Data-Wise · Data-Wise · Feb 24, 2026 · Feb 23, 2026 · Feb 23, 2026 · Feb 24, 2026
diff --git a/.STATUS b/.STATUS
@@ -1,15 +1,15 @@
 ---
 status: active
 priority: P1
-version: 1.19.0
+version: 1.20.0
 sprint: 37
 started: 2026-01-08
-updated: 2026-02-23
-released: 2026-02-23
+updated: 2026-02-24
+released: 2026-02-24
 editor: hybrid-markdown++
-next_focus: Settings Infrastructure Improvements (feature/settings-improvements)
-tests: 2255
-unit_tests: 2255
+next_focus: Fix 67 test file TypeScript errors
+tests: 2280
+unit_tests: 2280
 e2e_tests: 109
 test_file_errors: 67 (non-blocking, documented in docs/planning/TEST-FILE-TYPESCRIPT-ERRORS-2026-01-24.md)
 tags:
@@ -26,10 +26,6 @@ tags:
 
 ## Current Focus (Sprint 37)
 
-### In Progress
-
-1. **Settings Infrastructure Improvements** (WIP) — Extract reusable SettingsToggle, shortcut registry, usePreferences hook, pre-commit ORCHESTRATE guard. Branch: `feature/settings-improvements`. Spec: `docs/specs/SPEC-settings-improvements-2026-02-23.md`. ~3.5h total.
-
 ### Next Up
 
 1. **Fix 67 test file TypeScript errors** (~2.5h) — Non-blocking but noisy. Documented in `docs/planning/TEST-FILE-TYPESCRIPT-ERRORS-2026-01-24.md`
@@ -49,14 +45,30 @@ tags:
 
 ## Recently Completed
 
-### Pomodoro Focus Timer (2026-02-23) — PR #45 merged to dev
+### Session Timer Removal (2026-02-24) — PR #48
+
+- Removed legacy session timer from breadcrumb bar (⏸/▶/↺ controls)
+- Removed `sessionStartTime` prop chain from 5 components
+- StatsPanel Duration card → Pomodoro count from `usePomodoroStore`
+- Cleaned 4 localStorage keys and ~50 lines orphaned CSS
+- Net: -95 lines, 2,280 tests (2 session-duration tests removed)
+
+### Settings Infrastructure Improvements (2026-02-24) — PR #47
+
+- Reusable `SettingsToggle` component with full accessibility
+- `usePreferences` hook with cached state + event-based sync
+- `SHORTCUTS` registry (25 shortcuts) with `matchesShortcut()` helper
+- Migrated `SettingsModal.tsx` to `usePreferences` hook
+- 27 new tests (2,282 total)
+
+### v1.19.0 (2026-02-23) — Pomodoro Focus Timer (Released)
 
 - Pomodoro timer in editor status bar (start/pause click, reset right-click)
 - Zustand store with symmetric callbacks: `tick(onComplete, onBreakComplete)`
 - Auto-save on work completion, gentle break toasts
 - Focus Timer settings in General tab (5 new preferences)
 - Auto-pin new projects to sidebar
-- 62 new tests (2,255 total)
+- 62 new tests (2,282 total)
 
 ### v1.18.0 (2026-02-22) — Sidebar Vault Expansion Fix + DexieError2 Fix
 
@@ -127,8 +139,8 @@ tags:
 
 | Spec | Status | Target |
 |------|--------|--------|
-| Pomodoro Timer | Implemented (PR #45) | v1.19.0 |
-| Settings Improvements | In Progress | v1.19.0 |
+| Pomodoro Timer | Released | v1.19.0 |
+| Settings Improvements | In Progress | v1.20.0 |
 | Three-Tab Sidebar | Design Approved | v1.17.0 |
 | Quarto Enhancements | Partially Implemented | v1.15+ |
 | LaTeX Editor | Proposal | v2.0 |

diff --git a/.husky/pre-commit b/.husky/pre-commit
@@ -0,0 +1,11 @@
+#!/usr/bin/env sh
+
+# Guard: Block ORCHESTRATE files on dev/main branches
+if git diff --cached --name-only | grep -q '^ORCHESTRATE-'; then
+  branch=$(git branch --show-current)
+  if [ "$branch" = "dev" ] || [ "$branch" = "main" ]; then
+    echo "⚠️  ORCHESTRATE files should not be committed to $branch"
+    echo "   Remove with: git rm ORCHESTRATE-*.md"
+    exit 1
+  fi
+fi
diff --git a/BRAINSTORM-quarto-code-chunks-2026-02-24.md b/BRAINSTORM-quarto-code-chunks-2026-02-24.md
@@ -0,0 +1,184 @@
+# Brainstorm: VS Code-Style Quarto Code Chunks
+
+> **Date:** 2026-02-24
+> **Mode:** max | feat | save
+> **Duration:** ~12 min (research + 2 agents)
+> **Topic:** Implement VS Code Quarto-style code chunks with distinct background and code font
+
+## Problem Statement
+
+Scribe's code chunks (`\`\`\`{r}`, `\`\`\`{python}`) are nearly invisible. The current `rgba(0,0,0,0.04)` background blends into prose, making it hard to scan between text and code in long `.qmd` documents. VS Code's Quarto extension uses clear visual separation — distinct background color, monospace font, language indicators — that lets writers instantly identify code regions while editing.
+
+## Current State (Scribe)
+
+| Aspect | Current Implementation |
+|--------|----------------------|
+| **Background** | `rgba(0,0,0,0.04)` / `rgba(255,255,255,0.04)` — barely visible |
+| **Font** | JetBrains Mono via CSS, hardcoded in `index.css` |
+| **Detection** | CSS `:has(.tok-codeFence)` selectors (no ViewPlugin) |
+| **Left border** | 2px solid accent color |
+| **Theme integration** | `.dark` class override — not wired to theme CSS variables |
+| **Settings** | No code font preference (only prose font is configurable) |
+| **Chunk options** | `#| lines` styled via `:has(.tok-comment):has(.tok-monospace)` |
+| **Language badge** | None |
+| **Files** | `index.css:6231-6276`, `CodeMirrorEditor.tsx` (no dedicated plugin) |
+
+## VS Code Quarto Reference
+
+| Aspect | VS Code Implementation |
+|--------|----------------------|
+| **Background** | `#E1E1E166` light / `#40404066` dark — clearly visible |
+| **Font** | Fixed-width from `--vscode-editor-font-family` |
+| **Detection** | Markdown engine token parser via `background.ts` |
+| **Decoration** | `TextEditorDecorationType` with `isWholeLine: true` |
+| **CodeLens** | "Run Cell", "Run Next Cell", "Run Above" buttons above chunks |
+| **Theme** | Uses `notebook.selectedCellBackground` / `notebook.cellEditorBackground` |
+| **Config** | Background mode: default, theme-based, or off |
+
+Sources:
+- [Quarto VS Code Extension](https://marketplace.visualstudio.com/items?itemName=quarto.quarto)
+- [Quarto HTML Code Blocks docs](https://quarto.org/docs/output-formats/html-code.html)
+- [VS Code Notebook Editor](https://quarto.org/docs/tools/vscode/notebook.html)
+- [quarto-dev/quarto GitHub: background.ts](https://github.com/quarto-dev/quarto/blob/main/apps/vscode/src/providers/background.ts)
+- [quarto-dev/quarto GitHub: cell/codelens.ts](https://github.com/quarto-dev/quarto/blob/main/apps/vscode/src/providers/cell/codelens.ts)
+- [quarto-dev/quarto GitHub: theme.ts](https://github.com/quarto-dev/quarto/blob/main/apps/vscode-editor/src/theme.ts)
+
+## Quick Wins (< 30 min each)
+
+1. **Bump background opacity** — Change `rgba(0,0,0,0.04)` to `rgba(0,0,0,0.08)` in CSS. Zero-risk, immediate improvement.
+2. **Increase left border to 3px** — Thicker accent stripe improves scannability.
+3. **Add top/bottom margin on fence lines** — 8-12px spacing creates visual "breathing room" around chunks.
+
+## Medium Effort (1-2 hours each)
+
+4. **Add `--nexus-code-bg` CSS variable** — Computed in `applyTheme()` from existing `bgTertiary` values. Auto-adapts to all 10 themes.
+5. **Add `--code-font-family` CSS variable** — Separate code font from prose font, applied via `applyFontSettings()`.
+6. **Create `CodeChunkDecorationPlugin`** — ViewPlugin using `Decoration.line()` pattern (identical to existing callout system at line 554-597 of CodeMirrorEditor.tsx).
+
+## Long-term (Future sessions)
+
+7. **Language badge widget** — Small `[R]` / `[PY]` pill on fence lines. Uses existing `WidgetType` pattern.
+8. **Code font Settings UI** — Picker in Settings > Editor tab, filtered to mono fonts.
+9. **Chunk option collapsing** — Fold `#|` lines when cursor isn't on them (like heading mark hiding).
+10. **Code chunk line numbers** — Optional gutter numbers inside chunks only.
+
+## Architecture Decision: ViewPlugin vs CSS `:has()`
+
+**Decision: ViewPlugin for Quarto chunks, CSS `:has()` fallback for plain fences.**
+
+| Approach | Pros | Cons |
+|----------|------|------|
+| CSS `:has()` only | Simple, no JS | Can't extend bg beyond text, no badge widgets, browser compat edge cases |
+| ViewPlugin only | Full control, proven pattern in callouts | More code, need sort order discipline |
+| **Hybrid (recommended)** | Best of both — ViewPlugin for Quarto, CSS fallback for `\`\`\`js` | Two code paths |
+
+The hybrid approach matches how the codebase already works: callouts use `Decoration.line()` for rich treatment, while basic blockquotes use CSS.
+
+## Color Strategy
+
+**Approach: Derive `--nexus-code-bg` from `bgTertiary` in `applyTheme()`**
+
+For dark themes: `rgba(bgTertiary, 0.45)` — subtle but clearly distinct from `bgPrimary`
+For light themes: `rgba(bgTertiary, 0.5)` — visible tint without harsh contrast
+
+This auto-adapts to all 10 themes + custom themes without per-theme configuration.
+
+**Alternative considered:** `color-mix(in srgb, var(--nexus-bg-tertiary) 60%, var(--nexus-bg-primary) 40%)` — cleaner CSS but computed in CSS, not JS. Works in modern browsers but CSS `color-mix()` requires Chromium 111+ / Safari 16.2+.
+
+## Font Strategy
+
+| Element | Font | Size | Line Height |
+|---------|------|------|-------------|
+| Prose | User's choice (default: system sans, 15px) | `--editor-font-size` | 1.8 |
+| Code content | User's choice from mono fonts (default: JetBrains Mono) | `calc(editor-size * 0.88)` → ~13px | 1.5 |
+| Chunk options (`#|`) | Same as code, but smaller | `calc(editor-size * 0.82)` → ~12px | 1.5 |
+| Fence lines | Same as code | Same as code | 1.5 |
+
+The font size reduction (88%) plus line-height change (1.8→1.5) creates clear visual separation without being jarring.
+
+## What NOT to Include
+
+| VS Code Feature | Why Skip for Scribe |
+|----------------|---------------------|
+| Run Cell / CodeLens buttons | Scribe is for writing, not execution. VS Code handles running. |
+| Output cells | Quarto renders outputs separately. No inline output. |
+| Cell toolbar | Adds IDE complexity. Scribe is distraction-free. |
+| Gutter line numbers in chunks | Adds visual noise. Maybe as future opt-in. |
+| Drag handles | Not applicable to writing flow. |
+| Cell execution status | Scribe doesn't execute code. |
+
+## Agent Analysis Summary
+
+### Frontend Architect Agent
+
+Key findings:
+- The existing `RichMarkdownPlugin` (line 440-658) is the exact pattern to follow
+- `FencedCode` → `CodeInfo` syntax tree nodes provide language detection
+- `Decoration.line()` requires `range(line.from)` not a range — critical detail
+- Decorations MUST be sorted by `.from` position before `Decoration.set()`
+- `createEditorTheme()` is the canonical place for decoration class styles
+- `hexToRgb()` already exists at line 585 for color computation
+- `--nexus-code-bg` must be a complete `rgba()` string (CSS can't apply alpha to a variable)
+
+### UX Designer Agent
+
+Key findings:
+- Current `rgba(0,0,0,0.04)` is invisible — needs 4-8x increase
+- `color-mix()` approach auto-adapts to all themes without JS
+- Code font should be `--editor-font-size - 1px` (14px at default 15)
+- Chunk options (`#|`) should be italic + slightly smaller for hierarchy
+- Left border should increase from 2px→3px at 40% accent opacity
+- Language badge: `[R]`/`[PY]`/`[JL]` pill, 11px uppercase, always visible at 70% opacity
+- ADHD consideration: badge is "wayfinding anchor" for scanning — answers "what kind?" at a glance
+- Avoid all IDE chrome (run buttons, toolbars, status indicators)
+
+## Implementation Phases
+
+### Phase 1: CSS Variables Foundation (themes.ts)
+- Add `--nexus-code-bg` and `--nexus-code-border` in `applyTheme()`
+- Add `codeFamily`/`codeSize` to `FontSettings`
+- Add `--code-font-family` and `--code-font-size-ratio` in `applyFontSettings()`
+- Add `'jetbrains-mono'` to `FONT_FAMILIES` registry
+
+### Phase 2: ViewPlugin Core (CodeMirrorEditor.tsx)
+- Add `LanguageBadgeWidget extends WidgetType`
+- Add `CodeChunkDecorationPlugin` with `computeDecorations()`
+- Register in extensions array
+
+### Phase 3: Theme Styles (CodeMirrorEditor.tsx)
+- Add `.cm-quarto-*` classes in `createEditorTheme()`
+- Test across 4+ themes (dark + light)
+
+### Phase 4: CSS Cleanup (index.css)
+- Replace lines 6231-6276 with simplified plain-fence fallback
+- Remove `.dark` overrides
+
+### Phase 5: Settings UI (EditorSettingsTab.tsx)
+- Add Code Font section with mono-filtered picker
+- Add size ratio slider (0.75-1.0)
+
+### Phase 6: Validation
+- Cursor-on-fence behavior
+- Theme switching with visible chunks
+- Nested/adjacent chunks
+- Full test suite
+
+## Files Affected
+
+| File | Changes |
+|------|---------|
+| `src/renderer/src/lib/themes.ts` | `FontSettings` interface, `DEFAULT_FONT_SETTINGS`, `FONT_FAMILIES`, `applyTheme()`, `applyFontSettings()` |
+| `src/renderer/src/components/CodeMirrorEditor.tsx` | New `CodeChunkDecorationPlugin`, `LanguageBadgeWidget`, `createEditorTheme()` styles, extensions array |
+| `src/renderer/src/index.css` | Replace lines 6231-6276 with fallback-only CSS |
+| `src/renderer/src/components/Settings/EditorSettingsTab.tsx` | Add Code Font picker section |
+
+## Recommended Path
+
+> Start with Phase 1 (CSS variables) + Phase 4 (CSS cleanup) as a single commit. This alone makes code chunks visibly distinct across all themes with zero new JS. Then Phase 2+3 in a second commit for the ViewPlugin. Phase 5 (settings UI) can be a separate PR.
+
+## Open Questions
+
+1. Should `color-mix()` (CSS-only) or `rgba()` computation (JS in applyTheme) be used? The JS approach is more compatible but requires the `hexToRgb()` helper.
+2. Should language badges be cursor-reveal (hide when editing fence line) like heading marks?
+3. Should chunk option `#|` lines collapse when cursor isn't on them?
+4. What about inline executable code (`\`{r} 1+1\``)? The VS Code extension styles these too.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,29 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ---
 
+## [v1.20.0] - 2026-02-24 — Settings Infrastructure & Timer Cleanup
+
+### Added
+
+- **`SettingsToggle` component** — Reusable toggle switch with `role="switch"`, `aria-checked`, and `aria-label` accessibility attributes. Used by GeneralSettingsTab and EditorSettingsTab.
+- **`usePreferences` hook** — Cached preferences via React state with `preferences-changed` event listener for cross-component sync. Provides `prefs`, `updatePref()`, and `togglePref()`.
+- **`SHORTCUTS` registry** — Single source of truth for 25 keyboard shortcuts with `matchesShortcut(event, id)` helper for event matching. Replaces manual `e.metaKey && e.key` checks.
+
+### Changed
+
+- **StatsPanel Session section** — Duration card replaced with Pomodoro count card showing today's completed sessions from `usePomodoroStore`.
+- **WritingProgress** — No longer displays session elapsed time; shows word delta, progress bar, and streak only.
+- Migrated `SettingsModal.tsx` to use `usePreferences` hook (removed raw `loadPreferences` calls)
+
+### Removed
+
+- **Session timer** — Removed the legacy session timer from the breadcrumb bar (⏸/▶/↺ controls). Raw elapsed time persisted via localStorage causing confusing values like "2296:20" across restarts.
+- **sessionStartTime prop chain** — Removed from App.tsx, EditorOrchestrator, HybridEditor, WritingProgress, and StatsPanel interfaces.
+- **4 localStorage keys** — `sessionStart`, `timerPaused`, `pausedDuration`, `pauseStart`.
+- **~50 lines of CSS** — Orphaned `.focus-timer`, `.timer-btn`, `.timer-value` styles.
+
+---
+
 ## [v1.19.0] - 2026-02-23 — Pomodoro Focus Timer
 
 ### Added

diff --git a/README.md b/README.md
@@ -3,9 +3,9 @@
 > **ADHD-Friendly Distraction-Free Writer**
 
 [![Status](https://img.shields.io/badge/status-active-brightgreen)]()
-[![Version](https://img.shields.io/badge/version-1.19.0-blue)]()
+[![Version](https://img.shields.io/badge/version-1.20.0-blue)]()
 [![Progress](https://img.shields.io/badge/progress-100%25-brightgreen)]()
-[![Tests](https://img.shields.io/badge/tests-2255%20passing-brightgreen)]()
+[![Tests](https://img.shields.io/badge/tests-2280%20passing-brightgreen)]()
 [![Tauri](https://img.shields.io/badge/tauri-2-blue)]()
 [![React](https://img.shields.io/badge/react-18-blue)]()
 
@@ -240,7 +240,7 @@ scribe/
 
 ## Test Coverage
 
-**2,255 tests passing** across test files:
+**2,280 tests passing** across test files:
 
 | Test File | Tests |
 |-----------|-------|

diff --git a/docs/ARCHITECTURE.md b/docs/ARCHITECTURE.md
@@ -106,6 +106,45 @@ graph TD
 
 ---
 
+## Preferences System
+
+The preferences system provides lightweight, event-driven state management
+for user settings that persist to `localStorage`. It operates alongside
+the Zustand store but uses a simpler read/write model suited to key-value
+preferences.
+
+```mermaid
+flowchart LR
+    LS[localStorage] -->|loadPreferences| HP[usePreferences hook]
+    HP -->|React state| C[Components]
+    UP[updatePreferences / togglePref] -->|write-through| LS
+    UP -->|dispatch| E["preferences-changed event"]
+    E -->|listener| HP
+```
+
+### Key Modules
+
+| Module | File | Purpose |
+|--------|------|---------|
+| `preferences.ts` | `src/renderer/src/lib/preferences.ts` | Load, save, merge preferences to localStorage |
+| `usePreferences()` | `src/renderer/src/hooks/usePreferences.ts` | React hook — cached reads, event-based sync across components |
+| `shortcuts.ts` | `src/renderer/src/lib/shortcuts.ts` | `SHORTCUTS` registry — single source of truth for all 27 keyboard shortcuts |
+| `matchesShortcut()` | `src/renderer/src/lib/shortcuts.ts` | Registry-based `KeyboardEvent` matching (cmd/shift/alt modifiers) |
+| `SettingsToggle` | `src/renderer/src/components/Settings/SettingsToggle.tsx` | Reusable toggle switch component for boolean settings |
+
+### How It Works
+
+1. **`loadPreferences()`** reads from `localStorage`, merges with defaults so new fields get sensible values on upgrade.
+2. **`usePreferences()`** calls `loadPreferences()` once on mount and caches the result in React state. It listens for the `preferences-changed` custom event to stay in sync with other components.
+3. **`updatePreferences()` / `togglePref()`** write-through to `localStorage` and dispatch `preferences-changed`, triggering all mounted hooks to re-read.
+4. **`SHORTCUTS`** defines every keyboard shortcut with `key`, `mod`, and `label`. UI components reference `SHORTCUTS.xxx.label` for display; handlers call `matchesShortcut(event, shortcutId)` instead of manual key checks.
+
+### Pre-commit ORCHESTRATE Guard
+
+A husky `pre-commit` hook prevents accidental commits of `ORCHESTRATE-*.md` planning files to protected branches. These files belong on feature branches during development and are cleaned up on merge.
+
+---
+
 ## Data Flow
 
 ```mermaid
@@ -206,8 +245,13 @@ scribe/
 │           │   ├── SimpleTagAutocomplete.tsx
 │           │   └── CitationAutocomplete.tsx
 │           │
+│           ├── hooks/
+│           │   └── usePreferences.ts    # Cached prefs hook (event sync)
+│           │
 │           ├── lib/
 │           │   ├── api.ts               # Tauri IPC wrapper
+│           │   ├── preferences.ts       # localStorage preferences R/W
+│           │   ├── shortcuts.ts         # SHORTCUTS registry + matcher
 │           │   ├── themes.ts            # Theme definitions
 │           │   └── mathjax.ts           # KaTeX processing
 │           │