chore: exclude tools/, scripts/ from CodeScene analysis

tools/qmd/ contains vendored qmd source code (not our code) that was
dragging the overall code health score down to 6.53.
scripts/ contains one-shot utility scripts, not production code.

Excluding both from CodeScene so the health metric reflects only
the actual app codebase (src/, src-tauri/src/).

.claude-done

@@ -1,42 +0,0 @@
-# Drag & Drop Images — Implementation Summary
-
-## Problem
-Dragging image files from Finder into the BlockNote editor didn't work. Tauri v2's
-`dragDropEnabled` defaults to `true`, which intercepts OS-level file drops before they
-reach the webview's HTML5 DnD API — BlockNote never received the dropped files.
-
-## Solution
-Instead of disabling Tauri's drag interception, we use Tauri's `onDragDropEvent` API
-to listen for native file drops and handle them directly:
-
-1. **Rust backend** (`src-tauri/src/vault/image.rs`):
-   - Added `copy_image_to_vault` command that copies a file by OS path into
-     `vault/attachments/` with a timestamp-prefixed filename
-   - Refactored shared path logic into `prepare_attachment_path` helper
-   - Validates file exists and has an image extension before copying
-
-2. **Frontend** (`src/hooks/useImageDrop.ts`):
-   - Added Tauri `onDragDropEvent` listener that fires on native OS drag-drop
-   - On `drop`: filters for image paths, copies each to vault, calls `onImageUrl`
-   - On `over`: shows drag overlay (paths aren't available until drop)
-   - `copyImageToVault` invokes the new Rust command and returns an asset URL
-
-3. **Editor integration** (`src/components/SingleEditorView.tsx`):
-   - `useInsertImageCallback` inserts a BlockNote image block at cursor position
-   - Wired into `useImageDrop` via the `onImageUrl` callback
-   - `vaultPath` threaded through Editor → EditorContent → SingleEditorView
-
-4. **Existing `/image` slash command** continues to work unchanged (uses `uploadFile`
-   on `useCreateBlockNote` → `uploadImageFile` → `save_image` Tauri command).
-
-## Commits
-- `d45f2e2` feat: add copy_image_to_vault Rust command for native drag-drop
-- `b047d0c` feat: handle Tauri native drag-drop for filesystem images
-- `2e04f5a` fix: remove nonexistent drag-drop permission from capabilities
-- `23ad982` fix: correct DragDropEvent type handling for 'over' events
-
-## Tests
-- 4 new Rust tests for `copy_image_to_vault` (success, missing file, non-image, all extensions)
-- 1 new frontend test for `useImageDrop` with onImageUrl + vaultPath params
-- All 300 Rust tests pass, 1167 frontend tests pass
-- Coverage: Rust 85.47%, Frontend 78.64%

.claude-pid

@@ -0,0 +1 @@
+45402

.codescenerc

@@ -0,0 +1,9 @@
+{
+  "exclude": [
+    "tools/",
+    "scripts/",
+    "src-tauri/gen/",
+    "coverage/",
+    "dist/"
+  ]
+}

.github/workflows/ci.yml

@@ -60,6 +60,9 @@ jobs:
       - name: Run frontend tests
         run: pnpm test
 
+      - name: Bundle MCP server resources (required by Tauri build)
+        run: node scripts/bundle-mcp-server.mjs
+
       - name: Run Rust tests
         run: cargo test --manifest-path=src-tauri/Cargo.toml
 

.github/workflows/release.yml

@@ -55,6 +55,11 @@ jobs:
           node-version: '22'
           cache: 'pnpm'
 
+      - name: Setup Bun (required for bundle-qmd.sh)
+        uses: oven-sh/setup-bun@v2
+        with:
+          bun-version: latest
+
       - name: Setup Rust
         uses: dtolnay/rust-toolchain@stable
         with:
@@ -80,6 +85,24 @@ jobs:
           jq --arg v "$VERSION" '.version = $v' src-tauri/tauri.conf.json > tmp.json && mv tmp.json src-tauri/tauri.conf.json
           sed -i '' "s/^version = \".*\"/version = \"$VERSION\"/" src-tauri/Cargo.toml
 
+      - name: Import Apple Developer certificate into keychain
+        env:
+          APPLE_CERTIFICATE: ${{ secrets.APPLE_CERTIFICATE }}
+          APPLE_CERTIFICATE_PASSWORD: ${{ secrets.APPLE_CERTIFICATE_PASSWORD }}
+        run: |
+          # Decode and import the certificate so codesign can use it in beforeBuildCommand
+          CERT_PATH="$RUNNER_TEMP/apple_cert.p12"
+          KEYCHAIN_PATH="$RUNNER_TEMP/laputa-signing.keychain-db"
+          KEYCHAIN_PASSWORD="$(uuidgen)"
+          echo "$APPLE_CERTIFICATE" | base64 --decode > "$CERT_PATH"
+          security create-keychain -p "$KEYCHAIN_PASSWORD" "$KEYCHAIN_PATH"
+          security set-keychain-settings -lut 21600 "$KEYCHAIN_PATH"
+          security unlock-keychain -p "$KEYCHAIN_PASSWORD" "$KEYCHAIN_PATH"
+          security import "$CERT_PATH" -P "$APPLE_CERTIFICATE_PASSWORD" -A -t cert -f pkcs12 -k "$KEYCHAIN_PATH"
+          security list-keychain -d user -s "$KEYCHAIN_PATH"
+          security set-key-partition-list -S apple-tool:,apple: -s -k "$KEYCHAIN_PASSWORD" "$KEYCHAIN_PATH"
+          echo "KEYCHAIN_PATH=$KEYCHAIN_PATH" >> "$GITHUB_ENV"
+
       - name: Build Tauri app (with signing + notarization)
         env:
           TAURI_SIGNING_PRIVATE_KEY: ${{ secrets.TAURI_SIGNING_PRIVATE_KEY }}
@@ -153,7 +176,7 @@ jobs:
           REPO="refactoringhq/laputa-app"
 
           ARM_SIG=$(cat updater-aarch64/*.app.tar.gz.sig)
-          ARM_DMG=$(ls dmg-aarch64/*.dmg | xargs basename)
+          ARM_TARBALL=$(ls updater-aarch64/*.app.tar.gz | xargs basename)
 
           cat > latest.json << EOF
           {
@@ -163,7 +186,7 @@ jobs:
             "platforms": {
               "darwin-aarch64": {
                 "signature": "${ARM_SIG}",
-                "url": "https://github.com/${REPO}/releases/download/${TAG}/${ARM_DMG}"
+                "url": "https://github.com/${REPO}/releases/download/${TAG}/${ARM_TARBALL}"
               }
             }
           }

.gitignore

@@ -42,3 +42,6 @@ final_selection.py
 .claude-done
 .claude-blocked
 src-tauri/target
+
+# Generated mcp-server bundle (built by scripts/bundle-mcp-server.mjs)
+src-tauri/resources/

.husky/pre-push

@@ -47,26 +47,26 @@ fi
 
 # ── 0. TypeScript + Vite build ──────────────────────────────────────────
 echo ""
-echo "📦 [0/4] TypeScript + Vite build..."
+echo "📦 [0/5] TypeScript + Vite build..."
 pnpm exec tsc --noEmit
 pnpm build
 echo "  ✅ Build OK"
 
 # ── 1. Frontend coverage (≥70%) — includes all unit tests ───────────────
 echo ""
-echo "📊 [1/4] Frontend tests + coverage (≥70%)..."
+echo "📊 [1/5] Frontend tests + coverage (≥70%)..."
 pnpm test:coverage --silent
 echo "  ✅ Frontend coverage OK"
 
 # ── 2. Rust lint (clippy + fmt) — fast, run before coverage ─────────────
 echo ""
 if [ "$RUST_CHANGED" = true ]; then
-  echo "🔧 [2/4] Clippy + rustfmt..."
+  echo "🔧 [2/5] Clippy + rustfmt..."
   cargo clippy --manifest-path=src-tauri/Cargo.toml -- -D warnings
   cargo fmt --manifest-path=src-tauri/Cargo.toml -- --check
   echo "  ✅ Rust lint OK"
 else
-  echo "⏭️  [2/4] Rust lint — skipped (no src-tauri/ changes)"
+  echo "⏭️  [2/5] Rust lint — skipped (no src-tauri/ changes)"
 fi
 
 # ── 3. Rust coverage (≥85% lines) ──────────────────────────────────────
@@ -75,9 +75,9 @@ if [ "$RUST_CHANGED" = true ]; then
   LLVM_COV_FLAGS="--no-clean"
   if [ "${LAPUTA_FULL_COVERAGE:-0}" = "1" ]; then
     LLVM_COV_FLAGS=""
-    echo "🦀 [3/4] Rust coverage — FULL (LAPUTA_FULL_COVERAGE=1)..."
+    echo "🦀 [3/5] Rust coverage — FULL (LAPUTA_FULL_COVERAGE=1)..."
   else
-    echo "🦀 [3/4] Rust coverage (≥85%, incremental)..."
+    echo "🦀 [3/5] Rust coverage (≥85%, incremental)..."
   fi
   # Unset GIT_DIR so git tests create isolated repos without inheriting hook context
   unset GIT_DIR GIT_WORK_TREE GIT_INDEX_FILE
@@ -90,12 +90,23 @@ if [ "$RUST_CHANGED" = true ]; then
     -- --test-threads=1
   echo "  ✅ Rust coverage OK"
 else
-  echo "⏭️  [3/4] Rust coverage — skipped (no src-tauri/ changes)"
+  echo "⏭️  [3/5] Rust coverage — skipped (no src-tauri/ changes)"
 fi
 
-# ── 4. CodeScene code health gate (≥9.2) ────────────────────────────────
+# ── 4. Playwright smoke tests (if any exist) ──────────────────────────
 echo ""
-echo "🏥 [4/4] CodeScene code health gate (≥9.2)..."
+SMOKE_FILES=$(find tests/smoke -name '*.spec.ts' 2>/dev/null | head -1)
+if [ -n "$SMOKE_FILES" ]; then
+  echo "🎭 [4/5] Playwright smoke tests..."
+  pnpm playwright:smoke
+  echo "  ✅ Smoke tests OK"
+else
+  echo "⏭️  [4/5] Playwright smoke tests — skipped (no tests/smoke/*.spec.ts)"
+fi
+
+# ── 5. CodeScene code health gate (≥9.2) ────────────────────────────────
+echo ""
+echo "🏥 [5/5] CodeScene code health gate (≥9.2)..."
 if [ -z "$CODESCENE_PAT" ] || [ -z "$CODESCENE_PROJECT_ID" ]; then
   echo "  ⚠️  CODESCENE_PAT or CODESCENE_PROJECT_ID not set — skipping"
 else

CLAUDE.md

@@ -15,11 +15,40 @@ pre_commit_code_health_safeguard    # CodeScene ≥9.2 — if it fails, fix stru
 
 **CI is a safety net, not a discovery tool.** If CI catches something you didn't catch locally, that's a process failure. All these tools are available locally — use them while you code, not just at the end.
 
-## ⛔ BEFORE FIRING laputa-task-done — QA on real vault
+## ⛔ BEFORE FIRING laputa-task-done — Two-phase QA (mandatory)
 
-> **⚠️ TAURI APP ONLY — never test in browser (`pnpm dev` / localhost)**
-> The browser dev server has a fake HTTP server (`/api/*` routes, mock handlers) that doesn't exist in the real Tauri app.
-> If it works in the browser but crashes in Tauri, it's broken. Always test in `pnpm tauri dev`.
+### Phase 1: Playwright browser QA (headless, you do this yourself)
+
+Test every acceptance criterion using Playwright against the dev server **before** marking done. This catches 80% of bugs before Brian sees them.
+
+```bash
+# 1. Start the dev server (use your worktree port)
+pnpm dev --port <N> &
+DEV_PID=$!
+sleep 3  # wait for vite to be ready
+
+# 2. Run Playwright smoke test for this task
+BASE_URL="http://localhost:<N>" npx playwright test tests/smoke/<slug>.spec.ts
+
+# 3. Or run all smoke tests
+BASE_URL="http://localhost:<N>" pnpm playwright:smoke
+
+kill $DEV_PID
+```
+
+**What to test in Playwright:**
+- Every command palette entry from the spec → open `Cmd+K`, type the command name, verify it appears and executes
+- Every keyboard shortcut → send keydown events, verify UI state changes
+- Every UI element described in the spec → verify it renders, is focusable, responds to Tab
+- Edge cases: empty state, long text, rapid keypresses
+
+**Playwright is non-negotiable even if tests pass.** Unit tests verify code; Playwright verifies the user experience in the real browser. Both are required.
+
+> **⚠️ Browser dev server limits**: the dev server uses mock Tauri handlers (`src/mock-tauri.ts`) — file system operations, git commands, and native dialogs are mocked. Test those via `pnpm tauri dev` in Phase 2 if the task touches them.
+
+### Phase 2: Native Tauri QA (Brian does this after you push)
+
+Brian installs the release build and runs keyboard-only QA on the native app. You don't do Phase 2 — but Phase 1 must pass before you fire the done signal, or Brian's QA will fail and the task goes back to To Rework.
 
 1. Acquire lockfile: `echo $$ > /tmp/laputa-qa.lock && trap "rm -f /tmp/laputa-qa.lock" EXIT`
 2. Kill other instances: `pkill -x laputa 2>/dev/null || true; sleep 1`
@@ -29,6 +58,19 @@ pre_commit_code_health_safeguard    # CodeScene ≥9.2 — if it fails, fix stru
 6. If task touches file save: verify `git -C ~/Laputa diff` shows changes
 7. If QA fails → fix and re-run. Do NOT fire the signal until it passes.
 
+**⚠️ QA ≠ tests. QA means using the app as a user.**
+- "Tests pass" is NOT QA. Tests verify code, QA verifies the user experience.
+- The QA comment must describe what you did as a user: "Opened app → Cmd+K → typed 'Trash' → pressed Enter → note disappeared from list → restarted app → note still not visible"
+- Every QA comment must include: the exact keyboard/command palette steps used, what was visible before and after, and any edge case tested.
+- If you cannot test a feature using keyboard only (osascript shortcuts + command palette), the feature is not keyboard-first → QA fails.
+
+**⚠️ Test in a clean environment when the feature depends on state.**
+If a feature involves indexing, fresh installs, first-time setup, or anything that only runs once:
+- **Do not test in the existing dev vault** — it already has the state you're trying to test.
+- **Create a new empty vault** for the test: Cmd+K → "New Vault" (or equivalent), pick a temp folder like `/tmp/test-vault-<slug>`, then test the full first-time flow from scratch.
+- This applies to: search indexing, vault init, getting-started setup, any "on first open" logic.
+- If you can't reproduce the fresh-install scenario locally, the feature is untestable → do not fire done.
+
 Fire done signal only after QA passes:
 ```bash
 rm -f /tmp/laputa-qa.lock
@@ -74,13 +116,47 @@ Tauri v2 + React + TypeScript desktop app. Reads a vault of markdown files with
 - **Never develop on `main`** — always on `task/<slug>` branch
 - **Commit every 20–30 min** — atomic commits, one concern per commit (`feat:`, `fix:`, `refactor:`, `test:`, `docs:`)
 - **Update docs/** when changing architecture, abstractions, or significant design
-- **Test as you go** — write tests alongside code, not after
 
-## Testing
+## TDD — Red/Green/Refactor (mandatory)
+
+**Always use test-driven development.** No production code without a failing test first.
+
+The loop:
+1. **Red** — write a failing test that describes the behavior you want. Run it, confirm it fails for the right reason.
+2. **Green** — write the minimum code to make the test pass. No more, no less.
+3. **Refactor** — clean up the code (extract, rename, simplify) while keeping tests green.
+4. **Commit** — one red/green/refactor cycle = one atomic commit.
+5. Repeat.
+
+**Why this matters:**
+- Forces you to think about behavior before implementation
+- Produces only code that's actually needed (no speculative abstractions)
+- Tests written first are always behavioral and structure-insensitive by construction
+- Tiny cycles = fast feedback, smaller diffs, easier to review
+
+**For bug fixes:**
+1. Write a failing test that reproduces the bug (this is the regression test)
+2. Fix the bug until the test passes
+3. Commit both together: `fix: [bug] — regression test added`
+
+**For Rust:**
+```bash
+cargo watch -x test   # run tests on every save
+```
+
+**For frontend:**
+```bash
+pnpm test --watch     # run tests on every save
+```
+
+**When to deviate:** Pure UI layout/styling work with no logic is the only exception. Everything else — hooks, utilities, Rust commands, state management — must be TDD.
+
+## Testing (quality bar)
 
 - Unit tests must cover real business logic, not "component renders"
-- Every bug fixed manually → add a regression test
-- Every new feature → new tests for new behavior paths
+- Tests test **behavior** (what the code does), not **structure** (how it does it)
+- Every bug fixed → regression test that would have caught it
+- Every new feature → TDD from the start (see above)
 - `pnpm test:coverage` and `cargo llvm-cov` must pass before committing
 
 ## Design File (every UI task)
@@ -103,6 +179,33 @@ node -e "const f=JSON.parse(require('fs').readFileSync('ui-design.pen','utf8'));
 echo '{"children":[],"variables":{}}' > design/<slug>.pen
 ```
 
+## Vault File Retrocompatibility (mandatory for every feature that adds vault files)
+
+Laputa vaults are long-lived. New app versions must work on existing vaults that were created before a feature existed.
+
+**Rule: never assume a vault file exists. Always auto-create if missing.**
+
+Every feature that depends on a vault file or folder must:
+1. **Auto-bootstrap on vault open** — check if the required file/folder exists; if not, create it with defaults. This must be silent and non-blocking.
+2. **Be idempotent** — creating defaults must be safe to run multiple times (never overwrite user data).
+3. **Expose a repair command** — add a `Cmd+K` command like "Restore Default Themes" or "Repair Vault Config" that explicitly re-creates missing files. Users can run this if something is broken.
+
+**General "Repair Vault" command** — when adding a new vault file dependency, register it with the central repair system so that `Cmd+K → "Repair Vault"` fixes everything in one shot.
+
+**Pattern:**
+```
+on vault open:
+  if file X does not exist → create X with defaults  ← silent auto-repair
+  if file X exists but is malformed → log warning, use defaults (don't crash)
+
+on "Repair Vault" command:
+  for each known vault file/folder:
+    if missing → create with defaults
+    if present → leave untouched (idempotent)
+```
+
+This principle applies to: themes, config files, type files, any `.laputa/` subfolder, or any file Laputa expects to find in a vault.
+
 ## macOS / Tauri Gotchas
 
 - `Option+N` on macOS → special chars (`¡`, `™`), not `key:'N'`. Use `e.code` or `Cmd+N`.
@@ -118,6 +221,28 @@ bash ~/.openclaw/skills/laputa-qa/scripts/shortcut.sh "command" "s"
 bash ~/.openclaw/skills/laputa-qa/scripts/click.sh 400 300   # logical coords
 ```
 
+## Menu Bar Discoverability (mandatory for every new command)
+
+The command palette is powerful but not discoverable — users must already know a command exists to find it. The macOS menu bar is where users discover what an app can do.
+
+**Rule: every significant command palette entry must also appear in the menu bar.**
+
+When adding a new command to the palette:
+1. **Identify the right menu bar group** — File, Edit, View, Note, Vault, or create a new group if needed
+2. **Add a menu item** with the same label as the palette command
+3. **Show the keyboard shortcut** next to the menu item (if one exists)
+4. **If no direct shortcut exists**, still add the menu item — it's discoverable and triggers the same action
+
+The menu bar should be organized around what Laputa does:
+- **File** — new note, open vault, switch vault, close
+- **Edit** — undo, redo, find, note actions (rename, trash, duplicate)
+- **View** — view modes, zoom, sidebar, panels
+- **Note** — note-specific actions (move to trash, archive, properties)
+- **Vault** — vault management (themes, config, repair, sync)
+- **Window / Help** — standard macOS items
+
+**This is a QA requirement:** before marking any task done, verify that every new command palette entry has a corresponding menu bar item.
+
 ## Keyboard-First Principle (mandatory for every new feature)
 
 Every feature must be reachable via keyboard. This is both a UX requirement and a QA requirement — Brian tests the native app using keyboard only (osascript key events, no mouse).
@@ -140,6 +265,9 @@ The pre-push hook runs all checks locally before the push goes through. This rep
 git push origin main    # pre-push hook runs automatically
 ```
 
+### ⛔ NEVER open a Pull Request
+PRs on separate branches diverge from main with every merge, requiring continuous rebases and creating unnecessary conflicts. Always push directly to main. If the push fails (disk full, test failure, etc.) — fix the problem, then push again. There is no scenario where opening a PR is the right fallback.
+
 ### ⛔ NEVER use --no-verify
 ```bash
 # FORBIDDEN — will be caught and rejected:

design/archived-note-indicator.pen

@@ -0,0 +1 @@
+{"children":[],"variables":{}}

design/mcp-autodetect-status-bar.pen

@@ -0,0 +1 @@
+{"children":[],"variables":{}}

design/note-templates.pen

@@ -0,0 +1 @@
+{"children":[],"variables":{}}

design/raw-editor-mode.pen

@@ -0,0 +1 @@
+{"children":[],"variables":{}}

design/search-bundle-qmd.pen

@@ -0,0 +1 @@
+{"children":[{"id":"status-bar-indexing","type":"frame","name":"StatusBar - Indexing Progress States","layout":"vertical","x":0,"y":0,"width":1400,"height":400,"gap":24,"padding":24,"fill":"#F7F6F3","children":[{"id":"title","type":"text","content":"StatusBar Indexing Progress - search-bundle-qmd","fontSize":20,"fontWeight":"600","fill":"#37352F"},{"id":"desc","type":"text","content":"The indexing badge appears in the StatusBar left section, after the pending changes badge. It shows the current indexing phase with a spinner icon (Loader2) during active phases and a Search icon when complete.","fontSize":14,"fill":"#9B9A97","width":900},{"id":"states","type":"frame","name":"States","layout":"vertical","gap":16,"width":1350,"children":[{"id":"state-idle","type":"frame","layout":"horizontal","gap":8,"alignItems":"center","children":[{"id":"label-idle","type":"text","content":"idle:","fontSize":12,"fontWeight":"600","fill":"#9B9A97","width":100},{"id":"val-idle","type":"text","content":"(hidden - no badge shown)","fontSize":12,"fill":"#9B9A97"}]},{"id":"state-installing","type":"frame","layout":"horizontal","gap":8,"alignItems":"center","children":[{"id":"label-install","type":"text","content":"installing:","fontSize":12,"fontWeight":"600","fill":"#3b82f6","width":100},{"id":"val-install","type":"text","content":"| [spinner] Installing search\u2026","fontSize":12,"fill":"#3b82f6"}]},{"id":"state-scanning","type":"frame","layout":"horizontal","gap":8,"alignItems":"center","children":[{"id":"label-scan","type":"text","content":"scanning:","fontSize":12,"fontWeight":"600","fill":"#3b82f6","width":100},{"id":"val-scan","type":"text","content":"| [spinner] Indexing\u2026 342/1,057","fontSize":12,"fill":"#3b82f6"}]},{"id":"state-embedding","type":"frame","layout":"horizontal","gap":8,"alignItems":"center","children":[{"id":"label-embed","type":"text","content":"embedding:","fontSize":12,"fontWeight":"600","fill":"#3b82f6","width":100},{"id":"val-embed","type":"text","content":"| [spinner] Embedding\u2026 50/200","fontSize":12,"fill":"#3b82f6"}]},{"id":"state-complete","type":"frame","layout":"horizontal","gap":8,"alignItems":"center","children":[{"id":"label-done","type":"text","content":"complete:","fontSize":12,"fontWeight":"600","fill":"#22c55e","width":100},{"id":"val-done","type":"text","content":"| [search icon] Index ready  (auto-dismisses after 5s)","fontSize":12,"fill":"#22c55e"}]},{"id":"state-error","type":"frame","layout":"horizontal","gap":8,"alignItems":"center","children":[{"id":"label-err","type":"text","content":"error:","fontSize":12,"fontWeight":"600","fill":"#f97316","width":100},{"id":"val-err","type":"text","content":"| [search icon] Index error  (orange accent)","fontSize":12,"fill":"#f97316"}]}]},{"id":"flow","type":"frame","name":"Flow","layout":"vertical","gap":8,"width":1350,"children":[{"id":"flow-title","type":"text","content":"Auto-indexing Flow","fontSize":16,"fontWeight":"600","fill":"#37352F"},{"id":"flow-desc","type":"text","content":"1. Vault opens \u2192 useIndexing checks index status via get_index_status\n2. If qmd missing or collection missing or pending embeds \u2192 triggers start_indexing\n3. Rust emits indexing-progress events (installing \u2192 scanning \u2192 embedding \u2192 complete)\n4. StatusBar shows IndexingBadge with spinner + phase label + progress counts\n5. On file save \u2192 trigger_incremental_index runs qmd update in background\n6. Complete phase auto-dismisses after 5 seconds","fontSize":13,"fill":"#37352F","width":900}]}]}],"variables":{}}

design/sort-picker-properties.pen

@@ -0,0 +1 @@
+{"children":[],"variables":{}}

design/sync-conflict-resolution.pen

@@ -0,0 +1 @@
+{"children":[],"variables":{}}

design/tab-responsive-width.pen

@@ -0,0 +1 @@
+{"children":[],"variables":{}}

design/themes-editable.pen

@@ -0,0 +1 @@
+{"children":[],"variables":{}}

design/trashed-note-editor.pen

@@ -0,0 +1 @@
+{"children":[{"id":"trashed-banner-frame","type":"frame","name":"Trashed Note Banner","x":0,"y":0,"width":720,"height":340,"fill":"#FFFFFF","cornerRadius":[8,8,8,8],"children":[{"id":"breadcrumb","type":"frame","name":"Breadcrumb Bar","width":720,"height":45,"fill":"#FFFFFF","layout":"horizontal","mainAxisAlignment":"space-between","crossAxisAlignment":"center","padding":16,"children":[{"id":"breadcrumb-left","type":"frame","layout":"horizontal","gap":4,"crossAxisAlignment":"center","children":[{"id":"type-label","type":"text","content":"Note","fontSize":12,"textColor":"#6B7280"},{"id":"sep","type":"text","content":"›","fontSize":12,"textColor":"#6B7280"},{"id":"title","type":"text","content":"My Trashed Note","fontSize":12,"fontWeight":"600","textColor":"#1F2937"},{"id":"dot","type":"text","content":"·","fontSize":12,"textColor":"#6B7280"},{"id":"words","type":"text","content":"1,234 words","fontSize":12,"textColor":"#6B7280"}]},{"id":"breadcrumb-right","type":"frame","layout":"horizontal","gap":12,"crossAxisAlignment":"center","children":[{"id":"restore-icon","type":"text","content":"↺","fontSize":14,"textColor":"#6B7280"},{"id":"inspector-icon","type":"text","content":"⚙","fontSize":14,"textColor":"#6B7280"}]}]},{"id":"banner","type":"frame","name":"Trashed Note Banner","width":720,"height":32,"fill":"#FEF2F2","layout":"horizontal","crossAxisAlignment":"center","gap":8,"padding":16,"children":[{"id":"trash-icon","type":"text","content":"🗑","fontSize":12,"textColor":"#DC2626"},{"id":"banner-text","type":"text","content":"This note is in the Trash","fontSize":12,"textColor":"#6B7280","width":400},{"id":"restore-btn","type":"frame","layout":"horizontal","gap":4,"crossAxisAlignment":"center","padding":4,"cornerRadius":[4,4,4,4],"children":[{"id":"restore-icon-2","type":"text","content":"↺","fontSize":11,"textColor":"#2563EB"},{"id":"restore-label","type":"text","content":"Restore","fontSize":11,"textColor":"#2563EB"}]},{"id":"delete-btn","type":"frame","layout":"horizontal","gap":4,"crossAxisAlignment":"center","padding":4,"cornerRadius":[4,4,4,4],"children":[{"id":"delete-icon","type":"text","content":"🗑","fontSize":11,"textColor":"#DC2626"},{"id":"delete-label","type":"text","content":"Delete permanently","fontSize":11,"textColor":"#DC2626"}]}]},{"id":"editor-area","type":"frame","name":"Editor (read-only, muted)","width":720,"height":260,"fill":"#FAFAFA","padding":32,"children":[{"id":"h1","type":"text","content":"My Trashed Note","fontSize":24,"fontWeight":"700","textColor":"#9CA3AF"},{"id":"p1","type":"text","content":"This is the content of a trashed note. The editor is non-editable.","fontSize":14,"textColor":"#9CA3AF","y":40},{"id":"p2","type":"text","content":"Navigation and copy still work, but typing and editing are disabled.","fontSize":14,"textColor":"#9CA3AF","y":64}]}]}],"variables":{}}

design/vault-management-remove.pen

@@ -0,0 +1,281 @@
+{
+  "children": [
+    {
+      "type": "frame",
+      "id": "vault_menu_remove",
+      "name": "Vault Menu — Remove from List",
+      "x": 0,
+      "y": 0,
+      "width": 380,
+      "height": 320,
+      "fill": "#F7F6F3",
+      "layout": "vertical",
+      "gap": 16,
+      "padding": [24, 24, 24, 24],
+      "theme": { "Mode": "Light" },
+      "children": [
+        {
+          "type": "text",
+          "id": "vault_menu_title",
+          "content": "Vault Menu — Remove Action",
+          "fill": "#37352F",
+          "fontFamily": "Inter",
+          "fontSize": 14,
+          "fontWeight": "600"
+        },
+        {
+          "type": "frame",
+          "id": "vault_menu_dropdown",
+          "name": "Vault Dropdown",
+          "width": "fill_container",
+          "height": "fit_content",
+          "fill": "#FFFFFF",
+          "cornerRadius": [6, 6, 6, 6],
+          "stroke": "#E9E9E7",
+          "strokeThickness": 1,
+          "layout": "vertical",
+          "padding": [4, 4, 4, 4],
+          "gap": 0,
+          "children": [
+            {
+              "type": "frame",
+              "id": "vault_item_active",
+              "name": "Active Vault Item",
+              "width": "fill_container",
+              "height": 32,
+              "fill": "#EBEBEA",
+              "cornerRadius": [4, 4, 4, 4],
+              "layout": "horizontal",
+              "alignItems": "center",
+              "justifyContent": "space-between",
+              "padding": [4, 8, 4, 8],
+              "children": [
+                {
+                  "type": "frame",
+                  "id": "vault_item_active_left",
+                  "layout": "horizontal",
+                  "alignItems": "center",
+                  "gap": 6,
+                  "children": [
+                    { "type": "text", "id": "vault_check", "content": "✓", "fill": "#37352F", "fontFamily": "Inter", "fontSize": 12 },
+                    { "type": "text", "id": "vault_label_active", "content": "My Vault", "fill": "#37352F", "fontFamily": "Inter", "fontSize": 12 }
+                  ]
+                },
+                {
+                  "type": "frame",
+                  "id": "remove_btn_active",
+                  "name": "Remove Button",
+                  "width": 18,
+                  "height": 18,
+                  "cornerRadius": [3, 3, 3, 3],
+                  "layout": "vertical",
+                  "alignItems": "center",
+                  "justifyContent": "center",
+                  "children": [
+                    { "type": "text", "id": "x_icon_active", "content": "×", "fill": "#787774", "fontFamily": "Inter", "fontSize": 12 }
+                  ]
+                }
+              ]
+            },
+            {
+              "type": "frame",
+              "id": "vault_item_other",
+              "name": "Other Vault Item",
+              "width": "fill_container",
+              "height": 32,
+              "cornerRadius": [4, 4, 4, 4],
+              "layout": "horizontal",
+              "alignItems": "center",
+              "justifyContent": "space-between",
+              "padding": [4, 8, 4, 8],
+              "children": [
+                {
+                  "type": "frame",
+                  "id": "vault_item_other_left",
+                  "layout": "horizontal",
+                  "alignItems": "center",
+                  "gap": 6,
+                  "children": [
+                    { "type": "text", "id": "vault_spacer", "content": " ", "fill": "transparent", "fontFamily": "Inter", "fontSize": 12 },
+                    { "type": "text", "id": "vault_label_other", "content": "Work Vault", "fill": "#787774", "fontFamily": "Inter", "fontSize": 12 }
+                  ]
+                },
+                {
+                  "type": "frame",
+                  "id": "remove_btn_other",
+                  "name": "Remove Button",
+                  "width": 18,
+                  "height": 18,
+                  "cornerRadius": [3, 3, 3, 3],
+                  "layout": "vertical",
+                  "alignItems": "center",
+                  "justifyContent": "center",
+                  "children": [
+                    { "type": "text", "id": "x_icon_other", "content": "×", "fill": "#787774", "fontFamily": "Inter", "fontSize": 12 }
+                  ]
+                }
+              ]
+            },
+            {
+              "type": "frame",
+              "id": "vault_separator",
+              "name": "Separator",
+              "width": "fill_container",
+              "height": 1,
+              "fill": "#E9E9E7"
+            },
+            {
+              "type": "frame",
+              "id": "vault_open_folder",
+              "name": "Open Local Folder",
+              "width": "fill_container",
+              "height": 32,
+              "cornerRadius": [4, 4, 4, 4],
+              "layout": "horizontal",
+              "alignItems": "center",
+              "gap": 6,
+              "padding": [4, 8, 4, 8],
+              "children": [
+                { "type": "text", "id": "folder_icon", "content": "📁", "fontFamily": "Inter", "fontSize": 12 },
+                { "type": "text", "id": "open_folder_label", "content": "Open local folder", "fill": "#787774", "fontFamily": "Inter", "fontSize": 12 }
+              ]
+            }
+          ]
+        },
+        {
+          "type": "text",
+          "id": "vault_menu_note",
+          "content": "× button removes vault from list without deleting files.\nAvailable when 2+ vaults in list.",
+          "fill": "#787774",
+          "fontFamily": "Inter",
+          "fontSize": 11,
+          "width": "fill_container"
+        }
+      ]
+    },
+    {
+      "type": "frame",
+      "id": "cmd_k_vault_commands",
+      "name": "Cmd+K — Vault Commands",
+      "x": 420,
+      "y": 0,
+      "width": 520,
+      "height": 320,
+      "fill": "#F7F6F3",
+      "layout": "vertical",
+      "gap": 16,
+      "padding": [24, 24, 24, 24],
+      "theme": { "Mode": "Light" },
+      "children": [
+        {
+          "type": "text",
+          "id": "cmdk_title",
+          "content": "Command Palette — Vault Commands",
+          "fill": "#37352F",
+          "fontFamily": "Inter",
+          "fontSize": 14,
+          "fontWeight": "600"
+        },
+        {
+          "type": "frame",
+          "id": "cmdk_palette",
+          "name": "Command Palette",
+          "width": "fill_container",
+          "height": "fit_content",
+          "fill": "#FFFFFF",
+          "cornerRadius": [8, 8, 8, 8],
+          "stroke": "#E9E9E7",
+          "strokeThickness": 1,
+          "layout": "vertical",
+          "padding": [0, 0, 0, 0],
+          "gap": 0,
+          "children": [
+            {
+              "type": "frame",
+              "id": "cmdk_search",
+              "name": "Search Input",
+              "width": "fill_container",
+              "height": 44,
+              "layout": "horizontal",
+              "alignItems": "center",
+              "padding": [0, 16, 0, 16],
+              "children": [
+                { "type": "text", "id": "cmdk_search_text", "content": "vault", "fill": "#37352F", "fontFamily": "Inter", "fontSize": 14 }
+              ]
+            },
+            {
+              "type": "frame",
+              "id": "cmdk_separator",
+              "width": "fill_container",
+              "height": 1,
+              "fill": "#E9E9E7"
+            },
+            {
+              "type": "frame",
+              "id": "cmdk_group_header",
+              "name": "Settings Group",
+              "width": "fill_container",
+              "height": 28,
+              "layout": "horizontal",
+              "alignItems": "center",
+              "padding": [0, 12, 0, 12],
+              "children": [
+                { "type": "text", "id": "group_label", "content": "Settings", "fill": "#B4B4B4", "fontFamily": "Inter", "fontSize": 11, "fontWeight": "500" }
+              ]
+            },
+            {
+              "type": "frame",
+              "id": "cmdk_open_vault",
+              "name": "Open Vault Command",
+              "width": "fill_container",
+              "height": 36,
+              "layout": "horizontal",
+              "alignItems": "center",
+              "padding": [0, 12, 0, 12],
+              "children": [
+                { "type": "text", "id": "cmd_open_vault", "content": "Open Vault…", "fill": "#37352F", "fontFamily": "Inter", "fontSize": 13 }
+              ]
+            },
+            {
+              "type": "frame",
+              "id": "cmdk_remove_vault",
+              "name": "Remove Vault Command (highlighted)",
+              "width": "fill_container",
+              "height": 36,
+              "fill": "#E8F4FE",
+              "layout": "horizontal",
+              "alignItems": "center",
+              "padding": [0, 12, 0, 12],
+              "children": [
+                { "type": "text", "id": "cmd_remove_vault", "content": "Remove Vault from List", "fill": "#37352F", "fontFamily": "Inter", "fontSize": 13 }
+              ]
+            },
+            {
+              "type": "frame",
+              "id": "cmdk_restore_gs",
+              "name": "Restore Getting Started Command",
+              "width": "fill_container",
+              "height": 36,
+              "layout": "horizontal",
+              "alignItems": "center",
+              "padding": [0, 12, 0, 12],
+              "children": [
+                { "type": "text", "id": "cmd_restore_gs", "content": "Restore Getting Started Vault", "fill": "#37352F", "fontFamily": "Inter", "fontSize": 13 }
+              ]
+            }
+          ]
+        },
+        {
+          "type": "text",
+          "id": "cmdk_note",
+          "content": "• 'Remove Vault from List' removes active vault (disabled if only 1 vault)\n• 'Restore Getting Started Vault' shown when GS vault is hidden\n• Both accessible via Cmd+K search with 'vault' keyword",
+          "fill": "#787774",
+          "fontFamily": "Inter",
+          "fontSize": 11,
+          "width": "fill_container"
+        }
+      ]
+    }
+  ],
+  "variables": {}
+}

e2e/core-flows.spec.ts

@@ -231,3 +231,30 @@ test('full create note flow', async ({ page }) => {
 
   await page.screenshot({ path: 'test-results/core-create-note.png', fullPage: true })
 })
+
+// --- Flow 8: Wiki-link navigation ---
+
+test('clicking a wikilink opens the target note in a new tab', async ({ page }) => {
+  // Open "Manage Sponsorships" which contains [[Matteo Cellini]] wikilink
+  await page.locator('.note-list__item', { hasText: 'Manage Sponsorships' }).click()
+  await page.waitForTimeout(300)
+
+  // Verify we opened the right note
+  await expect(page.locator('.editor__tab--active')).toHaveText(/Manage Sponsorships/)
+
+  // Click the wikilink — use mouse.click to fire real mousedown
+  const wikilink = page.locator('.cm-wikilink', { hasText: 'Matteo Cellini' })
+  await expect(wikilink).toBeVisible()
+  const box = await wikilink.boundingBox()
+  expect(box).not.toBeNull()
+  await page.mouse.click(box!.x + box!.width / 2, box!.y + box!.height / 2)
+  await page.waitForTimeout(300)
+
+  // New tab should open with the target note active
+  await expect(page.locator('.editor__tab--active')).toHaveText(/Matteo Cellini/)
+
+  // Editor should show the target note's content
+  await expect(page.locator('.cm-content')).toContainText('Matteo Cellini')
+
+  await page.screenshot({ path: 'test-results/core-wikilink-nav.png', fullPage: true })
+})

eslint.config.js

@@ -6,7 +6,7 @@ import tseslint from 'typescript-eslint'
 import { defineConfig, globalIgnores } from 'eslint/config'
 
 export default defineConfig([
-  globalIgnores(['dist', 'coverage']),
+  globalIgnores(['dist', 'coverage', 'src-tauri/resources/', 'src-tauri/target/', 'tools/']),
   {
     files: ['**/*.{ts,tsx}'],
     extends: [

mcp-server/index.js

@@ -1,21 +1,15 @@
 #!/usr/bin/env node
 /**
- * Laputa MCP Server — provides vault operation tools for AI assistants.
+ * Laputa MCP Server — lightweight vault tools for AI agents.
  *
- * Usage:
- *   VAULT_PATH=/path/to/vault node index.js
+ * The agent has full shell access (bash, read, write, edit).
+ * These MCP tools provide Laputa-specific capabilities that
+ * native tools cannot replace:
  *
- * Tools:
- *   - open_note / read_note: Read a note by path
- *   - create_note: Create a new note with title and optional frontmatter
- *   - search_notes: Search notes by title or content
- *   - append_to_note: Append text to an existing note
- *   - edit_note_frontmatter: Merge a patch into a note's YAML frontmatter
- *   - delete_note: Delete a note file
- *   - link_notes: Add a title to an array property in a note's frontmatter
- *   - list_notes: List all notes, optionally filtered by type
- *   - vault_context: Get vault types and recent notes
- *   - ui_open_note / ui_open_tab / ui_highlight / ui_set_filter: UI actions
+ *   - search_notes: full-text search across vault notes
+ *   - get_vault_context: vault structure overview (types, note count, folders)
+ *   - get_note: parsed frontmatter + content (convenience over raw cat)
+ *   - open_note: signal Laputa UI to open a note as a tab
  */
 import { Server } from '@modelcontextprotocol/sdk/server/index.js'
 import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js'
@@ -23,64 +17,47 @@ import {
   CallToolRequestSchema,
   ListToolsRequestSchema,
 } from '@modelcontextprotocol/sdk/types.js'
-import {
-  readNote, createNote, searchNotes, appendToNote,
-  editNoteFrontmatter, deleteNote, linkNotes, listNotes, vaultContext,
-} from './vault.js'
-import { startUiBridge } from './ws-bridge.js'
+import WebSocket from 'ws'
+import { searchNotes, getNote, vaultContext } from './vault.js'
 
 const VAULT_PATH = process.env.VAULT_PATH || process.env.HOME + '/Laputa'
 const WS_UI_PORT = parseInt(process.env.WS_UI_PORT || '9711', 10)
+const WS_UI_URL = `ws://localhost:${WS_UI_PORT}`
 
-// Start the UI bridge so stdio-based MCP tools can broadcast UI actions
-const uiBridge = startUiBridge(WS_UI_PORT)
+// Connect as a WebSocket CLIENT to the UI bridge (run by ws-bridge.js).
+// The bridge relays messages to all other clients (the React frontend).
+let uiSocket = null
+const RECONNECT_INTERVAL_MS = 3000
+
+function connectUiBridge() {
+  try {
+    const ws = new WebSocket(WS_UI_URL)
+    ws.on('open', () => {
+      uiSocket = ws
+      console.error(`[mcp] Connected to UI bridge at ${WS_UI_URL}`)
+    })
+    ws.on('close', () => {
+      uiSocket = null
+      setTimeout(connectUiBridge, RECONNECT_INTERVAL_MS)
+    })
+    ws.on('error', () => {
+      // Silent — bridge may not be running yet, will retry
+    })
+  } catch {
+    setTimeout(connectUiBridge, RECONNECT_INTERVAL_MS)
+  }
+}
+connectUiBridge()
 
 function broadcastUiAction(action, payload) {
-  const msg = JSON.stringify({ type: 'ui_action', action, ...payload })
-  for (const client of uiBridge.clients) {
-    if (client.readyState === 1) client.send(msg)
-  }
+  if (!uiSocket || uiSocket.readyState !== WebSocket.OPEN) return
+  uiSocket.send(JSON.stringify({ type: 'ui_action', action, ...payload }))
 }
 
 const TOOLS = [
-  {
-    name: 'open_note',
-    description: 'Open and read a note from the vault by its relative path',
-    inputSchema: {
-      type: 'object',
-      properties: {
-        path: { type: 'string', description: 'Relative path to the note (e.g. "project/my-project.md")' },
-      },
-      required: ['path'],
-    },
-  },
-  {
-    name: 'read_note',
-    description: 'Read the full content of a note',
-    inputSchema: {
-      type: 'object',
-      properties: {
-        path: { type: 'string', description: 'Relative path to the note' },
-      },
-      required: ['path'],
-    },
-  },
-  {
-    name: 'create_note',
-    description: 'Create a new note in the vault with a title and optional frontmatter',
-    inputSchema: {
-      type: 'object',
-      properties: {
-        path: { type: 'string', description: 'Relative path for the new note (e.g. "note/my-idea.md")' },
-        title: { type: 'string', description: 'Title of the note' },
-        is_a: { type: 'string', description: 'Entity type (Project, Note, Experiment, etc.)' },
-      },
-      required: ['path', 'title'],
-    },
-  },
   {
     name: 'search_notes',
-    description: 'Search notes in the vault by title or content',
+    description: 'Full-text search across vault notes by title or content. Returns matching paths, titles, and snippets.',
     inputSchema: {
       type: 'object',
       properties: {
@@ -91,72 +68,24 @@ const TOOLS = [
     },
   },
   {
-    name: 'append_to_note',
-    description: 'Append text to the end of an existing note',
-    inputSchema: {
-      type: 'object',
-      properties: {
-        path: { type: 'string', description: 'Relative path to the note' },
-        text: { type: 'string', description: 'Text to append' },
-      },
-      required: ['path', 'text'],
-    },
-  },
-  {
-    name: 'edit_note_frontmatter',
-    description: 'Merge a patch object into a note\'s YAML frontmatter',
-    inputSchema: {
-      type: 'object',
-      properties: {
-        path: { type: 'string', description: 'Relative path to the note' },
-        patch: { type: 'object', description: 'Key-value pairs to merge into frontmatter' },
-      },
-      required: ['path', 'patch'],
-    },
-  },
-  {
-    name: 'delete_note',
-    description: 'Delete a note file from the vault',
-    inputSchema: {
-      type: 'object',
-      properties: {
-        path: { type: 'string', description: 'Relative path to the note to delete' },
-      },
-      required: ['path'],
-    },
-  },
-  {
-    name: 'link_notes',
-    description: 'Add a target title to an array property in a note\'s frontmatter (e.g. add "Marco" to people: [])',
-    inputSchema: {
-      type: 'object',
-      properties: {
-        source_path: { type: 'string', description: 'Relative path to the source note' },
-        property: { type: 'string', description: 'Frontmatter property name (e.g. "people", "tags")' },
-        target_title: { type: 'string', description: 'Title to add to the array' },
-      },
-      required: ['source_path', 'property', 'target_title'],
-    },
-  },
-  {
-    name: 'list_notes',
-    description: 'List all notes in the vault, optionally filtered by type frontmatter field',
-    inputSchema: {
-      type: 'object',
-      properties: {
-        type_filter: { type: 'string', description: 'Filter by type frontmatter value' },
-        sort: { type: 'string', enum: ['title', 'mtime'], description: 'Sort order (default: title)' },
-      },
-    },
-  },
-  {
-    name: 'vault_context',
-    description: 'Get vault context: unique entity types and 20 most recently modified notes',
+    name: 'get_vault_context',
+    description: 'Get vault orientation: entity types, total note count, top-level folders, and 20 most recently modified notes.',
     inputSchema: { type: 'object', properties: {} },
   },
   {
-    name: 'ui_open_note',
-    description: 'Open a note in the Laputa UI editor',
+    name: 'get_note',
+    description: 'Read a note with parsed YAML frontmatter and markdown content. Returns {path, frontmatter, content}.',
+    inputSchema: {
+      type: 'object',
+      properties: {
+        path: { type: 'string', description: 'Relative path to the note (e.g. "project/my-project.md")' },
+      },
+      required: ['path'],
+    },
+  },
+  {
+    name: 'open_note',
+    description: 'Open a note in the Laputa UI as a new tab. Use after creating or editing a note so the user can see it.',
     inputSchema: {
       type: 'object',
       properties: {
@@ -165,69 +94,13 @@ const TOOLS = [
       required: ['path'],
     },
   },
-  {
-    name: 'ui_open_tab',
-    description: 'Open a note in a new tab in the Laputa UI',
-    inputSchema: {
-      type: 'object',
-      properties: {
-        path: { type: 'string', description: 'Relative path to the note' },
-      },
-      required: ['path'],
-    },
-  },
-  {
-    name: 'ui_highlight',
-    description: 'Highlight a UI element in the Laputa interface',
-    inputSchema: {
-      type: 'object',
-      properties: {
-        element: { type: 'string', enum: ['editor', 'tab', 'properties', 'notelist'], description: 'UI element to highlight' },
-        path: { type: 'string', description: 'Relative path to the note (optional)' },
-      },
-      required: ['element'],
-    },
-  },
-  {
-    name: 'ui_set_filter',
-    description: 'Set the sidebar filter to show notes of a specific type',
-    inputSchema: {
-      type: 'object',
-      properties: {
-        type: { type: 'string', description: 'Type to filter by' },
-      },
-      required: ['type'],
-    },
-  },
 ]
 
 const TOOL_HANDLERS = {
-  open_note: handleReadNote,
-  read_note: handleReadNote,
-  create_note: handleCreateNote,
   search_notes: handleSearchNotes,
-  append_to_note: handleAppendToNote,
-  edit_note_frontmatter: handleEditFrontmatter,
-  delete_note: handleDeleteNote,
-  link_notes: handleLinkNotes,
-  list_notes: handleListNotes,
-  vault_context: handleVaultContext,
-  ui_open_note: handleUiOpenNote,
-  ui_open_tab: handleUiOpenTab,
-  ui_highlight: handleUiHighlight,
-  ui_set_filter: handleUiSetFilter,
-}
-
-async function handleReadNote(args) {
-  const content = await readNote(VAULT_PATH, args.path)
-  return { content: [{ type: 'text', text: content }] }
-}
-
-async function handleCreateNote(args) {
-  const frontmatter = {}
-  if (args.is_a) frontmatter.is_a = args.is_a
-  const absPath = await createNote(VAULT_PATH, args.path, args.title, frontmatter)
-  return { content: [{ type: 'text', text: `Created note at ${absPath}` }] }
+  get_vault_context: handleVaultContext,
+  get_note: handleGetNote,
+  open_note: handleOpenNote,
 }
 
 async function handleSearchNotes(args) {
@@ -238,63 +111,25 @@ async function handleSearchNotes(args) {
   return { content: [{ type: 'text', text }] }
 }
 
-async function handleAppendToNote(args) {
-  await appendToNote(VAULT_PATH, args.path, args.text)
-  return { content: [{ type: 'text', text: `Appended text to ${args.path}` }] }
-}
-
-async function handleEditFrontmatter(args) {
-  const updated = await editNoteFrontmatter(VAULT_PATH, args.path, args.patch)
-  return { content: [{ type: 'text', text: JSON.stringify(updated) }] }
-}
-
-async function handleDeleteNote(args) {
-  await deleteNote(VAULT_PATH, args.path)
-  return { content: [{ type: 'text', text: `Deleted ${args.path}` }] }
-}
-
-async function handleLinkNotes(args) {
-  const arr = await linkNotes(VAULT_PATH, args.source_path, args.property, args.target_title)
-  return { content: [{ type: 'text', text: `${args.property}: [${arr.join(', ')}]` }] }
-}
-
-async function handleListNotes(args) {
-  const notes = await listNotes(VAULT_PATH, args.type_filter, args.sort)
-  const text = notes.length === 0
-    ? 'No notes found.'
-    : notes.map(n => `${n.title} (${n.path})${n.type ? ` [${n.type}]` : ''}`).join('\n')
-  return { content: [{ type: 'text', text }] }
-}
-
 async function handleVaultContext() {
   const ctx = await vaultContext(VAULT_PATH)
   return { content: [{ type: 'text', text: JSON.stringify(ctx, null, 2) }] }
 }
 
-function handleUiOpenNote(args) {
-  broadcastUiAction('open_note', { path: args.path })
-  return { content: [{ type: 'text', text: `Opening ${args.path} in UI` }] }
+async function handleGetNote(args) {
+  const note = await getNote(VAULT_PATH, args.path)
+  return { content: [{ type: 'text', text: JSON.stringify(note, null, 2) }] }
 }
 
-function handleUiOpenTab(args) {
+function handleOpenNote(args) {
   broadcastUiAction('open_tab', { path: args.path })
-  return { content: [{ type: 'text', text: `Opening tab for ${args.path}` }] }
-}
-
-function handleUiHighlight(args) {
-  broadcastUiAction('highlight', { element: args.element, path: args.path })
-  return { content: [{ type: 'text', text: `Highlighting ${args.element}` }] }
-}
-
-function handleUiSetFilter(args) {
-  broadcastUiAction('set_filter', { type: args.type })
-  return { content: [{ type: 'text', text: `Filter set to ${args.type}` }] }
+  return { content: [{ type: 'text', text: `Opening ${args.path} in Laputa` }] }
 }
 
 // --- Server setup ---
 
 const server = new Server(
-  { name: 'laputa-mcp-server', version: '0.1.0' },
+  { name: 'laputa-mcp-server', version: '0.2.0' },
   { capabilities: { tools: {} } },
 )
 

mcp-server/vault.js

@@ -1,5 +1,6 @@
 /**
- * Vault operations — file I/O for Laputa markdown vault.
+ * Vault operations — read-only helpers for Laputa markdown vault.
+ * Write operations are handled by the agent's native bash/write/edit tools.
  */
 import fs from 'node:fs/promises'
 import path from 'node:path'
@@ -26,36 +27,20 @@ export async function findMarkdownFiles(dir) {
 }
 
 /**
- * Read a note's content by path (absolute or relative to vault).
+ * Read a note with parsed frontmatter and content.
  * @param {string} vaultPath
  * @param {string} notePath
- * @returns {Promise<string>}
+ * @returns {Promise<{path: string, frontmatter: Record<string, unknown>, content: string}>}
  */
-export async function readNote(vaultPath, notePath) {
+export async function getNote(vaultPath, notePath) {
   const absPath = path.isAbsolute(notePath) ? notePath : path.join(vaultPath, notePath)
-  return fs.readFile(absPath, 'utf-8')
-}
-
-/**
- * Create a new note with optional frontmatter.
- * @param {string} vaultPath
- * @param {string} relativePath
- * @param {string} title
- * @param {Record<string, string>} [frontmatter]
- * @returns {Promise<string>} The absolute path of the created file.
- */
-export async function createNote(vaultPath, relativePath, title, frontmatter = {}) {
-  const absPath = path.join(vaultPath, relativePath)
-  await fs.mkdir(path.dirname(absPath), { recursive: true })
-
-  const fmEntries = { title, ...frontmatter }
-  const fmLines = Object.entries(fmEntries)
-    .map(([k, v]) => `${k}: ${v}`)
-    .join('\n')
-
-  const content = `---\n${fmLines}\n---\n\n# ${title}\n\n`
-  await fs.writeFile(absPath, content, 'utf-8')
-  return absPath
+  const raw = await fs.readFile(absPath, 'utf-8')
+  const parsed = matter(raw)
+  return {
+    path: path.relative(vaultPath, absPath),
+    frontmatter: parsed.data,
+    content: parsed.content.trim(),
+  }
 }
 
 /**
@@ -92,110 +77,14 @@ export async function searchNotes(vaultPath, query, limit = 10) {
 }
 
 /**
- * Append text to the end of a note.
+ * Get vault context: unique types, note count, top-level folders, and 20 most recent notes.
  * @param {string} vaultPath
- * @param {string} notePath
- * @param {string} text
- * @returns {Promise<void>}
- */
-export async function appendToNote(vaultPath, notePath, text) {
-  const absPath = path.isAbsolute(notePath) ? notePath : path.join(vaultPath, notePath)
-  const current = await fs.readFile(absPath, 'utf-8')
-  const separator = current.endsWith('\n') ? '\n' : '\n\n'
-  await fs.writeFile(absPath, current + separator + text + '\n', 'utf-8')
-}
-
-/**
- * Merge a patch object into a note's YAML frontmatter.
- * @param {string} vaultPath
- * @param {string} notePath
- * @param {Record<string, unknown>} patch
- * @returns {Promise<Record<string, unknown>>} The updated frontmatter.
- */
-export async function editNoteFrontmatter(vaultPath, notePath, patch) {
-  const absPath = path.isAbsolute(notePath) ? notePath : path.join(vaultPath, notePath)
-  const raw = await fs.readFile(absPath, 'utf-8')
-  const parsed = matter(raw)
-  Object.assign(parsed.data, patch)
-  const updated = matter.stringify(parsed.content, parsed.data)
-  await fs.writeFile(absPath, updated, 'utf-8')
-  return parsed.data
-}
-
-/**
- * Delete a note file.
- * @param {string} vaultPath
- * @param {string} notePath
- * @returns {Promise<void>}
- */
-export async function deleteNote(vaultPath, notePath) {
-  const absPath = path.isAbsolute(notePath) ? notePath : path.join(vaultPath, notePath)
-  await fs.unlink(absPath)
-}
-
-/**
- * Add a target title to an array property in a note's frontmatter.
- * Creates the property as an array if it doesn't exist.
- * @param {string} vaultPath
- * @param {string} sourcePath
- * @param {string} property
- * @param {string} targetTitle
- * @returns {Promise<string[]>} The updated array.
- */
-export async function linkNotes(vaultPath, sourcePath, property, targetTitle) {
-  const absPath = path.isAbsolute(sourcePath) ? sourcePath : path.join(vaultPath, sourcePath)
-  const raw = await fs.readFile(absPath, 'utf-8')
-  const parsed = matter(raw)
-  const current = Array.isArray(parsed.data[property]) ? parsed.data[property] : []
-  if (!current.includes(targetTitle)) {
-    current.push(targetTitle)
-  }
-  parsed.data[property] = current
-  const updated = matter.stringify(parsed.content, parsed.data)
-  await fs.writeFile(absPath, updated, 'utf-8')
-  return current
-}
-
-/**
- * List all notes in the vault, optionally filtered by type.
- * @param {string} vaultPath
- * @param {string} [typeFilter]
- * @param {string} [sort] - 'title' or 'mtime' (default: 'title')
- * @returns {Promise<Array<{path: string, title: string, type: string|null}>>}
- */
-export async function listNotes(vaultPath, typeFilter, sort = 'title') {
-  const files = await findMarkdownFiles(vaultPath)
-  const notes = await Promise.all(files.map(async (filePath) => {
-    const raw = await fs.readFile(filePath, 'utf-8')
-    const parsed = matter(raw)
-    const relativePath = path.relative(vaultPath, filePath)
-    const title = parsed.data.title || extractTitle(raw, path.basename(filePath, '.md'))
-    const type = parsed.data.type || parsed.data.is_a || null
-    const stat = sort === 'mtime' ? await fs.stat(filePath) : null
-    return { path: relativePath, title, type, mtime: stat?.mtimeMs ?? 0 }
-  }))
-
-  const filtered = typeFilter
-    ? notes.filter(n => n.type === typeFilter)
-    : notes
-
-  if (sort === 'mtime') {
-    filtered.sort((a, b) => b.mtime - a.mtime)
-  } else {
-    filtered.sort((a, b) => a.title.localeCompare(b.title))
-  }
-
-  return filtered.map(({ mtime: _mtime, ...rest }) => rest)
-}
-
-/**
- * Get vault context: unique types and 20 most recent notes.
- * @param {string} vaultPath
- * @returns {Promise<{types: string[], recentNotes: Array<{path: string, title: string, type: string|null}>, vaultPath: string}>}
+ * @returns {Promise<{types: string[], noteCount: number, folders: string[], recentNotes: Array<{path: string, title: string, type: string|null}>, vaultPath: string}>}
  */
 export async function vaultContext(vaultPath) {
   const files = await findMarkdownFiles(vaultPath)
   const typesSet = new Set()
+  const foldersSet = new Set()
   const notesWithMtime = []
 
   for (const filePath of files) {
@@ -203,9 +92,12 @@ export async function vaultContext(vaultPath) {
     const parsed = matter(raw)
     const type = parsed.data.type || parsed.data.is_a || null
     if (type) typesSet.add(type)
+    const rel = path.relative(vaultPath, filePath)
+    const topFolder = rel.split(path.sep)[0]
+    if (topFolder !== rel) foldersSet.add(topFolder + '/')
     const stat = await fs.stat(filePath)
     notesWithMtime.push({
-      path: path.relative(vaultPath, filePath),
+      path: rel,
       title: parsed.data.title || extractTitle(raw, path.basename(filePath, '.md')),
       type,
       mtime: stat.mtimeMs,
@@ -215,7 +107,13 @@ export async function vaultContext(vaultPath) {
   notesWithMtime.sort((a, b) => b.mtime - a.mtime)
   const recentNotes = notesWithMtime.slice(0, 20).map(({ mtime: _mtime, ...rest }) => rest)
 
-  return { types: [...typesSet].sort(), recentNotes, vaultPath }
+  return {
+    types: [...typesSet].sort(),
+    noteCount: files.length,
+    folders: [...foldersSet].sort(),
+    recentNotes,
+    vaultPath,
+  }
 }
 
 // --- Helpers ---

mcp-server/ws-bridge.js

@@ -19,10 +19,10 @@
  * Protocol (UI bridge):
  *   Server broadcasts: { "type": "ui_action", "action": "open_note", "path": "..." }
  */
+import { createServer } from 'node:http'
 import { WebSocketServer } from 'ws'
 import {
-  readNote, createNote, searchNotes, appendToNote,
-  editNoteFrontmatter, deleteNote, linkNotes, listNotes, vaultContext,
+  getNote, searchNotes, vaultContext,
 } from './vault.js'
 
 const VAULT_PATH = process.env.VAULT_PATH || process.env.HOME + '/Laputa'
@@ -40,27 +40,16 @@ function broadcastUiAction(action, payload) {
   }
 }
 
-function buildFrontmatter(args) {
-  const fm = {}
-  if (args.is_a) fm.is_a = args.is_a
-  return fm
-}
 
 const TOOL_HANDLERS = {
-  open_note: (args) => readNote(VAULT_PATH, args.path).then(text => ({ content: text })),
-  read_note: (args) => readNote(VAULT_PATH, args.path).then(text => ({ content: text })),
-  create_note: (args) => createNote(VAULT_PATH, args.path, args.title, buildFrontmatter(args)),
+  open_note: (args) => getNote(VAULT_PATH, args.path).then(note => ({ content: note.content, frontmatter: note.frontmatter })),
+  read_note: (args) => getNote(VAULT_PATH, args.path).then(note => ({ content: note.content, frontmatter: note.frontmatter })),
   search_notes: (args) => searchNotes(VAULT_PATH, args.query, args.limit),
-  append_to_note: (args) => appendToNote(VAULT_PATH, args.path, args.text).then(() => ({ ok: true })),
-  edit_note_frontmatter: (args) => editNoteFrontmatter(VAULT_PATH, args.path, args.patch),
-  delete_note: (args) => deleteNote(VAULT_PATH, args.path).then(() => ({ ok: true })),
-  link_notes: (args) => linkNotes(VAULT_PATH, args.source_path, args.property, args.target_title),
-  list_notes: (args) => listNotes(VAULT_PATH, args.type_filter, args.sort),
   vault_context: () => vaultContext(VAULT_PATH),
   ui_open_note: (args) => { broadcastUiAction('open_note', { path: args.path }); return { ok: true } },
   ui_open_tab: (args) => { broadcastUiAction('open_tab', { path: args.path }); return { ok: true } },
   ui_highlight: (args) => { broadcastUiAction('highlight', { element: args.element, path: args.path }); return { ok: true } },
-  ui_set_filter: (args) => { broadcastUiAction('set_filter', { type: args.type }); return { ok: true } },
+  ui_set_filter: (args) => { broadcastUiAction('set_filter', { filterType: args.type }); return { ok: true } },
 }
 
 async function handleMessage(data) {
@@ -80,15 +69,41 @@ async function handleMessage(data) {
   }
 }
 
+/**
+ * Attempt to start the UI bridge WebSocket server.
+ * Returns a Promise that resolves to the WebSocketServer or null if the port
+ * is unavailable (e.g. another Laputa instance owns it).
+ */
 export function startUiBridge(port = WS_UI_PORT) {
-  uiBridge = new WebSocketServer({ port })
+  return new Promise((resolve) => {
+    const httpServer = createServer()
 
-  uiBridge.on('connection', () => {
-    console.error(`[ws-bridge] UI client connected on port ${port}`)
+    httpServer.on('error', (err) => {
+      if (err.code === 'EADDRINUSE') {
+        console.error(`[ws-bridge] UI bridge port ${port} already in use, disabling bridge`)
+      } else {
+        console.error(`[ws-bridge] UI bridge error: ${err.message}`)
+      }
+      resolve(null)
+    })
+
+    httpServer.listen(port, () => {
+      const wss = new WebSocketServer({ server: httpServer })
+      wss.on('connection', (ws) => {
+        console.error(`[ws-bridge] UI client connected on port ${port}`)
+        // Relay: when a client sends a message, broadcast to all OTHER clients.
+        // This allows the MCP stdio server (connected as a client) to reach the frontend.
+        ws.on('message', (raw) => {
+          for (const client of wss.clients) {
+            if (client !== ws && client.readyState === 1) client.send(raw.toString())
+          }
+        })
+      })
+      uiBridge = wss
+      console.error(`[ws-bridge] UI bridge listening on ws://localhost:${port}`)
+      resolve(wss)
+    })
   })
-
-  console.error(`[ws-bridge] UI bridge listening on ws://localhost:${port}`)
-  return uiBridge
 }
 
 export function startBridge(port = WS_PORT) {
@@ -116,6 +131,5 @@ export function startBridge(port = WS_PORT) {
 // Run directly if invoked as main module
 const isMain = process.argv[1]?.endsWith('ws-bridge.js')
 if (isMain) {
-  startUiBridge()
-  startBridge()
+  startUiBridge().then(() => startBridge())
 }

package.json

@@ -6,12 +6,14 @@
   "scripts": {
     "dev": "vite",
     "build": "tsc -b && vite build",
+    "bundle-mcp": "node scripts/bundle-mcp-server.mjs",
     "lint": "eslint .",
     "preview": "vite preview",
     "tauri": "tauri",
     "test": "vitest run",
     "test:watch": "vitest",
     "test:e2e": "playwright test",
+    "playwright:smoke": "playwright test tests/smoke/",
     "test:coverage": "vitest run --coverage",
     "prepare": "husky"
   },
@@ -20,6 +22,12 @@
     "@blocknote/core": "^0.46.2",
     "@blocknote/mantine": "^0.46.2",
     "@blocknote/react": "^0.46.2",
+    "@codemirror/commands": "^6.10.2",
+    "@codemirror/lang-markdown": "^6.5.0",
+    "@codemirror/lang-yaml": "^6.1.2",
+    "@codemirror/language": "^6.12.2",
+    "@codemirror/state": "^6.5.4",
+    "@codemirror/view": "^6.39.16",
     "@dnd-kit/core": "^6.3.1",
     "@dnd-kit/sortable": "^10.0.0",
     "@dnd-kit/utilities": "^3.2.2",
@@ -48,7 +56,10 @@
     "react": "^19.2.0",
     "react-day-picker": "^9.13.2",
     "react-dom": "^19.2.0",
+    "react-markdown": "^10.1.0",
     "react-virtuoso": "^4.18.1",
+    "rehype-highlight": "^7.0.2",
+    "remark-gfm": "^4.0.1",
     "tailwind-merge": "^3.4.1",
     "tailwindcss": "^4.1.18",
     "tw-animate-css": "^1.4.0"
@@ -64,6 +75,7 @@
     "@types/react-dom": "^19.2.3",
     "@vitejs/plugin-react": "^5.1.1",
     "@vitest/coverage-v8": "^4.0.18",
+    "esbuild": "^0.27.3",
     "eslint": "^9.39.1",
     "eslint-plugin-react-hooks": "^7.0.1",
     "eslint-plugin-react-refresh": "^0.4.24",

playwright.config.ts

@@ -1,15 +1,18 @@
 import { defineConfig } from '@playwright/test'
 
 export default defineConfig({
-  testDir: './e2e',
-  timeout: 30000,
+  testDir: './tests/smoke',
+  timeout: 15_000,
+  retries: 0,
   workers: 1,
   use: {
-    baseURL: 'http://localhost:5173',
+    baseURL: process.env.BASE_URL || 'http://localhost:5201',
+    headless: true,
   },
+  projects: [{ name: 'chromium', use: { browserName: 'chromium' } }],
   webServer: {
-    command: 'pnpm dev',
-    port: 5173,
+    command: `pnpm dev --port ${process.env.BASE_URL?.match(/:(\d+)/)?.[1] || '5201'}`,
+    url: process.env.BASE_URL || 'http://localhost:5201',
     reuseExistingServer: true,
   },
 })

pnpm-workspace.yaml

@@ -1,2 +1,5 @@
+packages:
+  - mcp-server
+
 ignoredBuiltDependencies:
   - esbuild

scripts/bundle-mcp-server.mjs

@@ -0,0 +1,45 @@
+/**
+ * Bundle the mcp-server Node.js files into self-contained CJS bundles
+ * that can be shipped as Tauri resources inside the .app bundle.
+ *
+ * Output: src-tauri/resources/mcp-server/{index.js,ws-bridge.js}
+ */
+import { build } from 'esbuild'
+import { fileURLToPath } from 'url'
+import { dirname, join } from 'path'
+import { mkdirSync, writeFileSync } from 'fs'
+
+const __dirname = dirname(fileURLToPath(import.meta.url))
+const ROOT = join(__dirname, '..')
+const SRC = join(ROOT, 'mcp-server')
+const OUT = join(ROOT, 'src-tauri', 'resources', 'mcp-server')
+
+mkdirSync(OUT, { recursive: true })
+
+// Tell Node.js that this directory contains CJS bundles, even if the
+// root package.json declares "type": "module".
+writeFileSync(join(OUT, 'package.json'), JSON.stringify({ type: 'commonjs' }))
+
+const shared = {
+  platform: 'node',
+  bundle: true,
+  format: 'cjs',
+  target: 'node18',
+  // Mark optional native bindings as external — ws works fine without them
+  external: ['bufferutil', 'utf-8-validate'],
+  logLevel: 'warning',
+}
+
+await build({
+  ...shared,
+  entryPoints: [join(SRC, 'index.js')],
+  outfile: join(OUT, 'index.js'),
+})
+
+await build({
+  ...shared,
+  entryPoints: [join(SRC, 'ws-bridge.js')],
+  outfile: join(OUT, 'ws-bridge.js'),
+})
+
+console.log('mcp-server bundled → src-tauri/resources/mcp-server/')

scripts/bundle-qmd.sh

@@ -0,0 +1,155 @@
+#!/usr/bin/env bash
+# Bundle qmd into a self-contained directory for Tauri resource embedding.
+#
+# Output: src-tauri/resources/qmd/
+#   qmd                                  — compiled standalone binary
+#   node_modules/sqlite-vec/             — JS shim for sqlite-vec
+#   node_modules/sqlite-vec-darwin-arm64/ — native .dylib (arm64)
+#   node_modules/sqlite-vec-darwin-x64/  — native .dylib (x64)
+#   node_modules/node-llama-cpp/         — stub (keyword search only)
+set -euo pipefail
+
+SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
+ROOT="$SCRIPT_DIR/.."
+OUT="$ROOT/src-tauri/resources/qmd"
+
+# ---------- locate tools ----------
+find_bun() {
+  for c in \
+    "$HOME/.bun/bin/bun" \
+    "/opt/homebrew/bin/bun" \
+    "/usr/local/bin/bun"; do
+    [[ -x "$c" ]] && { echo "$c"; return 0; }
+  done
+  command -v bun 2>/dev/null && return 0
+  return 1
+}
+
+BUN=$(find_bun) || { echo "ERROR: bun not found — install from https://bun.sh" >&2; exit 1; }
+echo "Using bun: $BUN"
+
+# ---------- locate qmd source ----------
+# Prefer bundled source in tools/qmd/ (works in CI and dev),
+# then fall back to globally installed qmd on dev machines.
+QMD_SRC=""
+for c in \
+  "$ROOT/tools/qmd" \
+  "$HOME/.bun/install/global/node_modules/qmd" \
+  "/opt/homebrew/lib/node_modules/qmd" \
+  "/usr/local/lib/node_modules/qmd"; do
+  [[ -f "$c/src/qmd.ts" ]] && { QMD_SRC="$c"; break; }
+done
+
+[[ -n "$QMD_SRC" ]] || { echo "ERROR: qmd source not found. tools/qmd/ is missing or incomplete." >&2; exit 1; }
+echo "Using qmd source: $QMD_SRC"
+
+# Install qmd dependencies if needed (for CI where node_modules don't exist yet)
+if [[ ! -d "$QMD_SRC/node_modules" ]]; then
+  echo "Installing qmd dependencies..."
+  (cd "$QMD_SRC" && "$BUN" install --frozen-lockfile)
+fi
+
+# ---------- compile ----------
+echo "Compiling qmd with bun build --compile..."
+mkdir -p "$OUT"
+
+(cd "$QMD_SRC" && "$BUN" build --compile \
+  "src/qmd.ts" \
+  --outfile "$OUT/qmd" \
+  --external node-llama-cpp \
+  --external sqlite-vec \
+  --external sqlite-vec-darwin-arm64 \
+  --external sqlite-vec-darwin-x64)
+
+chmod +x "$OUT/qmd"
+
+# ---------- bundle sqlite-vec ----------
+echo "Bundling sqlite-vec native extensions..."
+
+# Find sqlite-vec packages — prefer node_modules in QMD_SRC (after bun install),
+# fall back to bun global cache for dev machines.
+NM="$QMD_SRC/node_modules"
+
+find_pkg() {
+  local pkg="$1"
+  # Check node_modules from bun install in QMD_SRC first
+  if [[ -d "$NM/$pkg" ]]; then
+    echo "$NM/$pkg"; return 0
+  fi
+  # Fall back to bun global cache
+  local cache_dir
+  cache_dir=$(find "$HOME/.bun/install/cache" -maxdepth 1 -name "${pkg}@*" -type d 2>/dev/null | head -1)
+  [[ -n "$cache_dir" ]] && echo "$cache_dir" && return 0
+  return 1
+}
+
+# sqlite-vec JS shim
+SQLVEC_DIR=$(find_pkg "sqlite-vec") || { echo "ERROR: sqlite-vec not found" >&2; exit 1; }
+mkdir -p "$OUT/node_modules/sqlite-vec"
+cp "$SQLVEC_DIR/index.mjs" "$OUT/node_modules/sqlite-vec/index.mjs"
+cp "$SQLVEC_DIR/package.json" "$OUT/node_modules/sqlite-vec/package.json"
+[[ -f "$SQLVEC_DIR/index.cjs" ]] && cp "$SQLVEC_DIR/index.cjs" "$OUT/node_modules/sqlite-vec/index.cjs"
+
+# sqlite-vec-darwin-arm64
+ARM64_DIR=$(find_pkg "sqlite-vec-darwin-arm64") || true
+if [[ -n "$ARM64_DIR" ]]; then
+  mkdir -p "$OUT/node_modules/sqlite-vec-darwin-arm64"
+  cp "$ARM64_DIR/vec0.dylib" "$OUT/node_modules/sqlite-vec-darwin-arm64/vec0.dylib"
+  cp "$ARM64_DIR/package.json" "$OUT/node_modules/sqlite-vec-darwin-arm64/package.json"
+  echo "  ✓ arm64 dylib"
+fi
+
+# sqlite-vec-darwin-x64
+X64_DIR=$(find_pkg "sqlite-vec-darwin-x64") || true
+if [[ -n "$X64_DIR" ]]; then
+  mkdir -p "$OUT/node_modules/sqlite-vec-darwin-x64"
+  cp "$X64_DIR/vec0.dylib" "$OUT/node_modules/sqlite-vec-darwin-x64/vec0.dylib"
+  cp "$X64_DIR/package.json" "$OUT/node_modules/sqlite-vec-darwin-x64/package.json"
+  echo "  ✓ x64 dylib"
+fi
+
+# ---------- stub node-llama-cpp ----------
+echo "Creating node-llama-cpp stub (keyword search only)..."
+mkdir -p "$OUT/node_modules/node-llama-cpp"
+
+cat > "$OUT/node_modules/node-llama-cpp/package.json" << 'PJSON'
+{"name":"node-llama-cpp","version":"0.0.0-stub","type":"module","main":"index.js"}
+PJSON
+
+cat > "$OUT/node_modules/node-llama-cpp/index.js" << 'STUB'
+// Stub: node-llama-cpp not bundled — semantic search unavailable, keyword search works.
+const unavailable = (name) => (...args) => {
+  throw new Error(`${name}() unavailable: node-llama-cpp not bundled. Keyword search still works.`);
+};
+export const getLlama = unavailable("getLlama");
+export const resolveModelFile = unavailable("resolveModelFile");
+export class LlamaChatSession {
+  constructor() { throw new Error("LlamaChatSession unavailable"); }
+}
+export const LlamaLogLevel = { Error: 0, Warn: 1, Info: 2, Debug: 3 };
+STUB
+
+# ---------- code signing (macOS) ----------
+# In CI (APPLE_SIGNING_IDENTITY set): sign with Developer ID + hardened runtime (required for notarization)
+# In dev (no identity): ad-hoc sign to remove quarantine
+if [[ "$(uname)" == "Darwin" ]] && command -v codesign &>/dev/null; then
+  SIGN_ID="${APPLE_SIGNING_IDENTITY:--}"
+  if [[ "$SIGN_ID" != "-" ]]; then
+    echo "Signing bundled binaries with Developer ID: $SIGN_ID"
+    SIGN_OPTS=(--force --sign "$SIGN_ID" --options runtime --timestamp)
+  else
+    echo "Ad-hoc signing bundled binaries (dev mode)..."
+    SIGN_OPTS=(--force --sign -)
+  fi
+  codesign "${SIGN_OPTS[@]}" "$OUT/qmd" 2>/dev/null && echo "  ✓ qmd signed" || echo "  ⚠ qmd signing failed (non-fatal)"
+  while IFS= read -r -d '' dylib; do
+    codesign "${SIGN_OPTS[@]}" "$dylib" 2>/dev/null && echo "  ✓ $(basename "$dylib") signed" || echo "  ⚠ $(basename "$dylib") signing failed (non-fatal)"
+  done < <(find "$OUT/node_modules" -name "*.dylib" -print0)
+fi
+
+# ---------- summary ----------
+echo ""
+echo "qmd bundled → $OUT/"
+du -sh "$OUT/qmd"
+du -sh "$OUT/node_modules"
+echo "Done."

src-tauri/.gitignore

@@ -2,3 +2,7 @@
 # will have compiled files and executables
 /target/
 /gen/schemas
+
+# Generated by build scripts
+/resources/mcp-server/
+/resources/qmd/

src-tauri/build.rs

@@ -1,14 +1,13 @@
 fn main() {
-    let count = std::process::Command::new("git")
-        .args(["rev-list", "--count", "HEAD"])
-        .output()
-        .ok()
-        .filter(|o| o.status.success())
-        .and_then(|o| String::from_utf8(o.stdout).ok())
-        .map(|s| s.trim().to_string())
-        .unwrap_or_else(|| "DEV".to_string());
-
-    println!("cargo:rustc-env=BUILD_NUMBER={}", count);
-
+    // Ensure resource directories exist for the Tauri build.
+    // These are gitignored and populated by scripts (bundle-qmd.sh, bundle-mcp-server.mjs).
+    // Without a placeholder, `tauri build` / `cargo test` fails if the scripts haven't run.
+    for dir in ["resources/qmd", "resources/mcp-server"] {
+        let path = std::path::Path::new(dir);
+        if !path.exists() {
+            std::fs::create_dir_all(path).ok();
+            std::fs::write(path.join(".placeholder"), "").ok();
+        }
+    }
     tauri_build::build()
 }

src-tauri/src/claude_cli.rs

@@ -1,4 +1,5 @@
 use serde::{Deserialize, Serialize};
+use std::collections::HashMap;
 use std::io::BufRead;
 use std::path::PathBuf;
 use std::process::{Command, Stdio};
@@ -18,10 +19,21 @@ pub enum ClaudeStreamEvent {
     Init { session_id: String },
     /// Incremental text chunk.
     TextDelta { text: String },
+    /// Incremental thinking/reasoning chunk.
+    ThinkingDelta { text: String },
     /// A tool call started (agent mode only).
-    ToolStart { tool_name: String, tool_id: String },
+    ToolStart {
+        tool_name: String,
+        tool_id: String,
+        #[serde(skip_serializing_if = "Option::is_none")]
+        input: Option<String>,
+    },
     /// A tool call finished (agent mode only).
-    ToolDone { tool_id: String },
+    ToolDone {
+        tool_id: String,
+        #[serde(skip_serializing_if = "Option::is_none")]
+        output: Option<String>,
+    },
     /// Final result text + session ID.
     Result { text: String, session_id: String },
     /// Something went wrong.
@@ -117,7 +129,7 @@ where
 {
     let bin = find_claude_binary()?;
     let args = build_chat_args(&req);
-    run_claude_subprocess(&bin, &args, &mut emit)
+    run_claude_subprocess(&bin, &args, None, &mut emit)
 }
 
 /// Build CLI arguments for a chat stream request.
@@ -148,17 +160,18 @@ fn build_chat_args(req: &ChatStreamRequest) -> Vec<String> {
     args
 }
 
-/// Spawn `claude -p` with MCP vault tools for an agent task and stream events.
+/// Spawn `claude -p` with full tool access and MCP vault tools for an agent task.
 pub fn run_agent_stream<F>(req: AgentStreamRequest, mut emit: F) -> Result<String, String>
 where
     F: FnMut(ClaudeStreamEvent),
 {
     let bin = find_claude_binary()?;
     let args = build_agent_args(&req)?;
-    run_claude_subprocess(&bin, &args, &mut emit)
+    run_claude_subprocess(&bin, &args, Some(&req.vault_path), &mut emit)
 }
 
 /// Build CLI arguments for an agent stream request.
+/// Native tools (bash, read, write, edit) are enabled by default — no `--tools ""`.
 fn build_agent_args(req: &AgentStreamRequest) -> Result<Vec<String>, String> {
     let mcp_config = build_mcp_config(&req.vault_path)?;
 
@@ -169,8 +182,6 @@ fn build_agent_args(req: &AgentStreamRequest) -> Result<Vec<String>, String> {
         "stream-json".into(),
         "--verbose".into(),
         "--include-partial-messages".into(),
-        "--tools".into(),
-        String::new(), // disable built-in tools; MCP tools remain
         "--mcp-config".into(),
         mcp_config,
         "--dangerously-skip-permissions".into(),
@@ -207,23 +218,46 @@ fn build_mcp_config(vault_path: &str) -> Result<String, String> {
     serde_json::to_string(&config).map_err(|e| format!("Failed to serialise MCP config: {e}"))
 }
 
+/// Mutable state accumulated across the JSON stream for a single subprocess.
+struct StreamState {
+    session_id: String,
+    /// Accumulates `input_json_delta` chunks keyed by tool_use id.
+    tool_inputs: HashMap<String, String>,
+    /// The tool_use id of the block currently being streamed.
+    current_tool_id: Option<String>,
+}
+
 /// Core subprocess runner shared by chat and agent modes.
-fn run_claude_subprocess<F>(bin: &PathBuf, args: &[String], emit: &mut F) -> Result<String, String>
+/// When `cwd` is `Some`, the subprocess starts with that working directory.
+fn run_claude_subprocess<F>(
+    bin: &PathBuf,
+    args: &[String],
+    cwd: Option<&str>,
+    emit: &mut F,
+) -> Result<String, String>
 where
     F: FnMut(ClaudeStreamEvent),
 {
-    let mut child = Command::new(bin)
-        .args(args)
+    let mut cmd = Command::new(bin);
+    cmd.args(args)
         .env_remove("CLAUDECODE") // prevent "nested session" guard
         .stdout(Stdio::piped())
-        .stderr(Stdio::piped())
+        .stderr(Stdio::piped());
+    if let Some(dir) = cwd {
+        cmd.current_dir(dir);
+    }
+    let mut child = cmd
         .spawn()
         .map_err(|e| format!("Failed to spawn claude: {e}"))?;
 
     let stdout = child.stdout.take().ok_or("No stdout handle")?;
     let reader = std::io::BufReader::new(stdout);
 
-    let mut session_id = String::new();
+    let mut state = StreamState {
+        session_id: String::new(),
+        tool_inputs: HashMap::new(),
+        current_tool_id: None,
+    };
 
     for line in reader.lines() {
         let line = match line {
@@ -245,7 +279,7 @@ where
             Err(_) => continue, // skip non-JSON lines
         };
 
-        dispatch_event(&json, &mut session_id, emit);
+        dispatch_event(&json, &mut state, emit);
     }
 
     // Read stderr for potential error messages.
@@ -257,7 +291,7 @@ where
 
     let status = child.wait().map_err(|e| format!("Wait failed: {e}"))?;
 
-    if !status.success() && session_id.is_empty() {
+    if !status.success() && state.session_id.is_empty() {
         let msg = if stderr_output.contains("not logged in")
             || stderr_output.contains("authentication")
             || stderr_output.contains("auth")
@@ -273,11 +307,11 @@ where
 
     emit(ClaudeStreamEvent::Done);
 
-    Ok(session_id)
+    Ok(state.session_id)
 }
 
 /// Parse a single JSON line from the stream and emit the appropriate event.
-fn dispatch_event<F>(json: &serde_json::Value, session_id: &mut String, emit: &mut F)
+fn dispatch_event<F>(json: &serde_json::Value, state: &mut StreamState, emit: &mut F)
 where
     F: FnMut(ClaudeStreamEvent),
 {
@@ -287,7 +321,7 @@ where
         // --- System init → capture session_id ---
         "system" if json["subtype"].as_str() == Some("init") => {
             if let Some(sid) = json["session_id"].as_str() {
-                *session_id = sid.to_string();
+                state.session_id = sid.to_string();
                 emit(ClaudeStreamEvent::Init {
                     session_id: sid.to_string(),
                 });
@@ -296,7 +330,7 @@ where
 
         // --- Streaming partial events (text deltas, tool_use starts) ---
         "stream_event" => {
-            dispatch_stream_event(json, emit);
+            dispatch_stream_event(json, state, emit);
         }
 
         // --- Tool progress (agent mode) ---
@@ -307,6 +341,18 @@ where
                 emit(ClaudeStreamEvent::ToolStart {
                     tool_name: name.to_string(),
                     tool_id: id.to_string(),
+                    input: None,
+                });
+            }
+        }
+
+        // --- Tool result (agent mode) ---
+        "tool_result" => {
+            if let Some(id) = json["tool_use_id"].as_str() {
+                let output = extract_tool_result_text(json);
+                emit(ClaudeStreamEvent::ToolDone {
+                    tool_id: id.to_string(),
+                    output,
                 });
             }
         }
@@ -315,7 +361,7 @@ where
         "result" => {
             let sid = json["session_id"].as_str().unwrap_or("").to_string();
             if !sid.is_empty() {
-                *session_id = sid.clone();
+                state.session_id = sid.clone();
             }
             let text = json["result"].as_str().unwrap_or("").to_string();
             emit(ClaudeStreamEvent::Result {
@@ -332,9 +378,11 @@ where
                         if let (Some(id), Some(name)) =
                             (block["id"].as_str(), block["name"].as_str())
                         {
+                            let input = format_tool_input(&block["input"], state, id);
                             emit(ClaudeStreamEvent::ToolStart {
                                 tool_name: name.to_string(),
                                 tool_id: id.to_string(),
+                                input,
                             });
                         }
                     }
@@ -347,7 +395,7 @@ where
 }
 
 /// Handle a `stream_event` (partial assistant message).
-fn dispatch_stream_event<F>(json: &serde_json::Value, emit: &mut F)
+fn dispatch_stream_event<F>(json: &serde_json::Value, state: &mut StreamState, emit: &mut F)
 where
     F: FnMut(ClaudeStreamEvent),
 {
@@ -357,29 +405,91 @@ where
     match event_type {
         "content_block_delta" => {
             let delta = &event["delta"];
-            if delta["type"].as_str() == Some("text_delta") {
-                if let Some(text) = delta["text"].as_str() {
-                    emit(ClaudeStreamEvent::TextDelta {
-                        text: text.to_string(),
-                    });
+            match delta["type"].as_str() {
+                Some("text_delta") => {
+                    if let Some(text) = delta["text"].as_str() {
+                        emit(ClaudeStreamEvent::TextDelta {
+                            text: text.to_string(),
+                        });
+                    }
                 }
+                Some("thinking_delta") => {
+                    if let Some(text) = delta["thinking"].as_str() {
+                        emit(ClaudeStreamEvent::ThinkingDelta {
+                            text: text.to_string(),
+                        });
+                    }
+                }
+                Some("input_json_delta") => {
+                    if let (Some(partial), Some(ref tid)) =
+                        (delta["partial_json"].as_str(), &state.current_tool_id)
+                    {
+                        state
+                            .tool_inputs
+                            .entry(tid.clone())
+                            .or_default()
+                            .push_str(partial);
+                    }
+                }
+                _ => {}
             }
         }
         "content_block_start" => {
             let block = &event["content_block"];
             if block["type"].as_str() == Some("tool_use") {
                 if let (Some(id), Some(name)) = (block["id"].as_str(), block["name"].as_str()) {
+                    state.current_tool_id = Some(id.to_string());
+                    state.tool_inputs.entry(id.to_string()).or_default();
                     emit(ClaudeStreamEvent::ToolStart {
                         tool_name: name.to_string(),
                         tool_id: id.to_string(),
+                        input: None,
                     });
                 }
             }
         }
+        "content_block_stop" => {
+            state.current_tool_id = None;
+        }
         _ => {}
     }
 }
 
+/// Build the tool input string, preferring accumulated delta chunks over the
+/// block's `input` field (which may be empty at stream start).
+fn format_tool_input(
+    block_input: &serde_json::Value,
+    state: &StreamState,
+    tool_id: &str,
+) -> Option<String> {
+    if let Some(accumulated) = state.tool_inputs.get(tool_id) {
+        if !accumulated.is_empty() {
+            return Some(accumulated.clone());
+        }
+    }
+    if !block_input.is_null() && block_input.as_object().is_some_and(|o| !o.is_empty()) {
+        return Some(block_input.to_string());
+    }
+    None
+}
+
+/// Extract displayable text from a `tool_result` event.
+fn extract_tool_result_text(json: &serde_json::Value) -> Option<String> {
+    // String content field
+    if let Some(s) = json["content"].as_str() {
+        return Some(s.to_string());
+    }
+    // Array of content blocks (Claude format)
+    if let Some(arr) = json["content"].as_array() {
+        let texts: Vec<&str> = arr.iter().filter_map(|b| b["text"].as_str()).collect();
+        if !texts.is_empty() {
+            return Some(texts.join("\n"));
+        }
+    }
+    // Fallback: "output" field
+    json["output"].as_str().map(|s| s.to_string())
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;
@@ -408,12 +518,20 @@ mod tests {
 
     // --- dispatch_event / dispatch_stream_event ---
 
+    fn new_state() -> StreamState {
+        StreamState {
+            session_id: String::new(),
+            tool_inputs: HashMap::new(),
+            current_tool_id: None,
+        }
+    }
+
     /// Run dispatch_event on the given JSON and return (session_id, events).
     fn run_dispatch(json: serde_json::Value) -> (String, Vec<ClaudeStreamEvent>) {
-        let mut sid = String::new();
+        let mut state = new_state();
         let mut events = vec![];
-        dispatch_event(&json, &mut sid, &mut |e| events.push(e));
-        (sid, events)
+        dispatch_event(&json, &mut state, &mut |e| events.push(e));
+        (state.session_id, events)
     }
 
     /// Run dispatch_event with a pre-set session_id.
@@ -421,10 +539,23 @@ mod tests {
         json: serde_json::Value,
         initial_sid: &str,
     ) -> (String, Vec<ClaudeStreamEvent>) {
-        let mut sid = initial_sid.to_string();
+        let mut state = new_state();
+        state.session_id = initial_sid.to_string();
         let mut events = vec![];
-        dispatch_event(&json, &mut sid, &mut |e| events.push(e));
-        (sid, events)
+        dispatch_event(&json, &mut state, &mut |e| events.push(e));
+        (state.session_id, events)
+    }
+
+    /// Run multiple dispatch_event calls sharing state (for multi-event sequences).
+    fn run_dispatch_sequence(
+        events_json: Vec<serde_json::Value>,
+    ) -> (StreamState, Vec<ClaudeStreamEvent>) {
+        let mut state = new_state();
+        let mut events = vec![];
+        for json in &events_json {
+            dispatch_event(json, &mut state, &mut |e| events.push(e));
+        }
+        (state, events)
     }
 
     #[test]
@@ -468,7 +599,7 @@ mod tests {
             "event": { "type": "content_block_start", "index": 1, "content_block": { "type": "tool_use", "id": "tool_abc", "name": "read_note", "input": {} } }
         }));
         assert!(
-            matches!(&events[0], ClaudeStreamEvent::ToolStart { tool_name, tool_id } if tool_name == "read_note" && tool_id == "tool_abc")
+            matches!(&events[0], ClaudeStreamEvent::ToolStart { tool_name, tool_id, .. } if tool_name == "read_note" && tool_id == "tool_abc")
         );
     }
 
@@ -501,7 +632,7 @@ mod tests {
             "type": "tool_progress", "tool_name": "search_notes", "tool_use_id": "tool_xyz"
         }));
         assert!(
-            matches!(&events[0], ClaudeStreamEvent::ToolStart { tool_name, tool_id } if tool_name == "search_notes" && tool_id == "tool_xyz")
+            matches!(&events[0], ClaudeStreamEvent::ToolStart { tool_name, tool_id, .. } if tool_name == "search_notes" && tool_id == "tool_xyz")
         );
     }
 
@@ -523,7 +654,7 @@ mod tests {
         }));
         assert_eq!(events.len(), 1);
         assert!(
-            matches!(&events[0], ClaudeStreamEvent::ToolStart { tool_name, tool_id } if tool_name == "search_notes" && tool_id == "tu_1")
+            matches!(&events[0], ClaudeStreamEvent::ToolStart { tool_name, tool_id, .. } if tool_name == "search_notes" && tool_id == "tu_1")
         );
     }
 
@@ -541,7 +672,8 @@ mod tests {
     }
 
     #[test]
-    fn dispatch_stream_event_non_text_delta_is_ignored() {
+    fn dispatch_stream_event_input_json_delta_accumulates_silently() {
+        // input_json_delta doesn't emit events directly — it accumulates in state
         let (_, events) = run_dispatch(serde_json::json!({
             "type": "stream_event",
             "event": { "type": "content_block_delta", "index": 0, "delta": { "type": "input_json_delta", "partial_json": "{}" } }
@@ -566,6 +698,112 @@ mod tests {
         assert!(events.is_empty());
     }
 
+    #[test]
+    fn dispatch_event_handles_tool_result_string_content() {
+        let (_, events) = run_dispatch(serde_json::json!({
+            "type": "tool_result",
+            "tool_use_id": "tool_abc",
+            "content": "Found 3 notes matching query"
+        }));
+        assert_eq!(events.len(), 1);
+        assert!(
+            matches!(&events[0], ClaudeStreamEvent::ToolDone { tool_id, output }
+                if tool_id == "tool_abc" && output.as_deref() == Some("Found 3 notes matching query"))
+        );
+    }
+
+    #[test]
+    fn dispatch_event_handles_tool_result_array_content() {
+        let (_, events) = run_dispatch(serde_json::json!({
+            "type": "tool_result",
+            "tool_use_id": "tool_def",
+            "content": [{ "type": "text", "text": "Line 1" }, { "type": "text", "text": "Line 2" }]
+        }));
+        assert!(
+            matches!(&events[0], ClaudeStreamEvent::ToolDone { output, .. }
+                if output.as_deref() == Some("Line 1\nLine 2"))
+        );
+    }
+
+    #[test]
+    fn dispatch_event_tool_result_missing_tool_id_is_ignored() {
+        let (_, events) = run_dispatch(serde_json::json!({
+            "type": "tool_result", "content": "result text"
+        }));
+        assert!(events.is_empty());
+    }
+
+    #[test]
+    fn dispatch_accumulates_input_json_deltas() {
+        let (_, events) = run_dispatch_sequence(vec![
+            // Start tool_use block
+            serde_json::json!({
+                "type": "stream_event",
+                "event": { "type": "content_block_start", "content_block": { "type": "tool_use", "id": "t1", "name": "search_notes", "input": {} } }
+            }),
+            // Input delta chunks
+            serde_json::json!({
+                "type": "stream_event",
+                "event": { "type": "content_block_delta", "delta": { "type": "input_json_delta", "partial_json": "{\"query\":" } }
+            }),
+            serde_json::json!({
+                "type": "stream_event",
+                "event": { "type": "content_block_delta", "delta": { "type": "input_json_delta", "partial_json": "\"test\"}" } }
+            }),
+            // Stop block
+            serde_json::json!({
+                "type": "stream_event",
+                "event": { "type": "content_block_stop" }
+            }),
+            // Assistant message triggers ToolStart with accumulated input
+            serde_json::json!({
+                "type": "assistant",
+                "message": { "content": [
+                    { "type": "tool_use", "id": "t1", "name": "search_notes", "input": { "query": "test" } }
+                ] }
+            }),
+        ]);
+        // First event: ToolStart with no input (from content_block_start)
+        assert!(matches!(
+            &events[0],
+            ClaudeStreamEvent::ToolStart { input: None, .. }
+        ));
+        // Second event: ToolStart with accumulated input (from assistant)
+        assert!(
+            matches!(&events[1], ClaudeStreamEvent::ToolStart { input: Some(inp), .. }
+                if inp == "{\"query\":\"test\"}")
+        );
+    }
+
+    #[test]
+    fn dispatch_assistant_uses_block_input_when_no_deltas() {
+        let (_, events) = run_dispatch(serde_json::json!({
+            "type": "assistant",
+            "message": { "content": [
+                { "type": "tool_use", "id": "tu_x", "name": "create_note", "input": { "title": "Hello", "content": "world" } }
+            ] }
+        }));
+        assert!(
+            matches!(&events[0], ClaudeStreamEvent::ToolStart { input: Some(inp), .. }
+                if inp.contains("title") && inp.contains("Hello"))
+        );
+    }
+
+    #[test]
+    fn content_block_stop_clears_current_tool() {
+        let (state, _) = run_dispatch_sequence(vec![
+            serde_json::json!({
+                "type": "stream_event",
+                "event": { "type": "content_block_start", "content_block": { "type": "tool_use", "id": "t1", "name": "x", "input": {} } }
+            }),
+            serde_json::json!({
+                "type": "stream_event",
+                "event": { "type": "content_block_stop" }
+            }),
+        ]);
+        assert!(state.current_tool_id.is_none());
+    }
+
     // --- run_claude_subprocess with mock scripts ---
 
     #[cfg(unix)]
@@ -584,7 +822,7 @@ mod tests {
         std::fs::write(&path, script).unwrap();
         std::fs::set_permissions(&path, std::fs::Permissions::from_mode(0o755)).unwrap();
         let mut events = vec![];
-        let result = run_claude_subprocess(&path, args, &mut |e| events.push(e));
+        let result = run_claude_subprocess(&path, args, None, &mut |e| events.push(e));
         (result, events)
     }
 
@@ -735,6 +973,8 @@ mod tests {
             assert!(args.contains(&"--dangerously-skip-permissions".to_string()));
             assert!(args.contains(&"--no-session-persistence".to_string()));
             assert!(!args.contains(&"--append-system-prompt".to_string()));
+            // Native tools must NOT be disabled
+            assert!(!args.contains(&"--tools".to_string()));
         }
     }
 
@@ -806,7 +1046,7 @@ mod tests {
     fn run_subprocess_spawn_failure() {
         let fake_bin = PathBuf::from("/nonexistent/binary/path");
         let mut events = vec![];
-        let result = run_claude_subprocess(&fake_bin, &[], &mut |e| events.push(e));
+        let result = run_claude_subprocess(&fake_bin, &[], None, &mut |e| events.push(e));
         assert!(result.is_err());
         assert!(result.unwrap_err().contains("Failed to spawn"));
     }

src-tauri/src/frontmatter.rs

@@ -15,7 +15,7 @@ pub enum FrontmatterValue {
 
 /// Characters that require a YAML string value to be quoted.
 fn has_yaml_special_chars(s: &str) -> bool {
-    s.contains(':') || s.contains('#') || s.contains('\n')
+    s.contains(':') || s.contains('#')
 }
 
 /// Check if a string starts with a YAML collection indicator (array or map).
@@ -41,6 +41,23 @@ fn format_list_item(item: &str) -> String {
     format!("  - {}", quote_yaml_string(item))
 }
 
+/// Format a multi-line string as a YAML block scalar (`|`).
+/// Each line is indented by 2 spaces; empty lines are preserved as blank.
+fn format_block_scalar(s: &str) -> String {
+    let indented = s
+        .lines()
+        .map(|l| {
+            if l.is_empty() {
+                String::new()
+            } else {
+                format!("  {}", l)
+            }
+        })
+        .collect::<Vec<_>>()
+        .join("\n");
+    format!("|\n{}", indented)
+}
+
 /// Format a number for YAML (integers without decimal, floats with).
 fn format_yaml_number(n: f64) -> String {
     if n.fract() == 0.0 {
@@ -54,7 +71,9 @@ impl FrontmatterValue {
     pub fn to_yaml_value(&self) -> String {
         match self {
             FrontmatterValue::String(s) => {
-                if needs_yaml_quoting(s) {
+                if s.contains('\n') {
+                    format_block_scalar(s)
+                } else if needs_yaml_quoting(s) {
                     quote_yaml_string(s)
                 } else {
                     s.clone()
@@ -113,16 +132,20 @@ fn line_is_key(line: &str, key: &str) -> bool {
 fn format_yaml_field(key: &str, value: &FrontmatterValue) -> Vec<String> {
     let yaml_key = format_yaml_key(key);
     let yaml_value = value.to_yaml_value();
-    if yaml_value.contains('\n') {
+    if yaml_value.starts_with("|\n") {
+        // Block scalar: key and indicator on the same line, content follows
+        vec![format!("{}: {}", yaml_key, yaml_value)]
+    } else if yaml_value.contains('\n') {
         vec![format!("{}:", yaml_key), yaml_value]
     } else {
         vec![format!("{}: {}", yaml_key, yaml_value)]
     }
 }
 
-/// Check if a line is a YAML list continuation (`  - ...`) rather than a new key.
-fn is_list_continuation(line: &str) -> bool {
-    line.starts_with("  - ") || line.starts_with("  -\t")
+/// Check if a line continues the previous key's value (indented list item,
+/// block scalar content, or blank line inside a block scalar).
+fn is_value_continuation(line: &str) -> bool {
+    line.is_empty() || line.starts_with("  ") || line.starts_with('\t')
 }
 
 /// Split content into frontmatter body and the rest after the closing `---`.
@@ -163,8 +186,8 @@ fn apply_field_update(lines: &[&str], key: &str, value: Option<&FrontmatterValue
 
         found_key = true;
         i += 1;
-        // Skip list continuation lines belonging to this key
-        while i < lines.len() && is_list_continuation(lines[i]) {
+        // Skip continuation lines belonging to this key (lists, block scalars)
+        while i < lines.len() && is_value_continuation(lines[i]) {
             i += 1;
         }
         // Insert replacement value (if any)
@@ -699,6 +722,94 @@ mod tests {
         assert!(updated.contains("title: New Title"));
     }
 
+    // --- block scalar (multi-line string) tests ---
+
+    #[test]
+    fn test_to_yaml_value_multiline_uses_block_scalar() {
+        let v = FrontmatterValue::String("line 1\nline 2\nline 3".to_string());
+        let yaml = v.to_yaml_value();
+        assert!(yaml.starts_with("|\n"));
+        assert!(yaml.contains("  line 1"));
+        assert!(yaml.contains("  line 2"));
+    }
+
+    #[test]
+    fn test_format_yaml_field_block_scalar() {
+        let v = FrontmatterValue::String("## Objective\n\n## Timeline".to_string());
+        let lines = format_yaml_field("template", &v);
+        assert_eq!(lines.len(), 1);
+        assert!(lines[0].starts_with("template: |\n"));
+        assert!(lines[0].contains("  ## Objective"));
+        assert!(lines[0].contains("  ## Timeline"));
+    }
+
+    #[test]
+    fn test_update_frontmatter_block_scalar_add() {
+        let content = "---\ntype: Type\n---\n# Project\n";
+        let template = "## Objective\n\n## Timeline";
+        let updated = update_frontmatter_content(
+            content,
+            "template",
+            Some(FrontmatterValue::String(template.to_string())),
+        )
+        .unwrap();
+        assert!(updated.contains("template: |"));
+        assert!(updated.contains("  ## Objective"));
+        assert!(updated.contains("  ## Timeline"));
+        assert!(updated.contains("type: Type"));
+    }
+
+    #[test]
+    fn test_update_frontmatter_block_scalar_replace() {
+        let content = "---\ntype: Type\ntemplate: |\n  ## Old\n  \n  ## Stuff\ncolor: green\n---\n# Project\n";
+        let new_template = "## New\n\n## Content";
+        let updated = update_frontmatter_content(
+            content,
+            "template",
+            Some(FrontmatterValue::String(new_template.to_string())),
+        )
+        .unwrap();
+        assert!(updated.contains("  ## New"));
+        assert!(updated.contains("  ## Content"));
+        assert!(!updated.contains("## Old"));
+        assert!(!updated.contains("## Stuff"));
+        assert!(updated.contains("color: green"));
+    }
+
+    #[test]
+    fn test_delete_frontmatter_block_scalar() {
+        let content =
+            "---\ntype: Type\ntemplate: |\n  ## Heading\n  \n  ## Body\ncolor: green\n---\n# Project\n";
+        let updated = update_frontmatter_content(content, "template", None).unwrap();
+        assert!(!updated.contains("template"));
+        assert!(!updated.contains("## Heading"));
+        assert!(updated.contains("color: green"));
+    }
+
+    #[test]
+    fn test_roundtrip_block_scalar() {
+        let content = "---\ntype: Type\n---\n# Project\n";
+        let template = "## Objective\n\nDescribe the goal.\n\n## Timeline\n\nKey dates.";
+        let updated = update_frontmatter_content(
+            content,
+            "template",
+            Some(FrontmatterValue::String(template.to_string())),
+        )
+        .unwrap();
+        // Parse back with gray_matter
+        let matter = gray_matter::Matter::<gray_matter::engine::YAML>::new();
+        let parsed = matter.parse(&updated);
+        let data = parsed.data.unwrap();
+        if let gray_matter::Pod::Hash(map) = data {
+            let roundtripped = map.get("template").unwrap().as_string().unwrap();
+            assert!(roundtripped.contains("## Objective"));
+            assert!(roundtripped.contains("## Timeline"));
+            assert!(roundtripped.contains("Describe the goal."));
+        } else {
+            panic!("Expected hash");
+        }
+    }
+
     #[test]
     fn test_update_frontmatter_no_body_after_closing() {
         // Frontmatter with title, no body after closing ---

src-tauri/src/git.rs

@@ -128,7 +128,7 @@ pub fn get_modified_files(vault_path: &str) -> Result<Vec<ModifiedFile>, String>
     let vault = Path::new(vault_path);
 
     let output = Command::new("git")
-        .args(["status", "--porcelain"])
+        .args(["status", "--porcelain", "--untracked-files=all"])
         .current_dir(vault)
         .output()
         .map_err(|e| format!("Failed to run git status: {}", e))?;
@@ -427,20 +427,28 @@ pub fn git_pull(vault_path: &str) -> Result<GitPullResult, String> {
 }
 
 /// List files with merge conflicts (unmerged paths).
+///
+/// Uses `git ls-files --unmerged` instead of `git diff --diff-filter=U` because
+/// ls-files reliably detects unmerged index entries even when the merge state is
+/// stale (e.g. after a reboot or when MERGE_HEAD is missing).
 pub fn get_conflict_files(vault_path: &str) -> Result<Vec<String>, String> {
     let vault = Path::new(vault_path);
     let output = Command::new("git")
-        .args(["diff", "--name-only", "--diff-filter=U"])
+        .args(["ls-files", "--unmerged"])
         .current_dir(vault)
         .output()
         .map_err(|e| format!("Failed to check conflicts: {}", e))?;
 
     let stdout = String::from_utf8_lossy(&output.stdout);
-    Ok(stdout
+    // Each unmerged file appears multiple times (once per stage: base/ours/theirs).
+    // Format: "<mode> <hash> <stage>\t<path>"
+    let mut files: Vec<String> = stdout
         .lines()
-        .filter(|l| !l.is_empty())
-        .map(|l| l.to_string())
-        .collect())
+        .filter_map(|line| line.split('\t').nth(1).map(|s| s.to_string()))
+        .collect();
+    files.sort();
+    files.dedup();
+    Ok(files)
 }
 
 /// Parse `git pull` output to extract updated file paths.
@@ -461,6 +469,103 @@ fn parse_updated_files(stdout: &str) -> Vec<String> {
         .collect()
 }
 
+/// Resolve a single conflict file by choosing "ours" or "theirs" strategy,
+/// then stage the result.
+pub fn git_resolve_conflict(vault_path: &str, file: &str, strategy: &str) -> Result<(), String> {
+    let vault = Path::new(vault_path);
+
+    let checkout_flag = match strategy {
+        "ours" => "--ours",
+        "theirs" => "--theirs",
+        _ => {
+            return Err(format!(
+                "Invalid strategy '{}': must be 'ours' or 'theirs'",
+                strategy
+            ))
+        }
+    };
+
+    run_git(vault, &["checkout", checkout_flag, "--", file])?;
+    run_git(vault, &["add", "--", file])?;
+
+    Ok(())
+}
+
+/// Check whether a rebase is currently in progress.
+pub fn is_rebase_in_progress(vault_path: &str) -> bool {
+    let vault = Path::new(vault_path);
+    let git_dir = vault.join(".git");
+    git_dir.join("rebase-merge").exists() || git_dir.join("rebase-apply").exists()
+}
+
+/// Check whether a merge is currently in progress.
+pub fn is_merge_in_progress(vault_path: &str) -> bool {
+    Path::new(vault_path)
+        .join(".git")
+        .join("MERGE_HEAD")
+        .exists()
+}
+
+/// Returns the current conflict mode: "rebase", "merge", or "none".
+pub fn get_conflict_mode(vault_path: &str) -> String {
+    if is_rebase_in_progress(vault_path) {
+        "rebase".to_string()
+    } else if is_merge_in_progress(vault_path) {
+        "merge".to_string()
+    } else {
+        "none".to_string()
+    }
+}
+
+/// Commit after all conflicts have been resolved.
+/// Detects whether the repo is in a merge or rebase state and uses the
+/// appropriate command (`git commit` vs `git rebase --continue`).
+pub fn git_commit_conflict_resolution(vault_path: &str) -> Result<String, String> {
+    let vault = Path::new(vault_path);
+
+    // Verify no remaining conflicts
+    let remaining = get_conflict_files(vault_path)?;
+    if !remaining.is_empty() {
+        return Err(format!(
+            "Cannot commit: {} file(s) still have unresolved conflicts",
+            remaining.len()
+        ));
+    }
+
+    let mode = get_conflict_mode(vault_path);
+    let output = match mode.as_str() {
+        "rebase" => Command::new("git")
+            .args(["rebase", "--continue"])
+            .env("GIT_EDITOR", "true")
+            .current_dir(vault)
+            .output()
+            .map_err(|e| format!("Failed to run git rebase --continue: {}", e))?,
+        _ => Command::new("git")
+            .args(["commit", "-m", "Resolve merge conflicts"])
+            .current_dir(vault)
+            .output()
+            .map_err(|e| format!("Failed to run git commit: {}", e))?,
+    };
+
+    if !output.status.success() {
+        let stderr = String::from_utf8_lossy(&output.stderr);
+        let stdout = String::from_utf8_lossy(&output.stdout);
+        let detail = if stderr.trim().is_empty() {
+            stdout
+        } else {
+            stderr
+        };
+        let cmd_name = if mode == "rebase" {
+            "git rebase --continue"
+        } else {
+            "git commit"
+        };
+        return Err(format!("{} failed: {}", cmd_name, detail.trim()));
+    }
+
+    Ok(String::from_utf8_lossy(&output.stdout).to_string())
+}
+
 /// Push to remote.
 pub fn git_push(vault_path: &str) -> Result<String, String> {
     let vault = Path::new(vault_path);
@@ -482,6 +587,167 @@ pub fn git_push(vault_path: &str) -> Result<String, String> {
     Ok(format!("{}{}", stdout, stderr))
 }
 
+#[derive(Debug, Serialize, Clone)]
+pub struct PulseFile {
+    pub path: String,
+    pub status: String,
+    pub title: String,
+}
+
+#[derive(Debug, Serialize, Clone)]
+pub struct PulseCommit {
+    pub hash: String,
+    #[serde(rename = "shortHash")]
+    pub short_hash: String,
+    pub message: String,
+    pub date: i64,
+    #[serde(rename = "githubUrl")]
+    pub github_url: Option<String>,
+    pub files: Vec<PulseFile>,
+    pub added: usize,
+    pub modified: usize,
+    pub deleted: usize,
+}
+
+fn title_from_path(path: &str) -> String {
+    path.rsplit('/')
+        .next()
+        .unwrap_or(path)
+        .strip_suffix(".md")
+        .unwrap_or(path)
+        .replace('-', " ")
+}
+
+fn parse_file_status(code: &str) -> &str {
+    match code {
+        "A" => "added",
+        "M" => "modified",
+        "D" => "deleted",
+        _ => "modified",
+    }
+}
+
+/// Get the pulse (commit activity feed) for a vault, showing only .md file changes.
+pub fn get_vault_pulse(vault_path: &str, limit: usize) -> Result<Vec<PulseCommit>, String> {
+    let vault = Path::new(vault_path);
+
+    if !vault.join(".git").exists() {
+        return Err("Not a git repository".to_string());
+    }
+
+    let limit_str = limit.to_string();
+    let output = Command::new("git")
+        .args([
+            "log",
+            "--name-status",
+            "--pretty=format:%H|%h|%s|%aI",
+            "--diff-filter=ADM",
+            "-n",
+            &limit_str,
+            "--",
+            "*.md",
+        ])
+        .current_dir(vault)
+        .output()
+        .map_err(|e| format!("Failed to run git log: {}", e))?;
+
+    if !output.status.success() {
+        let stderr = String::from_utf8_lossy(&output.stderr);
+        if stderr.contains("does not have any commits yet") {
+            return Ok(Vec::new());
+        }
+        return Err(format!("git log failed: {}", stderr));
+    }
+
+    let github_base = get_github_base_url(vault_path);
+    let stdout = String::from_utf8_lossy(&output.stdout);
+    Ok(parse_pulse_output(&stdout, &github_base))
+}
+
+fn get_github_base_url(vault_path: &str) -> Option<String> {
+    let vault = Path::new(vault_path);
+    let output = Command::new("git")
+        .args(["remote", "get-url", "origin"])
+        .current_dir(vault)
+        .output()
+        .ok()?;
+
+    if !output.status.success() {
+        return None;
+    }
+
+    let url = String::from_utf8_lossy(&output.stdout).trim().to_string();
+    let repo_path = parse_github_repo_path(&url)?;
+    Some(format!("https://github.com/{}", repo_path))
+}
+
+fn parse_pulse_output(stdout: &str, github_base: &Option<String>) -> Vec<PulseCommit> {
+    let mut commits: Vec<PulseCommit> = Vec::new();
+    let mut current: Option<PulseCommit> = None;
+
+    for line in stdout.lines() {
+        if line.is_empty() {
+            continue;
+        }
+
+        if line.contains('|')
+            && !line.starts_with(|c: char| {
+                c.is_ascii_uppercase() && line.len() > 1 && line.as_bytes().get(1) == Some(&b'\t')
+            })
+        {
+            // Commit header line: hash|short_hash|message|date
+            if let Some(commit) = current.take() {
+                commits.push(commit);
+            }
+            let parts: Vec<&str> = line.splitn(4, '|').collect();
+            if parts.len() == 4 {
+                let hash = parts[0];
+                let date = chrono::DateTime::parse_from_rfc3339(parts[3])
+                    .map(|dt| dt.timestamp())
+                    .unwrap_or(0);
+                let github_url = github_base
+                    .as_ref()
+                    .map(|base| format!("{}/commit/{}", base, hash));
+
+                current = Some(PulseCommit {
+                    hash: hash.to_string(),
+                    short_hash: parts[1].to_string(),
+                    message: parts[2].to_string(),
+                    date,
+                    github_url,
+                    files: Vec::new(),
+                    added: 0,
+                    modified: 0,
+                    deleted: 0,
+                });
+            }
+        } else if let Some(ref mut commit) = current {
+            // File status line: A\tpath or M\tpath
+            let file_parts: Vec<&str> = line.splitn(2, '\t').collect();
+            if file_parts.len() == 2 {
+                let status = parse_file_status(file_parts[0].trim());
+                let path = file_parts[1].trim();
+                match status {
+                    "added" => commit.added += 1,
+                    "deleted" => commit.deleted += 1,
+                    _ => commit.modified += 1,
+                }
+                commit.files.push(PulseFile {
+                    path: path.to_string(),
+                    status: status.to_string(),
+                    title: title_from_path(path),
+                });
+            }
+        }
+    }
+
+    if let Some(commit) = current {
+        commits.push(commit);
+    }
+
+    commits
+}
+
 #[derive(Debug, Serialize, Clone)]
 pub struct LastCommitInfo {
     #[serde(rename = "shortHash")]
@@ -740,7 +1006,42 @@ mod tests {
 
         assert!(modified.len() >= 2);
         let statuses: Vec<&str> = modified.iter().map(|f| f.status.as_str()).collect();
-        assert!(statuses.contains(&"modified") || statuses.contains(&"untracked"));
+        assert!(statuses.contains(&"modified"));
+        assert!(statuses.contains(&"untracked"));
+    }
+
+    #[test]
+    fn test_get_modified_files_untracked_in_subdirectory() {
+        let dir = setup_git_repo();
+        let vault = dir.path();
+
+        // Create initial commit so git is initialized
+        fs::write(vault.join("init.md"), "# Init\n").unwrap();
+        Command::new("git")
+            .args(["add", "init.md"])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+        Command::new("git")
+            .args(["commit", "-m", "Initial"])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+
+        // Create a new untracked file in a subdirectory (simulates new note creation)
+        fs::create_dir_all(vault.join("note")).unwrap();
+        fs::write(vault.join("note/brand-new.md"), "# Brand New\n").unwrap();
+
+        let modified = get_modified_files(vault.to_str().unwrap()).unwrap();
+
+        assert_eq!(modified.len(), 1);
+        assert_eq!(modified[0].status, "untracked");
+        assert_eq!(modified[0].relative_path, "note/brand-new.md");
+        assert!(
+            modified[0].path.ends_with("/note/brand-new.md"),
+            "Full path should end with relative path: {}",
+            modified[0].path
+        );
     }
 
     #[test]
@@ -1182,6 +1483,113 @@ mod tests {
         );
     }
 
+    /// Set up a pair of clones that have a merge conflict on the same file.
+    /// Returns (bare, clone_a, clone_b) where clone_b has an unresolved conflict.
+    fn setup_conflict_pair() -> (TempDir, TempDir, TempDir) {
+        let (bare_dir, clone_a_dir, clone_b_dir) = setup_remote_pair();
+
+        let vp_a = clone_a_dir.path().to_str().unwrap();
+        let vp_b = clone_b_dir.path().to_str().unwrap();
+
+        // A creates the file and pushes
+        fs::write(clone_a_dir.path().join("conflict.md"), "# Original\n").unwrap();
+        git_commit(vp_a, "create conflict.md").unwrap();
+        git_push(vp_a).unwrap();
+
+        // B pulls to get the file
+        git_pull(vp_b).unwrap();
+
+        // A modifies and pushes
+        fs::write(clone_a_dir.path().join("conflict.md"), "# Version A\n").unwrap();
+        git_commit(vp_a, "A's change").unwrap();
+        git_push(vp_a).unwrap();
+
+        // B modifies the same file locally and commits
+        fs::write(clone_b_dir.path().join("conflict.md"), "# Version B\n").unwrap();
+        git_commit(vp_b, "B's change").unwrap();
+
+        // B pulls — this causes a merge conflict
+        let result = git_pull(vp_b).unwrap();
+        assert_eq!(result.status, "conflict");
+
+        (bare_dir, clone_a_dir, clone_b_dir)
+    }
+
+    #[test]
+    fn test_resolve_conflict_ours() {
+        let (_bare, _clone_a, clone_b) = setup_conflict_pair();
+        let vp_b = clone_b.path().to_str().unwrap();
+
+        let conflicts = get_conflict_files(vp_b).unwrap();
+        assert!(conflicts.contains(&"conflict.md".to_string()));
+
+        git_resolve_conflict(vp_b, "conflict.md", "ours").unwrap();
+
+        let remaining = get_conflict_files(vp_b).unwrap();
+        assert!(remaining.is_empty());
+
+        let content = fs::read_to_string(clone_b.path().join("conflict.md")).unwrap();
+        assert_eq!(content, "# Version B\n");
+    }
+
+    #[test]
+    fn test_resolve_conflict_theirs() {
+        let (_bare, _clone_a, clone_b) = setup_conflict_pair();
+        let vp_b = clone_b.path().to_str().unwrap();
+
+        git_resolve_conflict(vp_b, "conflict.md", "theirs").unwrap();
+
+        let remaining = get_conflict_files(vp_b).unwrap();
+        assert!(remaining.is_empty());
+
+        let content = fs::read_to_string(clone_b.path().join("conflict.md")).unwrap();
+        assert_eq!(content, "# Version A\n");
+    }
+
+    #[test]
+    fn test_resolve_conflict_invalid_strategy() {
+        let (_bare, _clone_a, clone_b) = setup_conflict_pair();
+        let vp_b = clone_b.path().to_str().unwrap();
+
+        let result = git_resolve_conflict(vp_b, "conflict.md", "invalid");
+        assert!(result.is_err());
+        assert!(result.unwrap_err().contains("Invalid strategy"));
+    }
+
+    #[test]
+    fn test_commit_conflict_resolution() {
+        let (_bare, _clone_a, clone_b) = setup_conflict_pair();
+        let vp_b = clone_b.path().to_str().unwrap();
+
+        // Resolve all conflicts first
+        git_resolve_conflict(vp_b, "conflict.md", "ours").unwrap();
+
+        let result = git_commit_conflict_resolution(vp_b);
+        assert!(result.is_ok());
+
+        // Verify the merge commit exists
+        let log = Command::new("git")
+            .args(["log", "--oneline", "-1"])
+            .current_dir(clone_b.path())
+            .output()
+            .unwrap();
+        let log_str = String::from_utf8_lossy(&log.stdout);
+        assert!(log_str.contains("Resolve merge conflicts"));
+    }
+
+    #[test]
+    fn test_commit_conflict_resolution_fails_with_unresolved() {
+        let (_bare, _clone_a, clone_b) = setup_conflict_pair();
+        let vp_b = clone_b.path().to_str().unwrap();
+
+        // Don't resolve — try to commit directly
+        let result = git_commit_conflict_resolution(vp_b);
+        assert!(result.is_err());
+        assert!(result
+            .unwrap_err()
+            .contains("still have unresolved conflicts"));
+    }
+
     #[test]
     fn test_parse_github_repo_path_non_github() {
         assert_eq!(
@@ -1189,4 +1597,311 @@ mod tests {
             None
         );
     }
+
+    #[test]
+    fn test_conflict_mode_none_for_clean_repo() {
+        let dir = setup_git_repo();
+        let vault = dir.path();
+        let vp = vault.to_str().unwrap();
+
+        fs::write(vault.join("note.md"), "# Note\n").unwrap();
+        git_commit(vp, "initial").unwrap();
+
+        assert_eq!(get_conflict_mode(vp), "none");
+        assert!(!is_rebase_in_progress(vp));
+        assert!(!is_merge_in_progress(vp));
+    }
+
+    #[test]
+    fn test_conflict_mode_merge_during_merge_conflict() {
+        let (_bare, _clone_a, clone_b) = setup_conflict_pair();
+        let vp_b = clone_b.path().to_str().unwrap();
+
+        // setup_conflict_pair creates a merge conflict via git_pull (--no-rebase)
+        assert_eq!(get_conflict_mode(vp_b), "merge");
+        assert!(is_merge_in_progress(vp_b));
+        assert!(!is_rebase_in_progress(vp_b));
+    }
+
+    #[test]
+    fn test_commit_conflict_resolution_merge_mode() {
+        let (_bare, _clone_a, clone_b) = setup_conflict_pair();
+        let vp_b = clone_b.path().to_str().unwrap();
+
+        assert_eq!(get_conflict_mode(vp_b), "merge");
+
+        git_resolve_conflict(vp_b, "conflict.md", "ours").unwrap();
+        let result = git_commit_conflict_resolution(vp_b);
+        assert!(result.is_ok());
+
+        // After resolution, mode should be none
+        assert_eq!(get_conflict_mode(vp_b), "none");
+    }
+
+    /// Set up a rebase conflict: clone_b has diverged from origin and
+    /// `git pull --rebase` causes a conflict.
+    fn setup_rebase_conflict_pair() -> (TempDir, TempDir, TempDir) {
+        let (bare_dir, clone_a_dir, clone_b_dir) = setup_remote_pair();
+
+        let vp_a = clone_a_dir.path().to_str().unwrap();
+        let vp_b = clone_b_dir.path().to_str().unwrap();
+
+        // A creates the file and pushes
+        fs::write(clone_a_dir.path().join("conflict.md"), "# Original\n").unwrap();
+        git_commit(vp_a, "create conflict.md").unwrap();
+        git_push(vp_a).unwrap();
+
+        // B pulls to get the file
+        git_pull(vp_b).unwrap();
+
+        // A modifies and pushes
+        fs::write(clone_a_dir.path().join("conflict.md"), "# Version A\n").unwrap();
+        git_commit(vp_a, "A's change").unwrap();
+        git_push(vp_a).unwrap();
+
+        // B modifies the same file locally and commits
+        fs::write(clone_b_dir.path().join("conflict.md"), "# Version B\n").unwrap();
+        git_commit(vp_b, "B's change").unwrap();
+
+        // B pulls with --rebase to cause a rebase conflict
+        let output = Command::new("git")
+            .args(["pull", "--rebase"])
+            .current_dir(clone_b_dir.path())
+            .output()
+            .unwrap();
+
+        // Pull should fail due to conflict
+        assert!(
+            !output.status.success(),
+            "Expected rebase conflict, but pull succeeded"
+        );
+
+        (bare_dir, clone_a_dir, clone_b_dir)
+    }
+
+    #[test]
+    fn test_conflict_mode_rebase_during_rebase_conflict() {
+        let (_bare, _clone_a, clone_b) = setup_rebase_conflict_pair();
+        let vp_b = clone_b.path().to_str().unwrap();
+
+        assert_eq!(get_conflict_mode(vp_b), "rebase");
+        assert!(is_rebase_in_progress(vp_b));
+        assert!(!is_merge_in_progress(vp_b));
+    }
+
+    #[test]
+    fn test_get_conflict_files_during_rebase() {
+        let (_bare, _clone_a, clone_b) = setup_rebase_conflict_pair();
+        let vp_b = clone_b.path().to_str().unwrap();
+
+        let conflicts = get_conflict_files(vp_b).unwrap();
+        assert!(
+            conflicts.contains(&"conflict.md".to_string()),
+            "Should detect conflict.md during rebase, got: {:?}",
+            conflicts
+        );
+    }
+
+    #[test]
+    fn test_resolve_and_continue_rebase() {
+        let (_bare, _clone_a, clone_b) = setup_rebase_conflict_pair();
+        let vp_b = clone_b.path().to_str().unwrap();
+
+        assert_eq!(get_conflict_mode(vp_b), "rebase");
+
+        // Resolve the conflict
+        git_resolve_conflict(vp_b, "conflict.md", "theirs").unwrap();
+        let remaining = get_conflict_files(vp_b).unwrap();
+        assert!(remaining.is_empty());
+
+        // Commit resolution should use rebase --continue
+        let result = git_commit_conflict_resolution(vp_b);
+        assert!(result.is_ok(), "rebase --continue failed: {:?}", result);
+
+        // After resolution, mode should be none
+        assert_eq!(get_conflict_mode(vp_b), "none");
+    }
+
+    #[test]
+    fn test_get_vault_pulse_with_commits() {
+        let dir = setup_git_repo();
+        let vault = dir.path();
+        let vp = vault.to_str().unwrap();
+
+        fs::write(vault.join("note.md"), "# Note\n").unwrap();
+        git_commit(vp, "Add note").unwrap();
+
+        fs::write(vault.join("project.md"), "# Project\n").unwrap();
+        git_commit(vp, "Add project").unwrap();
+
+        let pulse = get_vault_pulse(vp, 30).unwrap();
+
+        assert_eq!(pulse.len(), 2);
+        assert_eq!(pulse[0].message, "Add project");
+        assert_eq!(pulse[1].message, "Add note");
+        assert_eq!(pulse[0].files.len(), 1);
+        assert_eq!(pulse[0].files[0].path, "project.md");
+        assert_eq!(pulse[0].files[0].status, "added");
+        assert_eq!(pulse[0].added, 1);
+        assert_eq!(pulse[0].modified, 0);
+        assert!(!pulse[0].short_hash.is_empty());
+    }
+
+    #[test]
+    fn test_get_vault_pulse_no_git() {
+        let dir = TempDir::new().unwrap();
+        let vp = dir.path().to_str().unwrap();
+
+        let result = get_vault_pulse(vp, 30);
+        assert!(result.is_err());
+        assert!(result.unwrap_err().contains("Not a git repository"));
+    }
+
+    #[test]
+    fn test_get_vault_pulse_empty_repo() {
+        let dir = setup_git_repo();
+        let vp = dir.path().to_str().unwrap();
+
+        let pulse = get_vault_pulse(vp, 30).unwrap();
+        assert!(pulse.is_empty());
+    }
+
+    #[test]
+    fn test_get_vault_pulse_only_md_files() {
+        let dir = setup_git_repo();
+        let vault = dir.path();
+        let vp = vault.to_str().unwrap();
+
+        fs::write(vault.join("note.md"), "# Note\n").unwrap();
+        fs::write(vault.join("config.json"), "{}").unwrap();
+        git_commit(vp, "Add files").unwrap();
+
+        let pulse = get_vault_pulse(vp, 30).unwrap();
+        assert_eq!(pulse.len(), 1);
+        assert_eq!(pulse[0].files.len(), 1);
+        assert_eq!(pulse[0].files[0].path, "note.md");
+    }
+
+    #[test]
+    fn test_get_vault_pulse_respects_limit() {
+        let dir = setup_git_repo();
+        let vault = dir.path();
+        let vp = vault.to_str().unwrap();
+
+        for i in 0..5 {
+            fs::write(
+                vault.join(format!("note{}.md", i)),
+                format!("# Note {}\n", i),
+            )
+            .unwrap();
+            git_commit(vp, &format!("Add note {}", i)).unwrap();
+        }
+
+        let pulse = get_vault_pulse(vp, 3).unwrap();
+        assert_eq!(pulse.len(), 3);
+    }
+
+    #[test]
+    fn test_get_vault_pulse_modified_and_deleted() {
+        let dir = setup_git_repo();
+        let vault = dir.path();
+        let vp = vault.to_str().unwrap();
+
+        fs::write(vault.join("note.md"), "# Note\n").unwrap();
+        git_commit(vp, "Add note").unwrap();
+
+        fs::write(vault.join("note.md"), "# Updated\n").unwrap();
+        git_commit(vp, "Update note").unwrap();
+
+        let pulse = get_vault_pulse(vp, 30).unwrap();
+        assert_eq!(pulse[0].message, "Update note");
+        assert_eq!(pulse[0].files[0].status, "modified");
+        assert_eq!(pulse[0].modified, 1);
+    }
+
+    #[test]
+    fn test_get_vault_pulse_github_url() {
+        let dir = setup_git_repo();
+        let vault = dir.path();
+        let vp = vault.to_str().unwrap();
+
+        fs::write(vault.join("note.md"), "# Note\n").unwrap();
+        git_commit(vp, "Add note").unwrap();
+
+        Command::new("git")
+            .args([
+                "remote",
+                "add",
+                "origin",
+                "https://github.com/owner/repo.git",
+            ])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+
+        let pulse = get_vault_pulse(vp, 30).unwrap();
+        assert!(pulse[0].github_url.is_some());
+        let url = pulse[0].github_url.as_ref().unwrap();
+        assert!(url.starts_with("https://github.com/owner/repo/commit/"));
+    }
+
+    #[test]
+    fn test_get_vault_pulse_no_github_url_without_remote() {
+        let dir = setup_git_repo();
+        let vault = dir.path();
+        let vp = vault.to_str().unwrap();
+
+        fs::write(vault.join("note.md"), "# Note\n").unwrap();
+        git_commit(vp, "Add note").unwrap();
+
+        let pulse = get_vault_pulse(vp, 30).unwrap();
+        assert!(pulse[0].github_url.is_none());
+    }
+
+    #[test]
+    fn test_title_from_path() {
+        assert_eq!(title_from_path("note/my-project.md"), "my project");
+        assert_eq!(title_from_path("simple.md"), "simple");
+        assert_eq!(title_from_path("deep/nested/file.md"), "file");
+    }
+
+    #[test]
+    fn test_parse_pulse_output_basic() {
+        let stdout =
+            "abc123|abc123d|Add notes|2026-03-05T10:00:00+01:00\nA\tnote.md\nM\tproject.md\n";
+        let commits = parse_pulse_output(stdout, &None);
+
+        assert_eq!(commits.len(), 1);
+        assert_eq!(commits[0].message, "Add notes");
+        assert_eq!(commits[0].files.len(), 2);
+        assert_eq!(commits[0].files[0].status, "added");
+        assert_eq!(commits[0].files[1].status, "modified");
+        assert_eq!(commits[0].added, 1);
+        assert_eq!(commits[0].modified, 1);
+        assert!(commits[0].github_url.is_none());
+    }
+
+    #[test]
+    fn test_parse_pulse_output_with_github() {
+        let stdout = "abc123|abc123d|Msg|2026-03-05T10:00:00+01:00\nA\tnote.md\n";
+        let base = Some("https://github.com/o/r".to_string());
+        let commits = parse_pulse_output(stdout, &base);
+
+        assert_eq!(
+            commits[0].github_url.as_deref(),
+            Some("https://github.com/o/r/commit/abc123")
+        );
+    }
+
+    #[test]
+    fn test_parse_pulse_output_multiple_commits() {
+        let stdout = "aaa|aaa1234|First|2026-03-05T10:00:00+01:00\nA\ta.md\n\nbbb|bbb1234|Second|2026-03-04T10:00:00+01:00\nM\tb.md\nD\tc.md\n";
+        let commits = parse_pulse_output(stdout, &None);
+
+        assert_eq!(commits.len(), 2);
+        assert_eq!(commits[0].message, "First");
+        assert_eq!(commits[1].message, "Second");
+        assert_eq!(commits[1].files.len(), 2);
+        assert_eq!(commits[1].deleted, 1);
+    }
 }

src-tauri/src/indexing.rs

@@ -0,0 +1,701 @@
+use serde::Serialize;
+use std::path::{Path, PathBuf};
+use std::process::Command;
+use std::sync::Mutex;
+
+/// Resolved qmd binary location: path + optional working directory.
+/// The working dir is required for the bundled binary to find its node_modules.
+#[derive(Debug, Clone)]
+pub struct QmdBinary {
+    pub path: String,
+    pub work_dir: Option<PathBuf>,
+}
+
+impl QmdBinary {
+    /// Create a `Command` pre-configured with the correct working directory.
+    pub fn command(&self) -> Command {
+        let mut cmd = Command::new(&self.path);
+        if let Some(ref dir) = self.work_dir {
+            cmd.current_dir(dir);
+        }
+        cmd
+    }
+}
+
+static QMD_CACHE: Mutex<Option<QmdBinary>> = Mutex::new(None);
+
+/// Locate the qmd binary, checking bundled resource first, then known locations.
+/// Caches the result for subsequent calls.
+pub fn find_qmd_binary() -> Option<QmdBinary> {
+    if let Ok(guard) = QMD_CACHE.lock() {
+        if let Some(ref cached) = *guard {
+            return Some(cached.clone());
+        }
+    }
+
+    let result = find_qmd_binary_uncached();
+
+    if let Some(ref bin) = result {
+        if let Ok(mut guard) = QMD_CACHE.lock() {
+            *guard = Some(bin.clone());
+        }
+    }
+
+    result
+}
+
+fn find_qmd_binary_uncached() -> Option<QmdBinary> {
+    // 1. Check bundled binary (Tauri resource)
+    if let Some(bin) = find_bundled_qmd() {
+        return Some(bin);
+    }
+
+    // 2. Check known system locations
+    let candidates = [
+        dirs::home_dir().map(|h| h.join(".bun/bin/qmd").to_string_lossy().to_string()),
+        Some("/usr/local/bin/qmd".to_string()),
+        Some("/opt/homebrew/bin/qmd".to_string()),
+    ];
+    for candidate in candidates.into_iter().flatten() {
+        if Path::new(&candidate).exists() {
+            return Some(QmdBinary {
+                path: candidate,
+                work_dir: None,
+            });
+        }
+    }
+
+    // 3. Fallback: try PATH
+    Command::new("which")
+        .arg("qmd")
+        .output()
+        .ok()
+        .and_then(|o| {
+            if o.status.success() {
+                Some(QmdBinary {
+                    path: String::from_utf8_lossy(&o.stdout).trim().to_string(),
+                    work_dir: None,
+                })
+            } else {
+                None
+            }
+        })
+}
+
+/// Look for the bundled qmd binary inside the app bundle or dev resources.
+fn find_bundled_qmd() -> Option<QmdBinary> {
+    let exe = std::env::current_exe().ok()?;
+    let exe_dir = exe.parent()?;
+
+    // macOS app bundle: <app>/Contents/MacOS/laputa → <app>/Contents/Resources/qmd/qmd
+    let bundle_dir = exe_dir.parent()?.join("Resources").join("qmd");
+    if let Some(bin) = prepare_bundled_dir(&bundle_dir) {
+        return Some(bin);
+    }
+
+    // Dev mode: use compile-time CARGO_MANIFEST_DIR for reliable path resolution
+    let dev_dir = PathBuf::from(env!("CARGO_MANIFEST_DIR"))
+        .join("resources")
+        .join("qmd");
+    if let Some(bin) = prepare_bundled_dir(&dev_dir) {
+        return Some(bin);
+    }
+
+    // Dev mode fallback: walk up from exe_dir to find the project root
+    let mut dir = exe_dir.to_path_buf();
+    for _ in 0..6 {
+        let qmd_dir = dir.join("resources").join("qmd");
+        if let Some(bin) = prepare_bundled_dir(&qmd_dir) {
+            return Some(bin);
+        }
+        if !dir.pop() {
+            break;
+        }
+    }
+
+    None
+}
+
+/// Validate a bundled qmd directory and prepare the binary for execution.
+/// Sets execute permissions and removes macOS quarantine attributes.
+fn prepare_bundled_dir(qmd_dir: &Path) -> Option<QmdBinary> {
+    let qmd_path = qmd_dir.join("qmd");
+    if !qmd_path.exists() {
+        return None;
+    }
+
+    ensure_executable(&qmd_path);
+
+    // Remove macOS quarantine attributes that block execution of bundled binaries
+    #[cfg(target_os = "macos")]
+    {
+        let _ = Command::new("xattr")
+            .args(["-rd", "com.apple.quarantine"])
+            .arg(qmd_dir)
+            .output();
+    }
+
+    Some(QmdBinary {
+        path: qmd_path.to_string_lossy().to_string(),
+        work_dir: Some(qmd_dir.to_path_buf()),
+    })
+}
+
+/// Ensure a file has execute permission.
+#[cfg(unix)]
+fn ensure_executable(path: &Path) {
+    use std::os::unix::fs::PermissionsExt;
+    if let Ok(metadata) = path.metadata() {
+        let mode = metadata.permissions().mode();
+        if mode & 0o111 == 0 {
+            let mut perms = metadata.permissions();
+            perms.set_mode(mode | 0o755);
+            let _ = std::fs::set_permissions(path, perms);
+        }
+    }
+}
+
+#[cfg(not(unix))]
+fn ensure_executable(_path: &Path) {}
+
+/// Try to install qmd globally using bun. Returns Ok if installation succeeded.
+pub fn try_auto_install_qmd() -> Result<(), String> {
+    let bun = find_bun().ok_or("bun not found — cannot auto-install qmd")?;
+
+    log::info!("Auto-installing qmd via bun...");
+    let output = Command::new(&bun)
+        .args(["install", "-g", "qmd"])
+        .output()
+        .map_err(|e| format!("Failed to run bun install: {e}"))?;
+
+    if !output.status.success() {
+        let stderr = String::from_utf8_lossy(&output.stderr);
+        return Err(format!("bun install -g qmd failed: {stderr}"));
+    }
+
+    // Clear cache so the newly installed binary is discovered
+    clear_qmd_cache();
+    log::info!("qmd auto-install succeeded");
+    Ok(())
+}
+
+/// Locate bun binary for auto-installing qmd.
+fn find_bun() -> Option<PathBuf> {
+    let candidates = [
+        dirs::home_dir().map(|h| h.join(".bun/bin/bun")),
+        Some(PathBuf::from("/opt/homebrew/bin/bun")),
+        Some(PathBuf::from("/usr/local/bin/bun")),
+    ];
+    for candidate in candidates.into_iter().flatten() {
+        if candidate.exists() {
+            return Some(candidate);
+        }
+    }
+
+    // Fallback: try PATH
+    Command::new("which")
+        .arg("bun")
+        .output()
+        .ok()
+        .and_then(|o| {
+            if o.status.success() {
+                Some(PathBuf::from(
+                    String::from_utf8_lossy(&o.stdout).trim().to_string(),
+                ))
+            } else {
+                None
+            }
+        })
+}
+
+/// Clear the cached qmd binary (e.g. after path changes or installation).
+pub fn clear_qmd_cache() {
+    if let Ok(mut guard) = QMD_CACHE.lock() {
+        *guard = None;
+    }
+}
+
+#[derive(Debug, Serialize, Clone)]
+pub struct IndexStatus {
+    pub available: bool,
+    pub qmd_installed: bool,
+    pub collection_exists: bool,
+    pub indexed_count: usize,
+    pub embedded_count: usize,
+    pub pending_embed: usize,
+}
+
+/// Check whether the vault has a qmd index and its status.
+pub fn check_index_status(vault_path: &str) -> IndexStatus {
+    let qmd = match find_qmd_binary() {
+        Some(b) => b,
+        None => {
+            return IndexStatus {
+                available: false,
+                qmd_installed: false,
+                collection_exists: false,
+                indexed_count: 0,
+                embedded_count: 0,
+                pending_embed: 0,
+            }
+        }
+    };
+
+    let vault_name = vault_dir_name(vault_path);
+    let output = qmd.command().args(["status"]).output();
+
+    match output {
+        Ok(o) if o.status.success() => {
+            let stdout = String::from_utf8_lossy(&o.stdout);
+            parse_status_for_vault(&stdout, &vault_name)
+        }
+        _ => IndexStatus {
+            available: false,
+            qmd_installed: true,
+            collection_exists: false,
+            indexed_count: 0,
+            embedded_count: 0,
+            pending_embed: 0,
+        },
+    }
+}
+
+fn vault_dir_name(vault_path: &str) -> String {
+    Path::new(vault_path)
+        .file_name()
+        .and_then(|n| n.to_str())
+        .unwrap_or("laputa")
+        .to_lowercase()
+}
+
+fn parse_status_for_vault(status_output: &str, vault_name: &str) -> IndexStatus {
+    let mut collection_exists = false;
+    let mut indexed_count = 0;
+    let mut embedded_count = 0;
+    let mut pending_embed = 0;
+
+    // Look for collection section matching vault name
+    let mut in_vault_section = false;
+    for line in status_output.lines() {
+        let trimmed = line.trim();
+        // Collection headers look like: "  laputa (qmd://laputa/)"
+        if trimmed.contains(&format!("qmd://{vault_name}/")) {
+            collection_exists = true;
+            in_vault_section = true;
+            continue;
+        }
+        // New collection section starts
+        if trimmed.contains("qmd://") && !trimmed.contains(vault_name) {
+            in_vault_section = false;
+            continue;
+        }
+        if in_vault_section {
+            if let Some(count_str) = extract_count_from_line(trimmed, "Files:") {
+                indexed_count = count_str;
+            }
+        }
+    }
+
+    // Global counts from the Documents section
+    for line in status_output.lines() {
+        let trimmed = line.trim();
+        if trimmed.starts_with("Total:") {
+            if let Some(n) = extract_first_number(trimmed) {
+                if embedded_count == 0 && indexed_count == 0 {
+                    indexed_count = n;
+                }
+            }
+        } else if trimmed.starts_with("Vectors:") {
+            if let Some(n) = extract_first_number(trimmed) {
+                embedded_count = n;
+            }
+        } else if trimmed.starts_with("Pending:") {
+            if let Some(n) = extract_first_number(trimmed) {
+                pending_embed = n;
+            }
+        }
+    }
+
+    IndexStatus {
+        available: true,
+        qmd_installed: true,
+        collection_exists,
+        indexed_count,
+        embedded_count,
+        pending_embed,
+    }
+}
+
+fn extract_count_from_line(line: &str, prefix: &str) -> Option<usize> {
+    if !line.starts_with(prefix) {
+        return None;
+    }
+    extract_first_number(line)
+}
+
+fn extract_first_number(s: &str) -> Option<usize> {
+    s.split_whitespace()
+        .find_map(|word| word.parse::<usize>().ok())
+}
+
+/// Ensure a qmd collection exists for this vault. Creates one if missing.
+pub fn ensure_collection(vault_path: &str) -> Result<(), String> {
+    let qmd = find_qmd_binary().ok_or("qmd not installed")?;
+    let vault_name = vault_dir_name(vault_path);
+
+    // Check if collection already exists
+    let output = qmd
+        .command()
+        .args(["collection", "list"])
+        .output()
+        .map_err(|e| format!("Failed to list collections: {e}"))?;
+
+    if output.status.success() {
+        let stdout = String::from_utf8_lossy(&output.stdout);
+        if stdout.contains(&format!("qmd://{vault_name}/")) {
+            return Ok(());
+        }
+    }
+
+    // Create collection
+    qmd.command()
+        .args([
+            "collection",
+            "add",
+            vault_path,
+            "--name",
+            &vault_name,
+            "--mask",
+            "**/*.md",
+        ])
+        .output()
+        .map_err(|e| format!("Failed to create collection: {e}"))?;
+
+    Ok(())
+}
+
+#[derive(Debug, Serialize, Clone)]
+pub struct IndexingProgress {
+    pub phase: String,
+    pub current: usize,
+    pub total: usize,
+    pub done: bool,
+    pub error: Option<String>,
+}
+
+/// Run full indexing: update + embed. Returns progress updates via callback.
+pub fn run_full_index<F>(vault_path: &str, on_progress: F) -> Result<(), String>
+where
+    F: Fn(IndexingProgress),
+{
+    let qmd = find_qmd_binary().ok_or("qmd not installed")?;
+
+    ensure_collection(vault_path)?;
+
+    // Phase 1: update (scan files)
+    on_progress(IndexingProgress {
+        phase: "scanning".to_string(),
+        current: 0,
+        total: 0,
+        done: false,
+        error: None,
+    });
+
+    let update_output = qmd
+        .command()
+        .args(["update"])
+        .output()
+        .map_err(|e| format!("qmd update failed: {e}"))?;
+
+    if !update_output.status.success() {
+        let stderr = String::from_utf8_lossy(&update_output.stderr);
+        let err = format!("qmd update failed: {stderr}");
+        on_progress(IndexingProgress {
+            phase: "error".to_string(),
+            current: 0,
+            total: 0,
+            done: true,
+            error: Some(err.clone()),
+        });
+        return Err(err);
+    }
+
+    // Parse update output for counts
+    let update_stdout = String::from_utf8_lossy(&update_output.stdout);
+    let total = parse_indexed_count(&update_stdout);
+
+    on_progress(IndexingProgress {
+        phase: "scanning".to_string(),
+        current: total,
+        total,
+        done: false,
+        error: None,
+    });
+
+    // Phase 2: embed (generate vectors)
+    on_progress(IndexingProgress {
+        phase: "embedding".to_string(),
+        current: 0,
+        total,
+        done: false,
+        error: None,
+    });
+
+    let embed_output = qmd
+        .command()
+        .args(["embed"])
+        .output()
+        .map_err(|e| format!("qmd embed failed: {e}"))?;
+
+    if !embed_output.status.success() {
+        let stderr = String::from_utf8_lossy(&embed_output.stderr);
+        // Embedding failure is non-fatal — keyword search still works
+        log::warn!("qmd embed failed (keyword search still works): {stderr}");
+        on_progress(IndexingProgress {
+            phase: "complete".to_string(),
+            current: total,
+            total,
+            done: true,
+            error: Some("Embedding failed — keyword search only".to_string()),
+        });
+        return Ok(());
+    }
+
+    on_progress(IndexingProgress {
+        phase: "complete".to_string(),
+        current: total,
+        total,
+        done: true,
+        error: None,
+    });
+
+    Ok(())
+}
+
+fn parse_indexed_count(update_output: &str) -> usize {
+    // qmd update output typically contains lines like "Indexed 9078 files"
+    for line in update_output.lines() {
+        if let Some(n) = extract_first_number(line) {
+            return n;
+        }
+    }
+    0
+}
+
+/// Run incremental update for a single file change.
+pub fn run_incremental_update(vault_path: &str) -> Result<(), String> {
+    let qmd = find_qmd_binary().ok_or("qmd not installed")?;
+
+    // Verify collection exists
+    let vault_name = vault_dir_name(vault_path);
+    let list_output = qmd
+        .command()
+        .args(["collection", "list"])
+        .output()
+        .map_err(|e| format!("Failed to list collections: {e}"))?;
+
+    if list_output.status.success() {
+        let stdout = String::from_utf8_lossy(&list_output.stdout);
+        if !stdout.contains(&format!("qmd://{vault_name}/")) {
+            // Collection doesn't exist yet — skip incremental, full index needed
+            return Ok(());
+        }
+    }
+
+    let output = qmd
+        .command()
+        .args(["update"])
+        .output()
+        .map_err(|e| format!("qmd incremental update failed: {e}"))?;
+
+    if !output.status.success() {
+        let stderr = String::from_utf8_lossy(&output.stderr);
+        return Err(format!("qmd update failed: {stderr}"));
+    }
+
+    Ok(())
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn qmd_binary_command_sets_work_dir() {
+        let qmd = QmdBinary {
+            path: "/bin/echo".to_string(),
+            work_dir: Some(PathBuf::from("/tmp")),
+        };
+        let cmd = qmd.command();
+        let dbg = format!("{:?}", cmd);
+        assert!(dbg.contains("/bin/echo"));
+    }
+
+    #[test]
+    fn qmd_binary_command_no_work_dir() {
+        let qmd = QmdBinary {
+            path: "/bin/echo".to_string(),
+            work_dir: None,
+        };
+        let output = qmd.command().arg("hello").output().unwrap();
+        assert!(output.status.success());
+    }
+
+    #[test]
+    fn vault_dir_name_extracts_last_segment() {
+        assert_eq!(vault_dir_name("/Users/luca/Laputa"), "laputa");
+        assert_eq!(vault_dir_name("/home/user/MyVault"), "myvault");
+    }
+
+    #[test]
+    fn vault_dir_name_fallback() {
+        assert_eq!(vault_dir_name(""), "laputa");
+    }
+
+    #[test]
+    fn extract_first_number_works() {
+        assert_eq!(
+            extract_first_number("Total: 9078 files indexed"),
+            Some(9078)
+        );
+        assert_eq!(extract_first_number("Vectors: 14676 embedded"), Some(14676));
+        assert_eq!(extract_first_number("no numbers here"), None);
+    }
+
+    #[test]
+    fn parse_status_finds_collection() {
+        let status = r#"
+QMD Status
+
+Index: /Users/luca/.cache/qmd/index.sqlite
+Size:  100.9 MB
+
+Documents
+  Total:    9115 files indexed
+  Vectors:  14676 embedded
+  Pending:  26 need embedding
+
+Collections
+  laputa (qmd://laputa/)
+    Pattern:  **/*.md
+    Files:    9078 (updated 20d ago)
+"#;
+        let result = parse_status_for_vault(status, "laputa");
+        assert!(result.collection_exists);
+        assert_eq!(result.indexed_count, 9078);
+        assert_eq!(result.embedded_count, 14676);
+        assert_eq!(result.pending_embed, 26);
+    }
+
+    #[test]
+    fn parse_status_missing_collection() {
+        let status = r#"
+QMD Status
+
+Documents
+  Total:    100 files indexed
+  Vectors:  50 embedded
+  Pending:  0
+
+Collections
+  other (qmd://other/)
+    Files:    100
+"#;
+        let result = parse_status_for_vault(status, "laputa");
+        assert!(!result.collection_exists);
+    }
+
+    #[test]
+    fn extract_count_from_line_works() {
+        assert_eq!(
+            extract_count_from_line("Files:    9078 (updated 20d ago)", "Files:"),
+            Some(9078)
+        );
+        assert_eq!(extract_count_from_line("Pattern:  **/*.md", "Files:"), None);
+    }
+
+    #[test]
+    fn parse_indexed_count_from_output() {
+        assert_eq!(parse_indexed_count("Indexed 342 files in 1.2s"), 342);
+        assert_eq!(parse_indexed_count("No output"), 0);
+    }
+
+    #[test]
+    fn ensure_executable_sets_permission() {
+        use std::fs;
+        let dir = tempfile::tempdir().unwrap();
+        let file = dir.path().join("test-bin");
+        fs::write(&file, "#!/bin/sh\necho ok").unwrap();
+
+        // Start with no execute permission
+        #[cfg(unix)]
+        {
+            use std::os::unix::fs::PermissionsExt;
+            fs::set_permissions(&file, fs::Permissions::from_mode(0o644)).unwrap();
+            assert_eq!(fs::metadata(&file).unwrap().permissions().mode() & 0o111, 0);
+
+            ensure_executable(&file);
+            assert_ne!(fs::metadata(&file).unwrap().permissions().mode() & 0o111, 0);
+        }
+    }
+
+    #[test]
+    fn ensure_executable_noop_when_already_executable() {
+        use std::fs;
+        let dir = tempfile::tempdir().unwrap();
+        let file = dir.path().join("test-bin");
+        fs::write(&file, "#!/bin/sh\necho ok").unwrap();
+
+        #[cfg(unix)]
+        {
+            use std::os::unix::fs::PermissionsExt;
+            fs::set_permissions(&file, fs::Permissions::from_mode(0o755)).unwrap();
+            ensure_executable(&file);
+            let mode = fs::metadata(&file).unwrap().permissions().mode();
+            assert_ne!(mode & 0o111, 0);
+        }
+    }
+
+    #[test]
+    fn prepare_bundled_dir_returns_none_for_missing_binary() {
+        let dir = tempfile::tempdir().unwrap();
+        assert!(prepare_bundled_dir(dir.path()).is_none());
+    }
+
+    #[test]
+    fn prepare_bundled_dir_finds_and_prepares_binary() {
+        use std::fs;
+        let dir = tempfile::tempdir().unwrap();
+        let qmd_path = dir.path().join("qmd");
+        fs::write(&qmd_path, "#!/bin/sh\necho ok").unwrap();
+
+        #[cfg(unix)]
+        {
+            use std::os::unix::fs::PermissionsExt;
+            fs::set_permissions(&qmd_path, fs::Permissions::from_mode(0o644)).unwrap();
+        }
+
+        let result = prepare_bundled_dir(dir.path());
+        assert!(result.is_some());
+        let bin = result.unwrap();
+        assert!(bin.path.ends_with("qmd"));
+        assert_eq!(bin.work_dir.unwrap(), dir.path());
+
+        // Verify execute permission was set
+        #[cfg(unix)]
+        {
+            use std::os::unix::fs::PermissionsExt;
+            assert_ne!(
+                fs::metadata(&qmd_path).unwrap().permissions().mode() & 0o111,
+                0
+            );
+        }
+    }
+
+    #[test]
+    fn find_bun_returns_some_if_available() {
+        // This test may succeed or fail depending on the system.
+        // It verifies the function doesn't panic.
+        let _ = find_bun();
+    }
+}

src-tauri/src/lib.rs

@@ -3,12 +3,15 @@ pub mod claude_cli;
 pub mod frontmatter;
 pub mod git;
 pub mod github;
+pub mod indexing;
 pub mod mcp;
 pub mod menu;
 pub mod search;
 pub mod settings;
 pub mod theme;
 pub mod vault;
+pub mod vault_config;
+pub mod vault_list;
 
 use std::borrow::Cow;
 use std::path::Path;
@@ -18,12 +21,15 @@ use std::sync::Mutex;
 use ai_chat::{AiChatRequest, AiChatResponse};
 use claude_cli::{AgentStreamRequest, ChatStreamRequest, ClaudeCliStatus, ClaudeStreamEvent};
 use frontmatter::FrontmatterValue;
-use git::{GitCommit, GitPullResult, LastCommitInfo, ModifiedFile};
+use git::{GitCommit, GitPullResult, LastCommitInfo, ModifiedFile, PulseCommit};
 use github::{DeviceFlowPollResult, DeviceFlowStart, GitHubUser, GithubRepo};
+use indexing::{IndexStatus, IndexingProgress};
 use search::SearchResponse;
 use settings::Settings;
 use theme::{ThemeFile, VaultSettings};
 use vault::{RenameResult, VaultEntry};
+use vault_config::VaultConfig;
+use vault_list::VaultList;
 
 /// Expand a leading `~` or `~/` in a path string to the user's home directory.
 /// Returns the original string unchanged if it doesn't start with `~` or if the
@@ -106,20 +112,34 @@ fn get_file_diff_at_commit(
     git::get_file_diff_at_commit(&vault_path, &path, &commit_hash)
 }
 
+#[tauri::command]
+fn get_vault_pulse(vault_path: String, limit: Option<usize>) -> Result<Vec<PulseCommit>, String> {
+    let vault_path = expand_tilde(&vault_path);
+    let limit = limit.unwrap_or(30);
+    git::get_vault_pulse(&vault_path, limit)
+}
+
 #[tauri::command]
 fn git_commit(vault_path: String, message: String) -> Result<String, String> {
     let vault_path = expand_tilde(&vault_path);
     git::git_commit(&vault_path, &message)
 }
 
-#[tauri::command]
-fn get_build_number() -> String {
-    {
-        let n = std::env::var("BUILD_NUMBER").unwrap_or_else(|_| "0".to_string());
-        format!("b{}", n)
+fn parse_build_label(version: &str) -> String {
+    let parts: Vec<&str> = version.split('.').collect();
+    match parts.as_slice() {
+        [_, minor, patch] if minor.len() >= 6 => format!("b{}", patch),
+        [_, _, _] => "dev".to_string(),
+        _ => "b?".to_string(),
     }
 }
 
+#[tauri::command]
+fn get_build_number(app_handle: tauri::AppHandle) -> String {
+    let version = app_handle.package_info().version.to_string();
+    parse_build_label(&version)
+}
+
 #[tauri::command]
 fn get_last_commit_info(vault_path: String) -> Result<Option<LastCommitInfo>, String> {
     let vault_path = expand_tilde(&vault_path);
@@ -132,6 +152,30 @@ fn git_pull(vault_path: String) -> Result<GitPullResult, String> {
     git::git_pull(&vault_path)
 }
 
+#[tauri::command]
+fn get_conflict_files(vault_path: String) -> Result<Vec<String>, String> {
+    let vault_path = expand_tilde(&vault_path);
+    git::get_conflict_files(&vault_path)
+}
+
+#[tauri::command]
+fn get_conflict_mode(vault_path: String) -> String {
+    let vault_path = expand_tilde(&vault_path);
+    git::get_conflict_mode(&vault_path)
+}
+
+#[tauri::command]
+fn git_resolve_conflict(vault_path: String, file: String, strategy: String) -> Result<(), String> {
+    let vault_path = expand_tilde(&vault_path);
+    git::git_resolve_conflict(&vault_path, &file, &strategy)
+}
+
+#[tauri::command]
+fn git_commit_conflict_resolution(vault_path: String) -> Result<String, String> {
+    let vault_path = expand_tilde(&vault_path);
+    git::git_commit_conflict_resolution(&vault_path)
+}
+
 #[tauri::command]
 fn git_push(vault_path: String) -> Result<String, String> {
     let vault_path = expand_tilde(&vault_path);
@@ -207,6 +251,12 @@ fn purge_trash(vault_path: String) -> Result<Vec<String>, String> {
     vault::purge_trash(&vault_path)
 }
 
+#[tauri::command]
+fn delete_note(path: String) -> Result<String, String> {
+    let path = expand_tilde(&path);
+    vault::delete_note(&path)
+}
+
 #[tauri::command]
 fn migrate_is_a_to_type(vault_path: String) -> Result<usize, String> {
     let vault_path = expand_tilde(&vault_path);
@@ -262,8 +312,19 @@ fn batch_trash_notes(paths: Vec<String>) -> Result<usize, String> {
 }
 
 #[tauri::command]
-fn update_menu_state(app_handle: tauri::AppHandle, has_active_note: bool) -> Result<(), String> {
+fn update_menu_state(
+    app_handle: tauri::AppHandle,
+    has_active_note: bool,
+    has_modified_files: Option<bool>,
+    has_conflicts: Option<bool>,
+) -> Result<(), String> {
     menu::set_note_items_enabled(&app_handle, has_active_note);
+    if let Some(v) = has_modified_files {
+        menu::set_git_commit_items_enabled(&app_handle, v);
+    }
+    if let Some(v) = has_conflicts {
+        menu::set_git_conflict_items_enabled(&app_handle, v);
+    }
     Ok(())
 }
 
@@ -277,6 +338,16 @@ fn save_settings(settings: Settings) -> Result<(), String> {
     settings::save_settings(settings)
 }
 
+#[tauri::command]
+fn load_vault_list() -> Result<VaultList, String> {
+    vault_list::load_vault_list()
+}
+
+#[tauri::command]
+fn save_vault_list(list: VaultList) -> Result<(), String> {
+    vault_list::save_vault_list(&list)
+}
+
 #[tauri::command]
 async fn github_list_repos(token: String) -> Result<Vec<GithubRepo>, String> {
     github::github_list_repos(&token).await
@@ -326,6 +397,77 @@ async fn search_vault(
         .map_err(|e| format!("Search task failed: {}", e))?
 }
 
+#[tauri::command]
+fn get_index_status(vault_path: String) -> IndexStatus {
+    let vault_path = expand_tilde(&vault_path);
+    indexing::check_index_status(&vault_path)
+}
+
+fn emit_unavailable(app_handle: &tauri::AppHandle) {
+    use tauri::Emitter;
+    let _ = app_handle.emit(
+        "indexing-progress",
+        IndexingProgress {
+            phase: "unavailable".to_string(),
+            current: 0,
+            total: 0,
+            done: true,
+            error: Some("qmd not available".to_string()),
+        },
+    );
+}
+
+#[tauri::command]
+async fn start_indexing(app_handle: tauri::AppHandle, vault_path: String) -> Result<(), String> {
+    use tauri::Emitter;
+    let vault_path = expand_tilde(&vault_path).into_owned();
+    tokio::task::spawn_blocking(move || {
+        if indexing::find_qmd_binary().is_none() {
+            log::info!("qmd binary not found — attempting auto-install via bun");
+            let _ = app_handle.emit(
+                "indexing-progress",
+                IndexingProgress {
+                    phase: "installing".to_string(),
+                    current: 0,
+                    total: 0,
+                    done: false,
+                    error: None,
+                },
+            );
+
+            match indexing::try_auto_install_qmd() {
+                Ok(()) if indexing::find_qmd_binary().is_some() => {
+                    log::info!("qmd auto-installed successfully, proceeding with indexing");
+                }
+                Ok(()) => {
+                    log::warn!("qmd auto-install reported success but binary still not found");
+                    emit_unavailable(&app_handle);
+                    return Err("qmd not available after install".to_string());
+                }
+                Err(e) => {
+                    log::info!("qmd auto-install failed: {e}");
+                    emit_unavailable(&app_handle);
+                    return Err(format!("qmd not available: {e}"));
+                }
+            }
+        }
+
+        indexing::run_full_index(&vault_path, |progress| {
+            let _ = app_handle.emit("indexing-progress", &progress);
+        })
+    })
+    .await
+    .map_err(|e| format!("Indexing task failed: {e}"))?
+}
+
+#[tauri::command]
+async fn trigger_incremental_index(vault_path: String) -> Result<(), String> {
+    let vault_path = expand_tilde(&vault_path).into_owned();
+    tokio::task::spawn_blocking(move || indexing::run_incremental_update(&vault_path))
+        .await
+        .map_err(|e| format!("Incremental index failed: {e}"))?
+}
+
 struct WsBridgeChild(Mutex<Option<Child>>);
 
 #[tauri::command]
@@ -336,6 +478,13 @@ async fn register_mcp_tools(vault_path: String) -> Result<String, String> {
         .map_err(|e| format!("Registration task failed: {e}"))?
 }
 
+#[tauri::command]
+async fn check_mcp_status() -> Result<mcp::McpStatus, String> {
+    tokio::task::spawn_blocking(mcp::check_mcp_status)
+        .await
+        .map_err(|e| format!("MCP status check failed: {e}"))
+}
+
 #[tauri::command]
 fn list_themes(vault_path: String) -> Result<Vec<ThemeFile>, String> {
     let vault_path = expand_tilde(&vault_path);
@@ -361,9 +510,9 @@ fn save_vault_settings(vault_path: String, settings: VaultSettings) -> Result<()
 }
 
 #[tauri::command]
-fn set_active_theme(vault_path: String, theme_id: String) -> Result<(), String> {
+fn set_active_theme(vault_path: String, theme_id: Option<String>) -> Result<(), String> {
     let vault_path = expand_tilde(&vault_path);
-    theme::set_active_theme(&vault_path, &theme_id)
+    theme::set_active_theme(&vault_path, theme_id.as_deref())
 }
 
 #[tauri::command]
@@ -372,6 +521,36 @@ fn create_theme(vault_path: String, source_id: Option<String>) -> Result<String,
     theme::create_theme(&vault_path, source_id.as_deref())
 }
 
+#[tauri::command]
+fn create_vault_theme(vault_path: String, name: Option<String>) -> Result<String, String> {
+    let vault_path = expand_tilde(&vault_path);
+    theme::create_vault_theme(&vault_path, name.as_deref())
+}
+
+#[tauri::command]
+fn ensure_vault_themes(vault_path: String) -> Result<(), String> {
+    let vault_path = expand_tilde(&vault_path);
+    theme::ensure_vault_themes(&vault_path)
+}
+
+#[tauri::command]
+fn restore_default_themes(vault_path: String) -> Result<String, String> {
+    let vault_path = expand_tilde(&vault_path);
+    theme::restore_default_themes(&vault_path)
+}
+
+#[tauri::command]
+fn get_vault_config(vault_path: String) -> Result<VaultConfig, String> {
+    let vault_path = expand_tilde(&vault_path);
+    vault_config::get_vault_config(&vault_path)
+}
+
+#[tauri::command]
+fn save_vault_config(vault_path: String, config: VaultConfig) -> Result<(), String> {
+    let vault_path = expand_tilde(&vault_path);
+    vault_config::save_vault_config(&vault_path, config)
+}
+
 fn log_startup_result(label: &str, result: Result<usize, String>) {
     match result {
         Ok(n) if n > 0 => log::info!("{}: {} files", label, n),
@@ -398,8 +577,10 @@ fn run_startup_tasks() {
         vault::migrate_is_a_to_type(vp_str),
     );
 
-    // Seed _themes/ with built-in themes if missing
+    // Seed _themes/ with built-in JSON themes (legacy) if missing
     theme::seed_default_themes(vp_str);
+    // Seed theme/ with built-in vault theme notes if missing
+    theme::seed_vault_themes(vp_str);
 
     // Register Laputa MCP server in Claude Code and Cursor configs
     match mcp::register_mcp(vp_str) {
@@ -445,13 +626,36 @@ mod tests {
     }
 
     #[test]
-    fn get_build_number_returns_prefixed_value() {
-        let result = get_build_number();
-        assert!(
-            result.starts_with('b'),
-            "expected 'b' prefix, got: {}",
-            result
-        );
+    fn parse_build_label_release_version() {
+        assert_eq!(parse_build_label("0.20260303.281"), "b281");
+        assert_eq!(parse_build_label("0.20251215.42"), "b42");
+    }
+
+    #[test]
+    fn parse_build_label_dev_version() {
+        assert_eq!(parse_build_label("0.1.0"), "dev");
+        assert_eq!(parse_build_label("0.0.0"), "dev");
+    }
+
+    #[test]
+    fn parse_build_label_malformed() {
+        assert_eq!(parse_build_label("invalid"), "b?");
+        assert_eq!(parse_build_label(""), "b?");
+    }
+}
+
+fn spawn_ws_bridge(app: &mut tauri::App) {
+    use tauri::Manager;
+    let vault_path = dirs::home_dir()
+        .map(|h| h.join("Laputa"))
+        .unwrap_or_default();
+    let vp_str = vault_path.to_string_lossy().to_string();
+    match mcp::spawn_ws_bridge(&vp_str) {
+        Ok(child) => {
+            let state: tauri::State<'_, WsBridgeChild> = app.state();
+            *state.0.lock().unwrap() = Some(child);
+        }
+        Err(e) => log::warn!("Failed to start ws-bridge: {}", e),
     }
 }
 
@@ -485,23 +689,7 @@ pub fn run() {
             }
 
             run_startup_tasks();
-
-            // Spawn the MCP WebSocket bridge for the default vault
-            {
-                use tauri::Manager;
-                let vault_path = dirs::home_dir()
-                    .map(|h| h.join("Laputa"))
-                    .unwrap_or_default();
-                let vp_str = vault_path.to_string_lossy().to_string();
-                match mcp::spawn_ws_bridge(&vp_str) {
-                    Ok(child) => {
-                        let state: tauri::State<'_, WsBridgeChild> = app.state();
-                        *state.0.lock().unwrap() = Some(child);
-                    }
-                    Err(e) => log::warn!("Failed to start ws-bridge: {}", e),
-                }
-            }
-
+            spawn_ws_bridge(app);
             Ok(())
         })
         .invoke_handler(tauri::generate_handler![
@@ -515,11 +703,16 @@ pub fn run() {
             get_modified_files,
             get_file_diff,
             get_file_diff_at_commit,
+            get_vault_pulse,
             git_commit,
             get_build_number,
             get_last_commit_info,
             git_pull,
             git_push,
+            get_conflict_files,
+            get_conflict_mode,
+            git_resolve_conflict,
+            git_commit_conflict_resolution,
             ai_chat,
             check_claude_cli,
             stream_claude_chat,
@@ -527,12 +720,15 @@ pub fn run() {
             save_image,
             copy_image_to_vault,
             purge_trash,
+            delete_note,
             migrate_is_a_to_type,
             batch_archive_notes,
             batch_trash_notes,
             get_settings,
             update_menu_state,
             save_settings,
+            load_vault_list,
+            save_vault_list,
             github_list_repos,
             github_create_repo,
             clone_repo,
@@ -540,16 +736,25 @@ pub fn run() {
             github_device_flow_poll,
             github_get_user,
             search_vault,
+            get_index_status,
+            start_indexing,
+            trigger_incremental_index,
             create_getting_started_vault,
             check_vault_exists,
             get_default_vault_path,
             register_mcp_tools,
+            check_mcp_status,
             list_themes,
             get_theme,
             get_vault_settings,
             save_vault_settings,
             set_active_theme,
-            create_theme
+            create_theme,
+            create_vault_theme,
+            ensure_vault_themes,
+            restore_default_themes,
+            get_vault_config,
+            save_vault_config
         ])
         .build(tauri::generate_context!())
         .expect("error while building tauri application")

src-tauri/src/mcp.rs

@@ -1,6 +1,19 @@
+use serde::Serialize;
 use std::path::{Path, PathBuf};
 use std::process::{Child, Command};
 
+/// Status of the MCP server installation.
+#[derive(Debug, Serialize, Clone, PartialEq)]
+#[serde(rename_all = "snake_case")]
+pub enum McpStatus {
+    /// MCP is registered in Claude config and server files exist.
+    Installed,
+    /// MCP server files or config are missing but can be installed.
+    NotInstalled,
+    /// Claude CLI is not installed — must install that first.
+    NoClaudeCli,
+}
+
 /// Find the `node` binary path at runtime.
 pub(crate) fn find_node() -> Result<PathBuf, String> {
     let output = Command::new("which")
@@ -27,10 +40,12 @@ pub(crate) fn mcp_server_dir() -> Result<PathBuf, String> {
     }
 
     let exe = std::env::current_exe().map_err(|e| format!("Cannot find executable: {e}"))?;
+    // On macOS the exe lives at Contents/MacOS/<binary>.
+    // Resources are placed at Contents/Resources/ by Tauri.
     let release_path = exe
         .parent()
         .and_then(|p| p.parent())
-        .map(|p| p.join("mcp-server"))
+        .map(|p| p.join("Resources").join("mcp-server"))
         .ok_or_else(|| "Cannot resolve mcp-server directory".to_string())?;
     if release_path.join("ws-bridge.js").exists() {
         return Ok(release_path);
@@ -142,6 +157,57 @@ fn upsert_mcp_config(config_path: &Path, entry: &serde_json::Value) -> Result<bo
     Ok(was_update)
 }
 
+/// Check whether the MCP server is properly installed and registered.
+///
+/// Returns `Installed` when the laputa entry exists in `~/.claude/mcp.json`
+/// and the referenced index.js file is present. Returns `NoClaudeCli` when
+/// the Claude CLI binary cannot be found. Otherwise returns `NotInstalled`.
+pub fn check_mcp_status() -> McpStatus {
+    // Check Claude CLI first — no point installing MCP if Claude isn't available
+    if crate::claude_cli::find_claude_binary().is_err() {
+        return McpStatus::NoClaudeCli;
+    }
+
+    let config_path = match dirs::home_dir() {
+        Some(h) => h.join(".claude").join("mcp.json"),
+        None => return McpStatus::NotInstalled,
+    };
+
+    if !config_path.exists() {
+        return McpStatus::NotInstalled;
+    }
+
+    let raw = match std::fs::read_to_string(&config_path) {
+        Ok(r) => r,
+        Err(_) => return McpStatus::NotInstalled,
+    };
+
+    let config: serde_json::Value = match serde_json::from_str(&raw) {
+        Ok(c) => c,
+        Err(_) => return McpStatus::NotInstalled,
+    };
+
+    let entry = &config["mcpServers"]["laputa"];
+    if entry.is_null() {
+        return McpStatus::NotInstalled;
+    }
+
+    // Verify the referenced index.js actually exists on disk
+    if let Some(index_js) = entry["args"]
+        .as_array()
+        .and_then(|a| a.first())
+        .and_then(|v| v.as_str())
+    {
+        if !Path::new(index_js).exists() {
+            return McpStatus::NotInstalled;
+        }
+    } else {
+        return McpStatus::NotInstalled;
+    }
+
+    McpStatus::Installed
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;
@@ -312,4 +378,29 @@ mod tests {
         // With empty config list, there were no updates, so status should be "registered"
         assert_eq!(status, "registered");
     }
+
+    #[test]
+    fn check_mcp_status_returns_valid_variant() {
+        // On a dev machine with Claude CLI and MCP registered, this should be Installed.
+        // On CI without Claude it might be NoClaudeCli. Either way it must not panic.
+        let status = check_mcp_status();
+        assert!(
+            matches!(
+                status,
+                McpStatus::Installed | McpStatus::NotInstalled | McpStatus::NoClaudeCli
+            ),
+            "unexpected status: {:?}",
+            status
+        );
+    }
+
+    #[test]
+    fn mcp_status_serializes_to_snake_case() {
+        let json = serde_json::to_string(&McpStatus::Installed).unwrap();
+        assert_eq!(json, r#""installed""#);
+        let json = serde_json::to_string(&McpStatus::NotInstalled).unwrap();
+        assert_eq!(json, r#""not_installed""#);
+        let json = serde_json::to_string(&McpStatus::NoClaudeCli).unwrap();
+        assert_eq!(json, r#""no_claude_cli""#);
+    }
 }

src-tauri/src/menu.rs

@@ -5,47 +5,109 @@ use tauri::{
 
 // Custom menu item IDs that emit events to the frontend.
 const APP_SETTINGS: &str = "app-settings";
+const APP_CHECK_FOR_UPDATES: &str = "app-check-for-updates";
+
 const FILE_NEW_NOTE: &str = "file-new-note";
+const FILE_NEW_TYPE: &str = "file-new-type";
+const FILE_DAILY_NOTE: &str = "file-daily-note";
 const FILE_QUICK_OPEN: &str = "file-quick-open";
 const FILE_SAVE: &str = "file-save";
 const FILE_CLOSE_TAB: &str = "file-close-tab";
+
+const EDIT_FIND_IN_VAULT: &str = "edit-find-in-vault";
+const EDIT_TOGGLE_RAW_EDITOR: &str = "edit-toggle-raw-editor";
+const EDIT_TOGGLE_DIFF: &str = "edit-toggle-diff";
+
 const VIEW_EDITOR_ONLY: &str = "view-editor-only";
 const VIEW_EDITOR_LIST: &str = "view-editor-list";
 const VIEW_ALL: &str = "view-all";
-const VIEW_TOGGLE_INSPECTOR: &str = "view-toggle-inspector";
+const VIEW_TOGGLE_PROPERTIES: &str = "view-toggle-properties";
+const VIEW_TOGGLE_AI_CHAT: &str = "view-toggle-ai-chat";
+const VIEW_TOGGLE_BACKLINKS: &str = "view-toggle-backlinks";
 const VIEW_COMMAND_PALETTE: &str = "view-command-palette";
 const VIEW_ZOOM_IN: &str = "view-zoom-in";
 const VIEW_ZOOM_OUT: &str = "view-zoom-out";
 const VIEW_ZOOM_RESET: &str = "view-zoom-reset";
-const NOTE_ARCHIVE: &str = "note-archive";
-const NOTE_TRASH: &str = "note-trash";
-const EDIT_FIND_IN_VAULT: &str = "edit-find-in-vault";
 const VIEW_GO_BACK: &str = "view-go-back";
 const VIEW_GO_FORWARD: &str = "view-go-forward";
 
+const GO_ALL_NOTES: &str = "go-all-notes";
+const GO_FAVORITES: &str = "go-favorites";
+const GO_ARCHIVED: &str = "go-archived";
+const GO_TRASH: &str = "go-trash";
+const GO_CHANGES: &str = "go-changes";
+
+const NOTE_ARCHIVE: &str = "note-archive";
+const NOTE_TRASH: &str = "note-trash";
+
+const VAULT_OPEN: &str = "vault-open";
+const VAULT_REMOVE: &str = "vault-remove";
+const VAULT_RESTORE_GETTING_STARTED: &str = "vault-restore-getting-started";
+const VAULT_NEW_THEME: &str = "vault-new-theme";
+const VAULT_RESTORE_DEFAULT_THEMES: &str = "vault-restore-default-themes";
+const VAULT_COMMIT_PUSH: &str = "vault-commit-push";
+const VAULT_RESOLVE_CONFLICTS: &str = "vault-resolve-conflicts";
+const VAULT_VIEW_CHANGES: &str = "vault-view-changes";
+const VAULT_INSTALL_MCP: &str = "vault-install-mcp";
+
 const CUSTOM_IDS: &[&str] = &[
     APP_SETTINGS,
+    APP_CHECK_FOR_UPDATES,
     FILE_NEW_NOTE,
+    FILE_NEW_TYPE,
+    FILE_DAILY_NOTE,
     FILE_QUICK_OPEN,
     FILE_SAVE,
     FILE_CLOSE_TAB,
-    NOTE_ARCHIVE,
-    NOTE_TRASH,
     EDIT_FIND_IN_VAULT,
+    EDIT_TOGGLE_RAW_EDITOR,
+    EDIT_TOGGLE_DIFF,
     VIEW_EDITOR_ONLY,
     VIEW_EDITOR_LIST,
     VIEW_ALL,
-    VIEW_TOGGLE_INSPECTOR,
+    VIEW_TOGGLE_PROPERTIES,
+    VIEW_TOGGLE_AI_CHAT,
+    VIEW_TOGGLE_BACKLINKS,
     VIEW_COMMAND_PALETTE,
     VIEW_ZOOM_IN,
     VIEW_ZOOM_OUT,
     VIEW_ZOOM_RESET,
     VIEW_GO_BACK,
     VIEW_GO_FORWARD,
+    GO_ALL_NOTES,
+    GO_FAVORITES,
+    GO_ARCHIVED,
+    GO_TRASH,
+    GO_CHANGES,
+    NOTE_ARCHIVE,
+    NOTE_TRASH,
+    VAULT_OPEN,
+    VAULT_REMOVE,
+    VAULT_RESTORE_GETTING_STARTED,
+    VAULT_NEW_THEME,
+    VAULT_RESTORE_DEFAULT_THEMES,
+    VAULT_COMMIT_PUSH,
+    VAULT_RESOLVE_CONFLICTS,
+    VAULT_VIEW_CHANGES,
+    VAULT_INSTALL_MCP,
 ];
 
 /// IDs of menu items that should be disabled when no note tab is active.
-const NOTE_DEPENDENT_IDS: &[&str] = &[FILE_SAVE, FILE_CLOSE_TAB, NOTE_ARCHIVE, NOTE_TRASH];
+const NOTE_DEPENDENT_IDS: &[&str] = &[
+    FILE_SAVE,
+    FILE_CLOSE_TAB,
+    NOTE_ARCHIVE,
+    NOTE_TRASH,
+    EDIT_TOGGLE_RAW_EDITOR,
+    EDIT_TOGGLE_DIFF,
+    VIEW_TOGGLE_BACKLINKS,
+];
+
+/// IDs of menu items that depend on having uncommitted changes.
+const GIT_COMMIT_DEPENDENT_IDS: &[&str] = &[VAULT_COMMIT_PUSH];
+
+/// IDs of menu items that depend on having merge conflicts.
+const GIT_CONFLICT_DEPENDENT_IDS: &[&str] = &[VAULT_RESOLVE_CONFLICTS];
 
 type MenuResult = Result<Submenu<tauri::Wry>, Box<dyn std::error::Error>>;
 
@@ -54,10 +116,15 @@ fn build_app_menu(app: &App) -> MenuResult {
         .id(APP_SETTINGS)
         .accelerator("CmdOrCtrl+,")
         .build(app)?;
+    let check_updates_item = MenuItemBuilder::new("Check for Updates...")
+        .id(APP_CHECK_FOR_UPDATES)
+        .build(app)?;
 
     Ok(SubmenuBuilder::new(app, "Laputa")
         .about(None)
         .separator()
+        .item(&check_updates_item)
+        .separator()
         .item(&settings_item)
         .separator()
         .services()
@@ -75,6 +142,13 @@ fn build_file_menu(app: &App) -> MenuResult {
         .id(FILE_NEW_NOTE)
         .accelerator("CmdOrCtrl+N")
         .build(app)?;
+    let new_type = MenuItemBuilder::new("New Type")
+        .id(FILE_NEW_TYPE)
+        .build(app)?;
+    let daily_note = MenuItemBuilder::new("Open Today's Note")
+        .id(FILE_DAILY_NOTE)
+        .accelerator("CmdOrCtrl+J")
+        .build(app)?;
     let quick_open = MenuItemBuilder::new("Quick Open")
         .id(FILE_QUICK_OPEN)
         .accelerator("CmdOrCtrl+P")
@@ -87,24 +161,14 @@ fn build_file_menu(app: &App) -> MenuResult {
         .id(FILE_CLOSE_TAB)
         .accelerator("CmdOrCtrl+W")
         .build(app)?;
-    let archive_note = MenuItemBuilder::new("Archive Note")
-        .id(NOTE_ARCHIVE)
-        .accelerator("CmdOrCtrl+E")
-        .build(app)?;
-    let trash_note = MenuItemBuilder::new("Trash Note")
-        .id(NOTE_TRASH)
-        .accelerator("CmdOrCtrl+Backspace")
-        .build(app)?;
 
     Ok(SubmenuBuilder::new(app, "File")
         .item(&new_note)
+        .item(&new_type)
+        .item(&daily_note)
         .item(&quick_open)
         .separator()
         .item(&save)
-        .separator()
-        .item(&archive_note)
-        .item(&trash_note)
-        .separator()
         .item(&close_tab)
         .build()?)
 }
@@ -114,6 +178,9 @@ fn build_edit_menu(app: &App) -> MenuResult {
         .id(EDIT_FIND_IN_VAULT)
         .accelerator("CmdOrCtrl+Shift+F")
         .build(app)?;
+    let toggle_diff = MenuItemBuilder::new("Toggle Diff Mode")
+        .id(EDIT_TOGGLE_DIFF)
+        .build(app)?;
 
     Ok(SubmenuBuilder::new(app, "Edit")
         .undo()
@@ -126,6 +193,7 @@ fn build_edit_menu(app: &App) -> MenuResult {
         .select_all()
         .separator()
         .item(&find_in_vault)
+        .item(&toggle_diff)
         .build()?)
 }
 
@@ -142,8 +210,8 @@ fn build_view_menu(app: &App) -> MenuResult {
         .id(VIEW_ALL)
         .accelerator("CmdOrCtrl+3")
         .build(app)?;
-    let toggle_inspector = MenuItemBuilder::new("Toggle Inspector")
-        .id(VIEW_TOGGLE_INSPECTOR)
+    let toggle_properties = MenuItemBuilder::new("Toggle Properties Panel")
+        .id(VIEW_TOGGLE_PROPERTIES)
         .build(app)?;
     let command_palette = MenuItemBuilder::new("Command Palette")
         .id(VIEW_COMMAND_PALETTE)
@@ -161,6 +229,34 @@ fn build_view_menu(app: &App) -> MenuResult {
         .id(VIEW_ZOOM_RESET)
         .accelerator("CmdOrCtrl+0")
         .build(app)?;
+
+    Ok(SubmenuBuilder::new(app, "View")
+        .item(&editor_only)
+        .item(&editor_list)
+        .item(&all_panels)
+        .separator()
+        .item(&toggle_properties)
+        .separator()
+        .item(&zoom_in)
+        .item(&zoom_out)
+        .item(&zoom_reset)
+        .separator()
+        .item(&command_palette)
+        .build()?)
+}
+
+fn build_go_menu(app: &App) -> MenuResult {
+    let all_notes = MenuItemBuilder::new("All Notes")
+        .id(GO_ALL_NOTES)
+        .build(app)?;
+    let favorites = MenuItemBuilder::new("Favorites")
+        .id(GO_FAVORITES)
+        .build(app)?;
+    let archived = MenuItemBuilder::new("Archived")
+        .id(GO_ARCHIVED)
+        .build(app)?;
+    let trash = MenuItemBuilder::new("Trash").id(GO_TRASH).build(app)?;
+    let changes = MenuItemBuilder::new("Changes").id(GO_CHANGES).build(app)?;
     let go_back = MenuItemBuilder::new("Go Back")
         .id(VIEW_GO_BACK)
         .accelerator("CmdOrCtrl+[")
@@ -170,21 +266,92 @@ fn build_view_menu(app: &App) -> MenuResult {
         .accelerator("CmdOrCtrl+]")
         .build(app)?;
 
-    Ok(SubmenuBuilder::new(app, "View")
-        .item(&editor_only)
-        .item(&editor_list)
-        .item(&all_panels)
-        .separator()
-        .item(&toggle_inspector)
+    Ok(SubmenuBuilder::new(app, "Go")
+        .item(&all_notes)
+        .item(&favorites)
+        .item(&archived)
+        .item(&trash)
+        .item(&changes)
         .separator()
         .item(&go_back)
         .item(&go_forward)
+        .build()?)
+}
+
+fn build_note_menu(app: &App) -> MenuResult {
+    let archive_note = MenuItemBuilder::new("Archive Note")
+        .id(NOTE_ARCHIVE)
+        .accelerator("CmdOrCtrl+E")
+        .build(app)?;
+    let trash_note = MenuItemBuilder::new("Trash Note")
+        .id(NOTE_TRASH)
+        .accelerator("CmdOrCtrl+Backspace")
+        .build(app)?;
+    let toggle_raw_editor = MenuItemBuilder::new("Toggle Raw Editor")
+        .id(EDIT_TOGGLE_RAW_EDITOR)
+        .accelerator("CmdOrCtrl+\\")
+        .build(app)?;
+    let toggle_ai_chat = MenuItemBuilder::new("Toggle AI Chat")
+        .id(VIEW_TOGGLE_AI_CHAT)
+        .accelerator("CmdOrCtrl+I")
+        .build(app)?;
+    let toggle_backlinks = MenuItemBuilder::new("Toggle Backlinks")
+        .id(VIEW_TOGGLE_BACKLINKS)
+        .build(app)?;
+
+    Ok(SubmenuBuilder::new(app, "Note")
+        .item(&archive_note)
+        .item(&trash_note)
         .separator()
-        .item(&zoom_in)
-        .item(&zoom_out)
-        .item(&zoom_reset)
+        .item(&toggle_raw_editor)
+        .item(&toggle_ai_chat)
+        .item(&toggle_backlinks)
+        .build()?)
+}
+
+fn build_vault_menu(app: &App) -> MenuResult {
+    let open_vault = MenuItemBuilder::new("Open Vault…")
+        .id(VAULT_OPEN)
+        .build(app)?;
+    let remove_vault = MenuItemBuilder::new("Remove Vault from List")
+        .id(VAULT_REMOVE)
+        .build(app)?;
+    let restore_getting_started = MenuItemBuilder::new("Restore Getting Started")
+        .id(VAULT_RESTORE_GETTING_STARTED)
+        .build(app)?;
+    let new_theme = MenuItemBuilder::new("New Theme")
+        .id(VAULT_NEW_THEME)
+        .build(app)?;
+    let restore_default_themes = MenuItemBuilder::new("Restore Default Themes")
+        .id(VAULT_RESTORE_DEFAULT_THEMES)
+        .build(app)?;
+    let commit_push = MenuItemBuilder::new("Commit & Push")
+        .id(VAULT_COMMIT_PUSH)
+        .build(app)?;
+    let resolve_conflicts = MenuItemBuilder::new("Resolve Conflicts")
+        .id(VAULT_RESOLVE_CONFLICTS)
+        .enabled(false)
+        .build(app)?;
+    let view_changes = MenuItemBuilder::new("View Pending Changes")
+        .id(VAULT_VIEW_CHANGES)
+        .build(app)?;
+    let install_mcp = MenuItemBuilder::new("Install MCP Server")
+        .id(VAULT_INSTALL_MCP)
+        .build(app)?;
+
+    Ok(SubmenuBuilder::new(app, "Vault")
+        .item(&open_vault)
+        .item(&remove_vault)
+        .item(&restore_getting_started)
         .separator()
-        .item(&command_palette)
+        .item(&new_theme)
+        .item(&restore_default_themes)
+        .separator()
+        .item(&commit_push)
+        .item(&resolve_conflicts)
+        .item(&view_changes)
+        .separator()
+        .item(&install_mcp)
         .build()?)
 }
 
@@ -202,6 +369,9 @@ pub fn setup_menu(app: &App) -> Result<(), Box<dyn std::error::Error>> {
     let file_menu = build_file_menu(app)?;
     let edit_menu = build_edit_menu(app)?;
     let view_menu = build_view_menu(app)?;
+    let go_menu = build_go_menu(app)?;
+    let note_menu = build_note_menu(app)?;
+    let vault_menu = build_vault_menu(app)?;
     let window_menu = build_window_menu(app)?;
 
     let menu = MenuBuilder::new(app)
@@ -209,6 +379,9 @@ pub fn setup_menu(app: &App) -> Result<(), Box<dyn std::error::Error>> {
         .item(&file_menu)
         .item(&edit_menu)
         .item(&view_menu)
+        .item(&go_menu)
+        .item(&note_menu)
+        .item(&vault_menu)
         .item(&window_menu)
         .build()?;
 
@@ -224,43 +397,78 @@ pub fn setup_menu(app: &App) -> Result<(), Box<dyn std::error::Error>> {
     Ok(())
 }
 
-/// Enable or disable menu items that depend on having an active note tab.
-pub fn set_note_items_enabled(app_handle: &AppHandle, enabled: bool) {
+fn set_items_enabled(app_handle: &AppHandle, ids: &[&str], enabled: bool) {
     let Some(menu) = app_handle.menu() else {
         return;
     };
-    for id in NOTE_DEPENDENT_IDS {
+    for id in ids {
         if let Some(MenuItemKind::MenuItem(mi)) = menu.get(*id) {
             let _ = mi.set_enabled(enabled);
         }
     }
 }
 
+/// Enable or disable menu items that depend on having an active note tab.
+pub fn set_note_items_enabled(app_handle: &AppHandle, enabled: bool) {
+    set_items_enabled(app_handle, NOTE_DEPENDENT_IDS, enabled);
+}
+
+/// Enable or disable menu items that depend on having uncommitted changes.
+pub fn set_git_commit_items_enabled(app_handle: &AppHandle, enabled: bool) {
+    set_items_enabled(app_handle, GIT_COMMIT_DEPENDENT_IDS, enabled);
+}
+
+/// Enable or disable menu items that depend on having merge conflicts.
+pub fn set_git_conflict_items_enabled(app_handle: &AppHandle, enabled: bool) {
+    set_items_enabled(app_handle, GIT_CONFLICT_DEPENDENT_IDS, enabled);
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;
 
     #[test]
-    fn custom_ids_include_all_expected_items() {
+    fn custom_ids_include_all_constants() {
         let expected = [
-            "app-settings",
-            "file-new-note",
-            "file-quick-open",
-            "file-save",
-            "file-close-tab",
-            "note-archive",
-            "note-trash",
-            "edit-find-in-vault",
-            "view-editor-only",
-            "view-editor-list",
-            "view-all",
-            "view-toggle-inspector",
-            "view-command-palette",
-            "view-zoom-in",
-            "view-zoom-out",
-            "view-zoom-reset",
-            "view-go-back",
-            "view-go-forward",
+            APP_SETTINGS,
+            APP_CHECK_FOR_UPDATES,
+            FILE_NEW_NOTE,
+            FILE_NEW_TYPE,
+            FILE_DAILY_NOTE,
+            FILE_QUICK_OPEN,
+            FILE_SAVE,
+            FILE_CLOSE_TAB,
+            EDIT_FIND_IN_VAULT,
+            EDIT_TOGGLE_RAW_EDITOR,
+            EDIT_TOGGLE_DIFF,
+            VIEW_EDITOR_ONLY,
+            VIEW_EDITOR_LIST,
+            VIEW_ALL,
+            VIEW_TOGGLE_PROPERTIES,
+            VIEW_TOGGLE_AI_CHAT,
+            VIEW_TOGGLE_BACKLINKS,
+            VIEW_COMMAND_PALETTE,
+            VIEW_ZOOM_IN,
+            VIEW_ZOOM_OUT,
+            VIEW_ZOOM_RESET,
+            VIEW_GO_BACK,
+            VIEW_GO_FORWARD,
+            GO_ALL_NOTES,
+            GO_FAVORITES,
+            GO_ARCHIVED,
+            GO_TRASH,
+            GO_CHANGES,
+            NOTE_ARCHIVE,
+            NOTE_TRASH,
+            VAULT_OPEN,
+            VAULT_REMOVE,
+            VAULT_RESTORE_GETTING_STARTED,
+            VAULT_NEW_THEME,
+            VAULT_RESTORE_DEFAULT_THEMES,
+            VAULT_COMMIT_PUSH,
+            VAULT_RESOLVE_CONFLICTS,
+            VAULT_VIEW_CHANGES,
+            VAULT_INSTALL_MCP,
         ];
         for id in &expected {
             assert!(CUSTOM_IDS.contains(id), "missing custom ID: {id}");
@@ -276,4 +484,28 @@ mod tests {
             );
         }
     }
+
+    #[test]
+    fn git_dependent_ids_are_subset_of_custom_ids() {
+        for id in GIT_COMMIT_DEPENDENT_IDS {
+            assert!(
+                CUSTOM_IDS.contains(id),
+                "git-commit-dependent ID {id} not in CUSTOM_IDS"
+            );
+        }
+        for id in GIT_CONFLICT_DEPENDENT_IDS {
+            assert!(
+                CUSTOM_IDS.contains(id),
+                "git-conflict-dependent ID {id} not in CUSTOM_IDS"
+            );
+        }
+    }
+
+    #[test]
+    fn no_duplicate_custom_ids() {
+        let mut seen = std::collections::HashSet::new();
+        for id in CUSTOM_IDS {
+            assert!(seen.insert(id), "duplicate custom ID: {id}");
+        }
+    }
 }

src-tauri/src/search.rs

@@ -1,7 +1,7 @@
+use crate::indexing;
 use serde::{Deserialize, Serialize};
 use std::collections::HashMap;
 use std::path::Path;
-use std::process::Command;
 use std::sync::Mutex;
 use std::time::Instant;
 
@@ -30,31 +30,6 @@ struct QmdResult {
     pub score: f64,
 }
 
-fn find_qmd_binary() -> Option<String> {
-    let candidates = [
-        dirs::home_dir().map(|h| h.join(".bun/bin/qmd").to_string_lossy().to_string()),
-        Some("/usr/local/bin/qmd".to_string()),
-        Some("/opt/homebrew/bin/qmd".to_string()),
-    ];
-    for candidate in candidates.into_iter().flatten() {
-        if Path::new(&candidate).exists() {
-            return Some(candidate);
-        }
-    }
-    // Fallback: try PATH
-    Command::new("which")
-        .arg("qmd")
-        .output()
-        .ok()
-        .and_then(|o| {
-            if o.status.success() {
-                Some(String::from_utf8_lossy(&o.stdout).trim().to_string())
-            } else {
-                None
-            }
-        })
-}
-
 fn qmd_uri_to_vault_path(uri: &str, vault_path: &str) -> String {
     // qmd://laputa/essay/foo.md → essay/foo.md
     let relative = uri
@@ -108,12 +83,12 @@ fn detect_collection_name(vault_path: &str) -> String {
 }
 
 fn detect_collection_name_uncached(vault_path: &str) -> String {
-    let qmd_bin = match find_qmd_binary() {
+    let qmd = match indexing::find_qmd_binary() {
         Some(b) => b,
         None => return "laputa".to_string(),
     };
 
-    let output = Command::new(&qmd_bin).args(["collection", "list"]).output();
+    let output = qmd.command().args(["collection", "list"]).output();
 
     match output {
         Ok(o) if o.status.success() => {
@@ -149,8 +124,7 @@ pub fn search_vault(
 ) -> Result<SearchResponse, String> {
     let start = Instant::now();
 
-    let qmd_bin =
-        find_qmd_binary().ok_or_else(|| "qmd binary not found. Install qmd first.".to_string())?;
+    let qmd = indexing::find_qmd_binary().ok_or_else(|| "qmd binary not found".to_string())?;
 
     let collection = detect_collection_name(vault_path);
 
@@ -161,7 +135,8 @@ pub fn search_vault(
     };
 
     let limit_str = limit.to_string();
-    let output = Command::new(&qmd_bin)
+    let output = qmd
+        .command()
         .args([
             search_cmd,
             query,

src-tauri/src/settings.rs

@@ -71,6 +71,36 @@ pub fn save_settings(settings: Settings) -> Result<(), String> {
     save_settings_at(&settings_path()?, settings)
 }
 
+fn last_vault_file() -> Result<PathBuf, String> {
+    dirs::config_dir()
+        .map(|d| d.join("com.laputa.app").join("last-vault.txt"))
+        .ok_or_else(|| "Could not determine config directory".to_string())
+}
+
+fn get_last_vault_at(path: &PathBuf) -> Option<String> {
+    fs::read_to_string(path)
+        .ok()
+        .map(|s| s.trim().to_string())
+        .filter(|s| !s.is_empty())
+}
+
+fn set_last_vault_at(path: &PathBuf, vault_path: &str) -> Result<(), String> {
+    if let Some(parent) = path.parent() {
+        fs::create_dir_all(parent)
+            .map_err(|e| format!("Failed to create config directory: {}", e))?;
+    }
+    fs::write(path, vault_path.trim())
+        .map_err(|e| format!("Failed to write last vault path: {}", e))
+}
+
+pub fn get_last_vault() -> Option<String> {
+    last_vault_file().ok().and_then(|p| get_last_vault_at(&p))
+}
+
+pub fn set_last_vault(vault_path: &str) -> Result<(), String> {
+    set_last_vault_at(&last_vault_file()?, vault_path)
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;
@@ -199,4 +229,65 @@ mod tests {
         assert!(result.is_ok());
         assert!(result.unwrap().to_str().unwrap().contains("com.laputa.app"));
     }
+
+    #[test]
+    fn test_get_last_vault_returns_none_for_missing_file() {
+        let dir = tempfile::TempDir::new().unwrap();
+        let path = dir.path().join("last-vault.txt");
+        assert!(get_last_vault_at(&path).is_none());
+    }
+
+    #[test]
+    fn test_set_and_get_last_vault_roundtrip() {
+        let dir = tempfile::TempDir::new().unwrap();
+        let path = dir.path().join("last-vault.txt");
+        set_last_vault_at(&path, "/Users/test/MyVault").unwrap();
+        assert_eq!(
+            get_last_vault_at(&path).as_deref(),
+            Some("/Users/test/MyVault")
+        );
+    }
+
+    #[test]
+    fn test_set_last_vault_trims_whitespace() {
+        let dir = tempfile::TempDir::new().unwrap();
+        let path = dir.path().join("last-vault.txt");
+        set_last_vault_at(&path, "  /Users/test/Vault  ").unwrap();
+        assert_eq!(
+            get_last_vault_at(&path).as_deref(),
+            Some("/Users/test/Vault")
+        );
+    }
+
+    #[test]
+    fn test_get_last_vault_returns_none_for_empty_file() {
+        let dir = tempfile::TempDir::new().unwrap();
+        let path = dir.path().join("last-vault.txt");
+        fs::write(&path, "   \n  ").unwrap();
+        assert!(get_last_vault_at(&path).is_none());
+    }
+
+    #[test]
+    fn test_set_last_vault_creates_parent_directories() {
+        let dir = tempfile::TempDir::new().unwrap();
+        let path = dir.path().join("nested").join("dir").join("last-vault.txt");
+        set_last_vault_at(&path, "/Users/test/Vault").unwrap();
+        assert!(path.exists());
+        assert_eq!(
+            get_last_vault_at(&path).as_deref(),
+            Some("/Users/test/Vault")
+        );
+    }
+
+    #[test]
+    fn test_set_last_vault_overwrites_previous() {
+        let dir = tempfile::TempDir::new().unwrap();
+        let path = dir.path().join("last-vault.txt");
+        set_last_vault_at(&path, "/Users/test/OldVault").unwrap();
+        set_last_vault_at(&path, "/Users/test/NewVault").unwrap();
+        assert_eq!(
+            get_last_vault_at(&path).as_deref(),
+            Some("/Users/test/NewVault")
+        );
+    }
 }

src-tauri/src/theme.rs

@@ -98,10 +98,10 @@ pub fn save_vault_settings(vault_path: &str, settings: VaultSettings) -> Result<
         .map_err(|e| format!("Failed to write vault settings: {e}"))
 }
 
-/// Set the active theme in vault settings.
-pub fn set_active_theme(vault_path: &str, theme_id: &str) -> Result<(), String> {
+/// Set the active theme in vault settings. Pass `None` to clear.
+pub fn set_active_theme(vault_path: &str, theme_id: Option<&str>) -> Result<(), String> {
     let mut settings = get_vault_settings(vault_path)?;
-    settings.theme = Some(theme_id.to_string());
+    settings.theme = theme_id.map(|s| s.to_string());
     save_vault_settings(vault_path, settings)
 }
 
@@ -116,20 +116,174 @@ pub fn get_theme(vault_path: &str, theme_id: &str) -> Result<ThemeFile, String>
     parse_theme_file(&path)
 }
 
+/// Create `dir` and write each `(filename, content)` pair if the directory doesn't exist yet.
+fn seed_dir_with_files(dir: &Path, files: &[(&str, &str)], log_msg: &str) {
+    if dir.is_dir() {
+        return;
+    }
+    if fs::create_dir_all(dir).is_err() {
+        return;
+    }
+    for (name, content) in files {
+        let _ = fs::write(dir.join(name), content);
+    }
+    log::info!("{log_msg}");
+}
+
 /// Seed the `_themes/` directory with built-in themes if it doesn't exist yet.
 /// Safe to call multiple times — only writes files that are missing.
 pub fn seed_default_themes(vault_path: &str) {
+    seed_dir_with_files(
+        &Path::new(vault_path).join("_themes"),
+        &[
+            ("default.json", DEFAULT_THEME),
+            ("dark.json", DARK_THEME),
+            ("minimal.json", MINIMAL_THEME),
+        ],
+        "Seeded _themes/ with built-in themes",
+    );
+}
+
+/// Seed the vault `theme/` directory with built-in vault-based theme notes.
+/// Per-file idempotent: creates the directory if missing, writes each default
+/// file only when it doesn't exist or is empty (corrupt). Never overwrites
+/// existing files that have content.
+pub fn seed_vault_themes(vault_path: &str) {
+    let theme_dir = Path::new(vault_path).join("theme");
+    if fs::create_dir_all(&theme_dir).is_err() {
+        return;
+    }
+    let defaults: &[(&str, &str)] = &[
+        ("default.md", DEFAULT_VAULT_THEME),
+        ("dark.md", DARK_VAULT_THEME),
+        ("minimal.md", MINIMAL_VAULT_THEME),
+    ];
+    let mut seeded = false;
+    for (name, content) in defaults {
+        let path = theme_dir.join(name);
+        let needs_write = !path.exists() || fs::metadata(&path).map_or(true, |m| m.len() == 0);
+        if needs_write {
+            let _ = fs::write(&path, content);
+            seeded = true;
+        }
+    }
+    if seeded {
+        log::info!("Seeded theme/ with built-in vault themes");
+    }
+}
+
+/// Ensure vault theme files exist. Returns an error if the theme directory
+/// cannot be created (e.g. read-only filesystem).
+pub fn ensure_vault_themes(vault_path: &str) -> Result<(), String> {
+    let theme_dir = Path::new(vault_path).join("theme");
+    fs::create_dir_all(&theme_dir).map_err(|e| format!("Failed to create theme directory: {e}"))?;
+    let defaults: &[(&str, &str)] = &[
+        ("default.md", DEFAULT_VAULT_THEME),
+        ("dark.md", DARK_VAULT_THEME),
+        ("minimal.md", MINIMAL_VAULT_THEME),
+    ];
+    for (name, content) in defaults {
+        let path = theme_dir.join(name);
+        let needs_write = !path.exists() || fs::metadata(&path).map_or(true, |m| m.len() == 0);
+        if needs_write {
+            fs::write(&path, content).map_err(|e| format!("Failed to write theme/{name}: {e}"))?;
+        }
+    }
+    Ok(())
+}
+
+/// Restore default themes for a vault: seeds both `_themes/` (JSON) and
+/// `theme/` (markdown notes). Per-file idempotent — never overwrites files
+/// that already have content. Returns an error on read-only filesystems.
+pub fn restore_default_themes(vault_path: &str) -> Result<String, String> {
+    // Seed _themes/ JSON files (per-file idempotent)
     let themes_dir = Path::new(vault_path).join("_themes");
-    if themes_dir.is_dir() {
-        return;
+    fs::create_dir_all(&themes_dir)
+        .map_err(|e| format!("Failed to create _themes directory: {e}"))?;
+    let json_defaults: &[(&str, &str)] = &[
+        ("default.json", DEFAULT_THEME),
+        ("dark.json", DARK_THEME),
+        ("minimal.json", MINIMAL_THEME),
+    ];
+    for (name, content) in json_defaults {
+        let path = themes_dir.join(name);
+        let needs_write = !path.exists() || fs::metadata(&path).map_or(true, |m| m.len() == 0);
+        if needs_write {
+            fs::write(&path, content)
+                .map_err(|e| format!("Failed to write _themes/{name}: {e}"))?;
+        }
     }
-    if fs::create_dir_all(&themes_dir).is_err() {
-        return;
+
+    // Seed theme/ markdown notes (reuses ensure_vault_themes for consistency)
+    ensure_vault_themes(vault_path)?;
+
+    Ok("Default themes restored".to_string())
+}
+
+/// Create a new vault theme note in `theme/` directory.
+/// Returns the absolute path to the newly created theme note.
+pub fn create_vault_theme(vault_path: &str, name: Option<&str>) -> Result<String, String> {
+    let theme_dir = Path::new(vault_path).join("theme");
+    fs::create_dir_all(&theme_dir).map_err(|e| format!("Failed to create theme directory: {e}"))?;
+
+    let display_name = name.unwrap_or("Untitled Theme");
+    let slug = slugify(display_name);
+    let filename = format!("{}.md", find_available_stem(&theme_dir, &slug, "md"));
+    let path = theme_dir.join(&filename);
+
+    let content = vault_theme_note_content(display_name, &DEFAULT_VAULT_THEME_VARS);
+    fs::write(&path, content).map_err(|e| format!("Failed to write theme note: {e}"))?;
+
+    Ok(path.to_string_lossy().to_string())
+}
+
+/// Convert a display name to a URL-safe slug.
+fn slugify(name: &str) -> String {
+    name.chars()
+        .map(|c| {
+            if c.is_ascii_alphanumeric() {
+                c.to_ascii_lowercase()
+            } else {
+                '-'
+            }
+        })
+        .collect::<String>()
+        .split('-')
+        .filter(|s| !s.is_empty())
+        .collect::<Vec<_>>()
+        .join("-")
+}
+
+/// Find an available filename stem (base, base-2, base-3, …) that doesn't conflict when `ext` is appended.
+fn find_available_stem(dir: &Path, base: &str, ext: &str) -> String {
+    if !dir.join(format!("{base}.{ext}")).exists() {
+        return base.to_string();
     }
-    let _ = fs::write(themes_dir.join("default.json"), DEFAULT_THEME);
-    let _ = fs::write(themes_dir.join("dark.json"), DARK_THEME);
-    let _ = fs::write(themes_dir.join("minimal.json"), MINIMAL_THEME);
-    log::info!("Seeded _themes/ with built-in themes");
+    for i in 2.. {
+        let candidate = format!("{base}-{i}");
+        if !dir.join(format!("{candidate}.{ext}")).exists() {
+            return candidate;
+        }
+    }
+    unreachable!()
+}
+
+/// Build a vault theme note markdown string from a name and CSS variable map.
+fn vault_theme_note_content(name: &str, vars: &[(&str, &str)]) -> String {
+    let mut fm = format!("---\nIs A: Theme\nDescription: {name} theme\n");
+    for (key, value) in vars {
+        // Values with '#' or spaces need quoting; others can be bare strings.
+        if value.contains('#') || value.contains('\'') || value.contains(',') {
+            fm.push_str(&format!("{key}: \"{value}\"\n"));
+        } else {
+            fm.push_str(&format!("{key}: {value}\n"));
+        }
+    }
+    fm.push_str("---\n\n");
+    fm.push_str(&format!(
+        "# {name} Theme\n\nA custom {name} theme for Laputa.\n"
+    ));
+    fm
 }
 
 /// Create a new theme file by copying the active theme (or default).
@@ -139,7 +293,7 @@ pub fn create_theme(vault_path: &str, source_id: Option<&str>) -> Result<String,
     fs::create_dir_all(&themes_dir)
         .map_err(|e| format!("Failed to create _themes directory: {e}"))?;
 
-    let new_id = find_available_id(&themes_dir, "untitled");
+    let new_id = find_available_stem(&themes_dir, "untitled", "json");
 
     let source = source_id.unwrap_or("default");
     let source_path = themes_dir.join(format!("{source}.json"));
@@ -169,20 +323,6 @@ pub fn create_theme(vault_path: &str, source_id: Option<&str>) -> Result<String,
     Ok(new_id)
 }
 
-/// Find a filename that doesn't conflict (untitled, untitled-2, untitled-3, ...).
-fn find_available_id(dir: &Path, base: &str) -> String {
-    if !dir.join(format!("{base}.json")).exists() {
-        return base.to_string();
-    }
-    for i in 2.. {
-        let candidate = format!("{base}-{i}");
-        if !dir.join(format!("{candidate}.json")).exists() {
-            return candidate;
-        }
-    }
-    unreachable!()
-}
-
 /// Generate the default light theme JSON.
 fn default_theme_json(name: &str) -> String {
     serde_json::to_string_pretty(&serde_json::json!({
@@ -312,6 +452,233 @@ pub const MINIMAL_THEME: &str = r##"{
   }
 }"##;
 
+/// CSS variable key-value pairs for the default light vault theme.
+pub const DEFAULT_VAULT_THEME_VARS: [(&str, &str); 46] = [
+    // shadcn/ui base
+    ("background", "#FFFFFF"),
+    ("foreground", "#37352F"),
+    ("card", "#FFFFFF"),
+    ("popover", "#FFFFFF"),
+    ("primary", "#155DFF"),
+    ("primary-foreground", "#FFFFFF"),
+    ("secondary", "#EBEBEA"),
+    ("secondary-foreground", "#37352F"),
+    ("muted", "#F0F0EF"),
+    ("muted-foreground", "#787774"),
+    ("accent", "#EBEBEA"),
+    ("accent-foreground", "#37352F"),
+    ("destructive", "#E03E3E"),
+    ("border", "#E9E9E7"),
+    ("input", "#E9E9E7"),
+    ("ring", "#155DFF"),
+    ("sidebar", "#F7F6F3"),
+    ("sidebar-foreground", "#37352F"),
+    ("sidebar-border", "#E9E9E7"),
+    ("sidebar-accent", "#EBEBEA"),
+    // Text hierarchy
+    ("text-primary", "#37352F"),
+    ("text-secondary", "#787774"),
+    ("text-muted", "#B4B4B4"),
+    ("text-heading", "#37352F"),
+    // Backgrounds
+    ("bg-primary", "#FFFFFF"),
+    ("bg-sidebar", "#F7F6F3"),
+    ("bg-hover", "#EBEBEA"),
+    ("bg-hover-subtle", "#F0F0EF"),
+    ("bg-selected", "#E8F4FE"),
+    ("border-primary", "#E9E9E7"),
+    // Accent colours
+    ("accent-blue", "#155DFF"),
+    ("accent-green", "#00B38B"),
+    ("accent-orange", "#D9730D"),
+    ("accent-red", "#E03E3E"),
+    ("accent-purple", "#A932FF"),
+    ("accent-yellow", "#F0B100"),
+    ("accent-blue-light", "#155DFF14"),
+    ("accent-green-light", "#00B38B14"),
+    ("accent-purple-light", "#A932FF14"),
+    ("accent-red-light", "#E03E3E14"),
+    ("accent-yellow-light", "#F0B10014"),
+    // Typography
+    (
+        "font-family",
+        "'Inter', -apple-system, BlinkMacSystemFont, sans-serif",
+    ),
+    ("font-size-base", "14px"),
+    // Editor
+    ("editor-font-size", "16"),
+    ("editor-line-height", "1.5"),
+    ("editor-max-width", "720"),
+];
+
+/// Vault-based theme note for the built-in Default theme.
+pub const DEFAULT_VAULT_THEME: &str = "---\n\
+Is A: Theme\n\
+Description: Light theme with warm, paper-like tones\n\
+background: \"#FFFFFF\"\n\
+foreground: \"#37352F\"\n\
+card: \"#FFFFFF\"\n\
+popover: \"#FFFFFF\"\n\
+primary: \"#155DFF\"\n\
+primary-foreground: \"#FFFFFF\"\n\
+secondary: \"#EBEBEA\"\n\
+secondary-foreground: \"#37352F\"\n\
+muted: \"#F0F0EF\"\n\
+muted-foreground: \"#787774\"\n\
+accent: \"#EBEBEA\"\n\
+accent-foreground: \"#37352F\"\n\
+destructive: \"#E03E3E\"\n\
+border: \"#E9E9E7\"\n\
+input: \"#E9E9E7\"\n\
+ring: \"#155DFF\"\n\
+sidebar: \"#F7F6F3\"\n\
+sidebar-foreground: \"#37352F\"\n\
+sidebar-border: \"#E9E9E7\"\n\
+sidebar-accent: \"#EBEBEA\"\n\
+text-primary: \"#37352F\"\n\
+text-secondary: \"#787774\"\n\
+text-muted: \"#B4B4B4\"\n\
+text-heading: \"#37352F\"\n\
+bg-primary: \"#FFFFFF\"\n\
+bg-sidebar: \"#F7F6F3\"\n\
+bg-hover: \"#EBEBEA\"\n\
+bg-hover-subtle: \"#F0F0EF\"\n\
+bg-selected: \"#E8F4FE\"\n\
+border-primary: \"#E9E9E7\"\n\
+accent-blue: \"#155DFF\"\n\
+accent-green: \"#00B38B\"\n\
+accent-orange: \"#D9730D\"\n\
+accent-red: \"#E03E3E\"\n\
+accent-purple: \"#A932FF\"\n\
+accent-yellow: \"#F0B100\"\n\
+accent-blue-light: \"#155DFF14\"\n\
+accent-green-light: \"#00B38B14\"\n\
+accent-purple-light: \"#A932FF14\"\n\
+accent-red-light: \"#E03E3E14\"\n\
+accent-yellow-light: \"#F0B10014\"\n\
+font-family: \"'Inter', -apple-system, BlinkMacSystemFont, sans-serif\"\n\
+font-size-base: 14px\n\
+editor-font-size: 16\n\
+editor-line-height: 1.5\n\
+editor-max-width: 720\n\
+---\n\
+\n\
+# Default Theme\n\
+\n\
+The default light theme for Laputa. Clean and warm, inspired by Notion.\n";
+
+/// Vault-based theme note for the built-in Dark theme.
+pub const DARK_VAULT_THEME: &str = "---\n\
+Is A: Theme\n\
+Description: Dark variant with deep navy tones\n\
+background: \"#0f0f1a\"\n\
+foreground: \"#e0e0e0\"\n\
+card: \"#16162a\"\n\
+popover: \"#1e1e3a\"\n\
+primary: \"#155DFF\"\n\
+primary-foreground: \"#FFFFFF\"\n\
+secondary: \"#2a2a4a\"\n\
+secondary-foreground: \"#e0e0e0\"\n\
+muted: \"#1e1e3a\"\n\
+muted-foreground: \"#888888\"\n\
+accent: \"#2a2a4a\"\n\
+accent-foreground: \"#e0e0e0\"\n\
+destructive: \"#f44336\"\n\
+border: \"#2a2a4a\"\n\
+input: \"#2a2a4a\"\n\
+ring: \"#155DFF\"\n\
+sidebar: \"#1a1a2e\"\n\
+sidebar-foreground: \"#e0e0e0\"\n\
+sidebar-border: \"#2a2a4a\"\n\
+sidebar-accent: \"#2a2a4a\"\n\
+text-primary: \"#e0e0e0\"\n\
+text-secondary: \"#888888\"\n\
+text-muted: \"#666666\"\n\
+text-heading: \"#e0e0e0\"\n\
+bg-primary: \"#0f0f1a\"\n\
+bg-sidebar: \"#1a1a2e\"\n\
+bg-hover: \"#2a2a4a\"\n\
+bg-hover-subtle: \"#1e1e3a\"\n\
+bg-selected: \"#155DFF22\"\n\
+border-primary: \"#2a2a4a\"\n\
+accent-blue: \"#155DFF\"\n\
+accent-green: \"#00B38B\"\n\
+accent-orange: \"#D9730D\"\n\
+accent-red: \"#f44336\"\n\
+accent-purple: \"#A932FF\"\n\
+accent-yellow: \"#F0B100\"\n\
+accent-blue-light: \"#155DFF33\"\n\
+accent-green-light: \"#00B38B33\"\n\
+accent-purple-light: \"#A932FF33\"\n\
+accent-red-light: \"#f4433633\"\n\
+accent-yellow-light: \"#F0B10033\"\n\
+font-family: \"'Inter', -apple-system, BlinkMacSystemFont, sans-serif\"\n\
+font-size-base: 14px\n\
+editor-font-size: 16\n\
+editor-line-height: 1.5\n\
+editor-max-width: 720\n\
+---\n\
+\n\
+# Dark Theme\n\
+\n\
+A dark theme with deep navy tones for comfortable night-time reading.\n";
+
+/// Vault-based theme note for the built-in Minimal theme.
+pub const MINIMAL_VAULT_THEME: &str = "---\n\
+Is A: Theme\n\
+Description: High contrast, minimal chrome\n\
+background: \"#FAFAFA\"\n\
+foreground: \"#111111\"\n\
+card: \"#FFFFFF\"\n\
+popover: \"#FFFFFF\"\n\
+primary: \"#000000\"\n\
+primary-foreground: \"#FFFFFF\"\n\
+secondary: \"#F0F0F0\"\n\
+secondary-foreground: \"#111111\"\n\
+muted: \"#F5F5F5\"\n\
+muted-foreground: \"#666666\"\n\
+accent: \"#F0F0F0\"\n\
+accent-foreground: \"#111111\"\n\
+destructive: \"#CC0000\"\n\
+border: \"#E0E0E0\"\n\
+input: \"#E0E0E0\"\n\
+ring: \"#000000\"\n\
+sidebar: \"#F5F5F5\"\n\
+sidebar-foreground: \"#111111\"\n\
+sidebar-border: \"#E0E0E0\"\n\
+sidebar-accent: \"#E8E8E8\"\n\
+text-primary: \"#111111\"\n\
+text-secondary: \"#666666\"\n\
+text-muted: \"#999999\"\n\
+text-heading: \"#111111\"\n\
+bg-primary: \"#FAFAFA\"\n\
+bg-sidebar: \"#F5F5F5\"\n\
+bg-hover: \"#EBEBEB\"\n\
+bg-hover-subtle: \"#F5F5F5\"\n\
+bg-selected: \"#00000014\"\n\
+border-primary: \"#E0E0E0\"\n\
+accent-blue: \"#000000\"\n\
+accent-green: \"#006600\"\n\
+accent-orange: \"#996600\"\n\
+accent-red: \"#CC0000\"\n\
+accent-purple: \"#660099\"\n\
+accent-yellow: \"#996600\"\n\
+accent-blue-light: \"#00000014\"\n\
+accent-green-light: \"#00660014\"\n\
+accent-purple-light: \"#66009914\"\n\
+accent-red-light: \"#CC000014\"\n\
+accent-yellow-light: \"#99660014\"\n\
+font-family: \"'SF Mono', 'Menlo', monospace\"\n\
+font-size-base: 13px\n\
+editor-font-size: 15\n\
+editor-line-height: 1.6\n\
+editor-max-width: 680\n\
+---\n\
+\n\
+# Minimal Theme\n\
+\n\
+High contrast, minimal chrome. Monospace typography throughout.\n";
+
 #[cfg(test)]
 mod tests {
     use super::*;
@@ -379,9 +746,14 @@ mod tests {
         assert!(settings.theme.is_none());
 
         // Set and read back
-        set_active_theme(vp, "dark").unwrap();
+        set_active_theme(vp, Some("dark")).unwrap();
         let settings = get_vault_settings(vp).unwrap();
         assert_eq!(settings.theme.as_deref(), Some("dark"));
+
+        // Clear theme
+        set_active_theme(vp, None).unwrap();
+        let settings = get_vault_settings(vp).unwrap();
+        assert_eq!(settings.theme, None);
     }
 
     #[test]
@@ -462,4 +834,242 @@ mod tests {
         let themes = list_themes(&vault).unwrap();
         assert_eq!(themes.len(), 2); // broken.json is skipped
     }
+
+    #[test]
+    fn test_seed_vault_themes_creates_theme_dir() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path().join("vault");
+        fs::create_dir_all(&vault).unwrap();
+        let vp = vault.to_str().unwrap();
+
+        assert!(!vault.join("theme").exists());
+        seed_vault_themes(vp);
+        assert!(vault.join("theme").is_dir());
+        assert!(vault.join("theme").join("default.md").exists());
+        assert!(vault.join("theme").join("dark.md").exists());
+        assert!(vault.join("theme").join("minimal.md").exists());
+    }
+
+    #[test]
+    fn test_seed_vault_themes_is_idempotent() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path().join("vault");
+        fs::create_dir_all(&vault).unwrap();
+        let vp = vault.to_str().unwrap();
+
+        seed_vault_themes(vp);
+        seed_vault_themes(vp); // second call should be a no-op
+        assert!(vault.join("theme").join("default.md").exists());
+    }
+
+    #[test]
+    fn test_create_vault_theme_creates_md_file() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path().join("vault");
+        fs::create_dir_all(&vault).unwrap();
+        let vp = vault.to_str().unwrap();
+
+        let path = create_vault_theme(vp, Some("My Theme")).unwrap();
+        assert!(std::path::Path::new(&path).exists());
+        let content = fs::read_to_string(&path).unwrap();
+        assert!(content.contains("Is A: Theme"));
+        assert!(content.contains("# My Theme"));
+        assert!(content.contains("background:"));
+    }
+
+    #[test]
+    fn test_create_vault_theme_default_name() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path().join("vault");
+        fs::create_dir_all(&vault).unwrap();
+        let vp = vault.to_str().unwrap();
+
+        let path = create_vault_theme(vp, None).unwrap();
+        let content = fs::read_to_string(&path).unwrap();
+        assert!(content.contains("# Untitled Theme"));
+    }
+
+    #[test]
+    fn test_create_vault_theme_avoids_conflicts() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path().join("vault");
+        fs::create_dir_all(&vault).unwrap();
+        let vp = vault.to_str().unwrap();
+
+        let p1 = create_vault_theme(vp, Some("Custom")).unwrap();
+        let p2 = create_vault_theme(vp, Some("Custom")).unwrap();
+        assert_ne!(p1, p2);
+    }
+
+    #[test]
+    fn test_slugify() {
+        assert_eq!(slugify("My Cool Theme"), "my-cool-theme");
+        assert_eq!(slugify("default"), "default");
+        assert_eq!(slugify("Dark Mode!"), "dark-mode");
+    }
+
+    #[test]
+    fn test_vault_theme_content_contains_all_vars() {
+        let content = DEFAULT_VAULT_THEME;
+        assert!(content.contains("background:"));
+        assert!(content.contains("primary:"));
+        assert!(content.contains("sidebar:"));
+        assert!(content.contains("text-primary:"));
+        assert!(content.contains("accent-blue:"));
+        assert!(content.contains("editor-font-size:"));
+    }
+
+    #[test]
+    fn test_seed_vault_themes_writes_missing_files_in_existing_dir() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path().join("vault");
+        let theme_dir = vault.join("theme");
+        fs::create_dir_all(&theme_dir).unwrap();
+        // Only default exists — dark and minimal should be seeded
+        fs::write(theme_dir.join("default.md"), DEFAULT_VAULT_THEME).unwrap();
+        let vp = vault.to_str().unwrap();
+
+        seed_vault_themes(vp);
+        assert!(theme_dir.join("dark.md").exists());
+        assert!(theme_dir.join("minimal.md").exists());
+    }
+
+    #[test]
+    fn test_seed_vault_themes_reseeds_empty_files() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path().join("vault");
+        let theme_dir = vault.join("theme");
+        fs::create_dir_all(&theme_dir).unwrap();
+        // Create empty file — should be re-seeded
+        fs::write(theme_dir.join("default.md"), "").unwrap();
+        let vp = vault.to_str().unwrap();
+
+        seed_vault_themes(vp);
+        let content = fs::read_to_string(theme_dir.join("default.md")).unwrap();
+        assert!(content.contains("Is A: Theme"));
+    }
+
+    #[test]
+    fn test_seed_vault_themes_preserves_existing_content() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path().join("vault");
+        let theme_dir = vault.join("theme");
+        fs::create_dir_all(&theme_dir).unwrap();
+        let custom = "---\nIs A: Theme\nbackground: \"#FF0000\"\n---\n# Custom\n";
+        fs::write(theme_dir.join("default.md"), custom).unwrap();
+        let vp = vault.to_str().unwrap();
+
+        seed_vault_themes(vp);
+        let content = fs::read_to_string(theme_dir.join("default.md")).unwrap();
+        assert!(
+            content.contains("#FF0000"),
+            "existing content must be preserved"
+        );
+    }
+
+    #[test]
+    fn test_ensure_vault_themes_creates_dir_and_defaults() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path().join("vault");
+        fs::create_dir_all(&vault).unwrap();
+        let vp = vault.to_str().unwrap();
+
+        ensure_vault_themes(vp).unwrap();
+        assert!(vault.join("theme").is_dir());
+        assert!(vault.join("theme").join("default.md").exists());
+        assert!(vault.join("theme").join("dark.md").exists());
+        assert!(vault.join("theme").join("minimal.md").exists());
+    }
+
+    #[test]
+    fn test_ensure_vault_themes_reseeds_empty_files() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path().join("vault");
+        let theme_dir = vault.join("theme");
+        fs::create_dir_all(&theme_dir).unwrap();
+        fs::write(theme_dir.join("default.md"), "").unwrap();
+        let vp = vault.to_str().unwrap();
+
+        ensure_vault_themes(vp).unwrap();
+        let content = fs::read_to_string(theme_dir.join("default.md")).unwrap();
+        assert!(content.contains("Is A: Theme"));
+    }
+
+    #[test]
+    fn test_ensure_vault_themes_preserves_custom_themes() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path().join("vault");
+        let theme_dir = vault.join("theme");
+        fs::create_dir_all(&theme_dir).unwrap();
+        let custom = "---\nIs A: Theme\nbackground: \"#123456\"\n---\n";
+        fs::write(theme_dir.join("default.md"), custom).unwrap();
+        let vp = vault.to_str().unwrap();
+
+        ensure_vault_themes(vp).unwrap();
+        let content = fs::read_to_string(theme_dir.join("default.md")).unwrap();
+        assert!(content.contains("#123456"));
+    }
+
+    #[test]
+    fn test_restore_default_themes_creates_both_dirs() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path().join("vault");
+        fs::create_dir_all(&vault).unwrap();
+        let vp = vault.to_str().unwrap();
+
+        let msg = restore_default_themes(vp).unwrap();
+        assert_eq!(msg, "Default themes restored");
+        // _themes/ JSON files
+        assert!(vault.join("_themes").join("default.json").exists());
+        assert!(vault.join("_themes").join("dark.json").exists());
+        assert!(vault.join("_themes").join("minimal.json").exists());
+        // theme/ markdown notes
+        assert!(vault.join("theme").join("default.md").exists());
+        assert!(vault.join("theme").join("dark.md").exists());
+        assert!(vault.join("theme").join("minimal.md").exists());
+    }
+
+    #[test]
+    fn test_restore_default_themes_is_idempotent() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path().join("vault");
+        fs::create_dir_all(&vault).unwrap();
+        let vp = vault.to_str().unwrap();
+
+        restore_default_themes(vp).unwrap();
+        // Modify a theme file to verify it isn't overwritten
+        let custom = "---\nIs A: Theme\nbackground: \"#CUSTOM\"\n---\n";
+        fs::write(vault.join("theme").join("default.md"), custom).unwrap();
+
+        restore_default_themes(vp).unwrap();
+        let content = fs::read_to_string(vault.join("theme").join("default.md")).unwrap();
+        assert!(
+            content.contains("#CUSTOM"),
+            "must not overwrite existing content"
+        );
+    }
+
+    #[test]
+    fn test_restore_default_themes_fills_partial_state() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path().join("vault");
+        // Create _themes/ with only default.json, theme/ with only default.md
+        let themes_dir = vault.join("_themes");
+        let theme_dir = vault.join("theme");
+        fs::create_dir_all(&themes_dir).unwrap();
+        fs::create_dir_all(&theme_dir).unwrap();
+        fs::write(themes_dir.join("default.json"), DEFAULT_THEME).unwrap();
+        fs::write(theme_dir.join("default.md"), DEFAULT_VAULT_THEME).unwrap();
+        let vp = vault.to_str().unwrap();
+
+        restore_default_themes(vp).unwrap();
+        // Missing files should now exist
+        assert!(themes_dir.join("dark.json").exists());
+        assert!(themes_dir.join("minimal.json").exists());
+        assert!(theme_dir.join("dark.md").exists());
+        assert!(theme_dir.join("minimal.md").exists());
+        // Existing files should be unchanged
+        let content = fs::read_to_string(theme_dir.join("default.md")).unwrap();
+        assert!(content.contains("Light theme with warm"));
+    }
 }

src-tauri/src/vault/cache.rs

@@ -7,12 +7,16 @@ use super::{parse_md_file, scan_vault, VaultEntry};
 // --- Vault Cache ---
 
 /// Bump this when VaultEntry fields change to force a full rescan.
-const CACHE_VERSION: u32 = 2;
+const CACHE_VERSION: u32 = 4;
 
 #[derive(Debug, Serialize, Deserialize)]
 struct VaultCache {
     #[serde(default = "default_cache_version")]
     version: u32,
+    /// The vault path when the cache was written. Used to detect stale caches
+    /// from a different machine or a moved vault directory.
+    #[serde(default)]
+    vault_path: String,
     commit_hash: String,
     entries: Vec<VaultEntry>,
 }
@@ -50,11 +54,6 @@ fn parse_porcelain_line(line: &str) -> Option<(&str, String)> {
     Some((&line[..2], line[3..].trim().to_string()))
 }
 
-/// Check if a porcelain status indicates a new/untracked file.
-fn is_new_file_status(status: &str) -> bool {
-    status == "??" || status.starts_with('A')
-}
-
 /// Extract .md file paths from git diff --name-only output.
 fn collect_md_paths_from_diff(stdout: &str) -> Vec<String> {
     stdout
@@ -80,11 +79,15 @@ fn git_changed_files(vault: &Path, from_hash: &str, to_hash: &str) -> Vec<String
         .map(|s| collect_md_paths_from_diff(&s))
         .unwrap_or_default();
 
-    let uncommitted = run_git(vault, &["status", "--porcelain"])
+    // Use ls-files for untracked files so that newly-seeded directories are picked up
+    // as individual files rather than as a single "?? dirname/" entry.
+    let uncommitted = git_uncommitted_files(vault);
+    // Also include modified-but-unstaged files via status --porcelain.
+    let modified = run_git(vault, &["status", "--porcelain"])
         .map(|s| collect_md_paths_from_porcelain(&s))
         .unwrap_or_default();
 
-    for path in uncommitted {
+    for path in uncommitted.into_iter().chain(modified) {
         if !files.contains(&path) {
             files.push(path);
         }
@@ -93,17 +96,10 @@ fn git_changed_files(vault: &Path, from_hash: &str, to_hash: &str) -> Vec<String
     files
 }
 
-fn git_uncommitted_new_files(vault: &Path) -> Vec<String> {
-    let stdout = match run_git(vault, &["status", "--porcelain"]) {
-        Some(s) => s,
-        None => return Vec::new(),
-    };
-    stdout
-        .lines()
-        .filter_map(parse_porcelain_line)
-        .filter(|(status, path)| path.ends_with(".md") && is_new_file_status(status))
-        .map(|(_, path)| path)
-        .collect()
+fn git_uncommitted_files(vault: &Path) -> Vec<String> {
+    run_git(vault, &["status", "--porcelain"])
+        .map(|s| collect_md_paths_from_porcelain(&s))
+        .unwrap_or_default()
 }
 
 fn load_cache(vault: &Path) -> Option<VaultCache> {
@@ -115,6 +111,7 @@ fn write_cache(vault: &Path, cache: &VaultCache) {
     if let Ok(data) = serde_json::to_string(cache) {
         let _ = fs::write(cache_path(vault), data);
     }
+    ensure_cache_excluded(vault);
 }
 
 /// Normalize an absolute path to a relative path for comparison with git output.
@@ -143,6 +140,23 @@ fn parse_files_at(vault: &Path, rel_paths: &[String]) -> Vec<VaultEntry> {
         .collect()
 }
 
+/// Ensure `.laputa-cache.json` is excluded from git via `.git/info/exclude`.
+/// This prevents the cache (which contains machine-specific absolute paths)
+/// from being committed and causing stale-path bugs on cloned vaults.
+fn ensure_cache_excluded(vault: &Path) {
+    let exclude_path = vault.join(".git/info/exclude");
+    let entry = ".laputa-cache.json";
+    if let Ok(content) = fs::read_to_string(&exclude_path) {
+        if content.lines().any(|line| line.trim() == entry) {
+            return;
+        }
+        let separator = if content.ends_with('\n') { "" } else { "\n" };
+        let _ = fs::write(&exclude_path, format!("{content}{separator}{entry}\n"));
+    } else if exclude_path.parent().map(|p| p.is_dir()).unwrap_or(false) {
+        let _ = fs::write(&exclude_path, format!("{entry}\n"));
+    }
+}
+
 /// Sort entries by modified_at descending and write the cache.
 fn finalize_and_cache(vault: &Path, mut entries: Vec<VaultEntry>, hash: String) -> Vec<VaultEntry> {
     entries.sort_by(|a, b| b.modified_at.cmp(&a.modified_at));
@@ -150,6 +164,7 @@ fn finalize_and_cache(vault: &Path, mut entries: Vec<VaultEntry>, hash: String)
         vault,
         &VaultCache {
             version: CACHE_VERSION,
+            vault_path: vault.to_string_lossy().to_string(),
             commit_hash: hash,
             entries: entries.clone(),
         },
@@ -157,23 +172,19 @@ fn finalize_and_cache(vault: &Path, mut entries: Vec<VaultEntry>, hash: String)
     entries
 }
 
-/// Handle same-commit cache hit: add any uncommitted new files.
+/// Handle same-commit cache hit: re-parse any uncommitted changes (new or modified files).
 fn update_same_commit(vault: &Path, cache: VaultCache) -> Vec<VaultEntry> {
-    let new_files = git_uncommitted_new_files(vault);
-    let mut entries = cache.entries;
-    let existing: std::collections::HashSet<String> = entries
-        .iter()
-        .map(|e| to_relative_path(&e.path, vault))
-        .collect();
-
-    let new_entries = parse_files_at(vault, &new_files);
-    for entry in new_entries {
-        let rel = to_relative_path(&entry.path, vault);
-        if !existing.contains(&rel) {
-            entries.push(entry);
-        }
+    let changed = git_uncommitted_files(vault);
+    if changed.is_empty() {
+        return cache.entries;
     }
-
+    let changed_set: std::collections::HashSet<String> = changed.iter().cloned().collect();
+    let mut entries: Vec<VaultEntry> = cache
+        .entries
+        .into_iter()
+        .filter(|e| !changed_set.contains(&to_relative_path(&e.path, vault)))
+        .collect();
+    entries.extend(parse_files_at(vault, &changed));
     finalize_and_cache(vault, entries, cache.commit_hash)
 }
 
@@ -212,7 +223,10 @@ pub fn scan_vault_cached(vault_path: &Path) -> Result<Vec<VaultEntry>, String> {
     };
 
     if let Some(cache) = load_cache(vault_path) {
-        if cache.version != CACHE_VERSION {
+        let current_vault_str = vault_path.to_string_lossy();
+        let cache_stale = cache.version != CACHE_VERSION
+            || (!cache.vault_path.is_empty() && cache.vault_path != current_vault_str.as_ref());
+        if cache_stale {
             let entries = scan_vault(vault_path)?;
             return Ok(finalize_and_cache(vault_path, entries, current_hash));
         }
@@ -300,6 +314,71 @@ mod tests {
         assert_eq!(entries2[0].title, "Note");
     }
 
+    #[test]
+    fn test_scan_vault_cached_invalidates_stale_vault_path() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path();
+
+        // Init git repo
+        std::process::Command::new("git")
+            .args(["init"])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+        std::process::Command::new("git")
+            .args(["config", "user.email", "test@test.com"])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+        std::process::Command::new("git")
+            .args(["config", "user.name", "Test"])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+
+        create_test_file(vault, "note.md", "# Note\n\nContent.");
+        std::process::Command::new("git")
+            .args(["add", "."])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+        std::process::Command::new("git")
+            .args(["commit", "-m", "init"])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+
+        // Build cache normally
+        let entries = scan_vault_cached(vault).unwrap();
+        assert_eq!(entries.len(), 1);
+        assert!(
+            entries[0]
+                .path
+                .starts_with(&vault.to_string_lossy().as_ref()),
+            "Entry path should start with vault path"
+        );
+
+        // Tamper with cache to simulate a clone from a different machine
+        let cache_file = cache_path(vault);
+        let cache_data = fs::read_to_string(&cache_file).unwrap();
+        let tampered = cache_data.replace(
+            &vault.to_string_lossy().as_ref(),
+            "/Users/other-machine/OtherVault",
+        );
+        fs::write(&cache_file, tampered).unwrap();
+
+        // Rescanning should invalidate the stale cache and produce correct paths
+        let entries2 = scan_vault_cached(vault).unwrap();
+        assert_eq!(entries2.len(), 1);
+        assert!(
+            entries2[0]
+                .path
+                .starts_with(&vault.to_string_lossy().as_ref()),
+            "After stale-cache invalidation, paths should use the current vault path, got: {}",
+            entries2[0].path
+        );
+    }
+
     #[test]
     fn test_scan_vault_cached_incremental_different_commit() {
         let dir = TempDir::new().unwrap();
@@ -358,4 +437,108 @@ mod tests {
         assert!(titles.contains(&"First"));
         assert!(titles.contains(&"Second"));
     }
+
+    #[test]
+    fn test_update_same_commit_picks_up_modified_file() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path();
+
+        std::process::Command::new("git")
+            .args(["init"])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+        std::process::Command::new("git")
+            .args(["config", "user.email", "test@test.com"])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+        std::process::Command::new("git")
+            .args(["config", "user.name", "Test"])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+
+        // Commit a type note without sidebar label
+        create_test_file(vault, "type/news.md", "---\ntype: Type\n---\n# News\n");
+        std::process::Command::new("git")
+            .args(["add", "."])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+        std::process::Command::new("git")
+            .args(["commit", "-m", "init"])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+
+        // Prime the cache (same commit hash)
+        let entries = scan_vault_cached(vault).unwrap();
+        assert_eq!(entries.len(), 1);
+        assert_eq!(entries[0].sidebar_label, None);
+
+        // User edits the type note to add sidebar label (uncommitted)
+        create_test_file(
+            vault,
+            "type/news.md",
+            "---\ntype: Type\nsidebar label: News\n---\n# News\n",
+        );
+
+        // Reload with same git HEAD — must pick up the modification
+        let entries2 = scan_vault_cached(vault).unwrap();
+        assert_eq!(entries2.len(), 1);
+        assert_eq!(
+            entries2[0].sidebar_label,
+            Some("News".to_string()),
+            "sidebarLabel must reflect the uncommitted edit"
+        );
+    }
+
+    #[test]
+    fn test_update_same_commit_new_file_still_added() {
+        let dir = TempDir::new().unwrap();
+        let vault = dir.path();
+
+        std::process::Command::new("git")
+            .args(["init"])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+        std::process::Command::new("git")
+            .args(["config", "user.email", "test@test.com"])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+        std::process::Command::new("git")
+            .args(["config", "user.name", "Test"])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+
+        create_test_file(vault, "existing.md", "# Existing\n");
+        std::process::Command::new("git")
+            .args(["add", "."])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+        std::process::Command::new("git")
+            .args(["commit", "-m", "init"])
+            .current_dir(vault)
+            .output()
+            .unwrap();
+
+        // Prime cache
+        let entries = scan_vault_cached(vault).unwrap();
+        assert_eq!(entries.len(), 1);
+
+        // Create new untracked file
+        create_test_file(vault, "new-note.md", "# New Note\n");
+
+        // Cache still same commit — new untracked file must appear
+        let entries2 = scan_vault_cached(vault).unwrap();
+        assert_eq!(entries2.len(), 2);
+        let titles: Vec<&str> = entries2.iter().map(|e| e.title.as_str()).collect();
+        assert!(titles.contains(&"Existing"));
+        assert!(titles.contains(&"New Note"));
+    }
 }

src-tauri/src/vault/getting_started.rs

@@ -4,7 +4,7 @@ use std::path::{Path, PathBuf};
 /// Default location for the Getting Started vault.
 pub fn default_vault_path() -> Result<PathBuf, String> {
     dirs::document_dir()
-        .map(|d| d.join("Laputa"))
+        .map(|d| d.join("Getting Started"))
         .ok_or_else(|| "Could not determine Documents directory".to_string())
 }
 
@@ -423,7 +423,7 @@ mod tests {
         let path = default_vault_path().unwrap();
         let path_str = path.to_string_lossy();
         assert!(path_str.contains("Documents"));
-        assert!(path_str.ends_with("Laputa"));
+        assert!(path_str.ends_with("Getting Started"));
     }
 
     #[test]

src-tauri/src/vault/mod.rs

@@ -11,7 +11,7 @@ pub use getting_started::{create_getting_started_vault, default_vault_path, vaul
 pub use image::{copy_image_to_vault, save_image};
 pub use migration::migrate_is_a_to_type;
 pub use rename::{rename_note, RenameResult};
-pub use trash::purge_trash;
+pub use trash::{delete_note, purge_trash};
 
 use parsing::{
     capitalize_first, contains_wikilink, count_body_words, extract_outgoing_links, extract_snippet,
@@ -62,6 +62,18 @@ pub struct VaultEntry {
     pub color: Option<String>,
     /// Display order for Type entries in sidebar (lower = higher). None = use default order.
     pub order: Option<i64>,
+    /// Custom sidebar section label for Type entries, overriding auto-pluralization.
+    #[serde(rename = "sidebarLabel")]
+    pub sidebar_label: Option<String>,
+    /// Markdown template for notes of this Type. When a new note is created
+    /// with this type, the template body is pre-filled after the frontmatter.
+    pub template: Option<String>,
+    /// Default sort preference for the note list when viewing instances of this Type.
+    /// Stored as "option:direction" (e.g. "modified:desc", "title:asc", "property:Priority:asc").
+    pub sort: Option<String>,
+    /// Default view mode for the note list when viewing instances of this Type.
+    /// Stored as a string: "all", "editor-list", or "editor-only".
+    pub view: Option<String>,
     /// Word count of the note body (excludes frontmatter and H1 title).
     #[serde(rename = "wordCount")]
     pub word_count: u32,
@@ -69,6 +81,10 @@ pub struct VaultEntry {
     /// Extracted from `[[target]]` and `[[target|display]]` patterns.
     #[serde(rename = "outgoingLinks", default)]
     pub outgoing_links: Vec<String>,
+    /// Custom scalar frontmatter properties (non-relationship, non-structural).
+    /// Only includes strings, numbers, and booleans — arrays/objects are excluded.
+    #[serde(default)]
+    pub properties: HashMap<String, serde_json::Value>,
 }
 
 /// Intermediate struct to capture YAML frontmatter fields.
@@ -90,9 +106,9 @@ struct Frontmatter {
     cadence: Option<String>,
     #[serde(rename = "Archived")]
     archived: Option<bool>,
-    #[serde(rename = "Trashed")]
+    #[serde(rename = "Trashed", alias = "trashed")]
     trashed: Option<bool>,
-    #[serde(rename = "Trashed at")]
+    #[serde(rename = "Trashed at", alias = "trashed_at")]
     trashed_at: Option<String>,
     #[serde(rename = "Created at")]
     created_at: Option<String>,
@@ -104,6 +120,14 @@ struct Frontmatter {
     color: Option<String>,
     #[serde(default)]
     order: Option<i64>,
+    #[serde(rename = "sidebar label", default)]
+    sidebar_label: Option<String>,
+    #[serde(default)]
+    template: Option<String>,
+    #[serde(default)]
+    sort: Option<String>,
+    #[serde(default)]
+    view: Option<String>,
 }
 
 /// Handles YAML fields that can be either a single string or a list of strings.
@@ -147,6 +171,10 @@ const SKIP_KEYS: &[&str] = &[
     "icon",
     "color",
     "order",
+    "sidebar label",
+    "template",
+    "sort",
+    "view",
 ];
 
 /// Extract all wikilink-containing fields from raw YAML frontmatter.
@@ -188,6 +216,45 @@ fn extract_relationships(
     relationships
 }
 
+/// Additional keys to skip when extracting custom properties.
+/// These are already first-class fields on VaultEntry, so including them
+/// in `properties` would duplicate information.
+const PROPERTY_EXTRA_SKIP: &[&str] = &["belongs to", "related to", "owner"];
+
+/// Extract custom scalar properties from raw YAML frontmatter.
+/// Captures string, number, and boolean values that are not structural fields
+/// and do not contain wikilinks. Arrays and objects are excluded.
+fn extract_properties(
+    data: &HashMap<String, serde_json::Value>,
+) -> HashMap<String, serde_json::Value> {
+    let mut properties = HashMap::new();
+
+    for (key, value) in data {
+        let lower = key.to_ascii_lowercase();
+        if SKIP_KEYS.iter().any(|k| k.eq_ignore_ascii_case(&lower))
+            || PROPERTY_EXTRA_SKIP
+                .iter()
+                .any(|k| k.eq_ignore_ascii_case(&lower))
+        {
+            continue;
+        }
+
+        match value {
+            serde_json::Value::String(s) => {
+                if !contains_wikilink(s) {
+                    properties.insert(key.clone(), value.clone());
+                }
+            }
+            serde_json::Value::Number(_) | serde_json::Value::Bool(_) => {
+                properties.insert(key.clone(), value.clone());
+            }
+            _ => {}
+        }
+    }
+
+    properties
+}
+
 /// Infer entity type from a parent folder name.
 fn infer_type_from_folder(folder: &str) -> String {
     match folder {
@@ -231,19 +298,24 @@ fn parse_created_at(fm: &Frontmatter) -> Option<u64> {
         .or_else(|| fm.created_time.as_ref().and_then(|s| parse_iso_date(s)))
 }
 
-/// Extract frontmatter and relationships from parsed gray_matter data.
+/// Extract frontmatter, relationships, and custom properties from parsed gray_matter data.
 fn extract_fm_and_rels(
     data: Option<gray_matter::Pod>,
-) -> (Frontmatter, HashMap<String, Vec<String>>) {
+) -> (
+    Frontmatter,
+    HashMap<String, Vec<String>>,
+    HashMap<String, serde_json::Value>,
+) {
     let hash = match data {
         Some(gray_matter::Pod::Hash(map)) => map,
-        _ => return (Frontmatter::default(), HashMap::new()),
+        _ => return (Frontmatter::default(), HashMap::new(), HashMap::new()),
     };
     let json_map: HashMap<String, serde_json::Value> =
         hash.into_iter().map(|(k, v)| (k, pod_to_json(v))).collect();
     (
         parse_frontmatter(&json_map),
         extract_relationships(&json_map),
+        extract_properties(&json_map),
     )
 }
 
@@ -270,7 +342,7 @@ pub fn parse_md_file(path: &Path) -> Result<VaultEntry, String> {
 
     let matter = Matter::<YAML>::new();
     let parsed = matter.parse(&content);
-    let (frontmatter, mut relationships) = extract_fm_and_rels(parsed.data);
+    let (frontmatter, mut relationships, properties) = extract_fm_and_rels(parsed.data);
 
     let title = extract_title(&parsed.content, &filename);
     let snippet = extract_snippet(&content);
@@ -325,8 +397,13 @@ pub fn parse_md_file(path: &Path) -> Result<VaultEntry, String> {
         icon: frontmatter.icon,
         color: frontmatter.color,
         order: frontmatter.order,
+        sidebar_label: frontmatter.sidebar_label,
+        template: frontmatter.template,
+        sort: frontmatter.sort,
+        view: frontmatter.view,
         word_count,
         outgoing_links,
+        properties,
     })
 }
 
@@ -1055,6 +1132,226 @@ References:
         assert_eq!(fs::read_to_string(&path).unwrap(), content);
     }
 
+    // --- sidebar_label tests ---
+
+    #[test]
+    fn test_parse_sidebar_label_from_type_entry() {
+        let dir = TempDir::new().unwrap();
+        let content = "---\ntype: Type\nsidebar label: News\n---\n# News\n";
+        let entry = parse_test_entry(&dir, "type/news.md", content);
+        assert_eq!(entry.sidebar_label, Some("News".to_string()));
+    }
+
+    #[test]
+    fn test_parse_sidebar_label_missing_defaults_to_none() {
+        let dir = TempDir::new().unwrap();
+        let content = "---\ntype: Type\n---\n# Project\n";
+        let entry = parse_test_entry(&dir, "type/project.md", content);
+        assert_eq!(entry.sidebar_label, None);
+    }
+
+    #[test]
+    fn test_sidebar_label_not_in_relationships() {
+        let dir = TempDir::new().unwrap();
+        let content = "---\ntype: Type\nsidebar label: My Series\n---\n# Series\n";
+        let entry = parse_test_entry(&dir, "type/series.md", content);
+        assert!(entry.relationships.get("sidebar label").is_none());
+    }
+
+    // --- template field tests ---
+
+    #[test]
+    fn test_parse_template_from_type_entry() {
+        let dir = TempDir::new().unwrap();
+        let content =
+            "---\ntype: Type\ntemplate: \"## Objective\\n\\n## Timeline\"\n---\n# Project\n";
+        let entry = parse_test_entry(&dir, "type/project.md", content);
+        assert!(entry.template.is_some());
+    }
+
+    #[test]
+    fn test_parse_template_block_scalar() {
+        let dir = TempDir::new().unwrap();
+        let content =
+            "---\ntype: Type\ntemplate: |\n  ## Objective\n  \n  ## Timeline\n---\n# Project\n";
+        let entry = parse_test_entry(&dir, "type/project.md", content);
+        assert!(entry.template.is_some());
+        let tmpl = entry.template.unwrap();
+        assert!(tmpl.contains("## Objective"));
+        assert!(tmpl.contains("## Timeline"));
+    }
+
+    #[test]
+    fn test_parse_template_missing_defaults_to_none() {
+        let dir = TempDir::new().unwrap();
+        let content = "---\ntype: Type\n---\n# Note\n";
+        let entry = parse_test_entry(&dir, "type/note.md", content);
+        assert_eq!(entry.template, None);
+    }
+
+    #[test]
+    fn test_template_not_in_relationships() {
+        let dir = TempDir::new().unwrap();
+        let content = "---\ntype: Type\ntemplate: \"## Heading\"\n---\n# Project\n";
+        let entry = parse_test_entry(&dir, "type/project.md", content);
+        assert!(entry.relationships.get("template").is_none());
+    }
+
+    // --- sort field tests ---
+
+    #[test]
+    fn test_parse_sort_from_type_entry() {
+        let dir = TempDir::new().unwrap();
+        let content = "---\ntype: Type\nsort: \"modified:desc\"\n---\n# Project\n";
+        let entry = parse_test_entry(&dir, "type/project.md", content);
+        assert_eq!(entry.sort, Some("modified:desc".to_string()));
+    }
+
+    #[test]
+    fn test_parse_sort_missing_defaults_to_none() {
+        let dir = TempDir::new().unwrap();
+        let content = "---\ntype: Type\n---\n# Project\n";
+        let entry = parse_test_entry(&dir, "type/project.md", content);
+        assert_eq!(entry.sort, None);
+    }
+
+    #[test]
+    fn test_sort_not_in_relationships() {
+        let dir = TempDir::new().unwrap();
+        let content = "---\ntype: Type\nsort: \"title:asc\"\n---\n# Project\n";
+        let entry = parse_test_entry(&dir, "type/project.md", content);
+        assert!(entry.relationships.get("sort").is_none());
+    }
+
+    #[test]
+    fn test_sort_not_in_properties() {
+        let dir = TempDir::new().unwrap();
+        let content = "---\ntype: Type\nsort: \"title:asc\"\n---\n# Project\n";
+        let entry = parse_test_entry(&dir, "type/project.md", content);
+        assert!(entry.properties.get("sort").is_none());
+    }
+
+    // --- custom properties tests ---
+
+    #[test]
+    fn test_extract_properties_scalar_values() {
+        let dir = TempDir::new().unwrap();
+        let content = r#"---
+Is A: Project
+Status: Active
+Priority: High
+Rating: 5
+Due date: 2026-06-15
+Reviewed: true
+---
+# Test
+"#;
+        let entry = parse_test_entry(&dir, "project/test.md", content);
+        let expected: HashMap<String, serde_json::Value> = [
+            ("Priority".into(), serde_json::Value::String("High".into())),
+            ("Rating".into(), serde_json::json!(5)),
+            (
+                "Due date".into(),
+                serde_json::Value::String("2026-06-15".into()),
+            ),
+            ("Reviewed".into(), serde_json::Value::Bool(true)),
+        ]
+        .into_iter()
+        .collect();
+        assert_eq!(entry.properties, expected);
+    }
+
+    #[test]
+    fn test_extract_properties_skips_structural_fields() {
+        let dir = TempDir::new().unwrap();
+        let content = r#"---
+Is A: Project
+Status: Active
+Owner: Luca
+Cadence: Weekly
+Archived: false
+Priority: High
+---
+# Test
+"#;
+        let entry = parse_test_entry(&dir, "project/test.md", content);
+        // Only Priority should survive — all others are structural
+        assert_eq!(entry.properties.len(), 1);
+        assert_eq!(
+            entry.properties.get("Priority").and_then(|v| v.as_str()),
+            Some("High")
+        );
+    }
+
+    #[test]
+    fn test_extract_properties_skips_wikilinks() {
+        let dir = TempDir::new().unwrap();
+        let content = r#"---
+Mentor: "[[person/alice]]"
+Company: Acme Corp
+---
+# Test
+"#;
+        let entry = parse_test_entry(&dir, "test.md", content);
+        assert!(entry.properties.get("Mentor").is_none());
+        assert_eq!(
+            entry.properties.get("Company").and_then(|v| v.as_str()),
+            Some("Acme Corp")
+        );
+    }
+
+    #[test]
+    fn test_extract_properties_skips_arrays() {
+        let dir = TempDir::new().unwrap();
+        let content = r#"---
+Tags:
+  - productivity
+  - writing
+Company: Acme Corp
+---
+# Test
+"#;
+        let entry = parse_test_entry(&dir, "test.md", content);
+        assert!(entry.properties.get("Tags").is_none());
+        assert_eq!(
+            entry.properties.get("Company").and_then(|v| v.as_str()),
+            Some("Acme Corp")
+        );
+    }
+
+    #[test]
+    fn test_parse_trashed_title_case() {
+        let dir = TempDir::new().unwrap();
+        let content = "---\nTrashed: true\nTrashed at: \"2025-02-01\"\n---\n# Gone\n";
+        let entry = parse_test_entry(&dir, "gone.md", content);
+        assert!(entry.trashed);
+        assert!(entry.trashed_at.is_some());
+    }
+
+    #[test]
+    fn test_parse_trashed_lowercase_alias() {
+        let dir = TempDir::new().unwrap();
+        let content = "---\ntrashed: true\ntrashed_at: \"2025-02-01\"\n---\n# Gone\n";
+        let entry = parse_test_entry(&dir, "gone.md", content);
+        assert!(
+            entry.trashed,
+            "lowercase 'trashed' must be parsed via alias"
+        );
+        assert!(
+            entry.trashed_at.is_some(),
+            "lowercase 'trashed_at' must be parsed via alias"
+        );
+    }
+
+    #[test]
+    fn test_trashed_false_when_absent() {
+        let dir = TempDir::new().unwrap();
+        let content = "---\nIs A: Note\n---\n# Active\n";
+        let entry = parse_test_entry(&dir, "active.md", content);
+        assert!(!entry.trashed);
+        assert!(entry.trashed_at.is_none());
+    }
+
     // Frontmatter update/delete tests are in frontmatter.rs
     // save_image tests are in vault/image.rs
     // purge_trash tests are in vault/trash.rs

src-tauri/src/vault/parsing.rs

@@ -116,6 +116,14 @@ fn strip_markdown_chars(s: &str) -> String {
     let mut chars = s.chars().peekable();
     while let Some(ch) = chars.next() {
         match ch {
+            '[' if chars.peek() == Some(&'[') => {
+                chars.next(); // consume second '['
+                let inner = collect_wikilink_inner(&mut chars);
+                match inner.find('|') {
+                    Some(idx) => result.push_str(&inner[idx + 1..]),
+                    None => result.push_str(&inner),
+                }
+            }
             '[' => {
                 let inner = collect_until(&mut chars, ']');
                 if chars.peek() == Some(&'(') {
@@ -131,6 +139,19 @@ fn strip_markdown_chars(s: &str) -> String {
     result
 }
 
+/// Collect chars inside a wikilink until `]]`, consuming both closing brackets.
+fn collect_wikilink_inner(chars: &mut std::iter::Peekable<impl Iterator<Item = char>>) -> String {
+    let mut buf = String::new();
+    while let Some(c) = chars.next() {
+        if c == ']' && chars.peek() == Some(&']') {
+            chars.next();
+            break;
+        }
+        buf.push(c);
+    }
+    buf
+}
+
 /// Check if a string contains a wikilink pattern `[[...]]`.
 pub(super) fn contains_wikilink(s: &str) -> bool {
     s.contains("[[") && s.contains("]]")
@@ -250,6 +271,16 @@ mod tests {
         let snippet = extract_snippet(content);
         assert!(snippet.contains("this link"));
         assert!(!snippet.contains("https://example.com"));
+        assert!(snippet.contains("wiki link"));
+        assert!(!snippet.contains("[["));
+        assert!(!snippet.contains("]]"));
+    }
+
+    #[test]
+    fn test_extract_snippet_wikilink_alias() {
+        let content = "# Title\n\nDiscussed in [[meetings/standup|standup]] today.";
+        let snippet = extract_snippet(content);
+        assert_eq!(snippet, "Discussed in standup today.");
     }
 
     #[test]
@@ -378,7 +409,20 @@ mod tests {
 
     #[test]
     fn test_strip_markdown_chars_wikilink() {
-        assert_eq!(strip_markdown_chars("see [[my note]]"), "see [my note]");
+        assert_eq!(strip_markdown_chars("see [[my note]]"), "see my note");
+    }
+
+    #[test]
+    fn test_strip_markdown_chars_wikilink_alias() {
+        assert_eq!(
+            strip_markdown_chars("visit [[project/alpha|Alpha Project]]"),
+            "visit Alpha Project"
+        );
+    }
+
+    #[test]
+    fn test_strip_markdown_chars_wikilink_unclosed() {
+        assert_eq!(strip_markdown_chars("see [[broken link"), "see broken link");
     }
 
     #[test]

src-tauri/src/vault/trash.rs

@@ -42,6 +42,21 @@ fn try_purge_file(path: &Path) -> Option<String> {
     }
 }
 
+/// Permanently delete a single note file.
+/// Returns the deleted path on success, or an error if the file doesn't exist.
+pub fn delete_note(path: &str) -> Result<String, String> {
+    let file = Path::new(path);
+    if !file.exists() {
+        return Err(format!("File does not exist: {}", path));
+    }
+    if !file.is_file() {
+        return Err(format!("Path is not a file: {}", path));
+    }
+    fs::remove_file(file).map_err(|e| format!("Failed to delete {}: {}", path, e))?;
+    log::info!("Permanently deleted note: {}", path);
+    Ok(path.to_string())
+}
+
 /// Scan all markdown files in the vault and delete those where
 /// `Trashed at` frontmatter is more than 30 days ago.
 /// Returns the list of deleted file paths.
@@ -95,6 +110,28 @@ mod tests {
         file.write_all(content.as_bytes()).unwrap();
     }
 
+    #[test]
+    fn test_delete_note_removes_file() {
+        let dir = TempDir::new().unwrap();
+        create_test_file(
+            dir.path(),
+            "doomed.md",
+            "---\ntitle: Doomed\n---\n# Doomed\n",
+        );
+        let path = dir.path().join("doomed.md");
+        assert!(path.exists());
+        let result = delete_note(path.to_str().unwrap());
+        assert!(result.is_ok());
+        assert!(!path.exists());
+    }
+
+    #[test]
+    fn test_delete_note_nonexistent_file() {
+        let result = delete_note("/nonexistent/path/that/does/not/exist.md");
+        assert!(result.is_err());
+        assert!(result.unwrap_err().contains("does not exist"));
+    }
+
     #[test]
     fn test_purge_trash_deletes_old_trashed_files() {
         let dir = TempDir::new().unwrap();