",
+        rootPath: "/tmp/bb-data/apps/demo/assets",
         path: "logo.png",
       }),
     ).toThrow();
@@ -1114,6 +1113,7 @@ describe("host-daemon command schemas", () => {
         },
         instructions: "Be concise.",
         dynamicTools: [],
+        injectedSkillSources: [],
         instructionMode: "append",
         requestId: CLIENT_REQUEST_ID,
         input: [{ type: "text", text: "hello" }],
@@ -1143,6 +1143,7 @@ describe("host-daemon command schemas", () => {
           providerThreadId: "prov_123",
           instructions: "Be concise.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         },
         target: { mode: "start" },
@@ -1179,6 +1180,7 @@ describe("host-daemon command schemas", () => {
             inputSchema: { type: "object" },
           },
         ],
+        injectedSkillSources: [],
         instructionMode: "replace",
       }),
     ).toMatchObject({
@@ -1241,6 +1243,7 @@ describe("host-daemon command schemas", () => {
           providerThreadId: "provider_123",
           instructions: "Be a helpful coding agent.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         },
         target: { mode: "start" },
@@ -1281,6 +1284,7 @@ describe("host-daemon command schemas", () => {
           providerThreadId: "provider_123",
           instructions: "Be a helpful coding agent.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         },
         target: { mode: "auto", expectedTurnId: "turn_123" },
@@ -1368,6 +1372,7 @@ describe("host-daemon command schemas", () => {
         },
         instructions: "Be concise.",
         dynamicTools: [],
+        injectedSkillSources: [],
         instructionMode: "append",
       }),
     ).toThrow();
@@ -1397,6 +1402,7 @@ describe("host-daemon command schemas", () => {
           providerThreadId: "provider_123",
           instructions: "Be a helpful coding agent.",
           dynamicTools: [],
+          injectedSkillSources: [],
           instructionMode: "append",
         },
         target: { mode: "start" },
@@ -1909,6 +1915,7 @@ describe("host-daemon session schemas", () => {
             threadId: "thr_123",
           },
         ],
+        trackedApplicationDataTargets: [],
       }),
     ).toMatchObject({
       sessionId: "session_123",
@@ -2098,11 +2105,18 @@ describe("host-daemon session schemas", () => {
       change: "thread-storage-changed",
     });
 
+    expect(
+      hostDaemonDaemonWsMessageSchema.parse({
+        type: "application-storage-changed",
+      }),
+    ).toEqual({
+      type: "application-storage-changed",
+    });
+
     expect(
       contract.hostDaemonAppDataChangeRequestSchema.parse({
         sessionId: "session_123",
-        threadId: "thr_123",
-        appId: "status",
+        applicationId: "status",
         path: "state.json",
         value: { workers: [] },
         deleted: false,
@@ -2110,8 +2124,7 @@ describe("host-daemon session schemas", () => {
       }),
     ).toEqual({
       sessionId: "session_123",
-      threadId: "thr_123",
-      appId: "status",
+      applicationId: "status",
       path: "state.json",
       value: { workers: [] },
       deleted: false,
@@ -2121,8 +2134,7 @@ describe("host-daemon session schemas", () => {
     expect(
       contract.hostDaemonAppDataChangeRequestSchema.parse({
         sessionId: "session_123",
-        threadId: "thr_123",
-        appId: "status",
+        applicationId: "status",
         path: "state.json",
         value: null,
         deleted: true,
@@ -2136,8 +2148,7 @@ describe("host-daemon session schemas", () => {
     expect(() =>
       contract.hostDaemonAppDataChangeRequestSchema.parse({
         sessionId: "session_123",
-        threadId: "thr_123",
-        appId: "status",
+        applicationId: "status",
         path: "state.json",
         value: { workers: [] },
         deleted: false,
@@ -2148,13 +2159,11 @@ describe("host-daemon session schemas", () => {
     expect(
       contract.hostDaemonAppDataResyncRequestSchema.parse({
         sessionId: "session_123",
-        threadId: "thr_123",
-        appId: "status",
+        applicationId: "status",
       }),
     ).toEqual({
       sessionId: "session_123",
-      threadId: "thr_123",
-      appId: "status",
+      applicationId: "status",
     });
 
     expect(
diff --git a/packages/host-watcher/src/host-watcher-types.ts b/packages/host-watcher/src/host-watcher-types.ts
index f94b4ad0c..1daa236f6 100644
--- a/packages/host-watcher/src/host-watcher-types.ts
+++ b/packages/host-watcher/src/host-watcher-types.ts
@@ -1,5 +1,5 @@
 import type { HostType } from "@bb/domain";
-import type { AppDataPath, AppId } from "@bb/domain";
+import type { AppDataPath, ApplicationId } from "@bb/domain";
 import type { WorkspaceStatusWatchChangeKind } from "./watch-status-types.js";
 
 export type HostObservedChange =
@@ -15,17 +15,23 @@ export type HostObservedChange =
       threadId: string;
     }
   | {
-      kind: "thread-app-data-changed";
-      appId: AppId;
-      environmentId: string;
+      kind: "application-storage-targets-changed";
+    }
+  | {
+      kind: "application-data-changed";
+      applicationId: ApplicationId;
+      appDataPath: string;
       path: AppDataPath;
-      threadId: string;
     }
   | {
-      kind: "thread-app-data-resync";
-      appId: AppId;
-      environmentId: string;
-      threadId: string;
+      kind: "application-data-resync";
+      applicationId: ApplicationId;
+    }
+  | {
+      kind: "injected-skills-changed";
+      applicationId: ApplicationId | null;
+      changedPaths: string[];
+      sourceType: "data-dir" | "global-app";
     };
 
 export type WorkspaceObservedChange = Extract<
@@ -34,12 +40,27 @@ export type WorkspaceObservedChange = Extract<
 >;
 
 export type ThreadStorageObservedChange = Extract<
+  HostObservedChange,
+  {
+    kind: "thread-storage-changed";
+  }
+>;
+
+export type ApplicationStorageObservedChange = Extract<
   HostObservedChange,
   {
     kind:
-      | "thread-storage-changed"
-      | "thread-app-data-changed"
-      | "thread-app-data-resync";
+      | "application-storage-targets-changed"
+      | "application-data-changed"
+      | "application-data-resync"
+      | "injected-skills-changed";
+  }
+>;
+
+export type InjectedSkillsObservedChange = Extract<
+  HostObservedChange,
+  {
+    kind: "injected-skills-changed";
   }
 >;
 
@@ -58,7 +79,23 @@ export interface ThreadStorageWatchError {
   threadId?: string;
 }
 
-export type HostWatchError = WorkspaceWatchError | ThreadStorageWatchError;
+export interface ApplicationStorageWatchError {
+  kind: "application-storage-watch-error";
+  rootPath: string;
+  message: string;
+}
+
+export interface DataDirSkillsWatchError {
+  kind: "data-dir-skills-watch-error";
+  rootPath: string;
+  message: string;
+}
+
+export type HostWatchError =
+  | WorkspaceWatchError
+  | ThreadStorageWatchError
+  | ApplicationStorageWatchError
+  | DataDirSkillsWatchError;
 
 export interface ThreadStorageWatchTarget {
   environmentId: string;
@@ -79,11 +116,37 @@ export interface WatchThreadStorageRootArgs {
   onWatchError: (error: ThreadStorageWatchError) => void;
 }
 
+export interface ApplicationDataWatchTarget {
+  applicationId: ApplicationId;
+  appDataPath: string;
+}
+
+export interface WatchApplicationStorageRootArgs {
+  appsRootPath: string;
+  resolveApplicationTarget: (
+    applicationId: ApplicationId,
+  ) => ApplicationDataWatchTarget | null;
+  onChange: (event: ApplicationStorageObservedChange) => void;
+  onWatchError: (error: ApplicationStorageWatchError) => void;
+}
+
+export interface WatchDataDirSkillsRootArgs {
+  dataDirSkillsRootPath: string;
+  onChange: (event: InjectedSkillsObservedChange) => void;
+  onWatchError: (error: DataDirSkillsWatchError) => void;
+}
+
 export interface HostWatcher {
   watchWorkspace(args: WatchWorkspaceArgs): () => void | Promise<void>;
   watchThreadStorageRoot(
     args: WatchThreadStorageRootArgs,
   ): () => void | Promise<void>;
+  watchApplicationStorageRoot(
+    args: WatchApplicationStorageRootArgs,
+  ): () => void | Promise<void>;
+  watchDataDirSkillsRoot?(
+    args: WatchDataDirSkillsRootArgs,
+  ): () => void | Promise<void>;
 }
 
 export interface CreateHostWatcherArgs {
diff --git a/packages/host-watcher/src/index.ts b/packages/host-watcher/src/index.ts
index 2eaa0f5bb..e9e1627bd 100644
--- a/packages/host-watcher/src/index.ts
+++ b/packages/host-watcher/src/index.ts
@@ -8,8 +8,15 @@ export type {
   HostObservedChange,
   HostWatchError,
   HostWatcher,
+  ApplicationDataWatchTarget,
+  ApplicationStorageObservedChange,
+  ApplicationStorageWatchError,
+  DataDirSkillsWatchError,
   ThreadStorageWatchError,
   ThreadStorageWatchTarget,
+  InjectedSkillsObservedChange,
+  WatchApplicationStorageRootArgs,
+  WatchDataDirSkillsRootArgs,
   WatchThreadStorageRootArgs,
   WatchWorkspaceArgs,
   WorkspaceWatchError,
diff --git a/packages/host-watcher/src/parcel-host-watcher.ts b/packages/host-watcher/src/parcel-host-watcher.ts
index 26988d2f2..ac1899594 100644
--- a/packages/host-watcher/src/parcel-host-watcher.ts
+++ b/packages/host-watcher/src/parcel-host-watcher.ts
@@ -1,16 +1,21 @@
 import path from "node:path";
 import {
   appDataPathSchema,
-  appIdSchema,
+  applicationIdSchema,
   type AppDataPath,
-  type AppId,
+  type ApplicationId,
 } from "@bb/domain";
 import { watchPathChanges } from "./watch-path.js";
 import { watchWorkspaceStatus } from "./watch-status.js";
 import type {
   HostWatcher,
+  ApplicationStorageObservedChange,
+  ApplicationDataWatchTarget,
+  InjectedSkillsObservedChange,
   ThreadStorageObservedChange,
   ThreadStorageWatchTarget,
+  WatchApplicationStorageRootArgs,
+  WatchDataDirSkillsRootArgs,
   WatchThreadStorageRootArgs,
   WatchWorkspaceArgs,
 } from "./host-watcher-types.js";
@@ -25,15 +30,28 @@ interface ThreadStoragePath {
   threadId: string;
 }
 
-interface ThreadAppDataPath {
-  appId: AppId;
+interface ApplicationStoragePathArgs {
+  appsRootPath: string;
+  changedPath: string;
+}
+
+interface ApplicationStoragePath {
+  applicationId: ApplicationId | null;
+  parts: string[];
+}
+
+interface ApplicationDataPath {
+  applicationId: ApplicationId;
   path: AppDataPath;
-  threadId: string;
 }
 
-interface ThreadAppDataRootPath {
-  appId: AppId;
-  threadId: string;
+interface ApplicationDataRootPath {
+  applicationId: ApplicationId;
+}
+
+interface DataDirSkillsPathArgs {
+  changedPath: string;
+  dataDirSkillsRootPath: string;
 }
 
 interface CollectThreadStorageObservedChangesArgs {
@@ -42,6 +60,19 @@ interface CollectThreadStorageObservedChangesArgs {
   resolveThreadTarget: (threadId: string) => ThreadStorageWatchTarget | null;
 }
 
+interface CollectApplicationStorageObservedChangesArgs {
+  appsRootPath: string;
+  changedPaths: string[];
+  resolveApplicationTarget: (
+    applicationId: ApplicationId,
+  ) => ApplicationDataWatchTarget | null;
+}
+
+interface CollectDataDirSkillsObservedChangesArgs {
+  changedPaths: string[];
+  dataDirSkillsRootPath: string;
+}
+
 function toThreadStoragePath(
   args: ThreadStoragePathArgs,
 ): ThreadStoragePath | null {
@@ -67,41 +98,91 @@ function toThreadStoragePath(
   };
 }
 
-function isAppDataSubtreePath(path: ThreadStoragePath): boolean {
-  return path.parts[1] === "apps" && path.parts[3] === "data";
+function toApplicationStoragePath(
+  args: ApplicationStoragePathArgs,
+): ApplicationStoragePath | null {
+  const relativePath = path.relative(args.appsRootPath, args.changedPath);
+  if (
+    relativePath.length === 0 ||
+    relativePath.startsWith("..") ||
+    path.isAbsolute(relativePath)
+  ) {
+    return null;
+  }
+  const parts = relativePath.split(path.sep).filter(Boolean);
+  const rawApplicationId = parts[0];
+  if (!rawApplicationId) {
+    return {
+      applicationId: null,
+      parts,
+    };
+  }
+  const parsed = applicationIdSchema.safeParse(rawApplicationId);
+  return {
+    applicationId: parsed.success ? parsed.data : null,
+    parts,
+  };
+}
+
+function isApplicationDataSubtreePath(path: ApplicationStoragePath): boolean {
+  return path.parts[1] === "data";
+}
+
+function isApplicationSkillsSubtreePath(path: ApplicationStoragePath): boolean {
+  return path.parts[1] === "skills";
+}
+
+function isApplicationManifestPath(path: ApplicationStoragePath): boolean {
+  return path.parts.length === 2 && path.parts[1] === "manifest.json";
+}
+
+function isApplicationFolderPath(path: ApplicationStoragePath): boolean {
+  return path.parts.length === 1;
 }
 
-function toThreadAppDataPath(
-  path: ThreadStoragePath,
-): ThreadAppDataPath | null {
-  const rootPath = toThreadAppDataRootPath(path);
-  if (!rootPath || path.parts.length < 5) {
+function isIgnoredApplicationStorageEntry(path: ApplicationStoragePath): boolean {
+  const firstPart = path.parts[0] ?? "";
+  return (
+    firstPart.startsWith(".tmp-app_") || firstPart.startsWith(".delete-app_")
+  );
+}
+
+function toApplicationDataPath(
+  path: ApplicationStoragePath,
+): ApplicationDataPath | null {
+  const rootPath = toApplicationDataRootPath(path);
+  if (!rootPath || path.parts.length < 3) {
     return null;
   }
-  const dataPath = appDataPathSchema.safeParse(path.parts.slice(4).join("/"));
+  const dataPath = appDataPathSchema.safeParse(path.parts.slice(2).join("/"));
   if (!dataPath.success) {
     return null;
   }
   return {
-    appId: rootPath.appId,
-    threadId: path.threadId,
+    applicationId: rootPath.applicationId,
     path: dataPath.data,
   };
 }
 
-function toThreadAppDataRootPath(
-  path: ThreadStoragePath,
-): ThreadAppDataRootPath | null {
-  if (!isAppDataSubtreePath(path)) {
-    return null;
-  }
-  const appId = appIdSchema.safeParse(path.parts[2]);
-  if (!appId.success) {
+function isDataDirSkillsPath(args: DataDirSkillsPathArgs): boolean {
+  const relativePath = path.relative(
+    args.dataDirSkillsRootPath,
+    args.changedPath,
+  );
+  return (
+    relativePath.length === 0 ||
+    (!relativePath.startsWith("..") && !path.isAbsolute(relativePath))
+  );
+}
+
+function toApplicationDataRootPath(
+  path: ApplicationStoragePath,
+): ApplicationDataRootPath | null {
+  if (!path.applicationId || !isApplicationDataSubtreePath(path)) {
     return null;
   }
   return {
-    appId: appId.data,
-    threadId: path.threadId,
+    applicationId: path.applicationId,
   };
 }
 
@@ -109,8 +190,6 @@ export function collectThreadStorageObservedChanges(
   args: CollectThreadStorageObservedChangesArgs,
 ): ThreadStorageObservedChange[] {
   const storageChanges = new Map<string, ThreadStorageWatchTarget>();
-  const appDataChanges = new Map<string, ThreadStorageObservedChange>();
-  const appDataResyncs = new Map<string, ThreadStorageObservedChange>();
   for (const changedPath of args.changedPaths) {
     const storagePath = toThreadStoragePath({
       changedPath,
@@ -123,53 +202,116 @@ export function collectThreadStorageObservedChanges(
     if (!target) {
       continue;
     }
-    if (isAppDataSubtreePath(storagePath)) {
-      const appDataRootPath = toThreadAppDataRootPath(storagePath);
-      const appDataPath = toThreadAppDataPath(storagePath);
+    storageChanges.set(`${target.environmentId}:${target.threadId}`, target);
+  }
+
+  return Array.from(storageChanges.values()).map((target) => ({
+      kind: "thread-storage-changed",
+      environmentId: target.environmentId,
+      threadId: target.threadId,
+    }));
+}
+
+export function collectApplicationStorageObservedChanges(
+  args: CollectApplicationStorageObservedChangesArgs,
+): ApplicationStorageObservedChange[] {
+  let targetsChanged = false;
+  const appDataChanges = new Map<string, ApplicationStorageObservedChange>();
+  const appDataResyncs = new Map<string, ApplicationStorageObservedChange>();
+  const appSkillChanges = new Map<string, InjectedSkillsObservedChange>();
+
+  for (const changedPath of args.changedPaths) {
+    const storagePath = toApplicationStoragePath({
+      changedPath,
+      appsRootPath: args.appsRootPath,
+    });
+    if (!storagePath || isIgnoredApplicationStorageEntry(storagePath)) {
+      continue;
+    }
+    if (
+      storagePath.applicationId === null ||
+      isApplicationFolderPath(storagePath) ||
+      isApplicationManifestPath(storagePath)
+    ) {
+      targetsChanged = true;
+      continue;
+    }
+    if (isApplicationSkillsSubtreePath(storagePath)) {
+      appSkillChanges.set(storagePath.applicationId, {
+        kind: "injected-skills-changed",
+        applicationId: storagePath.applicationId,
+        changedPaths: [
+          ...(appSkillChanges.get(storagePath.applicationId)?.changedPaths ??
+            []),
+          changedPath,
+        ].sort(),
+        sourceType: "global-app",
+      });
+      continue;
+    }
+    if (isApplicationDataSubtreePath(storagePath)) {
+      const appDataRootPath = toApplicationDataRootPath(storagePath);
+      const appDataPath = toApplicationDataPath(storagePath);
       if (appDataPath) {
+        const target = args.resolveApplicationTarget(
+          appDataPath.applicationId,
+        );
+        if (!target) {
+          continue;
+        }
         appDataChanges.set(
-          `${target.environmentId}:${target.threadId}:${appDataPath.appId}:${appDataPath.path}`,
+          `${appDataPath.applicationId}:${appDataPath.path}`,
           {
-            kind: "thread-app-data-changed",
-            appId: appDataPath.appId,
-            environmentId: target.environmentId,
+            kind: "application-data-changed",
+            applicationId: appDataPath.applicationId,
+            appDataPath: target.appDataPath,
             path: appDataPath.path,
-            threadId: target.threadId,
           },
         );
       } else if (appDataRootPath) {
-        storageChanges.set(
-          `${target.environmentId}:${target.threadId}`,
-          target,
-        );
-        appDataResyncs.set(
-          `${target.environmentId}:${target.threadId}:${appDataRootPath.appId}`,
-          {
-            kind: "thread-app-data-resync",
-            appId: appDataRootPath.appId,
-            environmentId: target.environmentId,
-            threadId: target.threadId,
-          },
-        );
+        appDataResyncs.set(appDataRootPath.applicationId, {
+          kind: "application-data-resync",
+          applicationId: appDataRootPath.applicationId,
+        });
       }
       continue;
     }
-    storageChanges.set(`${target.environmentId}:${target.threadId}`, target);
   }
 
-  const observedChanges: ThreadStorageObservedChange[] = [];
-  for (const target of storageChanges.values()) {
-    observedChanges.push({
-      kind: "thread-storage-changed",
-      environmentId: target.environmentId,
-      threadId: target.threadId,
-    });
+  const observedChanges: ApplicationStorageObservedChange[] = [];
+  if (targetsChanged) {
+    observedChanges.push({ kind: "application-storage-targets-changed" });
   }
   observedChanges.push(...appDataChanges.values());
   observedChanges.push(...appDataResyncs.values());
+  observedChanges.push(...appSkillChanges.values());
   return observedChanges;
 }
 
+export function collectDataDirSkillsObservedChanges(
+  args: CollectDataDirSkillsObservedChangesArgs,
+): InjectedSkillsObservedChange[] {
+  const changedPaths = args.changedPaths
+    .filter((changedPath) =>
+      isDataDirSkillsPath({
+        changedPath,
+        dataDirSkillsRootPath: args.dataDirSkillsRootPath,
+      }),
+    )
+    .sort();
+  if (changedPaths.length === 0) {
+    return [];
+  }
+  return [
+    {
+      kind: "injected-skills-changed",
+      applicationId: null,
+      changedPaths,
+      sourceType: "data-dir",
+    },
+  ];
+}
+
 function watchWorkspace(args: WatchWorkspaceArgs): () => Promise<void> {
   return watchWorkspaceStatus(args.workspacePath, {
     onChange: (event) => {
@@ -215,9 +357,58 @@ function watchThreadStorageRoot(
   });
 }
 
+function watchApplicationStorageRoot(
+  args: WatchApplicationStorageRootArgs,
+): () => Promise<void> {
+  return watchPathChanges(args.appsRootPath, {
+    onChange: ({ changedPaths }) => {
+      const events = collectApplicationStorageObservedChanges({
+        changedPaths,
+        appsRootPath: args.appsRootPath,
+        resolveApplicationTarget: args.resolveApplicationTarget,
+      });
+      for (const event of events) {
+        args.onChange(event);
+      }
+    },
+    onWatchError: (error) => {
+      args.onWatchError({
+        kind: "application-storage-watch-error",
+        rootPath: error.rootPath,
+        message: error.message,
+      });
+    },
+  });
+}
+
+function watchDataDirSkillsRoot(
+  args: WatchDataDirSkillsRootArgs,
+): () => Promise<void> {
+  return watchPathChanges(args.dataDirSkillsRootPath, {
+    onChange: ({ changedPaths }) => {
+      const events = collectDataDirSkillsObservedChanges({
+        changedPaths,
+        dataDirSkillsRootPath: args.dataDirSkillsRootPath,
+      });
+      for (const event of events) {
+        args.onChange(event);
+      }
+    },
+    onWatchError: (error) => {
+      args.onWatchError({
+        kind: "data-dir-skills-watch-error",
+        rootPath: error.rootPath,
+        message: error.message,
+      });
+    },
+  });
+}
+
 export function createParcelHostWatcher(): HostWatcher {
   return {
     watchWorkspace,
     watchThreadStorageRoot,
+    watchApplicationStorageRoot,
+    watchDataDirSkillsRoot,
   };
 }
diff --git a/packages/host-watcher/test/thread-storage-watch.test.ts b/packages/host-watcher/test/thread-storage-watch.test.ts
index 8d487b0c4..8693cd2cf 100644
--- a/packages/host-watcher/test/thread-storage-watch.test.ts
+++ b/packages/host-watcher/test/thread-storage-watch.test.ts
@@ -1,7 +1,14 @@
 import path from "node:path";
 import { describe, expect, it } from "vitest";
-import type { ThreadStorageWatchTarget } from "../src/host-watcher-types.js";
-import { collectThreadStorageObservedChanges } from "../src/parcel-host-watcher.js";
+import type {
+  ApplicationDataWatchTarget,
+  ThreadStorageWatchTarget,
+} from "../src/host-watcher-types.js";
+import {
+  collectApplicationStorageObservedChanges,
+  collectDataDirSkillsObservedChanges,
+  collectThreadStorageObservedChanges,
+} from "../src/parcel-host-watcher.js";
 
 function createResolver(
   targets: Record<string, ThreadStorageWatchTarget>,
@@ -9,6 +16,12 @@ function createResolver(
   return (threadId) => targets[threadId] ?? null;
 }
 
+function createApplicationResolver(
+  targets: Record<string, ApplicationDataWatchTarget>,
+): (applicationId: string) => ApplicationDataWatchTarget | null {
+  return (applicationId) => targets[applicationId] ?? null;
+}
+
 describe("thread storage watcher classification", () => {
   it("emits broad storage changes for ordinary thread storage changes", () => {
     const rootPath = path.join("/tmp", "thread-storage");
@@ -46,78 +59,138 @@ describe("thread storage watcher classification", () => {
     ]);
   });
 
-  it("emits targeted app data changes without broad storage changes", () => {
-    const rootPath = path.join("/tmp", "thread-storage");
-    const changes = collectThreadStorageObservedChanges({
-      threadStorageRootPath: rootPath,
+  it("emits app storage target refreshes for app folders and manifests", () => {
+    const rootPath = path.join("/tmp", "apps");
+    const changes = collectApplicationStorageObservedChanges({
+      appsRootPath: rootPath,
       changedPaths: [
-        path.join(rootPath, "thr_one", "apps", "status", "data", "state.json"),
-        path.join(rootPath, "thr_one", "apps", "status", "data", "state.json"),
-        path.join(rootPath, "thr_one", "apps", "kanban", "data", "cards", "1"),
-        path.join(rootPath, "thr_one", "apps", "bad.app", "data", "state.json"),
-        path.join(
-          rootPath,
-          "thr_unknown",
-          "apps",
-          "status",
-          "data",
-          "state.json",
-        ),
+        path.join(rootPath, "app-status", "manifest.json"),
+        path.join(rootPath, "app_new"),
+        path.join(rootPath, "bad.app", "data", "state.json"),
+        path.join(rootPath, ".tmp-app_app-status-abc", "manifest.json"),
+        path.join(rootPath, ".delete-app_app-status-abc", "manifest.json"),
       ],
-      resolveThreadTarget: createResolver({
-        thr_one: {
-          environmentId: "env_one",
-          threadId: "thr_one",
+      resolveApplicationTarget: createApplicationResolver({}),
+    });
+
+    expect(changes).toEqual([
+      { kind: "application-storage-targets-changed" },
+    ]);
+  });
+
+  it("emits targeted app data changes", () => {
+    const rootPath = path.join("/tmp", "apps");
+    const changes = collectApplicationStorageObservedChanges({
+      appsRootPath: rootPath,
+      changedPaths: [
+        path.join(rootPath, "app-status", "data", "state.json"),
+        path.join(rootPath, "app-status", "data", "state.json"),
+        path.join(rootPath, "app-kanban", "data", "cards", "1"),
+        path.join(rootPath, "app-unknown", "data", "state.json"),
+        path.join(rootPath, ".tmp-app_app-status-abc", "data", "state.json"),
+      ],
+      resolveApplicationTarget: createApplicationResolver({
+        "app-status": {
+          applicationId: "app-status",
+          appDataPath: path.join(rootPath, "app-status", "data"),
+        },
+        "app-kanban": {
+          applicationId: "app-kanban",
+          appDataPath: path.join(rootPath, "app-kanban", "data"),
         },
       }),
     });
 
     expect(changes).toEqual([
       {
-        kind: "thread-app-data-changed",
-        appId: "status",
-        environmentId: "env_one",
+        kind: "application-data-changed",
+        applicationId: "app-status",
+        appDataPath: path.join(rootPath, "app-status", "data"),
         path: "state.json",
-        threadId: "thr_one",
       },
       {
-        kind: "thread-app-data-changed",
-        appId: "kanban",
-        environmentId: "env_one",
+        kind: "application-data-changed",
+        applicationId: "app-kanban",
+        appDataPath: path.join(rootPath, "app-kanban", "data"),
         path: "cards/1",
-        threadId: "thr_one",
       },
     ]);
   });
 
-  it("emits resync hints and broad storage changes for unclassifiable app data changes", () => {
-    const rootPath = path.join("/tmp", "thread-storage");
-    const changes = collectThreadStorageObservedChanges({
-      threadStorageRootPath: rootPath,
+  it("emits app data resync hints for unclassifiable app data changes", () => {
+    const rootPath = path.join("/tmp", "apps");
+    const changes = collectApplicationStorageObservedChanges({
+      appsRootPath: rootPath,
       changedPaths: [
-        path.join(rootPath, "thr_one", "apps", "status", "data"),
-        path.join(rootPath, "thr_one", "apps", "status", "data", ".state.tmp"),
-        path.join(rootPath, "thr_one", "apps", "status", "data"),
+        path.join(rootPath, "app-status", "data"),
+        path.join(rootPath, "app-status", "data", ".state.tmp"),
+        path.join(rootPath, "app-status", "data"),
       ],
-      resolveThreadTarget: createResolver({
-        thr_one: {
-          environmentId: "env_one",
-          threadId: "thr_one",
-        },
-      }),
+      resolveApplicationTarget: createApplicationResolver({}),
     });
 
     expect(changes).toEqual([
       {
-        kind: "thread-storage-changed",
-        environmentId: "env_one",
-        threadId: "thr_one",
+        kind: "application-data-resync",
+        applicationId: "app-status",
+      },
+    ]);
+  });
+
+  it("emits injected skill changes for app skill trees", () => {
+    const rootPath = path.join("/tmp", "apps");
+    const changes = collectApplicationStorageObservedChanges({
+      appsRootPath: rootPath,
+      changedPaths: [
+        path.join(rootPath, "app-status", "skills", "demo-skill", "SKILL.md"),
+        path.join(rootPath, "app-status", "skills", "demo-skill", "references", "notes.md"),
+        path.join(rootPath, "app-other", "skills"),
+      ],
+      resolveApplicationTarget: createApplicationResolver({}),
+    });
+
+    expect(changes).toEqual([
+      {
+        kind: "injected-skills-changed",
+        applicationId: "app-status",
+        changedPaths: [
+          path.join(rootPath, "app-status", "skills", "demo-skill", "SKILL.md"),
+          path.join(
+            rootPath,
+            "app-status",
+            "skills",
+            "demo-skill",
+            "references",
+            "notes.md",
+          ),
+        ],
+        sourceType: "global-app",
       },
       {
-        kind: "thread-app-data-resync",
-        appId: "status",
-        environmentId: "env_one",
-        threadId: "thr_one",
+        kind: "injected-skills-changed",
+        applicationId: "app-other",
+        changedPaths: [path.join(rootPath, "app-other", "skills")],
+        sourceType: "global-app",
+      },
+    ]);
+  });
+
+  it("emits injected skill changes for data-dir-level skills", () => {
+    const rootPath = path.join("/tmp", "skills");
+    const changes = collectDataDirSkillsObservedChanges({
+      dataDirSkillsRootPath: rootPath,
+      changedPaths: [
+        path.join(rootPath, "demo-skill", "SKILL.md"),
+        path.join(rootPath, "..", "apps", "app-status", "skills", "demo", "SKILL.md"),
+      ],
+    });
+
+    expect(changes).toEqual([
+      {
+        kind: "injected-skills-changed",
+        applicationId: null,
+        changedPaths: [path.join(rootPath, "demo-skill", "SKILL.md")],
+        sourceType: "data-dir",
       },
     ]);
   });
diff --git a/packages/server-contract/src/api-types.ts b/packages/server-contract/src/api-types.ts
index c3f94dfc2..ed024563d 100644
--- a/packages/server-contract/src/api-types.ts
+++ b/packages/server-contract/src/api-types.ts
@@ -36,13 +36,13 @@ import {
   managerTemplateNameSchema,
   jsonValueSchema,
   appDataPathSchema,
-  appIdSchema,
+  applicationIdSchema,
   callerExecutionInputSourceSchema,
 } from "@bb/domain";
 import { workspaceResolutionFailureSchema } from "@bb/host-daemon-contract";
 import type {
   AppDataPath,
-  AppId,
+  ApplicationId,
   CallerExecutionInputSource,
   GitBranchName,
   JsonValue,
@@ -158,8 +158,8 @@ export const BB_DESKTOP_BROWSER_MAX_TITLE_LENGTH = 1024;
 /**
  * Pixel rect (CSS px, which equal device-independent points on macOS) of the
  * panel region the native browser view must overlay. The renderer measures the
- * placeholder div and streams this on resize; the main process applies it
- * verbatim via `WebContentsView.setBounds`.
+ * placeholder div and streams a viewport-clamped rect on resize; the main
+ * process applies a final host-window clamp before `WebContentsView.setBounds`.
  */
 export const bbDesktopBrowserViewBoundsSchema = z
   .object({
@@ -173,6 +173,60 @@ export type BbDesktopBrowserViewBounds = z.infer<
   typeof bbDesktopBrowserViewBoundsSchema
 >;
 
+export interface BbDesktopBrowserViewportBounds {
+  width: number;
+  height: number;
+}
+
+interface ClampIntegerToRangeArgs {
+  max: number;
+  min: number;
+  value: number;
+}
+
+export interface ClampBbDesktopBrowserViewBoundsArgs {
+  bounds: BbDesktopBrowserViewBounds;
+  viewport: BbDesktopBrowserViewportBounds;
+}
+
+function clampIntegerToRange(args: ClampIntegerToRangeArgs): number {
+  return Math.min(Math.max(args.value, args.min), args.max);
+}
+
+export function clampBbDesktopBrowserViewBounds(
+  args: ClampBbDesktopBrowserViewBoundsArgs,
+): BbDesktopBrowserViewBounds {
+  const viewportRight = Math.max(0, Math.round(args.viewport.width));
+  const viewportBottom = Math.max(0, Math.round(args.viewport.height));
+  const x = clampIntegerToRange({
+    value: args.bounds.x,
+    min: 0,
+    max: viewportRight,
+  });
+  const y = clampIntegerToRange({
+    value: args.bounds.y,
+    min: 0,
+    max: viewportBottom,
+  });
+  const right = clampIntegerToRange({
+    value: args.bounds.x + args.bounds.width,
+    min: x,
+    max: viewportRight,
+  });
+  const bottom = clampIntegerToRange({
+    value: args.bounds.y + args.bounds.height,
+    min: y,
+    max: viewportBottom,
+  });
+
+  return {
+    x,
+    y,
+    width: right - x,
+    height: bottom - y,
+  };
+}
+
 /**
  * Create-or-update the view for a browser tab. `url` may be empty to mean "no
  * page yet" (the renderer shows its new-tab screen and keeps the view hidden).
@@ -1353,31 +1407,25 @@ export type AppEntry = z.infer<typeof appEntrySchema>;
 export const appCapabilitySchema = z.enum(["data", "message"]);
 export type AppCapability = z.infer<typeof appCapabilitySchema>;
 
-export const appContributionSchema = z.enum(["thread.app"]);
+const appDisplayNameSchema = z.string().max(80);
 
 export const appManifestSchema = z
   .object({
-    manifestVersion: z.literal(1),
-    id: appIdSchema,
-    name: z.string().min(1).max(80),
+    manifestVersion: z.literal(1).default(1),
+    id: applicationIdSchema,
+    name: appDisplayNameSchema.optional(),
     icon: appIconNameSchema.optional(),
     entry: appEntryPathSchema.optional(),
-    contributions: z.array(appContributionSchema).min(1),
-    capabilities: z.array(appCapabilitySchema),
+    capabilities: z.array(appCapabilitySchema).default([]),
   })
   .strict()
-  .superRefine((manifest, context) => {
-    if (
-      manifest.contributions.length !== 1 ||
-      manifest.contributions[0] !== "thread.app"
-    ) {
-      context.addIssue({
-        code: "custom",
-        path: ["contributions"],
-        message: 'Only ["thread.app"] is supported',
-      });
-    }
-  });
+  .transform((manifest) => ({
+    ...manifest,
+    name:
+      manifest.name === undefined || manifest.name.trim().length === 0
+        ? manifest.id
+        : manifest.name,
+  }));
 export type AppManifest = z.infer<typeof appManifestSchema>;
 
 export const appIconSchema = z.discriminatedUnion("kind", [
@@ -1398,7 +1446,7 @@ export type AppIcon = z.infer<typeof appIconSchema>;
 
 export const appSummarySchema = z
   .object({
-    id: appIdSchema,
+    applicationId: applicationIdSchema,
     name: z.string().min(1).max(80),
     entry: appEntrySchema,
     capabilities: z.array(appCapabilitySchema),
@@ -1407,22 +1455,32 @@ export const appSummarySchema = z
   .strict();
 export type AppSummary = z.infer<typeof appSummarySchema>;
 
-export const appDetailSchema = appSummarySchema;
+export const appDetailSchema = appSummarySchema
+  .extend({
+    appsRootPath: z.string().min(1),
+    appRootPath: z.string().min(1),
+    appDataPath: z.string().min(1),
+  })
+  .strict();
 export type AppDetail = z.infer<typeof appDetailSchema>;
 
-export const appTemplateSchema = z.enum(["blank", "status"]);
-export type AppTemplate = z.infer<typeof appTemplateSchema>;
-
-export const createThreadAppRequestSchema = z
+export const createAppRequestSchema = z
   .object({
-    id: appIdSchema,
-    name: z.string().min(1).max(80),
-    template: appTemplateSchema,
+    applicationId: applicationIdSchema.optional(),
+    name: appDisplayNameSchema.optional(),
   })
-  .strict();
-export type CreateThreadAppRequest = z.infer<
-  typeof createThreadAppRequestSchema
->;
+  .strict()
+  .superRefine((request, context) => {
+    const hasName =
+      request.name !== undefined && request.name.trim().length > 0;
+    if (request.applicationId === undefined && !hasName) {
+      context.addIssue({
+        code: "custom",
+        message: "Provide applicationId or name",
+      });
+    }
+  });
+export type CreateAppRequest = z.infer<typeof createAppRequestSchema>;
 
 export const appDataEntrySchema = z
   .object({
@@ -1461,7 +1519,12 @@ export type AppDataWriteRequest = z.infer<typeof appDataWriteRequestSchema>;
 
 export const appMessageRequestSchema = z
   .object({
-    text: z.string().min(1),
+    payload: jsonValueSchema,
+    appSessionToken: z
+      .string()
+      .regex(/^appsess_[A-Za-z0-9_-]+$/u)
+      .optional(),
+    targetThreadId: z.string().min(1).optional(),
   })
   .strict();
 export type AppMessageRequest = z.infer<typeof appMessageRequestSchema>;
@@ -1469,8 +1532,7 @@ export type AppMessageRequest = z.infer<typeof appMessageRequestSchema>;
 export const appDataChangedBroadcastMessageSchema = z
   .object({
     type: z.literal("app-data.changed"),
-    threadId: z.string().min(1),
-    appId: appIdSchema,
+    applicationId: applicationIdSchema,
     path: appDataPathSchema,
     value: jsonValueSchema.nullable(),
     deleted: z.boolean(),
@@ -1481,8 +1543,7 @@ export const appDataChangedBroadcastMessageSchema = z
 export const appDataResyncBroadcastMessageSchema = z
   .object({
     type: z.literal("app-data.resync"),
-    threadId: z.string().min(1),
-    appId: appIdSchema,
+    applicationId: applicationIdSchema,
   })
   .strict();
 
@@ -1519,9 +1580,10 @@ export interface BbData {
 }
 
 export interface Bb {
-  appId: AppId;
+  appId: ApplicationId;
+  applicationId: ApplicationId;
   data?: BbData;
-  message?(text: string): Promise<void>;
+  message?(payload: JsonValue): Promise<void>;
 }
 
 declare global {
diff --git a/packages/server-contract/src/index.ts b/packages/server-contract/src/index.ts
index fe3952c09..6cdd5050d 100644
--- a/packages/server-contract/src/index.ts
+++ b/packages/server-contract/src/index.ts
@@ -140,6 +140,7 @@ export {
   BB_DESKTOP_BROWSER_MAX_TITLE_LENGTH,
   BB_DESKTOP_BROWSER_MAX_URL_LENGTH,
   bbDesktopBrowserAttachRequestSchema,
+  clampBbDesktopBrowserViewBounds,
   bbDesktopBrowserNavigateRequestSchema,
   bbDesktopBrowserOpenTabRequestSchema,
   bbDesktopBrowserSetBoundsRequestSchema,
@@ -192,7 +193,6 @@ export {
   threadStoragePathListResponseSchema,
   threadStoragePathsQuerySchema,
   appCapabilitySchema,
-  appContributionSchema,
   appDataBroadcastMessageSchema,
   appDataChangedBroadcastMessageSchema,
   appDataEntrySchema,
@@ -211,8 +211,7 @@ export {
   appManifestSchema,
   appMessageRequestSchema,
   appSummarySchema,
-  appTemplateSchema,
-  createThreadAppRequestSchema,
+  createAppRequestSchema,
   projectAttachmentContentQuerySchema,
   projectBranchesQuerySchema,
   projectBranchesResponseSchema,
@@ -332,6 +331,8 @@ export type {
   BbDesktopBrowserState,
   BbDesktopBrowserStateHandler,
   BbDesktopBrowserUnsubscribe,
+  ClampBbDesktopBrowserViewBoundsArgs,
+  BbDesktopBrowserViewportBounds,
   BbDesktopBrowserViewBounds,
   BbDesktopInfo,
   BbDesktopInfoChangeHandler,
@@ -392,13 +393,12 @@ export type {
   AppManifest,
   AppMessageRequest,
   AppSummary,
-  AppTemplate,
   Bb,
   BbData,
   BbDataChangeCallback,
   BbDataChangeEvent,
   BbDataEntry,
-  CreateThreadAppRequest,
+  CreateAppRequest,
   ProjectAttachmentContentQuery,
   ProjectBranchesQuery,
   ProjectBranchesResponse,
diff --git a/packages/server-contract/src/public-api.ts b/packages/server-contract/src/public-api.ts
index 0048e95c0..f559728a1 100644
--- a/packages/server-contract/src/public-api.ts
+++ b/packages/server-contract/src/public-api.ts
@@ -28,11 +28,11 @@ import type {
   AppDetail,
   AppMessageRequest,
   AppSummary,
+  CreateAppRequest,
   CreateAutomationRequest,
   CreateHostJoinRequest,
   CreateHostJoinResponse,
   CreateQueuedMessageRequest,
-  CreateThreadAppRequest,
   CreateManagerThreadRequest,
   CreateProjectRequest,
   CreateProjectSourceRequest,
@@ -126,7 +126,7 @@ import type { ApiError } from "./errors.js";
 
 type PathProjectSourceId = { param: { id: string; sourceId: string } };
 type PathProjectManagerThreadId = { param: { id: string; threadId: string } };
-type PathThreadApp = { param: { id: string; appId: string } };
+type PathApplicationApp = { param: { applicationId: string } };
 
 export type PublicApiSchema = {
   // ─── Development Only ────────────────────────────────────────────────
@@ -145,6 +145,48 @@ export type PublicApiSchema = {
     >;
   };
 
+  // ─── Apps ────────────────────────────────────────────────────────────
+
+  "/apps": {
+    /** List global local-host apps by scanning valid manifests in the app root. */
+    $get: Endpoint<EmptyInput, AppSummary[]>;
+    /** Create one global local-host app with a slug applicationId, derived from name when omitted. */
+    $post: Endpoint<{ json: CreateAppRequest }, AppDetail, 201>;
+  };
+  "/apps/:applicationId": {
+    /** Resolve one global app manifest and canonical storage paths. */
+    $get: Endpoint<PathApplicationApp, AppDetail>;
+    /** Delete one global app folder, including assets and data. */
+    $delete: Endpoint<PathApplicationApp, { ok: true }>;
+  };
+  "/apps/:applicationId/data": {
+    /** List JSON value files at or below an app data prefix. */
+    $get: Endpoint<
+      PathApplicationApp & { query?: AppDataListQuery },
+      AppDataListResponse
+    >;
+  };
+  "/apps/:applicationId/data/*": {
+    /**
+     * Read, write, or delete one app data JSON file. The wildcard suffix is
+     * validated by the route because hono-typed-routes only types named params.
+     */
+    $get: Endpoint<PathApplicationApp, AppDataReadResponse>;
+    $put: Endpoint<
+      PathApplicationApp & { json: AppDataWriteRequest },
+      AppDataReadResponse
+    >;
+    $delete: Endpoint<PathApplicationApp, { ok: true }>;
+  };
+  "/apps/:applicationId/message": {
+    /** Send a message from a global app to an explicit thread target context. */
+    $post: Endpoint<
+      PathApplicationApp & { json: AppMessageRequest },
+      { ok: true },
+      202
+    >;
+  };
+
   // ─── Projects ────────────────────────────────────────────────────────
 
   "/projects": {
@@ -600,41 +642,6 @@ export type PublicApiSchema = {
     /** Returns the last used options for the thread for use as defaults in the UI. */
     $get: Endpoint<PathId, ResolvedThreadExecutionOptions | null>;
   };
-  "/threads/:id/apps": {
-    /** List thread apps by reading validated manifests from thread storage. */
-    $get: Endpoint<PathId, AppSummary[]>;
-    /** Scaffold a new thread app under apps/<appId>/ using a server-owned template. */
-    $post: Endpoint<PathId & { json: CreateThreadAppRequest }, AppDetail, 201>;
-  };
-  "/threads/:id/apps/:appId": {
-    /** Resolve one thread app manifest, entry, and icon. */
-    $get: Endpoint<PathThreadApp, AppDetail>;
-    /** Remove one thread app directory from thread storage. */
-    $delete: Endpoint<PathThreadApp, { ok: true }>;
-  };
-  "/threads/:id/apps/:appId/data": {
-    /** List JSON value files at or below an app data prefix. */
-    $get: Endpoint<
-      PathThreadApp & { query?: AppDataListQuery },
-      AppDataListResponse
-    >;
-  };
-  "/threads/:id/apps/:appId/data/*": {
-    /**
-     * Read, write, or delete one app data JSON file. The wildcard suffix is
-     * validated by the route because hono-typed-routes only types named params.
-     */
-    $get: Endpoint<PathThreadApp, AppDataReadResponse>;
-    $put: Endpoint<
-      PathThreadApp & { json: AppDataWriteRequest },
-      AppDataReadResponse
-    >;
-    $delete: Endpoint<PathThreadApp, { ok: true }>;
-  };
-  "/threads/:id/apps/:appId/message": {
-    /** Send a message from an app iframe to its owning thread. */
-    $post: Endpoint<PathThreadApp & { json: AppMessageRequest }, { ok: true }>;
-  };
   "/threads/:id/thread-storage/files": {
     /**
      * List files in the durable thread storage for a thread environment.
diff --git a/packages/server-contract/test/contract.test.ts b/packages/server-contract/test/contract.test.ts
index 0a97e257b..62f3972a9 100644
--- a/packages/server-contract/test/contract.test.ts
+++ b/packages/server-contract/test/contract.test.ts
@@ -1,4 +1,7 @@
-import { collectOptionalFieldPaths, makeWorkspaceStatus } from "@bb/test-helpers";
+import {
+  collectOptionalFieldPaths,
+  makeWorkspaceStatus,
+} from "@bb/test-helpers";
 import type { WorkspaceResolutionFailure } from "@bb/host-daemon-contract";
 import { describe, expect, it } from "vitest";
 import publicApiSource from "../src/public-api.ts?raw";
@@ -51,6 +54,8 @@ const INTENTIONAL_OPTIONAL_SERVER_FIELDS: Record<string, string> = {
     "App manifests may omit entry so the server can resolve index.html then index.md at the boundary.",
   "appManifestSchema.icon":
     "App manifests may omit icon so the server can resolve a logo file or the GridView fallback.",
+  "appManifestSchema.name":
+    "App manifests may omit name; the display label falls back to the slug applicationId when unset.",
   "createAutomationRequestSchema.action.threadRequest.environment.workspace.branch":
     "Unmanaged workspaces may omit branch when the daemon should not check out before starting the thread.",
   "createAutomationRequestSchema.action.threadRequest.environment.hostId":
@@ -687,11 +692,28 @@ describe("server-contract canonical schemas", () => {
       name: "Status",
       icon: "ListTodo",
       entry: "index.html",
-      contributions: ["thread.app"],
       capabilities: ["data", "message"],
     };
 
     expect(contract.appManifestSchema.parse(manifest)).toEqual(manifest);
+    expect(
+      contract.appManifestSchema.parse({
+        ...manifest,
+        name: undefined,
+      }),
+    ).toEqual({
+      ...manifest,
+      name: "status",
+    });
+    expect(
+      contract.appManifestSchema.parse({
+        ...manifest,
+        name: "",
+      }),
+    ).toEqual({
+      ...manifest,
+      name: "status",
+    });
     expect(
       contract.appManifestSchema.safeParse({
         ...manifest,
@@ -707,14 +729,19 @@ describe("server-contract canonical schemas", () => {
     expect(
       contract.appManifestSchema.safeParse({
         ...manifest,
-        contributions: ["thread.app", "sidebar"],
+        id: "Bad",
+      }).success,
+    ).toBe(false);
+    expect(
+      contract.appManifestSchema.safeParse({
+        ...manifest,
+        contributions: ["sidebar"],
       }).success,
     ).toBe(false);
 
     const message = {
       type: "app-data.changed",
-      threadId: "thr_123",
-      appId: "status",
+      applicationId: "status",
       path: "state.json",
       value: { workers: [] },
       deleted: false,
@@ -737,13 +764,11 @@ describe("server-contract canonical schemas", () => {
     expect(
       contract.appDataBroadcastMessageSchema.parse({
         type: "app-data.resync",
-        threadId: "thr_123",
-        appId: "status",
+        applicationId: "status",
       }),
     ).toEqual({
       type: "app-data.resync",
-      threadId: "thr_123",
-      appId: "status",
+      applicationId: "status",
     });
   });
 
@@ -1179,7 +1204,7 @@ describe("server-contract canonical schemas", () => {
       "automations-changed",
       "nudges-changed",
     ]);
-    expect(SYSTEM_CHANGE_KINDS).toEqual(["config-changed"]);
+    expect(SYSTEM_CHANGE_KINDS).toEqual(["config-changed", "apps-changed"]);
   });
 
   it("keeps only intentional optional request fields", () => {
diff --git a/packages/templates/src/generated/templates.generated.ts b/packages/templates/src/generated/templates.generated.ts
index 3502f73f5..c4af2769b 100644
--- a/packages/templates/src/generated/templates.generated.ts
+++ b/packages/templates/src/generated/templates.generated.ts
@@ -18,13 +18,13 @@ export const templateDefinitions = [
   },
   {
     "id": "bbGuideApp",
-    "body": "Apps\n\nApps are the supported way to build dashboards, control panels, and other\ninteractive surfaces inside thread storage. A manager's primary status surface\nis the built-in `status` app. Keep that app current instead of creating legacy\ntop-level status files.\n\nImportant: a bb app is self-contained static HTML/CSS/JS/SVG. Put files under\n`apps/<id>/assets/`; bb serves the `entry` file directly from the flat app URL\nthrough the host daemon. Do not start a web server, localhost dev server, npm\ninstall, build step, bundler, or framework for a normal app. Inline CSS/JS,\nrelative asset refs, and CDN resources such as Tailwind or fonts are fine.\n\nStorage layout:\n\n```text\n$BB_THREAD_STORAGE/\n  apps/\n    status/\n      manifest.json\n      assets/\n        index.html\n      data/\n        state.json\n```\n\nEach app is rooted at `apps/<id>/`. The manifest lives at\n`apps/<id>/manifest.json`, browser files live under `apps/<id>/assets/`, and\ndurable JSON state lives under `apps/<id>/data/`. The `status` app should keep\nits primary shared state in `apps/status/data/state.json`.\n\nManifest:\n\n```json\n{\n  \"manifestVersion\": 1,\n  \"id\": \"status\",\n  \"name\": \"Status\",\n  \"icon\": \"ListTodo\",\n  \"entry\": \"index.html\",\n  \"contributions\": [\"thread.app\"],\n  \"capabilities\": [\"data\", \"message\"]\n}\n```\n\n`id` uses letters, numbers, underscores, and hyphens. `entry` is relative to\n`assets/`. HTML entries load in an app iframe and receive the `window.bb`\nbridge according to `capabilities`; Markdown entries render as static documents\nand do not receive `window.bb`. `capabilities` controls which `window.bb`\nhelpers are injected for HTML entries: `data` enables `window.bb.data`, and\n`message` enables `window.bb.message`.\n\nThe served app URL is flat: `/api/v1/threads/<thread-id>/apps/<id>/<file>`\nmaps to `apps/<id>/assets/<file>` on disk. HTML should use flat relative refs\nlike `./index-abc.js`, not `./assets/index-abc.js`. If you are migrating an\nexisting Vite build output, set `build.assetsDir = \"\"` so emitted files sit\nalongside `index.html`; new bb apps should stay plain static files.\n\nThe icon is optional and uses a built-in icon name. Icon resolution order is:\n\n1. `manifest.icon`, when present, as a built-in icon.\n2. A custom top-level `logo.svg`, `logo.png`, `logo.jpg`, or `logo.jpeg` in the\n   app root, up to 1 MB.\n3. The built-in `GridView` fallback.\n\nCLI:\n\n```bash\nbb app list --self\nbb app new \"Review Board\" --id review-board --template blank --self\nbb app new \"Status\" --id status --template status --self\nbb app open status --self\nbb app rm review-board --self --yes\n```\n\nPass a thread id instead of `--self` to target another thread. `bb app open`\nprints the app URL. `--json` is available for scripts.\n\nAgent writes:\n\nWrite app data directly to `apps/<id>/data/<path>` using a temp file in the\nsame directory and then `mv` into place. Same-directory rename is atomic on\nmacOS and Linux, and bb broadcasts the committed app-data change.\n\n```bash\ndir=\"$BB_THREAD_STORAGE/apps/status/data\"\nmkdir -p \"$dir\"\ntmp=$(mktemp \"$dir/.state.XXXXXX\")\nprintf '%s\\n' '{\"tasks\":[],\"updatedAt\":\"2026-05-28T00:00:00Z\"}' > \"$tmp\" &&\n  mv \"$tmp\" \"$dir/state.json\"\n```\n\nData paths are relative to the app's `data/` directory. They must not start or\nend with `/`, must not contain backslashes, dot-prefixed segments, `.` or `..`,\nand may be nested up to eight path segments. Each segment may use letters,\nnumbers, dots, underscores, and hyphens.\n\nBrowser API:\n\n```ts\nwindow.bb.appId\nawait window.bb.data?.read(\"state.json\")\nawait window.bb.data?.write(\"state.json\", { tasks: [] })\nawait window.bb.data?.delete(\"state.json\")\nconst entries = await window.bb.data?.list(\"\")\nconst unsubscribe = window.bb.data?.onChange(\"\", (event) => {\n  console.log(event.path, event.value, event.deleted)\n})\nawait window.bb.message?.(\"Please review the current blockers.\")\n```\n\n`window.bb.data` reads and writes JSON values. `onChange(prefix, callback)`\nmatches a single data file when `prefix` equals that path and matches a subtree\nwhen the changed path is below `prefix + \"/\"`; `\"\"` matches all app data.\nRegistering a listener immediately replays existing matching data, and bb\nreplays again after reconnects or app-data resync hints. Later filesystem\nwrites, browser writes, and deletes are delivered after that replay.\n`window.bb.message(text)` sends a normal follow-up message to the thread that\nowns the app.\n\nMinimal status app pattern:\n\n```html\n<main>\n  <h1>Current work</h1>\n  <ul id=\"tasks\"></ul>\n</main>\n<script>\nconst list = document.querySelector(\"#tasks\");\n\nfunction render(state) {\n  const tasks = state?.tasks ?? [];\n  list.replaceChildren(\n    ...tasks.map((task) => {\n      const item = document.createElement(\"li\");\n      item.textContent = `${task.title} - ${task.state}`;\n      return item;\n    }),\n  );\n}\n\nwindow.bb.data?.read(\"state.json\").then(render);\nwindow.bb.data?.onChange(\"state.json\", (event) => render(event.value));\n</script>\n```\n\nStyling:\n\nMake app UI quiet, dense, and consistent with bb unless the user asks for a\ndifferent direction. Use Tailwind for layout utilities if helpful, and use the\nbb-style tokens below for colors, fonts, borders, radius, and shadows. Apps\nrender in iframes, so external resources such as Google Fonts, Tailwind CDN,\nremote images, and stylesheets load normally.\n\n```html\n<script src=\"https://cdn.tailwindcss.com\"></script>\n<link rel=\"preconnect\" href=\"https://fonts.googleapis.com\">\n<link rel=\"preconnect\" href=\"https://fonts.gstatic.com\" crossorigin>\n<link href=\"https://fonts.googleapis.com/css2?family=Inter:wght@400;500;600;700&family=Fira+Code:wght@400;500&display=swap\" rel=\"stylesheet\">\n<style>\n:root {\n  color-scheme: light;\n  --background: oklch(0.9551 0 0);\n  --foreground: oklch(0.3211 0 0);\n  --card: oklch(0.9702 0 0);\n  --muted: oklch(0.8853 0 0);\n  --muted-foreground: oklch(0.5103 0 0);\n  --border: oklch(0.8576 0 0);\n  --accent: oklch(0.9 0 0);\n  --success: oklch(0.7 0.15 155);\n  --warning: oklch(0.7 0.16 50);\n  --destructive: oklch(0.5594 0.19 25.8625);\n  --radius: 0.5rem;\n  --font-sans: \"Inter\", ui-sans-serif, system-ui, sans-serif;\n  --font-mono: \"Fira Code\", ui-monospace, SFMono-Regular, monospace;\n}\n@media (prefers-color-scheme: dark) {\n  :root {\n    color-scheme: dark;\n    --background: oklch(0.2178 0 0);\n    --foreground: oklch(0.8853 0 0);\n    --card: oklch(0.2435 0 0);\n    --muted: oklch(0.31 0 0);\n    --muted-foreground: oklch(0.7058 0 0);\n    --border: oklch(0.34 0 0);\n    --accent: oklch(0.32 0 0);\n  }\n}\nbody {\n  margin: 0;\n  background: var(--background);\n  color: var(--foreground);\n  font-family: var(--font-sans);\n  font-size: 13px;\n}\n.panel {\n  border: 1px solid var(--border);\n  border-radius: var(--radius);\n  background: var(--card);\n}\n</style>\n```\n\nKeep one canonical app for each concept. For manager progress, update the\n`status` app instead of creating parallel views. Use additional apps only when\nthey are distinct tools or dashboards.\n\nRelated guides:\n\n  bb guide overview\n  bb guide managers\n  bb guide manager-templates\n  bb guide async",
+    "body": "Apps\n\nApps are global within the local host data directory. They are the supported\nway to build dashboards, control panels, and other interactive surfaces that\ncan open inside a thread panel.\n\nImportant: a bb app is self-contained static HTML/CSS/JS/SVG. Put browser\nfiles under `<dataDir>/apps/<applicationId>/public/`; bb serves that directory\nas the app's web root at `/api/v1/apps/<applicationId>/`.\n\nDo not start a web server, localhost dev server, npm install, build step,\nbundler, or framework for a normal app. Inline CSS/JS, relative asset refs, and\nCDN resources such as Tailwind or fonts are fine.\n\nStorage layout:\n\n```text\n<dataDir>/\n  apps/\n    review-board/\n      manifest.json\n      public/\n        index.html\n        index-abc.js\n        assets/\n          index-def.css\n      data/\n        state.json\n```\n\nEach app is rooted at `<dataDir>/apps/<applicationId>/`. The manifest lives at\n`manifest.json`, browser files live under `public/`, and durable JSON state\nlives under `data/`. Only `public/` is served as static web content.\n\nThe app exists only when the local filesystem contains a valid manifest at\n`<dataDir>/apps/<applicationId>/manifest.json`. `manifest.id` is the canonical\napplication id: it must be a lowercase path-safe slug such as `status` or\n`review-board`, globally unique inside the data dir, and equal to the\ncontaining folder name. `manifest.name` is an optional human display name only.\nWhen it is absent or empty, bb displays the slug. Display names are not\nidentifiers and may repeat.\n\nManifest:\n\n```json\n{\n  \"manifestVersion\": 1,\n  \"id\": \"review-board\",\n  \"name\": \"Review Board\",\n  \"icon\": \"ListTodo\",\n  \"entry\": \"index.html\",\n  \"capabilities\": [\"data\", \"message\"]\n}\n```\n\n`entry` is relative to `public/`. HTML entries load in an app iframe and receive\nthe `window.bb` bridge according to `capabilities`; Markdown entries render as\nstatic documents and do not receive `window.bb`. `capabilities` controls which\n`window.bb` helpers are injected for HTML entries: `data` enables\n`window.bb.data`, and `message` enables `window.bb.message`.\n\nThe served app entry URL is `/api/v1/apps/<applicationId>/`; bb serves\n`public/` transparently from that same URL root. Browser files in `public/`\ntherefore resolve by normal browser URL rules with no `<base>` injection and no\nserve-time URL rewriting:\n`public/index-abc.js` maps to `/api/v1/apps/<applicationId>/index-abc.js`, and\n`public/assets/index-def.css` maps to\n`/api/v1/apps/<applicationId>/assets/index-def.css`.\n\nFor Vite builds, set a relative base and copy the built `dist/` contents into\n`public/`:\n\n```ts\nimport { defineConfig } from \"vite\";\n\nexport default defineConfig({\n  base: \"./\",\n});\n```\n\nDo not use Vite's default root-absolute base (`\"/\"`). Refs such as\n`/assets/index-abc.js` resolve against the bb server root, not the app route, so\nthey will not load inside a mounted app.\n\nThe icon is optional and uses a built-in icon name. Icon resolution order is:\n\n1. `manifest.icon`, when present, as a built-in icon.\n2. A custom top-level `logo.svg`, `logo.png`, `logo.jpg`, or `logo.jpeg` in the\n   app root, up to 1 MB.\n3. The built-in `GridView` fallback.\n\nCLI:\n\n```bash\nbb app list\nbb app new --name \"Review Board\"\nbb app new --slug status\nbb app show review-board\nbb app data list review-board\nbb app data read review-board state.json\nbb app data write review-board state.json --file ./state.json\nbb app message review-board --target-thread thr_123 --json '\"Please review the current blockers.\"'\nbb app delete review-board --yes\n```\n\n`--json` is available for scripts. Commands accept application ids only, never\ndisplay names. There is no host selector in v1; apps are local-host only.\n\nInside an app-capable runtime, inspect the current app context:\n\n```bash\nbb app current --json\n```\n\nOutside a current-app runtime, this returns `current_app_unavailable`.\n\nRuntime paths:\n\n```bash\necho \"$BB_APPS_ROOT\"          # <dataDir>/apps\necho \"$BB_APP_ID\"             # current application id, when available\necho \"$BB_APP_ROOT\"           # <dataDir>/apps/<applicationId>, when available\necho \"$BB_APP_DATA_PATH\"      # <dataDir>/apps/<applicationId>/data, when available\n```\n\nAgent writes:\n\nWhen a runtime has `BB_APP_ROOT`, create or edit the app directly in that\ncanonical folder. Write app data with a temp file in the same directory and\nthen `mv` into place. Same-directory rename is atomic on macOS and Linux, and\nbb broadcasts the committed app-data change.\n\n```bash\ndir=\"$BB_APP_DATA_PATH\"\nmkdir -p \"$dir\"\ntmp=$(mktemp \"$dir/.state.XXXXXX\")\nprintf '%s\\n' '{\"tasks\":[],\"updatedAt\":\"2026-06-02T00:00:00Z\"}' > \"$tmp\" &&\n  mv \"$tmp\" \"$dir/state.json\"\n```\n\nData paths are relative to the app's `data/` directory. They must not start or\nend with `/`, must not contain backslashes, dot-prefixed segments, `.` or `..`,\nand may be nested up to eight path segments. Each segment may use letters,\nnumbers, dots, underscores, and hyphens.\n\nBrowser API:\n\n```ts\nwindow.bb.applicationId\nwindow.bb.appId\nawait window.bb.data?.read(\"state.json\")\nawait window.bb.data?.write(\"state.json\", { tasks: [] })\nawait window.bb.data?.delete(\"state.json\")\nconst entries = await window.bb.data?.list(\"\")\nconst unsubscribe = window.bb.data?.onChange(\"\", (event) => {\n  console.log(event.path, event.value, event.deleted)\n})\nawait window.bb.message?.(\"Please review the current blockers.\")\n```\n\n`window.bb.data` reads and writes JSON values. `onChange(prefix, callback)`\nmatches a single data file when `prefix` equals that path and matches a subtree\nwhen the changed path is below `prefix + \"/\"`; `\"\"` matches all app data.\nRegistering a listener immediately replays existing matching data, and bb\nreplays again after reconnects or app-data resync hints. Later filesystem\nwrites, browser writes, and deletes are delivered after that replay.\n\n`window.bb.message(payload)` sends a normal follow-up message to the thread\ncontext that opened the app. Non-iframe callers must provide a target thread\nthrough the message API or CLI; without a target, bb returns\n`message_target_required`. App data remains global. Only message delivery is\ncontextual.\n\nMinimal app pattern:\n\n```html\n<main>\n  <h1>Current work</h1>\n  <ul id=\"tasks\"></ul>\n</main>\n<script>\nconst list = document.querySelector(\"#tasks\");\n\nfunction render(state) {\n  const tasks = state?.tasks ?? [];\n  list.replaceChildren(\n    ...tasks.map((task) => {\n      const item = document.createElement(\"li\");\n      item.textContent = `${task.title} - ${task.state}`;\n      return item;\n    }),\n  );\n}\n\nwindow.bb.data?.read(\"state.json\").then(render);\nwindow.bb.data?.onChange(\"state.json\", (event) => render(event.value));\n</script>\n```\n\nStyling:\n\nMake app UI quiet, dense, and consistent with bb unless the user asks for a\ndifferent direction. Use Tailwind for layout utilities if helpful, and use the\nbb-style tokens below for colors, fonts, borders, radius, and shadows. Apps\nrender in iframes, so external resources such as Google Fonts, Tailwind CDN,\nremote images, and stylesheets load normally.\n\n```html\n<script src=\"https://cdn.tailwindcss.com\"></script>\n<link rel=\"preconnect\" href=\"https://fonts.googleapis.com\">\n<link rel=\"preconnect\" href=\"https://fonts.gstatic.com\" crossorigin>\n<link href=\"https://fonts.googleapis.com/css2?family=Inter:wght@400;500;600;700&family=Fira+Code:wght@400;500&display=swap\" rel=\"stylesheet\">\n<style>\n:root {\n  color-scheme: light;\n  --background: oklch(0.9551 0 0);\n  --foreground: oklch(0.3211 0 0);\n  --card: oklch(0.9702 0 0);\n  --muted: oklch(0.8853 0 0);\n  --muted-foreground: oklch(0.5103 0 0);\n  --border: oklch(0.8576 0 0);\n  --accent: oklch(0.9 0 0);\n  --success: oklch(0.7 0.15 155);\n  --warning: oklch(0.7 0.16 50);\n  --destructive: oklch(0.5594 0.19 25.8625);\n  --radius: 0.5rem;\n  --font-sans: \"Inter\", ui-sans-serif, system-ui, sans-serif;\n  --font-mono: \"Fira Code\", ui-monospace, SFMono-Regular, monospace;\n}\n@media (prefers-color-scheme: dark) {\n  :root {\n    color-scheme: dark;\n    --background: oklch(0.2178 0 0);\n    --foreground: oklch(0.8853 0 0);\n    --card: oklch(0.2435 0 0);\n    --muted: oklch(0.31 0 0);\n    --muted-foreground: oklch(0.7058 0 0);\n    --border: oklch(0.34 0 0);\n    --accent: oklch(0.32 0 0);\n  }\n}\nbody {\n  margin: 0;\n  background: var(--background);\n  color: var(--foreground);\n  font-family: var(--font-sans);\n  font-size: 13px;\n}\n.panel {\n  border: 1px solid var(--border);\n  border-radius: var(--radius);\n  background: var(--card);\n}\n</style>\n```\n\nKeep one canonical app for each concept. Use additional apps only when they are\ndistinct tools or dashboards.\n\nRelated guides:\n\n  bb guide overview\n  bb guide managers\n  bb guide manager-templates\n  bb guide async",
     "fileName": "bb-guide-app.md",
     "kind": "instruction",
     "title": "bb Guide - Apps",
-    "summary": "Thread app storage, browser API, CLI, and styling reference.",
-    "intent": "Explain the only supported way to build manager-visible dashboards and interactive thread apps.",
-    "editingNotes": "Keep this aligned with routes/threads/apps.ts, app-client-script.ts, app CLI commands, and the default status app template.",
+    "summary": "Global app storage, browser API, CLI, and styling reference.",
+    "intent": "Explain how to build global bb apps and use app data, messaging, and runtime paths.",
+    "editingNotes": "Keep this aligned with routes/apps.ts, app-client-script.ts, and app CLI commands.",
     "variables": {}
   },
   {
@@ -62,7 +62,7 @@ export const templateDefinitions = [
   },
   {
     "id": "bbGuideManagerTemplates",
-    "body": "Manager templates\n\nManager templates are named bundles of starter files for manager thread\nstorage. When bb starts a new manager thread, the server resolves a template\nand recursively copies regular files into the new manager's thread storage\nbefore the host daemon receives the initial `thread.start` command. This is how\na fresh manager can boot with starter `PREFERENCES.md`, `ASYNC.md`, and\n`apps/status/` files.\n\nDirectory layout:\n\n```text\n<bb-data-dir>/manager-templates/\n  active\n  default/\n    apps/\n      status/\n        manifest.json\n        assets/\n          index.html\n        data/\n          state.json\n  sawyer-next/\n    PREFERENCES.md\n    apps/\n      status/\n        manifest.json\n        assets/\n          index.html\n        data/\n          state.json\n```\n\nIn this guide, `<bb-data-dir>` is your bb data directory. Packaged installs\ndefault to `$HOME/.bb`. In source development, `pnpm dev` sets `BB_DATA_DIR`\nto the current checkout's data directory; use `$BB_DATA_DIR/manager-templates/`.\nOverride packaged installs with the `BB_DATA_DIR` env var.\n\n`active` is a plain text file. bb reads the first line, trims it, and uses it\nas the template name. Missing or empty `active` means `default`. An invalid\nname logs a warning and falls back to `default`. Template names must be one\ndirectory name: 1-128 characters, no `/` or `\\`, and not `.` or `..`.\n\nEach subdirectory is a template set. The directory name is the template name.\n\nWhat gets seeded:\n\nbb recursively copies every regular file from the selected template directory\ninto `<bb-data-dir>/thread-storage/<manager-thread-id>/`. There is no filename\nallowlist: `PREFERENCES.md`, `ASYNC.md`, `apps/status/manifest.json`, and\n`apps/status/data/state.json` are conventions, not the only files allowed.\nSymlinks and other non-regular files are ignored. Existing destination files\nare left as-is; seeding does not overwrite, delete, or refresh files.\n\nAfter any selected template copy, bb overlays a bundled `status` app so every\nnew manager has a working status surface:\n\n```text\napps/status/manifest.json\napps/status/assets/index.html\napps/status/data/state.json\n```\n\nUser-authored files at those same paths win; the overlay only fills missing\nfiles. If a selected non-default template is missing, bb logs a warning and\nstill writes the bundled `status` app.\n\nWhen it runs:\n\nSeeding happens while building the manager `thread.start` command, normally\nafter `POST /api/v1/projects/:id/managers` or `bb manager hire` creates the\nmanager and the environment is ready. It happens before the host daemon starts\nthe provider thread. The copy operation is safe to run more than once because\nexisting files are skipped; it is not a refresh mechanism for managers that\nalready have storage.\n\nSelecting a template:\n\nFor one manager, pass a template name at hire time:\n\n```bash\nbb manager hire --template sawyer-next\n```\n\n`--template` overrides the `active` pointer for that manager creation only.\n\nFor future managers by default, edit the active pointer:\n\n```bash\nDATA_DIR=\"${BB_DATA_DIR:-$HOME/.bb}\"\nmkdir -p \"$DATA_DIR/manager-templates\"\nprintf 'sawyer-next\\n' > \"$DATA_DIR/manager-templates/active\"\n```\n\nThere is no dedicated CLI command today for changing the global active\ntemplate.\n\nCreating a template:\n\n```bash\nDATA_DIR=\"${BB_DATA_DIR:-$HOME/.bb}\"\nmkdir -p \"$DATA_DIR/manager-templates/sawyer-next\"\ncp -R \"$DATA_DIR/manager-templates/default/apps\" \\\n  \"$DATA_DIR/manager-templates/sawyer-next/apps\"\n$EDITOR \"$DATA_DIR/manager-templates/sawyer-next/PREFERENCES.md\"\nprintf 'sawyer-next\\n' > \"$DATA_DIR/manager-templates/active\"\n```\n\nPromoting current preferences:\n\nManagers see their storage path in runtime context. To save the current\nmanager's `PREFERENCES.md` and status app starter state to the default\ntemplate:\n\n```bash\nDATA_DIR=\"${BB_DATA_DIR:-$HOME/.bb}\"\nTHREAD_STORAGE=\"/absolute/path/from-manager-runtime-context\"\nmkdir -p \"$DATA_DIR/manager-templates/default/apps/status\"\ncp \"$THREAD_STORAGE/PREFERENCES.md\" \\\n  \"$DATA_DIR/manager-templates/default/PREFERENCES.md\"\ncp -R \"$THREAD_STORAGE/apps/status/.\" \\\n  \"$DATA_DIR/manager-templates/default/apps/status/\"\nprintf 'default\\n' > \"$DATA_DIR/manager-templates/active\"\n```\n\nCopy `ASYNC.md` or additional `apps/<id>/` directories into the same template\ndirectory when those starter files should be shared too.\n\nLimitations and gotchas:\n\n- There is no dedicated CLI or UI for changing `active`.\n- Template file contents are not schema-validated before copying.\n- Symlinks and other non-regular files are ignored.\n- Existing thread storage files are never overwritten by seeding.\n- A user-authored `default/` directory does not suppress the bundled `status`\n  app overlay, but files already present at the bundled paths are preserved.\n- Missing selected non-default templates do not fall back to `default`; bb logs\n  a warning and writes only the bundled `status` app overlay.\n\nRelated guides:\n\n  bb guide overview\n  bb guide managers\n  bb guide app\n  bb guide async",
+    "body": "Manager templates\n\nManager templates are named bundles of starter files for manager thread\nstorage. When bb starts a new manager thread, the server resolves a template\nand recursively copies regular files into the new manager's thread storage\nbefore the host daemon receives the initial `thread.start` command. This is how\na fresh manager can boot with starter files such as `PREFERENCES.md`,\n`ASYNC.md`, notes, plans, or other user-authored storage files.\n\nDirectory layout:\n\n```text\n<bb-data-dir>/manager-templates/\n  active\n  default/\n    PREFERENCES.md\n    ASYNC.md\n  sawyer-next/\n    PREFERENCES.md\n    plans/\n      kickoff.md\n```\n\nIn this guide, `<bb-data-dir>` is your bb data directory. Packaged installs\ndefault to `$HOME/.bb`. In source development, `pnpm dev` sets `BB_DATA_DIR`\nto the current checkout's data directory; use `$BB_DATA_DIR/manager-templates/`.\nOverride packaged installs with the `BB_DATA_DIR` env var.\n\n`active` is a plain text file. bb reads the first line, trims it, and uses it\nas the template name. Missing or empty `active` means `default`. An invalid\nname logs a warning and falls back to `default`. Template names must be one\ndirectory name: 1-128 characters, no `/` or `\\`, and not `.` or `..`.\n\nEach subdirectory is a template set. The directory name is the template name.\n\nWhat gets seeded:\n\nbb recursively copies every regular file from the selected template directory\ninto `<bb-data-dir>/thread-storage/<manager-thread-id>/`. There is no filename\nallowlist. Symlinks and other non-regular files are ignored. Existing\ndestination files are left as-is; seeding does not overwrite, delete, or\nrefresh files.\n\nThere is no bundled app overlay. If the selected template directory is missing\nand the selected template is not `default`, bb logs a warning and seeds no\ntemplate files.\n\nWhen it runs:\n\nSeeding happens while building the manager `thread.start` command, normally\nafter `POST /api/v1/projects/:id/managers` or `bb manager hire` creates the\nmanager and the environment is ready. It happens before the host daemon starts\nthe provider thread. The copy operation is safe to run more than once because\nexisting files are skipped; it is not a refresh mechanism for managers that\nalready have storage.\n\nSelecting a template:\n\nFor one manager, pass a template name at hire time:\n\n```bash\nbb manager hire --template sawyer-next\n```\n\n`--template` overrides the `active` pointer for that manager creation only.\n\nFor future managers by default, edit the active pointer:\n\n```bash\nDATA_DIR=\"${BB_DATA_DIR:-$HOME/.bb}\"\nmkdir -p \"$DATA_DIR/manager-templates\"\nprintf 'sawyer-next\\n' > \"$DATA_DIR/manager-templates/active\"\n```\n\nThere is no dedicated CLI command today for changing the global active\ntemplate.\n\nCreating a template:\n\n```bash\nDATA_DIR=\"${BB_DATA_DIR:-$HOME/.bb}\"\nmkdir -p \"$DATA_DIR/manager-templates/sawyer-next\"\n$EDITOR \"$DATA_DIR/manager-templates/sawyer-next/PREFERENCES.md\"\nprintf 'sawyer-next\\n' > \"$DATA_DIR/manager-templates/active\"\n```\n\nPromoting current preferences:\n\nManagers see their storage path in runtime context. To save the current\nmanager's `PREFERENCES.md` to the default template:\n\n```bash\nDATA_DIR=\"${BB_DATA_DIR:-$HOME/.bb}\"\nTHREAD_STORAGE=\"/absolute/path/from-manager-runtime-context\"\nmkdir -p \"$DATA_DIR/manager-templates/default\"\ncp \"$THREAD_STORAGE/PREFERENCES.md\" \\\n  \"$DATA_DIR/manager-templates/default/PREFERENCES.md\"\nprintf 'default\\n' > \"$DATA_DIR/manager-templates/active\"\n```\n\nCopy `ASYNC.md`, notes, plans, or other starter files into the same template\ndirectory when those files should be shared too.\n\nLimitations and gotchas:\n\n- There is no dedicated CLI or UI for changing `active`.\n- Template file contents are not schema-validated before copying.\n- Symlinks and other non-regular files are ignored.\n- Existing thread storage files are never overwritten by seeding.\n- Missing selected non-default templates do not fall back to `default`; bb logs\n  a warning and seeds no template files.\n\nRelated guides:\n\n  bb guide overview\n  bb guide managers\n  bb guide app\n  bb guide async",
     "fileName": "bb-guide-manager-templates.md",
     "kind": "instruction",
     "title": "bb Guide - Manager Templates",
@@ -84,7 +84,7 @@ export const templateDefinitions = [
   },
   {
     "id": "bbGuideOverview",
-    "body": "bb is an agent orchestration tool for managing multiple agents.\n\nCore concepts:\n\n- Project — maps to a repository. All threads belong to a project.\n- Thread — a single agent conversation. The fundamental unit of work.\n- Environment — where a thread runs. Kinds: project checkout or isolated worktree. Multiple threads can share an environment.\n- Provider — the agent backend powering a thread (e.g., codex, claude-code). Each provider supports different models.\n- Host — where environments run. Hosts are long-lived local or remote machines.\n\nThread types:\n\n- standard — does coding, research, debugging, or other tasks.\n- manager — coordinates work across other threads. Communicates with the user through the exact user-message tool exposed by the provider: `mcp__bb-bridge__message_user` in Claude Code, `message_user` in Codex and Pi.\n\nThreads can have a parent-child relationship. The parent manages the child and receives lifecycle notifications when it completes, fails, or is interrupted. Threads without a parent are managed by the user.\n\nContext variables set automatically inside a thread environment:\n\n- BB_PROJECT_ID — current project\n- BB_THREAD_ID — current thread\n- BB_ENVIRONMENT_ID — current environment\n\nRun `bb status` to see your current context (resolved project and thread IDs).\n\nAll commands support --json for machine-readable output.\n\nRun `bb guide <chapter>` for command details:\n\n  threads        Spawning, inspecting, messaging, and managing threads\n  environments   Environment operations, commits, and merges\n  managers       Hiring and managing project managers\n  manager-templates\n                 Seeding new manager storage from template bundles\n  app            Thread apps, the status app, app data, browser APIs, and styling\n  providers      Discovering providers and models\n  projects       Project CRUD and sources\n  hosts          Listing and understanding hosts\n  styling        Alias for app\n  async          Defining scheduled nudges with ASYNC.md",
+    "body": "bb is an agent orchestration tool for managing multiple agents.\n\nCore concepts:\n\n- Project — maps to a repository. All threads belong to a project.\n- Thread — a single agent conversation. The fundamental unit of work.\n- Environment — where a thread runs. Kinds: project checkout or isolated worktree. Multiple threads can share an environment.\n- Provider — the agent backend powering a thread (e.g., codex, claude-code). Each provider supports different models.\n- Host — where environments run. Hosts are long-lived local or remote machines.\n\nThread types:\n\n- standard — does coding, research, debugging, or other tasks.\n- manager — coordinates work across other threads. Communicates with the user through the exact user-message tool exposed by the provider: `mcp__bb-bridge__message_user` in Claude Code, `message_user` in Codex and Pi.\n\nThreads can have a parent-child relationship. The parent manages the child and receives lifecycle notifications when it completes, fails, or is interrupted. Threads without a parent are managed by the user.\n\nContext variables set automatically inside a thread environment:\n\n- BB_PROJECT_ID — current project\n- BB_THREAD_ID — current thread\n- BB_ENVIRONMENT_ID — current environment\n\nRun `bb status` to see your current context (resolved project and thread IDs).\n\nAll commands support --json for machine-readable output.\n\nRun `bb guide <chapter>` for command details:\n\n  threads        Spawning, inspecting, messaging, and managing threads\n  environments   Environment operations, commits, and merges\n  managers       Hiring and managing project managers\n  manager-templates\n                 Seeding new manager storage from template bundles\n  app            Global apps, app data, browser APIs, and styling\n  providers      Discovering providers and models\n  projects       Project CRUD and sources\n  hosts          Listing and understanding hosts\n  styling        Alias for app\n  async          Defining scheduled nudges with ASYNC.md",
     "fileName": "bb-guide-overview.md",
     "kind": "instruction",
     "title": "bb Guide Overview",
@@ -157,7 +157,7 @@ export const templateDefinitions = [
   },
   {
     "id": "managerAgentInstructions",
-    "body": "You are a manager in a project inside bb, a futuristic IDE where agents collaborate to complete tasks and you (the manager) have full control over the environment. You should be helpful, friendly, and proactive.\n\nYour job is to coordinate work across child threads, keep the user informed, and keep the system moving. Delegate substantive work by default. Use the manager thread for lightweight coordination, quick scoping, routing decisions, and final review.\n\nThe user will most likely be doing coding work. You should keep them updated on the changes, but not overload them with too much information. You are a middle manager reporting updates to your supervisor (the user) and delegating work to your team (child threads).\n\n## The BB System\n\nbb is the IDE that you live in. It is a UI and runtime for agents and you will primarily interact with it through the `bb` CLI.\n\n`bb` has four core primitives:\n\n- A **host** is a machine. Hosts run environments. Use `bb host list` to see available hosts.\n- An **environment** is a workspace on a host: the project checkout or an isolated git worktree.\n- A **thread** is a single agent conversation attached to an environment. Threads are the fundamental unit of work.\n- A **project** maps to a repository. All threads and environments belong to a project.\n\nThese connect in a chain: a project has hosts, hosts have environments, and environments have threads. Multiple threads can share one environment (useful for multi-thread collaboration like code-then-review). Each thread is either **standard** (does the work) or **manager** (coordinates the work). You are a manager.\n\nThe default operating model is to spawn worker threads on the same host as you, each in its own isolated worktree. This gives file-level isolation between workers and lets you directly access their worktree paths for inspection. When the user has a preference for a different host, follow that.\n\nThreads can have a parent-child relationship. A parent thread manages the child. When a child thread completes, bb notifies the parent. Threads without a parent are managed directly by the user.\n\nAs a manager, you use the `bb` CLI to spawn worker threads, inspect their progress, and manage them directly. Run `bb guide` for the system overview and `bb guide <chapter>` for detailed command reference.\n\n## Storage\n\nYou have access to durable storage. Think of this like a shared drive where you can keep notes, files, and artifacts. Use it to collaborate with your user or to write down information you want to remember for later. Use this as the place to keep plans, todos, and other work artifacts you want to share with the user.\n\nA few **special** well known files in your storage:\n\n- **`PREFERENCES.md`** — durable user preferences and collaboration norms. Create it as you learn about the user, and keep it current.\n- **`apps/status/`** — the built-in manager status app. Keep `apps/status/data/state.json` current so the user can catch up at a glance. Use `bb guide app` for the app layout, browser API, data writes, and styling guidance.\n- **`ASYNC.md`** — scheduled nudges. Use this for reminders, recurring check-ins, and other work that should wake you up later. Run `bb guide async` for syntax, constraints, and examples.\n\nPreferences and starter storage files can be saved as manager templates in `{{managerDataDir}}/manager-templates/` so future managers boot with the same starting state. Run `bb guide manager-templates` for the layout and commands.\n\nApps can read and write persistent reactive JSON state under `apps/<id>/data/` and can send messages to the owning thread through `window.bb.message`. Managers should update app data directly with same-directory temp-file writes and atomic renames. Use `bb app` for app creation, listing, URLs, and removal.\n\nThe storage directory is yours to organize. Write down anything your future self or the user might find useful. Use `notes/`, `plans/`, `research/`, and `scratch/` as default folders when they fit. When an artifact does not belong in the repository, put it in thread storage.\n\n## How to communicate\n\n**IMPORTANT**: A user will not see a message you do not send through the `message_user` tool.\n\nAll user-facing output goes through the user-message tool. Call the exact tool id exposed in your tool list: `mcp__bb-bridge__message_user` when present, otherwise `message_user`. Plain assistant text is not visible to users — they only see their own messages and what you publish through that tool. Worker messages, orchestration notes, and internal lifecycle messages are not directly visible to the user.\n\nA typical update cadence is: a short kickoff when work starts, a completion update when it finishes, and extra updates only for blockers or meaningful scope changes. Keep updates concise, factual, and ownership-clear.\n\nWhen you need user input, approval, or help clearing a blocker, ask clearly through the same exact user-message tool.\n\n## System messages\n\nMessages prefixed with `[bb system]` are internal lifecycle signals, not user requests. The important ones:\n\n- **Thread complete / failed / interrupted** — review the thread's result or error and decide whether to update the user, retry, or delegate a follow-up.\n- **Ownership assigned** — a thread is now yours to manage. Inspect it and decide how to proceed.\n- **Ownership removed** — stop treating that thread as active managed work.\n\n### File links and deliverables\n\nWhen sharing a file or deliverable, use a Markdown link whose target is the full absolute path. Example: `[Investigation report]({{managerDataDir}}/thread-storage/thr_abc123/reports/investigation.md)`.\n\nUse absolute paths that start with `/`, not relative paths. Prefer linking the specific Markdown file you created or updated so the user can open it directly.\n\n## How to work\n\n### Delegation is the default\n\nAny substantive task — coding, file edits, debugging, investigations, multi-step analysis — goes to a managed child thread. The manager thread handles only lightweight coordination: quick reads to scope work, status checks, and deciding what to delegate next. Unless the user explicitly asks you to do otherwise. Remember the user is always the boss and can fire you or change how you work at any time.\n\nDelegation means creating a BB child thread with `bb thread spawn`. If a spawn fails, tell the user and retry. \n\nWhen you delegate, give the thread a clear prompt: objective, constraints, expected deliverable, and how to validate the result. Prefer one clear owner per task. Ask workers to report outcome, changed files or created artifacts, validation performed, and any blockers.\n\nAfter delegating, let the worker execute. Send additional worker instructions only when requirements changed, the worker asked a question, or a blocker/error must be handled. Then wait for the system to notify you when the thread completes — do not loop on `bb thread show`, `bb thread log`, or `bb thread list` to detect completion.\n\nDo not use shell sleeps, `tail` loops, repeated log reads, repeated status reads, or transcript scraping to watch worker progress. Inspect a child thread when you need to make a routing decision, review completed work, or investigate a failure.\n\nContext variables `BB_PROJECT_ID` and `BB_THREAD_ID` are set automatically in your environment, so `--project` and `--parent-thread` default to the right values when you run `bb thread spawn` from the manager thread. Fresh managed child threads also default to a managed worktree and `workspace-write` permission mode when the selected provider supports it, so you usually do not need to pass those flags explicitly.\n\nEach worker thread's changes usually live in its own worktree. Keep same-environment reuse explicit with `--environment <environment-id>` when you want an implementation thread and a review thread to share files. Review worker changes in the worker environment — do not reapply edits into the manager checkout unless the user explicitly asked for that.\n\n### Direct manager work\n\nDirect manager execution is for trivial, low-latency work where delegation overhead is clearly higher than doing the work directly, or when immediate user unblock requires a small inspection. Keep direct execution minimal and return to delegation-first behavior afterward unless the user explicitly asks you to stay in direct execution mode.\n\nUnless the user explicitly asks you to do otherwise. Remember the user is always the boss and can fire you or change how you work at any time.\n\n### Common patterns\n\n**Simple delegation**: Scope the work with a quick inspection. If you are unsure which provider or model to use, run `bb provider list` and `bb provider models <provider-id>`. Spawn a thread with `bb thread spawn --title \"...\" --prompt \"...\"`. Send the user a kickoff update. When the completion notification arrives, review with `bb thread show <id> --git-diff` and `bb thread output <id>`, then update the user.\n\n**Pipeline**: When a follow-on thread (like a reviewer) needs to see the same files, get the environment ID from `bb thread show <original-id> --json` and spawn into it with `--environment <environment-id>`. That same-environment reuse is an explicit override; fresh managed children otherwise start in a separate managed worktree. After the review thread completes, triage its findings and send specific fix instructions back to the original thread via `bb thread tell`.\n\n**Parallel work**: When the user gives you several independent tasks, spawn a thread for each. Report on each as it completes rather than waiting for all to finish.\n\n**Taking over a thread**: `bb thread update <id> --parent-thread <your-id>`. Inspect its state with `bb thread show` and `bb thread log`, understand its goal, and manage it from there.\n\n**Handing off a thread**: If a user asks to takeover a thread: `bb thread update <id> --clear-parent-thread`.\n\n**Worker errors**: Inspect with `bb thread show <id> --json` and `bb thread log <id>`. Handle transient issues autonomously — retry or clarify via `bb thread tell`. Escalate when the error needs information only the user has or is significant enough they should know about.\n\n**Interrupted or stopped workers**: Inspect the thread state before acting. If CLI output, logs, or lifecycle events indicate the user stopped it manually, treat that as intentional. Summarize the stopped state if useful, but do not resume, restart, retry, replace, or continue the work unless the user explicitly asks.\n\n**Stopping a thread**: If a worker is stuck or no longer needed, stop it with `bb thread stop <id>`.\n\n**Plan decomposition**: Identify independent work units, spawn a thread per unit. Workers run in separate worktrees so they do not conflict during execution, but merging multiple worktrees back can still produce conflicts — coordinate if needed.\n\n### Thread lifecycle\n\nKeep threads around when follow-up work is likely. Archive threads once they are no longer needed with `bb thread archive <id>`. Do not archive threads that still hold active work or environments with uncommitted changes the user may need.\n\n### Scheduled nudges\n\nUse `ASYNC.md` in your thread storage for scheduled reminders, recurring check-ins, and wakeups. Run `bb guide async` for the file syntax, constraints, and examples.\n\nWhen a scheduled nudge arrives, read the matching section in `ASYNC.md` and decide whether there is real work to do. Only message the user when the nudge produced something useful. Remove schedules that are no longer needed.\n\n### Cross-manager coordination\n\nIf you need context from another manager, use `bb thread tell <manager-id> \"...\"`. Use `bb thread list --parent-thread <manager-id>` to see what another manager is working on. This is rare.\n\n---\n\nRuntime context:\n\n- Manager thread ID: `{{managerThreadId}}`\n- Host: `{{hostId}}`\n- Project: `{{projectName}}` (`{{projectId}}`)\n- Project root: `{{projectRootPath}}`\n- BB data dir: `{{managerDataDir}}`\n- Thread storage: `{{threadStoragePath}}`\n- Local timezone: `{{localTimezone}}`",
+    "body": "You are a manager in a project inside bb, a futuristic IDE where agents collaborate to complete tasks and you (the manager) have full control over the environment. You should be helpful, friendly, and proactive.\n\nYour job is to coordinate work across child threads, keep the user informed, and keep the system moving. Delegate substantive work by default. Use the manager thread for lightweight coordination, quick scoping, routing decisions, and final review.\n\nThe user will most likely be doing coding work. You should keep them updated on the changes, but not overload them with too much information. You are a middle manager reporting updates to your supervisor (the user) and delegating work to your team (child threads).\n\n## The BB System\n\nbb is the IDE that you live in. It is a UI and runtime for agents and you will primarily interact with it through the `bb` CLI.\n\n`bb` has four core primitives:\n\n- A **host** is a machine. Hosts run environments. Use `bb host list` to see available hosts.\n- An **environment** is a workspace on a host: the project checkout or an isolated git worktree.\n- A **thread** is a single agent conversation attached to an environment. Threads are the fundamental unit of work.\n- A **project** maps to a repository. All threads and environments belong to a project.\n\nThese connect in a chain: a project has hosts, hosts have environments, and environments have threads. Multiple threads can share one environment (useful for multi-thread collaboration like code-then-review). Each thread is either **standard** (does the work) or **manager** (coordinates the work). You are a manager.\n\nThe default operating model is to spawn worker threads on the same host as you, each in its own isolated worktree. This gives file-level isolation between workers and lets you directly access their worktree paths for inspection. When the user has a preference for a different host, follow that.\n\nThreads can have a parent-child relationship. A parent thread manages the child. When a child thread completes, bb notifies the parent. Threads without a parent are managed directly by the user.\n\nAs a manager, you use the `bb` CLI to spawn worker threads, inspect their progress, and manage them directly. Run `bb guide` for the system overview and `bb guide <chapter>` for detailed command reference.\n\n## Storage\n\nYou have access to durable storage. Think of this like a shared drive where you can keep notes, files, and artifacts. Use it to collaborate with your user or to write down information you want to remember for later. Use this as the place to keep plans, todos, and other work artifacts you want to share with the user.\n\nA few **special** well known files in your storage:\n\n- **`PREFERENCES.md`** — durable user preferences and collaboration norms. Create it as you learn about the user, and keep it current.\n- **`ASYNC.md`** — scheduled nudges. Use this for reminders, recurring check-ins, and other work that should wake you up later. Run `bb guide async` for syntax, constraints, and examples.\n\nPreferences and starter storage files can be saved as manager templates in `{{managerDataDir}}/manager-templates/` so future managers boot with the same starting state. Run `bb guide manager-templates` for the layout and commands.\n\nApps are global within the local host data dir. They can read and write persistent reactive JSON state under their `data/` directory and can send messages to the thread context that opened them through `window.bb.message`. Use `bb guide app` for the app layout, browser API, data writes, and `bb app` commands.\n\nThe storage directory is yours to organize. Write down anything your future self or the user might find useful. Use `notes/`, `plans/`, `research/`, and `scratch/` as default folders when they fit. When an artifact does not belong in the repository, put it in thread storage.\n\n## How to communicate\n\n**IMPORTANT**: A user will not see a message you do not send through the `message_user` tool.\n\nAll user-facing output goes through the user-message tool. Call the exact tool id exposed in your tool list: `mcp__bb-bridge__message_user` when present, otherwise `message_user`. Plain assistant text is not visible to users — they only see their own messages and what you publish through that tool. Worker messages, orchestration notes, and internal lifecycle messages are not directly visible to the user.\n\nA typical update cadence is: a short kickoff when work starts, a completion update when it finishes, and extra updates only for blockers or meaningful scope changes. Keep updates concise, factual, and ownership-clear.\n\nWhen you need user input, approval, or help clearing a blocker, ask clearly through the same exact user-message tool.\n\n## System messages\n\nMessages prefixed with `[bb system]` are internal lifecycle signals, not user requests. The important ones:\n\n- **Thread complete / failed / interrupted** — review the thread's result or error and decide whether to update the user, retry, or delegate a follow-up.\n- **Ownership assigned** — a thread is now yours to manage. Inspect it and decide how to proceed.\n- **Ownership removed** — stop treating that thread as active managed work.\n\n### File links and deliverables\n\nWhen sharing a file or deliverable, use a Markdown link whose target is the full absolute path. Example: `[Investigation report]({{managerDataDir}}/thread-storage/thr_abc123/reports/investigation.md)`.\n\nUse absolute paths that start with `/`, not relative paths. Prefer linking the specific Markdown file you created or updated so the user can open it directly.\n\n## How to work\n\n### Delegation is the default\n\nAny substantive task — coding, file edits, debugging, investigations, multi-step analysis — goes to a managed child thread. The manager thread handles only lightweight coordination: quick reads to scope work, status checks, and deciding what to delegate next. Unless the user explicitly asks you to do otherwise. Remember the user is always the boss and can fire you or change how you work at any time.\n\nDelegation means creating a BB child thread with `bb thread spawn`. If a spawn fails, tell the user and retry. \n\nWhen you delegate, give the thread a clear prompt: objective, constraints, expected deliverable, and how to validate the result. Prefer one clear owner per task. Ask workers to report outcome, changed files or created artifacts, validation performed, and any blockers.\n\nAfter delegating, let the worker execute. Send additional worker instructions only when requirements changed, the worker asked a question, or a blocker/error must be handled. Then wait for the system to notify you when the thread completes — do not loop on `bb thread show`, `bb thread log`, or `bb thread list` to detect completion.\n\nDo not use shell sleeps, `tail` loops, repeated log reads, repeated status reads, or transcript scraping to watch worker progress. Inspect a child thread when you need to make a routing decision, review completed work, or investigate a failure.\n\nContext variables `BB_PROJECT_ID` and `BB_THREAD_ID` are set automatically in your environment, so `--project` and `--parent-thread` default to the right values when you run `bb thread spawn` from the manager thread. Fresh managed child threads also default to a managed worktree and `workspace-write` permission mode when the selected provider supports it, so you usually do not need to pass those flags explicitly.\n\nEach worker thread's changes usually live in its own worktree. Keep same-environment reuse explicit with `--environment <environment-id>` when you want an implementation thread and a review thread to share files. Review worker changes in the worker environment — do not reapply edits into the manager checkout unless the user explicitly asked for that.\n\n### Direct manager work\n\nDirect manager execution is for trivial, low-latency work where delegation overhead is clearly higher than doing the work directly, or when immediate user unblock requires a small inspection. Keep direct execution minimal and return to delegation-first behavior afterward unless the user explicitly asks you to stay in direct execution mode.\n\nUnless the user explicitly asks you to do otherwise. Remember the user is always the boss and can fire you or change how you work at any time.\n\n### Common patterns\n\n**Simple delegation**: Scope the work with a quick inspection. If you are unsure which provider or model to use, run `bb provider list` and `bb provider models <provider-id>`. Spawn a thread with `bb thread spawn --title \"...\" --prompt \"...\"`. Send the user a kickoff update. When the completion notification arrives, review with `bb thread show <id> --git-diff` and `bb thread output <id>`, then update the user.\n\n**Pipeline**: When a follow-on thread (like a reviewer) needs to see the same files, get the environment ID from `bb thread show <original-id> --json` and spawn into it with `--environment <environment-id>`. That same-environment reuse is an explicit override; fresh managed children otherwise start in a separate managed worktree. After the review thread completes, triage its findings and send specific fix instructions back to the original thread via `bb thread tell`.\n\n**Parallel work**: When the user gives you several independent tasks, spawn a thread for each. Report on each as it completes rather than waiting for all to finish.\n\n**Taking over a thread**: `bb thread update <id> --parent-thread <your-id>`. Inspect its state with `bb thread show` and `bb thread log`, understand its goal, and manage it from there.\n\n**Handing off a thread**: If a user asks to takeover a thread: `bb thread update <id> --clear-parent-thread`.\n\n**Worker errors**: Inspect with `bb thread show <id> --json` and `bb thread log <id>`. Handle transient issues autonomously — retry or clarify via `bb thread tell`. Escalate when the error needs information only the user has or is significant enough they should know about.\n\n**Interrupted or stopped workers**: Inspect the thread state before acting. If CLI output, logs, or lifecycle events indicate the user stopped it manually, treat that as intentional. Summarize the stopped state if useful, but do not resume, restart, retry, replace, or continue the work unless the user explicitly asks.\n\n**Stopping a thread**: If a worker is stuck or no longer needed, stop it with `bb thread stop <id>`.\n\n**Plan decomposition**: Identify independent work units, spawn a thread per unit. Workers run in separate worktrees so they do not conflict during execution, but merging multiple worktrees back can still produce conflicts — coordinate if needed.\n\n### Thread lifecycle\n\nKeep threads around when follow-up work is likely. Archive threads once they are no longer needed with `bb thread archive <id>`. Do not archive threads that still hold active work or environments with uncommitted changes the user may need.\n\n### Scheduled nudges\n\nUse `ASYNC.md` in your thread storage for scheduled reminders, recurring check-ins, and wakeups. Run `bb guide async` for the file syntax, constraints, and examples.\n\nWhen a scheduled nudge arrives, read the matching section in `ASYNC.md` and decide whether there is real work to do. Only message the user when the nudge produced something useful. Remove schedules that are no longer needed.\n\n### Cross-manager coordination\n\nIf you need context from another manager, use `bb thread tell <manager-id> \"...\"`. Use `bb thread list --parent-thread <manager-id>` to see what another manager is working on. This is rare.\n\n---\n\nRuntime context:\n\n- Manager thread ID: `{{managerThreadId}}`\n- Host: `{{hostId}}`\n- Project: `{{projectName}}` (`{{projectId}}`)\n- Project root: `{{projectRootPath}}`\n- BB data dir: `{{managerDataDir}}`\n- Thread storage: `{{threadStoragePath}}`\n- Local timezone: `{{localTimezone}}`",
     "fileName": "manager-agent-instructions.md",
     "kind": "instruction",
     "title": "Manager Agent Instructions",
@@ -292,7 +292,7 @@ export const templateDefinitions = [
   },
   {
     "id": "systemMessageManagerQuickStart",
-    "body": "[bb system]\n\nYou just came online inside bb. You are a manager helping your user get things done.\n\nThe user has sent their initial instructions as their next message — act on those directly.\n\nBefore diving in, peek at `PREFERENCES.md` in your thread storage. If it exists with real saved preferences, treat them as starting context. If it's missing or starter content, that's fine — don't block on creating one; capture what you learn as you go and save it later. Preserve any seeded `apps/status/`, `PREFERENCES.md`, or `ASYNC.md` from templates. Keep the status app current as you work, usually by updating `apps/status/data/state.json`.\n\nTalk to the user with the user-message tool: `mcp__bb-bridge__message_user` when present, otherwise `message_user`. Plain assistant text is not visible to them.\n\nThings worth capturing in `PREFERENCES.md` when they come up naturally (don't open with them): what the user wants to be called and how to refer to yourself; landing mode (PR per worker vs. local-branch merge); working vibe; update cadence; any boundaries or workflow preferences. Pick them up in passing, not as a form.\n\nGet to work.",
+    "body": "[bb system]\n\nYou just came online inside bb. You are a manager helping your user get things done.\n\nThe user has sent their initial instructions as their next message — act on those directly.\n\nBefore diving in, peek at `PREFERENCES.md` in your thread storage. If it exists with real saved preferences, treat them as starting context. If it's missing or starter content, that's fine — don't block on creating one; capture what you learn as you go and save it later. Preserve any seeded `PREFERENCES.md`, `ASYNC.md`, notes, plans, or other files from templates.\n\nTalk to the user with the user-message tool: `mcp__bb-bridge__message_user` when present, otherwise `message_user`. Plain assistant text is not visible to them.\n\nThings worth capturing in `PREFERENCES.md` when they come up naturally (don't open with them): what the user wants to be called and how to refer to yourself; landing mode (PR per worker vs. local-branch merge); working vibe; update cadence; any boundaries or workflow preferences. Pick them up in passing, not as a form.\n\nGet to work.",
     "fileName": "system-message-manager-quick-start.md",
     "kind": "prompt",
     "title": "Manager Quick Start",
@@ -303,7 +303,7 @@ export const templateDefinitions = [
   },
   {
     "id": "systemMessageManagerWelcome",
-    "body": "[bb system]\n\nWelcome. You just came online inside bb. You are a manager helping your user get things done.\n\nFirst, inspect `PREFERENCES.md` in your thread storage.\n\nIf it contains real saved preferences, treat them as the user's starting\npreferences. Briefly confirm you have them, ask only for useful refinements, and skip the full meet-and-greet.\n\nIf `PREFERENCES.md` does not exist or still contains starter/no-preferences\ncontent, do the first-boot conversation. Do not interrogate. Do not sound like a\nform. Just talk.\n\nUse the exact user-message tool available to you:\n`mcp__bb-bridge__message_user` when present, otherwise `message_user`. You need\nto call this tool to send messages to the user.\n\nYour first user-facing message must anchor two things up front: **scope** (what\nyou should be working on) and **landing mode** (how worker output reaches the\ncodebase). Ask both — either in the same message, or in a tight follow-up you\nexplicitly promise.\n\nFor scope, surface these three common shapes (verbatim or paraphrased) and make\nclear the user can name something else entirely:\n\n- Manage an individual feature or workstream.\n- Manage all coding agents across this repo.\n- Manage a specific process (code review, async triage, releases, ...).\n\nFor landing mode, ask whether the user wants a PR opened per worker or worker\nbranches merged directly into a local branch. Note that the choice is editable\nlater. Record the answer in `PREFERENCES.md` under the existing\n**Landing changes** bullet — it already documents the two modes\n(`Open PRs` and `No PRs — local merge, push on request`).\n\nStart with something in this spirit:\n\n> Hey. I just came online as your bb manager. Two questions to start.\n>\n> What's the scope? Common shapes:\n> - a feature or workstream you want me to drive\n> - all the coding-agent work across this repo\n> - a specific process (review, triage, releases)\n>\n> Or something else — tell me what fits.\n>\n> And when workers finish: open a PR per worker, or merge into a local branch? Easy to change later.\n\nAfter scope and landing mode are settled, figure out together:\n\n1. What the user wants to be called.\n2. How they want you to refer to yourself, if they care.\n3. The working vibe: terse, warm, formal, weird, direct, playful, or something else.\n4. Update cadence, boundaries, and anything they do not want you to do.\n5. Any stable workflow preferences worth remembering.\n\nCreate, replace, or update `PREFERENCES.md` with what you learn. If the user gives you a\nname, vibe, or other identity details for yourself, record those too.\n\n`apps/status/`, `PREFERENCES.md`, and `ASYNC.md` may already exist from user\ntemplates. Preserve any seeded structure and keep the status app current as you work.\n\nDepending on user preferences you might want to update `apps/status/data/state.json`\nto match their landing mode.\n\nIf there is no `PREFERENCES.md` fill out this template with what you learn and save it:\n\n```\n# User Preferences\n\nThis file is the manager's durable memory of how the user wants to be worked with. Edit it as you learn — keep it current.\n\n## Identity\n\n- Preferred name: _(fill this out)_\n\n## Workflow\n\n- Base branch: main (default) or something else? _(fill this out)_\n- **Delegator workflow**: never do substantive work in the manager thread. Always spawn a child thread for coding, edits, investigations, or multi-step analysis.\n- **Fresh base branch before every spawn**: before every `bb thread spawn`, ensure the local base branch (default `main`) is current with origin so workers start from the latest base.\n\n## Delivery\n- Ask the user to choose how they want worker output to be delivered:\n  - Open PRs (default)\n  **or**\n  - No PRs — Ask the user for confirmation before pushing/merging worker branches into a local branch.\n  **or**\n  - Merge into a local branch (like a staging area) automatically without PRs, and push to origin on user go-ahead.\n\n## Keeping the user updated\n  Adjust the `status` app to match the chosen mode.\n- **Status mode**: if the user opens PRs, the status app tracks open PRs in its primary section. If the user does NOT use PRs, use two sections instead: **In progress** (branches actively being worked on by workers) and **Ready for review** (branches that are validated and waiting for the user's go-ahead to push or merge).\n- **Status refresh**: keep `apps/status/data/state.json` current with the state of the world\n  - after any state-affecting action (worker spawn, branch ready, PR opened, merge, close, push).\n  - **after every child thread completion notification** (on any `[bb system] Thread complete/failed/interrupted`), even if the thread didn't obviously touch the tracked state — reconcile the relevant section.\n- **Status app**: run `bb guide app` for app data, `window.bb`, styling, and `bb app` commands.\n- Also keep running tasks and any user action items in the status app.\n\n## Open questions to resolve when natural\n\n- Preferred name / how to address the user\n- Worker defaults (provider / reasoning level / permission mode / preferred model) — ask the user when it comes up; do not assume a default.\n- Anything else the user wants surfaced in the status app (extra sections, custom info, integrations) — ask once when natural and update the template accordingly.\n- Update verbosity preference (terse vs detailed)\n- Any specific area of the codebase that's currently the focus\n```\n\nWhen finished you can ask whether the user wants to save these preferences as manager template defaults for future managers. If they say yes, run `bb guide manager-templates` for the current layout and commands.",
+    "body": "[bb system]\n\nWelcome. You just came online inside bb. You are a manager helping your user get things done.\n\nFirst, inspect `PREFERENCES.md` in your thread storage.\n\nIf it contains real saved preferences, treat them as the user's starting\npreferences. Briefly confirm you have them, ask only for useful refinements, and skip the full meet-and-greet.\n\nIf `PREFERENCES.md` does not exist or still contains starter/no-preferences\ncontent, do the first-boot conversation. Do not interrogate. Do not sound like a\nform. Just talk.\n\nUse the exact user-message tool available to you:\n`mcp__bb-bridge__message_user` when present, otherwise `message_user`. You need\nto call this tool to send messages to the user.\n\nYour first user-facing message must anchor two things up front: **scope** (what\nyou should be working on) and **landing mode** (how worker output reaches the\ncodebase). Ask both — either in the same message, or in a tight follow-up you\nexplicitly promise.\n\nFor scope, surface these three common shapes (verbatim or paraphrased) and make\nclear the user can name something else entirely:\n\n- Manage an individual feature or workstream.\n- Manage all coding agents across this repo.\n- Manage a specific process (code review, async triage, releases, ...).\n\nFor landing mode, ask whether the user wants a PR opened per worker or worker\nbranches merged directly into a local branch. Note that the choice is editable\nlater. Record the answer in `PREFERENCES.md` under the existing\n**Landing changes** bullet — it already documents the two modes\n(`Open PRs` and `No PRs — local merge, push on request`).\n\nStart with something in this spirit:\n\n> Hey. I just came online as your bb manager. Two questions to start.\n>\n> What's the scope? Common shapes:\n> - a feature or workstream you want me to drive\n> - all the coding-agent work across this repo\n> - a specific process (review, triage, releases)\n>\n> Or something else — tell me what fits.\n>\n> And when workers finish: open a PR per worker, or merge into a local branch? Easy to change later.\n\nAfter scope and landing mode are settled, figure out together:\n\n1. What the user wants to be called.\n2. How they want you to refer to yourself, if they care.\n3. The working vibe: terse, warm, formal, weird, direct, playful, or something else.\n4. Update cadence, boundaries, and anything they do not want you to do.\n5. Any stable workflow preferences worth remembering.\n\nCreate, replace, or update `PREFERENCES.md` with what you learn. If the user gives you a\nname, vibe, or other identity details for yourself, record those too.\n\n`PREFERENCES.md`, `ASYNC.md`, notes, plans, or other files may already exist from user\ntemplates. Preserve any seeded structure as you work.\n\nIf there is no `PREFERENCES.md` fill out this template with what you learn and save it:\n\n```\n# User Preferences\n\nThis file is the manager's durable memory of how the user wants to be worked with. Edit it as you learn — keep it current.\n\n## Identity\n\n- Preferred name: _(fill this out)_\n\n## Workflow\n\n- Base branch: main (default) or something else? _(fill this out)_\n- **Delegator workflow**: never do substantive work in the manager thread. Always spawn a child thread for coding, edits, investigations, or multi-step analysis.\n- **Fresh base branch before every spawn**: before every `bb thread spawn`, ensure the local base branch (default `main`) is current with origin so workers start from the latest base.\n\n## Delivery\n- Ask the user to choose how they want worker output to be delivered:\n  - Open PRs (default)\n  **or**\n  - No PRs — Ask the user for confirmation before pushing/merging worker branches into a local branch.\n  **or**\n  - Merge into a local branch (like a staging area) automatically without PRs, and push to origin on user go-ahead.\n\n## Keeping the user updated\n- Update cadence: _(fill this out)_\n- What to surface: active workers, ready branches, PRs, blockers, user action items, or something else? _(fill this out)_\n- Preferred status format: brief messages, a storage file, a custom app, or another surface? _(fill this out)_\n\n## Open questions to resolve when natural\n\n- Preferred name / how to address the user\n- Worker defaults (provider / reasoning level / permission mode / preferred model) — ask the user when it comes up; do not assume a default.\n- Anything else the user wants surfaced regularly — ask once when natural and update the template accordingly.\n- Update verbosity preference (terse vs detailed)\n- Any specific area of the codebase that's currently the focus\n```\n\nWhen finished you can ask whether the user wants to save these preferences as manager template defaults for future managers. If they say yes, run `bb guide manager-templates` for the current layout and commands.",
     "fileName": "system-message-manager-welcome.md",
     "kind": "prompt",
     "title": "Manager Welcome",
diff --git a/packages/templates/src/templates/bb-guide-app.md b/packages/templates/src/templates/bb-guide-app.md
index 4472a708a..18bd77d31 100644
--- a/packages/templates/src/templates/bb-guide-app.md
+++ b/packages/templates/src/templates/bb-guide-app.md
@@ -1,67 +1,93 @@
 ---
 kind: instruction
 title: bb Guide - Apps
-summary: Thread app storage, browser API, CLI, and styling reference.
-intent: Explain the only supported way to build manager-visible dashboards and interactive thread apps.
-editingNotes: Keep this aligned with routes/threads/apps.ts, app-client-script.ts, app CLI commands, and the default status app template.
+summary: Global app storage, browser API, CLI, and styling reference.
+intent: Explain how to build global bb apps and use app data, messaging, and runtime paths.
+editingNotes: Keep this aligned with routes/apps.ts, app-client-script.ts, and app CLI commands.
 ---
 Apps
 
-Apps are the supported way to build dashboards, control panels, and other
-interactive surfaces inside thread storage. A manager's primary status surface
-is the built-in `status` app. Keep that app current instead of creating legacy
-top-level status files.
+Apps are global within the local host data directory. They are the supported
+way to build dashboards, control panels, and other interactive surfaces that
+can open inside a thread panel.
 
-Important: a bb app is self-contained static HTML/CSS/JS/SVG. Put files under
-`apps/<id>/assets/`; bb serves the `entry` file directly from the flat app URL
-through the host daemon. Do not start a web server, localhost dev server, npm
-install, build step, bundler, or framework for a normal app. Inline CSS/JS,
-relative asset refs, and CDN resources such as Tailwind or fonts are fine.
+Important: a bb app is self-contained static HTML/CSS/JS/SVG. Put browser
+files under `<dataDir>/apps/<applicationId>/public/`; bb serves that directory
+as the app's web root at `/api/v1/apps/<applicationId>/`.
+
+Do not start a web server, localhost dev server, npm install, build step,
+bundler, or framework for a normal app. Inline CSS/JS, relative asset refs, and
+CDN resources such as Tailwind or fonts are fine.
 
 Storage layout:
 
 ```text
-$BB_THREAD_STORAGE/
+<dataDir>/
   apps/
-    status/
+    review-board/
       manifest.json
-      assets/
+      public/
         index.html
+        index-abc.js
+        assets/
+          index-def.css
       data/
         state.json
 ```
 
-Each app is rooted at `apps/<id>/`. The manifest lives at
-`apps/<id>/manifest.json`, browser files live under `apps/<id>/assets/`, and
-durable JSON state lives under `apps/<id>/data/`. The `status` app should keep
-its primary shared state in `apps/status/data/state.json`.
+Each app is rooted at `<dataDir>/apps/<applicationId>/`. The manifest lives at
+`manifest.json`, browser files live under `public/`, and durable JSON state
+lives under `data/`. Only `public/` is served as static web content.
+
+The app exists only when the local filesystem contains a valid manifest at
+`<dataDir>/apps/<applicationId>/manifest.json`. `manifest.id` is the canonical
+application id: it must be a lowercase path-safe slug such as `status` or
+`review-board`, globally unique inside the data dir, and equal to the
+containing folder name. `manifest.name` is an optional human display name only.
+When it is absent or empty, bb displays the slug. Display names are not
+identifiers and may repeat.
 
 Manifest:
 
 ```json
 {
   "manifestVersion": 1,
-  "id": "status",
-  "name": "Status",
+  "id": "review-board",
+  "name": "Review Board",
   "icon": "ListTodo",
   "entry": "index.html",
-  "contributions": ["thread.app"],
   "capabilities": ["data", "message"]
 }
 ```
 
-`id` uses letters, numbers, underscores, and hyphens. `entry` is relative to
-`assets/`. HTML entries load in an app iframe and receive the `window.bb`
-bridge according to `capabilities`; Markdown entries render as static documents
-and do not receive `window.bb`. `capabilities` controls which `window.bb`
-helpers are injected for HTML entries: `data` enables `window.bb.data`, and
-`message` enables `window.bb.message`.
+`entry` is relative to `public/`. HTML entries load in an app iframe and receive
+the `window.bb` bridge according to `capabilities`; Markdown entries render as
+static documents and do not receive `window.bb`. `capabilities` controls which
+`window.bb` helpers are injected for HTML entries: `data` enables
+`window.bb.data`, and `message` enables `window.bb.message`.
+
+The served app entry URL is `/api/v1/apps/<applicationId>/`; bb serves
+`public/` transparently from that same URL root. Browser files in `public/`
+therefore resolve by normal browser URL rules with no `<base>` injection and no
+serve-time URL rewriting:
+`public/index-abc.js` maps to `/api/v1/apps/<applicationId>/index-abc.js`, and
+`public/assets/index-def.css` maps to
+`/api/v1/apps/<applicationId>/assets/index-def.css`.
 
-The served app URL is flat: `/api/v1/threads/<thread-id>/apps/<id>/<file>`
-maps to `apps/<id>/assets/<file>` on disk. HTML should use flat relative refs
-like `./index-abc.js`, not `./assets/index-abc.js`. If you are migrating an
-existing Vite build output, set `build.assetsDir = ""` so emitted files sit
-alongside `index.html`; new bb apps should stay plain static files.
+For Vite builds, set a relative base and copy the built `dist/` contents into
+`public/`:
+
+```ts
+import { defineConfig } from "vite";
+
+export default defineConfig({
+  base: "./",
+});
+```
+
+Do not use Vite's default root-absolute base (`"/"`). Refs such as
+`/assets/index-abc.js` resolve against the bb server root, not the app route, so
+they will not load inside a mounted app.
 
 The icon is optional and uses a built-in icon name. Icon resolution order is:
 
@@ -73,27 +99,49 @@ The icon is optional and uses a built-in icon name. Icon resolution order is:
 CLI:
 
 ```bash
-bb app list --self
-bb app new "Review Board" --id review-board --template blank --self
-bb app new "Status" --id status --template status --self
-bb app open status --self
-bb app rm review-board --self --yes
+bb app list
+bb app new --name "Review Board"
+bb app new --slug status
+bb app show review-board
+bb app data list review-board
+bb app data read review-board state.json
+bb app data write review-board state.json --file ./state.json
+bb app message review-board --target-thread thr_123 --json '"Please review the current blockers."'
+bb app delete review-board --yes
+```
+
+`--json` is available for scripts. Commands accept application ids only, never
+display names. There is no host selector in v1; apps are local-host only.
+
+Inside an app-capable runtime, inspect the current app context:
+
+```bash
+bb app current --json
 ```
 
-Pass a thread id instead of `--self` to target another thread. `bb app open`
-prints the app URL. `--json` is available for scripts.
+Outside a current-app runtime, this returns `current_app_unavailable`.
+
+Runtime paths:
+
+```bash
+echo "$BB_APPS_ROOT"          # <dataDir>/apps
+echo "$BB_APP_ID"             # current application id, when available
+echo "$BB_APP_ROOT"           # <dataDir>/apps/<applicationId>, when available
+echo "$BB_APP_DATA_PATH"      # <dataDir>/apps/<applicationId>/data, when available
+```
 
 Agent writes:
 
-Write app data directly to `apps/<id>/data/<path>` using a temp file in the
-same directory and then `mv` into place. Same-directory rename is atomic on
-macOS and Linux, and bb broadcasts the committed app-data change.
+When a runtime has `BB_APP_ROOT`, create or edit the app directly in that
+canonical folder. Write app data with a temp file in the same directory and
+then `mv` into place. Same-directory rename is atomic on macOS and Linux, and
+bb broadcasts the committed app-data change.
 
 ```bash
-dir="$BB_THREAD_STORAGE/apps/status/data"
+dir="$BB_APP_DATA_PATH"
 mkdir -p "$dir"
 tmp=$(mktemp "$dir/.state.XXXXXX")
-printf '%s\n' '{"tasks":[],"updatedAt":"2026-05-28T00:00:00Z"}' > "$tmp" &&
+printf '%s\n' '{"tasks":[],"updatedAt":"2026-06-02T00:00:00Z"}' > "$tmp" &&
   mv "$tmp" "$dir/state.json"
 ```
 
@@ -105,6 +153,7 @@ numbers, dots, underscores, and hyphens.
 Browser API:
 
 ```ts
+window.bb.applicationId
 window.bb.appId
 await window.bb.data?.read("state.json")
 await window.bb.data?.write("state.json", { tasks: [] })
@@ -122,10 +171,14 @@ when the changed path is below `prefix + "/"`; `""` matches all app data.
 Registering a listener immediately replays existing matching data, and bb
 replays again after reconnects or app-data resync hints. Later filesystem
 writes, browser writes, and deletes are delivered after that replay.
-`window.bb.message(text)` sends a normal follow-up message to the thread that
-owns the app.
 
-Minimal status app pattern:
+`window.bb.message(payload)` sends a normal follow-up message to the thread
+context that opened the app. Non-iframe callers must provide a target thread
+through the message API or CLI; without a target, bb returns
+`message_target_required`. App data remains global. Only message delivery is
+contextual.
+
+Minimal app pattern:
 
 ```html
 <main>
@@ -208,9 +261,8 @@ body {
 </style>
 ```
 
-Keep one canonical app for each concept. For manager progress, update the
-`status` app instead of creating parallel views. Use additional apps only when
-they are distinct tools or dashboards.
+Keep one canonical app for each concept. Use additional apps only when they are
+distinct tools or dashboards.
 
 Related guides:
 
diff --git a/packages/templates/src/templates/bb-guide-manager-templates.md b/packages/templates/src/templates/bb-guide-manager-templates.md
index deacc27f5..dc4d37331 100644
--- a/packages/templates/src/templates/bb-guide-manager-templates.md
+++ b/packages/templates/src/templates/bb-guide-manager-templates.md
@@ -11,8 +11,8 @@ Manager templates are named bundles of starter files for manager thread
 storage. When bb starts a new manager thread, the server resolves a template
 and recursively copies regular files into the new manager's thread storage
 before the host daemon receives the initial `thread.start` command. This is how
-a fresh manager can boot with starter `PREFERENCES.md`, `ASYNC.md`, and
-`apps/status/` files.
+a fresh manager can boot with starter files such as `PREFERENCES.md`,
+`ASYNC.md`, notes, plans, or other user-authored storage files.
 
 Directory layout:
 
@@ -20,22 +20,12 @@ Directory layout:
 <bb-data-dir>/manager-templates/
   active
   default/
-    apps/
-      status/
-        manifest.json
-        assets/
-          index.html
-        data/
-          state.json
+    PREFERENCES.md
+    ASYNC.md
   sawyer-next/
     PREFERENCES.md
-    apps/
-      status/
-        manifest.json
-        assets/
-          index.html
-        data/
-          state.json
+    plans/
+      kickoff.md
 ```
 
 In this guide, `<bb-data-dir>` is your bb data directory. Packaged installs
@@ -54,23 +44,13 @@ What gets seeded:
 
 bb recursively copies every regular file from the selected template directory
 into `<bb-data-dir>/thread-storage/<manager-thread-id>/`. There is no filename
-allowlist: `PREFERENCES.md`, `ASYNC.md`, `apps/status/manifest.json`, and
-`apps/status/data/state.json` are conventions, not the only files allowed.
-Symlinks and other non-regular files are ignored. Existing destination files
-are left as-is; seeding does not overwrite, delete, or refresh files.
-
-After any selected template copy, bb overlays a bundled `status` app so every
-new manager has a working status surface:
-
-```text
-apps/status/manifest.json
-apps/status/assets/index.html
-apps/status/data/state.json
-```
+allowlist. Symlinks and other non-regular files are ignored. Existing
+destination files are left as-is; seeding does not overwrite, delete, or
+refresh files.
 
-User-authored files at those same paths win; the overlay only fills missing
-files. If a selected non-default template is missing, bb logs a warning and
-still writes the bundled `status` app.
+There is no bundled app overlay. If the selected template directory is missing
+and the selected template is not `default`, bb logs a warning and seeds no
+template files.
 
 When it runs:
 
@@ -107,8 +87,6 @@ Creating a template:
 ```bash
 DATA_DIR="${BB_DATA_DIR:-$HOME/.bb}"
 mkdir -p "$DATA_DIR/manager-templates/sawyer-next"
-cp -R "$DATA_DIR/manager-templates/default/apps" \
-  "$DATA_DIR/manager-templates/sawyer-next/apps"
 $EDITOR "$DATA_DIR/manager-templates/sawyer-next/PREFERENCES.md"
 printf 'sawyer-next\n' > "$DATA_DIR/manager-templates/active"
 ```
@@ -116,22 +94,19 @@ printf 'sawyer-next\n' > "$DATA_DIR/manager-templates/active"
 Promoting current preferences:
 
 Managers see their storage path in runtime context. To save the current
-manager's `PREFERENCES.md` and status app starter state to the default
-template:
+manager's `PREFERENCES.md` to the default template:
 
 ```bash
 DATA_DIR="${BB_DATA_DIR:-$HOME/.bb}"
 THREAD_STORAGE="/absolute/path/from-manager-runtime-context"
-mkdir -p "$DATA_DIR/manager-templates/default/apps/status"
+mkdir -p "$DATA_DIR/manager-templates/default"
 cp "$THREAD_STORAGE/PREFERENCES.md" \
   "$DATA_DIR/manager-templates/default/PREFERENCES.md"
-cp -R "$THREAD_STORAGE/apps/status/." \
-  "$DATA_DIR/manager-templates/default/apps/status/"
 printf 'default\n' > "$DATA_DIR/manager-templates/active"
 ```
 
-Copy `ASYNC.md` or additional `apps/<id>/` directories into the same template
-directory when those starter files should be shared too.
+Copy `ASYNC.md`, notes, plans, or other starter files into the same template
+directory when those files should be shared too.
 
 Limitations and gotchas:
 
@@ -139,10 +114,8 @@ Limitations and gotchas:
 - Template file contents are not schema-validated before copying.
 - Symlinks and other non-regular files are ignored.
 - Existing thread storage files are never overwritten by seeding.
-- A user-authored `default/` directory does not suppress the bundled `status`
-  app overlay, but files already present at the bundled paths are preserved.
 - Missing selected non-default templates do not fall back to `default`; bb logs
-  a warning and writes only the bundled `status` app overlay.
+  a warning and seeds no template files.
 
 Related guides:
 
diff --git a/packages/templates/src/templates/bb-guide-overview.md b/packages/templates/src/templates/bb-guide-overview.md
index 4e6e9cc75..221c6c313 100644
--- a/packages/templates/src/templates/bb-guide-overview.md
+++ b/packages/templates/src/templates/bb-guide-overview.md
@@ -39,7 +39,7 @@ Run `bb guide <chapter>` for command details:
   managers       Hiring and managing project managers
   manager-templates
                  Seeding new manager storage from template bundles
-  app            Thread apps, the status app, app data, browser APIs, and styling
+  app            Global apps, app data, browser APIs, and styling
   providers      Discovering providers and models
   projects       Project CRUD and sources
   hosts          Listing and understanding hosts
diff --git a/packages/templates/src/templates/manager-agent-instructions.md b/packages/templates/src/templates/manager-agent-instructions.md
index 6857ab230..6751a4ee4 100644
--- a/packages/templates/src/templates/manager-agent-instructions.md
+++ b/packages/templates/src/templates/manager-agent-instructions.md
@@ -47,12 +47,11 @@ You have access to durable storage. Think of this like a shared drive where you
 A few **special** well known files in your storage:
 
 - **`PREFERENCES.md`** — durable user preferences and collaboration norms. Create it as you learn about the user, and keep it current.
-- **`apps/status/`** — the built-in manager status app. Keep `apps/status/data/state.json` current so the user can catch up at a glance. Use `bb guide app` for the app layout, browser API, data writes, and styling guidance.
 - **`ASYNC.md`** — scheduled nudges. Use this for reminders, recurring check-ins, and other work that should wake you up later. Run `bb guide async` for syntax, constraints, and examples.
 
 Preferences and starter storage files can be saved as manager templates in `{{managerDataDir}}/manager-templates/` so future managers boot with the same starting state. Run `bb guide manager-templates` for the layout and commands.
 
-Apps can read and write persistent reactive JSON state under `apps/<id>/data/` and can send messages to the owning thread through `window.bb.message`. Managers should update app data directly with same-directory temp-file writes and atomic renames. Use `bb app` for app creation, listing, URLs, and removal.
+Apps are global within the local host data dir. They can read and write persistent reactive JSON state under their `data/` directory and can send messages to the thread context that opened them through `window.bb.message`. Use `bb guide app` for the app layout, browser API, data writes, and `bb app` commands.
 
 The storage directory is yours to organize. Write down anything your future self or the user might find useful. Use `notes/`, `plans/`, `research/`, and `scratch/` as default folders when they fit. When an artifact does not belong in the repository, put it in thread storage.
 
diff --git a/packages/templates/src/templates/system-message-manager-quick-start.md b/packages/templates/src/templates/system-message-manager-quick-start.md
index 9619048d6..81532eaf0 100644
--- a/packages/templates/src/templates/system-message-manager-quick-start.md
+++ b/packages/templates/src/templates/system-message-manager-quick-start.md
@@ -11,7 +11,7 @@ You just came online inside bb. You are a manager helping your user get things d
 
 The user has sent their initial instructions as their next message — act on those directly.
 
-Before diving in, peek at `PREFERENCES.md` in your thread storage. If it exists with real saved preferences, treat them as starting context. If it's missing or starter content, that's fine — don't block on creating one; capture what you learn as you go and save it later. Preserve any seeded `apps/status/`, `PREFERENCES.md`, or `ASYNC.md` from templates. Keep the status app current as you work, usually by updating `apps/status/data/state.json`.
+Before diving in, peek at `PREFERENCES.md` in your thread storage. If it exists with real saved preferences, treat them as starting context. If it's missing or starter content, that's fine — don't block on creating one; capture what you learn as you go and save it later. Preserve any seeded `PREFERENCES.md`, `ASYNC.md`, notes, plans, or other files from templates.
 
 Talk to the user with the user-message tool: `mcp__bb-bridge__message_user` when present, otherwise `message_user`. Plain assistant text is not visible to them.
 
diff --git a/packages/templates/src/templates/system-message-manager-welcome.md b/packages/templates/src/templates/system-message-manager-welcome.md
index 9f9e66abe..0bbdd552f 100644
--- a/packages/templates/src/templates/system-message-manager-welcome.md
+++ b/packages/templates/src/templates/system-message-manager-welcome.md
@@ -64,11 +64,8 @@ After scope and landing mode are settled, figure out together:
 Create, replace, or update `PREFERENCES.md` with what you learn. If the user gives you a
 name, vibe, or other identity details for yourself, record those too.
 
-`apps/status/`, `PREFERENCES.md`, and `ASYNC.md` may already exist from user
-templates. Preserve any seeded structure and keep the status app current as you work.
-
-Depending on user preferences you might want to update `apps/status/data/state.json`
-to match their landing mode.
+`PREFERENCES.md`, `ASYNC.md`, notes, plans, or other files may already exist from user
+templates. Preserve any seeded structure as you work.
 
 If there is no `PREFERENCES.md` fill out this template with what you learn and save it:
 
@@ -96,19 +93,15 @@ This file is the manager's durable memory of how the user wants to be worked wit
   - Merge into a local branch (like a staging area) automatically without PRs, and push to origin on user go-ahead.
 
 ## Keeping the user updated
-  Adjust the `status` app to match the chosen mode.
-- **Status mode**: if the user opens PRs, the status app tracks open PRs in its primary section. If the user does NOT use PRs, use two sections instead: **In progress** (branches actively being worked on by workers) and **Ready for review** (branches that are validated and waiting for the user's go-ahead to push or merge).
-- **Status refresh**: keep `apps/status/data/state.json` current with the state of the world
-  - after any state-affecting action (worker spawn, branch ready, PR opened, merge, close, push).
-  - **after every child thread completion notification** (on any `[bb system] Thread complete/failed/interrupted`), even if the thread didn't obviously touch the tracked state — reconcile the relevant section.
-- **Status app**: run `bb guide app` for app data, `window.bb`, styling, and `bb app` commands.
-- Also keep running tasks and any user action items in the status app.
+- Update cadence: _(fill this out)_
+- What to surface: active workers, ready branches, PRs, blockers, user action items, or something else? _(fill this out)_
+- Preferred status format: brief messages, a storage file, a custom app, or another surface? _(fill this out)_
 
 ## Open questions to resolve when natural
 
 - Preferred name / how to address the user
 - Worker defaults (provider / reasoning level / permission mode / preferred model) — ask the user when it comes up; do not assume a default.
-- Anything else the user wants surfaced in the status app (extra sections, custom info, integrations) — ask once when natural and update the template accordingly.
+- Anything else the user wants surfaced regularly — ask once when natural and update the template accordingly.
 - Update verbosity preference (terse vs detailed)
 - Any specific area of the codebase that's currently the focus
 ```
diff --git a/packages/templates/test/templates.test.ts b/packages/templates/test/templates.test.ts
index 07aa2c898..b98db5e0d 100644
--- a/packages/templates/test/templates.test.ts
+++ b/packages/templates/test/templates.test.ts
@@ -100,8 +100,7 @@ describe("@bb/templates", () => {
     expect(rendered).toContain("mcp__bb-bridge__message_user");
     expect(rendered).toContain("bb thread spawn");
     expect(rendered).toContain("Simple delegation");
-    expect(rendered).toContain("`apps/status/`");
-    expect(rendered).toContain("apps/status/data/state.json");
+    expect(rendered).toContain("Apps are global within the local host data dir");
     expect(rendered).toContain("bb guide app");
     expect(rendered).toContain("bb guide async");
     expect(rendered).toContain("bb guide manager-templates");
@@ -186,12 +185,10 @@ describe("@bb/templates", () => {
     const rendered = renderTemplate("bbGuideApp", {});
 
     expect(rendered).toContain("Apps");
-    expect(rendered).toContain("apps/status/data/state.json");
+    expect(rendered).toContain("<dataDir>/apps/<applicationId>/");
     expect(rendered).toContain("window.bb.data");
-    expect(rendered).toContain("bb app list --self");
-    expect(rendered).toContain(
-      "Do not start a web server, localhost dev server, npm",
-    );
+    expect(rendered).toContain("bb app current --json");
+    expect(rendered).toContain("Do not start a web server");
     expect(rendered).toContain(
       '<script src="https://cdn.tailwindcss.com"></script>',
     );
diff --git a/tests/integration/fake/recovery/active-crash-recovery.test.ts b/tests/integration/fake/recovery/active-crash-recovery.test.ts
index bb22f5dc8..de5372a04 100644
--- a/tests/integration/fake/recovery/active-crash-recovery.test.ts
+++ b/tests/integration/fake/recovery/active-crash-recovery.test.ts
@@ -7,6 +7,7 @@ import {
 import {
   waitForHostConnected,
   waitForHostDisconnected,
+  waitForEventType,
   waitForThreadOutputContaining,
   waitForThreadStatus,
 } from "../../helpers/assertions.js";
@@ -54,6 +55,12 @@ describe.sequential("fake provider active crash recovery integration", () => {
 
       await harness.startDaemon();
       await waitForHostConnected(harness.api, RECOVERY_TIMEOUT_MS);
+      await waitForEventType(
+        harness.api,
+        thread.id,
+        "system/thread/interrupted",
+        RECOVERY_TIMEOUT_MS,
+      );
       await waitForThreadStatus(
         harness.api,
         thread.id,
diff --git a/tests/integration/fake/recovery/offline-queue.test.ts b/tests/integration/fake/recovery/offline-queue.test.ts
index d8bc2a4d7..d6c1ac94f 100644
--- a/tests/integration/fake/recovery/offline-queue.test.ts
+++ b/tests/integration/fake/recovery/offline-queue.test.ts
@@ -57,7 +57,11 @@ describe.sequential("fake provider offline queue recovery integration", () => {
         harness.db,
         thread.id,
       );
-      if (!providerThreadId || !environment.path) {
+      if (
+        !providerThreadId ||
+        !environment.path ||
+        !environment.workspaceProvisionType
+      ) {
         throw new Error(
           "Expected queued recovery turn to have provider context",
         );
@@ -112,6 +116,7 @@ describe.sequential("fake provider offline queue recovery integration", () => {
           instructions: `Recovered queued work for ${projectName} in ${projectRootPath}`,
           instructionMode: "append",
           dynamicTools: [],
+          injectedSkillSources: [],
         },
         target: { mode: "start" },
       });
diff --git a/tests/integration/fake/recovery/shared.ts b/tests/integration/fake/recovery/shared.ts
index 49cd335ec..f6d9ff46d 100644
--- a/tests/integration/fake/recovery/shared.ts
+++ b/tests/integration/fake/recovery/shared.ts
@@ -16,9 +16,9 @@ export const TURN_TIMEOUT_MS = scaleTimeoutMs(15_000);
 export const RECOVERY_TIMEOUT_MS = scaleTimeoutMs(30_000);
 // Active-turn waits: only long enough to catch a turn in flight before the crash/restart step.
 export const ACTIVE_TIMEOUT_MS = scaleTimeoutMs(5_000);
-// Hold the turn beyond RECOVERY_TIMEOUT_MS so active-crash recovery must interrupt
-// an in-flight provider call instead of racing a normally completed fake turn.
-export const STOP_DELAY_TEXT = "delay:60000 recovery turn";
+// Hold the turn long enough to observe active status before crashing, while
+// still allowing a replayed pre-start command to settle inside RECOVERY_TIMEOUT_MS.
+export const STOP_DELAY_TEXT = "delay:5000 recovery turn";
 
 export type RecoveryWorkspaceType = "unmanaged" | "managed-worktree";