diff --git a/src/cli/mod.ts b/src/cli/mod.ts
index 62fe44f5..9f176947 100644
--- a/src/cli/mod.ts
+++ b/src/cli/mod.ts
@@ -191,6 +191,13 @@ export function commandNeedsExtensions(args: string[]): boolean {
   return !SKIP_EXTENSION_COMMANDS.has(commandInfo.command);
 }
 
+/** A deferred warning message to emit after logging is initialized. */
+export interface DeferredWarning {
+  kind: "model" | "vault" | "driver" | "datastore" | "report";
+  file: string;
+  error: string;
+}
+
 /**
  * Load user models from configured directory.
  */
@@ -198,6 +205,7 @@ async function loadUserModels(
   repoDir: string,
   marker: RepoMarkerData | null,
   denoRuntime: EmbeddedDenoRuntime,
+  deferredWarnings: DeferredWarning[],
 ): Promise<void> {
   try {
     const modelsDir = resolveModelsDir(marker);
@@ -209,18 +217,16 @@ async function loadUserModels(
     const loader = new UserModelLoader(denoRuntime, repoDir);
     const result = await loader.loadModels(absoluteModelsDir);
 
-    // Log extension successes at debug level
-    for (const file of result.extended) {
-      logger.debug`Extended model type from ${file}`;
-    }
-
-    // Log failures as warnings (don't block CLI startup)
+    // Collect failures for deferred logging (logging not yet initialized)
     for (const failure of result.failed) {
-      logger.warn`Failed to load user model ${failure.file}: ${failure.error}`;
+      deferredWarnings.push({
+        kind: "model",
+        file: failure.file,
+        error: failure.error,
+      });
     }
-  } catch (error) {
-    // Not in a swamp repo or other error - log at debug level for troubleshooting
-    logger.debug`Skipping user models: ${error}`;
+  } catch {
+    // Not in a swamp repo or models dir doesn't exist — not an error
   }
 }
 
@@ -231,6 +237,7 @@ async function loadUserVaults(
   repoDir: string,
   marker: RepoMarkerData | null,
   denoRuntime: EmbeddedDenoRuntime,
+  deferredWarnings: DeferredWarning[],
 ): Promise<void> {
   try {
     const vaultsDir = resolveVaultsDir(marker);
@@ -241,18 +248,15 @@ async function loadUserVaults(
     const loader = new UserVaultLoader(denoRuntime, repoDir);
     const result = await loader.loadVaults(absoluteVaultsDir);
 
-    // Log successes at debug level
-    for (const file of result.loaded) {
-      logger.debug`Loaded user vault type from ${file}`;
-    }
-
-    // Log failures as warnings (don't block CLI startup)
     for (const failure of result.failed) {
-      logger.warn`Failed to load user vault ${failure.file}: ${failure.error}`;
+      deferredWarnings.push({
+        kind: "vault",
+        file: failure.file,
+        error: failure.error,
+      });
     }
-  } catch (error) {
-    // Not in a swamp repo or other error - log at debug level for troubleshooting
-    logger.debug`Skipping user vaults: ${error}`;
+  } catch {
+    // Not in a swamp repo or vaults dir doesn't exist — not an error
   }
 }
 
@@ -260,6 +264,7 @@ async function loadUserDrivers(
   repoDir: string,
   marker: RepoMarkerData | null,
   denoRuntime: EmbeddedDenoRuntime,
+  deferredWarnings: DeferredWarning[],
 ): Promise<void> {
   try {
     const driversDir = resolveDriversDir(marker);
@@ -270,18 +275,15 @@ async function loadUserDrivers(
     const loader = new UserDriverLoader(denoRuntime, repoDir);
     const result = await loader.loadDrivers(absoluteDriversDir);
 
-    // Log successes at debug level
-    for (const file of result.loaded) {
-      logger.debug`Loaded user driver type from ${file}`;
-    }
-
-    // Log failures as warnings (don't block CLI startup)
     for (const failure of result.failed) {
-      logger.warn`Failed to load user driver ${failure.file}: ${failure.error}`;
+      deferredWarnings.push({
+        kind: "driver",
+        file: failure.file,
+        error: failure.error,
+      });
     }
-  } catch (error) {
-    // Not in a swamp repo or other error - log at debug level for troubleshooting
-    logger.debug`Skipping user drivers: ${error}`;
+  } catch {
+    // Not in a swamp repo or drivers dir doesn't exist — not an error
   }
 }
 
@@ -289,6 +291,7 @@ async function loadUserDatastores(
   repoDir: string,
   marker: RepoMarkerData | null,
   denoRuntime: EmbeddedDenoRuntime,
+  deferredWarnings: DeferredWarning[],
 ): Promise<void> {
   try {
     const datastoresDir = resolveDatastoresDir(marker);
@@ -299,19 +302,15 @@ async function loadUserDatastores(
     const loader = new UserDatastoreLoader(denoRuntime, repoDir);
     const result = await loader.loadDatastores(absoluteDatastoresDir);
 
-    // Log successes at debug level
-    for (const file of result.loaded) {
-      logger.debug`Loaded user datastore type from ${file}`;
-    }
-
-    // Log failures as warnings (don't block CLI startup)
     for (const failure of result.failed) {
-      logger
-        .warn`Failed to load user datastore ${failure.file}: ${failure.error}`;
+      deferredWarnings.push({
+        kind: "datastore",
+        file: failure.file,
+        error: failure.error,
+      });
     }
-  } catch (error) {
-    // Not in a swamp repo or other error - log at debug level for troubleshooting
-    logger.debug`Skipping user datastores: ${error}`;
+  } catch {
+    // Not in a swamp repo or datastores dir doesn't exist — not an error
   }
 }
 
@@ -319,6 +318,7 @@ async function loadUserReports(
   repoDir: string,
   marker: RepoMarkerData | null,
   denoRuntime: EmbeddedDenoRuntime,
+  deferredWarnings: DeferredWarning[],
 ): Promise<void> {
   try {
     const reportsDir = resolveReportsDir(marker);
@@ -329,18 +329,15 @@ async function loadUserReports(
     const loader = new UserReportLoader(denoRuntime, repoDir);
     const result = await loader.loadReports(absoluteReportsDir);
 
-    // Log successes at debug level
-    for (const file of result.loaded) {
-      logger.debug`Loaded user report from ${file}`;
-    }
-
-    // Log failures as warnings (don't block CLI startup)
     for (const failure of result.failed) {
-      logger.warn`Failed to load user report ${failure.file}: ${failure.error}`;
+      deferredWarnings.push({
+        kind: "report",
+        file: failure.file,
+        error: failure.error,
+      });
     }
-  } catch (error) {
-    // Not in a swamp repo or other error - log at debug level for troubleshooting
-    logger.debug`Skipping user reports: ${error}`;
+  } catch {
+    // Not in a swamp repo or reports dir doesn't exist — not an error
   }
 }
 
@@ -496,15 +493,17 @@ export async function runCli(args: string[]): Promise<void> {
     // Not in a swamp repo - marker stays null
   }
 
-  // Load user extensions in parallel (skip for commands that don't need them)
+  // Load user extensions in parallel (skip for commands that don't need them).
+  // Collect warnings because logging is not yet initialized at this point.
+  const deferredWarnings: DeferredWarning[] = [];
   if (commandNeedsExtensions(args)) {
     const denoRuntime = new EmbeddedDenoRuntime();
     await Promise.all([
-      loadUserModels(repoDir, marker, denoRuntime),
-      loadUserVaults(repoDir, marker, denoRuntime),
-      loadUserDrivers(repoDir, marker, denoRuntime),
-      loadUserDatastores(repoDir, marker, denoRuntime),
-      loadUserReports(repoDir, marker, denoRuntime),
+      loadUserModels(repoDir, marker, denoRuntime, deferredWarnings),
+      loadUserVaults(repoDir, marker, denoRuntime, deferredWarnings),
+      loadUserDrivers(repoDir, marker, denoRuntime, deferredWarnings),
+      loadUserDatastores(repoDir, marker, denoRuntime, deferredWarnings),
+      loadUserReports(repoDir, marker, denoRuntime, deferredWarnings),
     ]);
   }
 
@@ -602,6 +601,12 @@ export async function runCli(args: string[]): Promise<void> {
         jsonMode: options.json ?? false,
         noColor,
       });
+
+      // Emit deferred warnings now that logging is initialized
+      for (const warning of deferredWarnings) {
+        logger
+          .warn`Failed to load user ${warning.kind} ${warning.file}: ${warning.error}`;
+      }
     })
     .error(unknownCommandErrorHandler)
     .action(function () {
diff --git a/src/domain/extensions/extension_content_extractor.ts b/src/domain/extensions/extension_content_extractor.ts
index 5e58c669..c6d137d3 100644
--- a/src/domain/extensions/extension_content_extractor.ts
+++ b/src/domain/extensions/extension_content_extractor.ts
@@ -325,19 +325,45 @@ function extractVaultFromSource(
 
 /**
  * Extracts method definitions from the source.
- * Matches the `methods: { name: { description: "..." } }` pattern.
+ * Handles three patterns:
+ *   1. Inline: `methods: { name: { description: "..." } }`
+ *   2. Shorthand property: `methods,` (references a variable named `methods`)
+ *   3. Variable reference: `methods: someVar` (references a named variable)
  */
 function extractMethods(content: string): ExtractedMethod[] {
+  // Try inline methods block first: methods: { ... }
+  const inlineMethods = extractMethodsFromBlock(content, content);
+  if (inlineMethods.length > 0) return inlineMethods;
+
+  // Try variable reference: methods: someVar or shorthand methods,
+  const refName = resolveMethodsReference(content);
+  if (!refName) return [];
+
+  // Look up the referenced variable in the same file
+  const varBlock = findVariableObjectBody(content, refName);
+  if (varBlock) {
+    return extractMethodsFromBlock(varBlock, content);
+  }
+
+  return [];
+}
+
+/**
+ * Extracts methods from an inline `methods: { ... }` block within the content.
+ */
+function extractMethodsFromBlock(
+  searchContent: string,
+  fullContent: string,
+): ExtractedMethod[] {
   const methods: ExtractedMethod[] = [];
 
-  // Find the methods block
-  const methodsBlockMatch = content.match(/methods:\s*\{/);
+  const methodsBlockMatch = searchContent.match(/methods:\s*\{/);
   if (!methodsBlockMatch || methodsBlockMatch.index === undefined) {
     return methods;
   }
 
   const methodsStart = methodsBlockMatch.index + methodsBlockMatch[0].length;
-  const methodsBlock = extractBalancedBraces(content, methodsStart);
+  const methodsBlock = extractBalancedBraces(searchContent, methodsStart);
   if (!methodsBlock) return methods;
 
   // Match individual method entries: methodName: { description: "..." }
@@ -351,7 +377,7 @@ function extractMethods(content: string): ExtractedMethod[] {
     // Try to extract arguments for this method
     const methodEntry = extractMethodEntry(methodsBlock, name);
     const args = methodEntry
-      ? extractMethodArguments(methodEntry, content)
+      ? extractMethodArguments(methodEntry, fullContent)
       : [];
 
     methods.push({ name, description, arguments: args });
@@ -360,6 +386,61 @@ function extractMethods(content: string): ExtractedMethod[] {
   return methods;
 }
 
+/**
+ * Resolves the variable name referenced by the `methods` property.
+ * Returns the variable name for `methods: someVar` or `methods` (shorthand).
+ * Returns null if methods are defined inline or not found.
+ */
+function resolveMethodsReference(content: string): string | null {
+  // Match shorthand property: methods, or methods } (end of object)
+  // This pattern appears when an imported variable named `methods` is used
+  // as a shorthand property in the model object literal.
+  const shorthandMatch = content.match(
+    /(?:export\s+const\s+(?:model|extension)\s*=\s*\{[\s\S]*?)(?<![.\w])methods\s*[,}]/,
+  );
+  if (shorthandMatch) {
+    // Verify it's not `methods: {` (inline) or `methods: someRef` (reference)
+    const beforeMethods = content.slice(
+      0,
+      (shorthandMatch.index ?? 0) + shorthandMatch[0].length,
+    );
+    if (!beforeMethods.match(/methods\s*:\s*[{\w]/)) {
+      return "methods";
+    }
+  }
+
+  // Match reference: methods: someVar (not followed by { which is inline)
+  const refMatch = content.match(/methods:\s*(\w+)\s*[,}\n]/);
+  if (refMatch && refMatch[1] !== "{") {
+    return refMatch[1];
+  }
+
+  return null;
+}
+
+/**
+ * Finds the body of a `const varName = { ... }` or `export const varName = { ... }`
+ * declaration and returns the full declaration text including `varName: { ... }` wrapper
+ * so that extractMethodsFromBlock can find `methodName: { description: ... }` entries.
+ */
+function findVariableObjectBody(
+  content: string,
+  varName: string,
+): string | null {
+  const pattern = new RegExp(
+    `(?:export\\s+)?(?:const|let)\\s+${varName}\\s*=\\s*\\{`,
+  );
+  const match = content.match(pattern);
+  if (!match || match.index === undefined) return null;
+
+  const start = match.index + match[0].length;
+  const body = extractBalancedBraces(content, start);
+  if (!body) return null;
+
+  // Wrap as `methods: { <body> }` so the method extraction regex works
+  return `methods: {${body}}`;
+}
+
 /**
  * Extracts the full text of a single method entry from the methods block.
  */
diff --git a/src/domain/extensions/extension_content_extractor_test.ts b/src/domain/extensions/extension_content_extractor_test.ts
index 83602824..ebc939f5 100644
--- a/src/domain/extensions/extension_content_extractor_test.ts
+++ b/src/domain/extensions/extension_content_extractor_test.ts
@@ -1389,3 +1389,85 @@ Deno.test("extractContentMetadata skips datastore without type", async () => {
     await Deno.remove(tmpDir, { recursive: true });
   }
 });
+
+Deno.test("extractContentMetadata: extracts methods from shorthand property", async () => {
+  const tmpDir = await Deno.makeTempDir();
+  try {
+    const modelsDir = join(tmpDir, "models");
+    await Deno.mkdir(modelsDir, { recursive: true });
+
+    const modelFile = join(modelsDir, "mymodel.ts");
+    await Deno.writeTextFile(
+      modelFile,
+      [
+        'import { z } from "npm:zod@4";',
+        "const methods = {",
+        "  list: {",
+        '    description: "List resources",',
+        "    arguments: z.object({}),",
+        "    execute: async () => ({ dataHandles: [] }),",
+        "  },",
+        "  create: {",
+        '    description: "Create a resource",',
+        "    arguments: z.object({}),",
+        "    execute: async () => ({ dataHandles: [] }),",
+        "  },",
+        "};",
+        "export const model = {",
+        '  type: "@test/mymodel",',
+        '  version: "2026.03.26.1",',
+        "  methods,",
+        "};",
+      ].join("\n"),
+    );
+
+    const result = await extractContentMetadata([modelFile], modelsDir, []);
+    assertEquals(result.models.length, 1);
+    assertEquals(result.models[0].methods.length, 2);
+    assertEquals(result.models[0].methods[0].name, "list");
+    assertEquals(result.models[0].methods[0].description, "List resources");
+    assertEquals(result.models[0].methods[1].name, "create");
+    assertEquals(
+      result.models[0].methods[1].description,
+      "Create a resource",
+    );
+  } finally {
+    await Deno.remove(tmpDir, { recursive: true });
+  }
+});
+
+Deno.test("extractContentMetadata: extracts methods from variable reference", async () => {
+  const tmpDir = await Deno.makeTempDir();
+  try {
+    const modelsDir = join(tmpDir, "models");
+    await Deno.mkdir(modelsDir, { recursive: true });
+
+    const modelFile = join(modelsDir, "refmodel.ts");
+    await Deno.writeTextFile(
+      modelFile,
+      [
+        'import { z } from "npm:zod@4";',
+        "const myMethods = {",
+        "  sync: {",
+        '    description: "Sync data",',
+        "    arguments: z.object({}),",
+        "    execute: async () => ({ dataHandles: [] }),",
+        "  },",
+        "};",
+        "export const model = {",
+        '  type: "@test/refmodel",',
+        '  version: "2026.03.26.1",',
+        "  methods: myMethods,",
+        "};",
+      ].join("\n"),
+    );
+
+    const result = await extractContentMetadata([modelFile], modelsDir, []);
+    assertEquals(result.models.length, 1);
+    assertEquals(result.models[0].methods.length, 1);
+    assertEquals(result.models[0].methods[0].name, "sync");
+    assertEquals(result.models[0].methods[0].description, "Sync data");
+  } finally {
+    await Deno.remove(tmpDir, { recursive: true });
+  }
+});
diff --git a/src/libswamp/extensions/push.ts b/src/libswamp/extensions/push.ts
index 5c88d891..e585d1d4 100644
--- a/src/libswamp/extensions/push.ts
+++ b/src/libswamp/extensions/push.ts
@@ -418,7 +418,7 @@ export async function extensionPushPrepare(
   let contentMetadata: ExtensionContentMetadata | undefined;
   try {
     contentMetadata = await deps.extractContentMetadata(
-      input.allModelFiles,
+      input.modelEntryPoints,
       input.modelsDir,
       input.workflowFiles,
       input.allVaultFiles,