fix: remove --resume from AI chat to fix conversation history

The AI chat was using both --resume (CLI session resumption) AND formatted
conversation history in the prompt simultaneously. This dual-context approach
confused the model — it saw the conversation twice (from session + from prompt
markup), leading to "I don't have context" responses on follow-ups.

Fix: remove --resume entirely from chat mode. Each CLI call is now independent,
with full conversation history formatted into the prompt via
<conversation_history> markup. trimHistory handles graceful truncation.

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

.claude-pid

@@ -1 +1 @@
-33549
+66070

mcp-server/index.js

@@ -10,6 +10,8 @@
  *   - 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
+ *   - highlight_editor: visually highlight a UI element (editor, tab, etc.)
+ *   - refresh_vault: trigger vault rescan so new/modified files appear
  */
 import { Server } from '@modelcontextprotocol/sdk/server/index.js'
 import { StdioServerTransport } from '@modelcontextprotocol/sdk/server/stdio.js'
@@ -94,6 +96,28 @@ const TOOLS = [
       required: ['path'],
     },
   },
+  {
+    name: 'highlight_editor',
+    description: 'Visually highlight a UI element in Laputa (editor, tab, properties panel, or note list). The highlight auto-clears after a short delay.',
+    inputSchema: {
+      type: 'object',
+      properties: {
+        element: { type: 'string', enum: ['editor', 'tab', 'properties', 'notelist'], description: 'Which UI element to highlight' },
+        path: { type: 'string', description: 'Optional note path to associate with the highlight' },
+      },
+      required: ['element'],
+    },
+  },
+  {
+    name: 'refresh_vault',
+    description: 'Trigger a vault rescan so new or modified files appear immediately in the Laputa note list.',
+    inputSchema: {
+      type: 'object',
+      properties: {
+        path: { type: 'string', description: 'Optional specific note path that changed' },
+      },
+    },
+  },
 ]
 
 const TOOL_HANDLERS = {
@@ -101,6 +125,8 @@ const TOOL_HANDLERS = {
   get_vault_context: handleVaultContext,
   get_note: handleGetNote,
   open_note: handleOpenNote,
+  highlight_editor: handleHighlightEditor,
+  refresh_vault: handleRefreshVault,
 }
 
 async function handleSearchNotes(args) {
@@ -126,10 +152,20 @@ function handleOpenNote(args) {
   return { content: [{ type: 'text', text: `Opening ${args.path} in Laputa` }] }
 }
 
+function handleHighlightEditor(args) {
+  broadcastUiAction('highlight', { element: args.element, path: args.path })
+  return { content: [{ type: 'text', text: `Highlighting ${args.element}` }] }
+}
+
+function handleRefreshVault(args) {
+  broadcastUiAction('vault_changed', { path: args?.path })
+  return { content: [{ type: 'text', text: 'Vault refresh triggered' }] }
+}
+
 // --- Server setup ---
 
 const server = new Server(
-  { name: 'laputa-mcp-server', version: '0.2.0' },
+  { name: 'laputa-mcp-server', version: '0.3.0' },
   { capabilities: { tools: {} } },
 )
 

mcp-server/test.js

@@ -4,8 +4,7 @@ import fs from 'node:fs/promises'
 import path from 'node:path'
 import os from 'node:os'
 import {
-  readNote, createNote, searchNotes, appendToNote, findMarkdownFiles,
-  editNoteFrontmatter, deleteNote, linkNotes, listNotes, vaultContext,
+  findMarkdownFiles, getNote, searchNotes, vaultContext,
 } from './vault.js'
 
 let tmpDir
@@ -65,39 +64,23 @@ describe('findMarkdownFiles', () => {
   })
 })
 
-describe('readNote', () => {
-  it('should read a note by relative path', async () => {
-    const content = await readNote(tmpDir, 'project/test-project.md')
-    assert.ok(content.includes('Test Project'))
-    assert.ok(content.includes('is_a: Project'))
+describe('getNote', () => {
+  it('should read a note with parsed frontmatter', async () => {
+    const note = await getNote(tmpDir, 'project/test-project.md')
+    assert.equal(note.path, 'project/test-project.md')
+    assert.equal(note.frontmatter.title, 'Test Project')
+    assert.equal(note.frontmatter.is_a, 'Project')
+    assert.ok(note.content.includes('test project for the MCP server'))
   })
 
   it('should throw for missing notes', async () => {
     await assert.rejects(
-      () => readNote(tmpDir, 'nonexistent.md'),
+      () => getNote(tmpDir, 'nonexistent.md'),
       { code: 'ENOENT' }
     )
   })
 })
 
-describe('createNote', () => {
-  it('should create a note with frontmatter', async () => {
-    const absPath = await createNote(tmpDir, 'note/new-note.md', 'My New Note', { is_a: 'Note' })
-    assert.ok(absPath.endsWith('new-note.md'))
-
-    const content = await fs.readFile(absPath, 'utf-8')
-    assert.ok(content.includes('title: My New Note'))
-    assert.ok(content.includes('is_a: Note'))
-    assert.ok(content.includes('# My New Note'))
-  })
-
-  it('should create parent directories', async () => {
-    const absPath = await createNote(tmpDir, 'deep/nested/dir/note.md', 'Deep Note')
-    const content = await fs.readFile(absPath, 'utf-8')
-    assert.ok(content.includes('# Deep Note'))
-  })
-})
-
 describe('searchNotes', () => {
   it('should find notes matching title', async () => {
     const results = await searchNotes(tmpDir, 'Test Project')
@@ -121,123 +104,6 @@ describe('searchNotes', () => {
   })
 })
 
-describe('appendToNote', () => {
-  it('should append text to a note', async () => {
-    await appendToNote(tmpDir, 'note/daily-log.md', '## Evening Update\nFinished testing.')
-    const content = await readNote(tmpDir, 'note/daily-log.md')
-    assert.ok(content.includes('## Evening Update'))
-    assert.ok(content.includes('Finished testing.'))
-  })
-})
-
-describe('editNoteFrontmatter', () => {
-  it('should merge a patch into frontmatter', async () => {
-    const updated = await editNoteFrontmatter(tmpDir, 'project/test-project.md', { status: 'Completed', priority: 'High' })
-    assert.equal(updated.status, 'Completed')
-    assert.equal(updated.priority, 'High')
-    assert.equal(updated.title, 'Test Project')
-  })
-
-  it('should preserve existing frontmatter fields', async () => {
-    const content = await readNote(tmpDir, 'project/test-project.md')
-    assert.ok(content.includes('is_a: Project'))
-    assert.ok(content.includes('status: Completed'))
-  })
-
-  it('should throw for missing file', async () => {
-    await assert.rejects(
-      () => editNoteFrontmatter(tmpDir, 'nonexistent.md', { foo: 'bar' }),
-      { code: 'ENOENT' }
-    )
-  })
-})
-
-describe('deleteNote', () => {
-  it('should delete an existing note', async () => {
-    const delPath = 'note/to-delete.md'
-    await createNote(tmpDir, delPath, 'To Delete')
-    const absPath = path.join(tmpDir, delPath)
-
-    // Verify it exists
-    await fs.access(absPath)
-
-    await deleteNote(tmpDir, delPath)
-
-    await assert.rejects(
-      () => fs.access(absPath),
-      { code: 'ENOENT' }
-    )
-  })
-
-  it('should throw for missing file', async () => {
-    await assert.rejects(
-      () => deleteNote(tmpDir, 'nonexistent.md'),
-      { code: 'ENOENT' }
-    )
-  })
-})
-
-describe('linkNotes', () => {
-  it('should add a target to an array property', async () => {
-    const linkPath = 'project/link-test.md'
-    await createNote(tmpDir, linkPath, 'Link Test', { is_a: 'Project' })
-
-    const result = await linkNotes(tmpDir, linkPath, 'related_to', '[[note/daily-log]]')
-    assert.deepEqual(result, ['[[note/daily-log]]'])
-  })
-
-  it('should not duplicate existing links', async () => {
-    const linkPath = 'project/link-test.md'
-
-    await linkNotes(tmpDir, linkPath, 'related_to', '[[note/daily-log]]')
-    const result = await linkNotes(tmpDir, linkPath, 'related_to', '[[note/daily-log]]')
-    assert.equal(result.length, 1)
-  })
-
-  it('should add multiple distinct links', async () => {
-    const linkPath = 'project/link-test.md'
-
-    await linkNotes(tmpDir, linkPath, 'related_to', '[[project/test-project]]')
-    const result = await linkNotes(tmpDir, linkPath, 'related_to', '[[project/test-project]]')
-    // Should have daily-log and test-project
-    assert.ok(result.includes('[[note/daily-log]]'))
-    assert.ok(result.includes('[[project/test-project]]'))
-    assert.equal(result.length, 2)
-  })
-})
-
-describe('listNotes', () => {
-  it('should list all notes sorted by title', async () => {
-    const notes = await listNotes(tmpDir)
-    assert.ok(notes.length >= 3)
-    // Verify sorted by title
-    for (let i = 1; i < notes.length; i++) {
-      assert.ok(notes[i - 1].title.localeCompare(notes[i].title) <= 0)
-    }
-  })
-
-  it('should filter by type', async () => {
-    const projects = await listNotes(tmpDir, 'Project')
-    assert.ok(projects.length >= 1)
-    for (const n of projects) {
-      assert.equal(n.type, 'Project')
-    }
-  })
-
-  it('should return empty for unknown type', async () => {
-    const notes = await listNotes(tmpDir, 'UnknownType12345')
-    assert.equal(notes.length, 0)
-  })
-
-  it('should support mtime sorting', async () => {
-    const notes = await listNotes(tmpDir, undefined, 'mtime')
-    assert.ok(notes.length >= 1)
-    // Just verify it returns results without crashing
-    assert.ok(notes[0].path)
-    assert.ok(notes[0].title)
-  })
-})
-
 describe('vaultContext', () => {
   it('should return types, recent notes, and vault path', async () => {
     const ctx = await vaultContext(tmpDir)
@@ -264,4 +130,15 @@ describe('vaultContext', () => {
       assert.ok(note.title)
     }
   })
+
+  it('should include folders', async () => {
+    const ctx = await vaultContext(tmpDir)
+    assert.ok(ctx.folders.includes('project/'))
+    assert.ok(ctx.folders.includes('note/'))
+  })
+
+  it('should report correct note count', async () => {
+    const ctx = await vaultContext(tmpDir)
+    assert.equal(ctx.noteCount, 3)
+  })
 })

mcp-server/ws-bridge.js

@@ -50,6 +50,8 @@ const TOOL_HANDLERS = {
   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', { filterType: args.type }); return { ok: true } },
+  highlight_editor: (args) => { broadcastUiAction('highlight', { element: args.element, path: args.path }); return { ok: true } },
+  refresh_vault: (args) => { broadcastUiAction('vault_changed', { path: args?.path }); return { ok: true } },
 }
 
 async function handleMessage(data) {

src-tauri/src/commands.rs

@@ -5,7 +5,9 @@ use crate::claude_cli::{
     AgentStreamRequest, ChatStreamRequest, ClaudeCliStatus, ClaudeStreamEvent,
 };
 use crate::frontmatter::FrontmatterValue;
-use crate::git::{GitCommit, GitPullResult, LastCommitInfo, ModifiedFile, PulseCommit};
+use crate::git::{
+    GitCommit, GitPullResult, GitPushResult, LastCommitInfo, ModifiedFile, PulseCommit,
+};
 use crate::github::{DeviceFlowPollResult, DeviceFlowStart, GitHubUser, GithubRepo};
 use crate::indexing::{IndexStatus, IndexingProgress};
 use crate::search::SearchResponse;
@@ -276,7 +278,7 @@ pub fn git_commit_conflict_resolution(vault_path: String) -> Result<String, Stri
 }
 
 #[tauri::command]
-pub fn git_push(vault_path: String) -> Result<String, String> {
+pub fn git_push(vault_path: String) -> Result<GitPushResult, String> {
     let vault_path = expand_tilde(&vault_path);
     git::git_push(&vault_path)
 }

src-tauri/src/frontmatter/yaml.rs

@@ -193,8 +193,8 @@ mod tests {
 
     #[test]
     fn test_to_yaml_value_number_float() {
-        let v = FrontmatterValue::Number(3.14);
-        assert_eq!(v.to_yaml_value(), "3.14");
+        let v = FrontmatterValue::Number(3.125);
+        assert_eq!(v.to_yaml_value(), "3.125");
     }
 
     #[test]

src-tauri/src/git/mod.rs

@@ -15,7 +15,7 @@ pub use conflict::{
 };
 pub use history::{get_file_diff, get_file_diff_at_commit, get_file_history};
 pub use pulse::{get_last_commit_info, get_vault_pulse, LastCommitInfo, PulseCommit, PulseFile};
-pub use remote::{git_pull, git_push, has_remote, GitPullResult};
+pub use remote::{git_pull, git_push, has_remote, GitPullResult, GitPushResult};
 pub use status::{get_modified_files, ModifiedFile};
 
 use serde::Serialize;

src-tauri/src/git/pulse.rs

@@ -54,7 +54,11 @@ fn parse_file_status(code: &str) -> &str {
 
 /// Get the pulse (commit activity feed) for a vault, showing only .md file changes.
 /// `skip` offsets into the commit list for pagination; `limit` caps how many to return.
-pub fn get_vault_pulse(vault_path: &str, limit: usize, skip: usize) -> Result<Vec<PulseCommit>, String> {
+pub fn get_vault_pulse(
+    vault_path: &str,
+    limit: usize,
+    skip: usize,
+) -> Result<Vec<PulseCommit>, String> {
     let vault = Path::new(vault_path);
 
     if !vault.join(".git").exists() {

src-tauri/src/git/remote.rs

@@ -110,8 +110,74 @@ fn parse_updated_files(stdout: &str) -> Vec<String> {
         .collect()
 }
 
+#[derive(Debug, Serialize, Deserialize, Clone, PartialEq)]
+pub struct GitPushResult {
+    pub status: String, // "ok" | "rejected" | "auth_error" | "network_error" | "error"
+    pub message: String,
+}
+
+/// Classify a git push stderr message into a user-friendly status and message.
+pub fn classify_push_error(stderr: &str) -> GitPushResult {
+    let lower = stderr.to_lowercase();
+
+    if lower.contains("non-fast-forward")
+        || lower.contains("[rejected]")
+        || lower.contains("fetch first")
+        || lower.contains("failed to push some refs")
+            && (lower.contains("updates were rejected") || lower.contains("non-fast-forward"))
+    {
+        return GitPushResult {
+            status: "rejected".to_string(),
+            message: "Push rejected: remote has new commits. Pull first, then push.".to_string(),
+        };
+    }
+
+    if lower.contains("authentication failed")
+        || lower.contains("could not read username")
+        || lower.contains("permission denied")
+        || lower.contains("403")
+        || lower.contains("invalid credentials")
+    {
+        return GitPushResult {
+            status: "auth_error".to_string(),
+            message: "Push failed: authentication error. Check your credentials.".to_string(),
+        };
+    }
+
+    if lower.contains("could not resolve host")
+        || lower.contains("unable to access")
+        || lower.contains("connection refused")
+        || lower.contains("network is unreachable")
+        || lower.contains("timed out")
+    {
+        return GitPushResult {
+            status: "network_error".to_string(),
+            message: "Push failed: network error. Check your connection and try again.".to_string(),
+        };
+    }
+
+    // Fallback: extract the hint line if present, otherwise use the full stderr
+    let hint_line = stderr
+        .lines()
+        .find(|l| l.trim_start().starts_with("hint:"))
+        .map(|l| l.trim_start().strip_prefix("hint:").unwrap_or(l).trim())
+        .unwrap_or("")
+        .to_string();
+
+    let detail = if hint_line.is_empty() {
+        stderr.trim().to_string()
+    } else {
+        hint_line
+    };
+
+    GitPushResult {
+        status: "error".to_string(),
+        message: format!("Push failed: {detail}"),
+    }
+}
+
 /// Push to remote.
-pub fn git_push(vault_path: &str) -> Result<String, String> {
+pub fn git_push(vault_path: &str) -> Result<GitPushResult, String> {
     let vault = Path::new(vault_path);
 
     let output = Command::new("git")
@@ -122,13 +188,13 @@ pub fn git_push(vault_path: &str) -> Result<String, String> {
 
     if !output.status.success() {
         let stderr = String::from_utf8_lossy(&output.stderr);
-        return Err(format!("git push failed: {}", stderr));
+        return Ok(classify_push_error(&stderr));
     }
 
-    // git push often writes to stderr even on success
-    let stdout = String::from_utf8_lossy(&output.stdout);
-    let stderr = String::from_utf8_lossy(&output.stderr);
-    Ok(format!("{}{}", stdout, stderr))
+    Ok(GitPushResult {
+        status: "ok".to_string(),
+        message: "Pushed to remote".to_string(),
+    })
 }
 
 #[cfg(test)]
@@ -227,6 +293,104 @@ mod tests {
         assert!(files.is_empty());
     }
 
+    #[test]
+    fn test_classify_push_error_non_fast_forward() {
+        let stderr = r#"To github.com:user/repo.git
+ ! [rejected]        main -> main (non-fast-forward)
+error: failed to push some refs to 'github.com:user/repo.git'
+hint: Updates were rejected because the remote contains work that you do not
+hint: have locally."#;
+        let result = classify_push_error(stderr);
+        assert_eq!(result.status, "rejected");
+        assert!(result.message.contains("Pull first"));
+    }
+
+    #[test]
+    fn test_classify_push_error_fetch_first() {
+        let stderr = "error: failed to push some refs\nhint: Updates were rejected because the tip of your current branch is behind\nhint: its remote counterpart. Integrate the remote changes (e.g.\nhint: 'git pull ...') before pushing again.\nhint: See the 'Note about fast-forwards' in 'git push --help' for details.\n ! [rejected]        main -> main (fetch first)\n";
+        let result = classify_push_error(stderr);
+        assert_eq!(result.status, "rejected");
+    }
+
+    #[test]
+    fn test_classify_push_error_auth_failure() {
+        let stderr = "remote: Permission denied to user/repo.git\nfatal: unable to access 'https://github.com/user/repo.git/': The requested URL returned error: 403";
+        let result = classify_push_error(stderr);
+        assert_eq!(result.status, "auth_error");
+        assert!(result.message.contains("authentication"));
+    }
+
+    #[test]
+    fn test_classify_push_error_network() {
+        let stderr = "fatal: unable to access 'https://github.com/user/repo.git/': Could not resolve host: github.com";
+        let result = classify_push_error(stderr);
+        assert_eq!(result.status, "network_error");
+        assert!(result.message.contains("network"));
+    }
+
+    #[test]
+    fn test_classify_push_error_unknown() {
+        let stderr = "error: something unexpected happened\nhint: Try again later";
+        let result = classify_push_error(stderr);
+        assert_eq!(result.status, "error");
+        assert!(result.message.contains("Try again later"));
+    }
+
+    #[test]
+    fn test_classify_push_error_unknown_no_hint() {
+        let stderr = "error: something totally weird";
+        let result = classify_push_error(stderr);
+        assert_eq!(result.status, "error");
+        assert!(result.message.contains("something totally weird"));
+    }
+
+    #[test]
+    fn test_git_push_result_serialization() {
+        let result = GitPushResult {
+            status: "rejected".to_string(),
+            message: "Push rejected".to_string(),
+        };
+        let json = serde_json::to_string(&result).unwrap();
+        assert!(json.contains("\"rejected\""));
+        let parsed: GitPushResult = serde_json::from_str(&json).unwrap();
+        assert_eq!(parsed.status, "rejected");
+    }
+
+    #[test]
+    fn test_git_push_success_returns_ok() {
+        let (_bare, clone_a, _clone_b) = setup_remote_pair();
+        let vp_a = clone_a.path().to_str().unwrap();
+
+        fs::write(clone_a.path().join("note.md"), "# Note\n").unwrap();
+        git_commit(vp_a, "initial").unwrap();
+        let result = git_push(vp_a).unwrap();
+        assert_eq!(result.status, "ok");
+    }
+
+    #[test]
+    fn test_git_push_rejected_returns_rejected() {
+        let (_bare, clone_a, clone_b) = setup_remote_pair();
+        let vp_a = clone_a.path().to_str().unwrap();
+        let vp_b = clone_b.path().to_str().unwrap();
+
+        // Both clones commit and push — second push should be rejected
+        fs::write(clone_a.path().join("note.md"), "# A\n").unwrap();
+        git_commit(vp_a, "from A").unwrap();
+        git_push(vp_a).unwrap();
+
+        git_pull(vp_b).unwrap();
+        fs::write(clone_b.path().join("note.md"), "# B\n").unwrap();
+        git_commit(vp_b, "from B").unwrap();
+        git_push(vp_b).unwrap();
+
+        // Now A has a new commit but hasn't pulled B's changes
+        fs::write(clone_a.path().join("other.md"), "# Other\n").unwrap();
+        git_commit(vp_a, "from A again").unwrap();
+        let result = git_push(vp_a).unwrap();
+        assert_eq!(result.status, "rejected");
+        assert!(result.message.contains("Pull first"));
+    }
+
     #[test]
     fn test_git_pull_result_serialization() {
         let result = GitPullResult {

src-tauri/src/indexing.rs

@@ -1,4 +1,4 @@
-use serde::Serialize;
+use serde::{Deserialize, Serialize};
 use std::path::{Path, PathBuf};
 use std::process::Command;
 use std::sync::Mutex;
@@ -223,10 +223,72 @@ pub struct IndexStatus {
     pub indexed_count: usize,
     pub embedded_count: usize,
     pub pending_embed: usize,
+    pub last_indexed_commit: Option<String>,
+    pub last_indexed_at: Option<u64>,
+}
+
+// --- Index metadata persistence ---
+
+#[derive(Debug, Serialize, Deserialize, Default)]
+struct IndexMetadata {
+    #[serde(default)]
+    last_indexed_commit: Option<String>,
+    #[serde(default)]
+    last_indexed_at: Option<u64>,
+}
+
+fn index_metadata_path(vault_path: &str) -> PathBuf {
+    Path::new(vault_path).join(".laputa-index.json")
+}
+
+fn load_index_metadata(vault_path: &str) -> IndexMetadata {
+    let path = index_metadata_path(vault_path);
+    std::fs::read_to_string(&path)
+        .ok()
+        .and_then(|s| serde_json::from_str(&s).ok())
+        .unwrap_or_default()
+}
+
+fn save_index_metadata(vault_path: &str, meta: &IndexMetadata) -> Result<(), String> {
+    let path = index_metadata_path(vault_path);
+    let json =
+        serde_json::to_string_pretty(meta).map_err(|e| format!("Failed to serialize: {e}"))?;
+    std::fs::write(&path, json).map_err(|e| format!("Failed to write index metadata: {e}"))
+}
+
+/// Get the current HEAD commit hash for a vault.
+fn get_head_commit(vault_path: &str) -> Option<String> {
+    let output = Command::new("git")
+        .args(["rev-parse", "HEAD"])
+        .current_dir(vault_path)
+        .output()
+        .ok()?;
+    if output.status.success() {
+        Some(String::from_utf8_lossy(&output.stdout).trim().to_string())
+    } else {
+        None
+    }
+}
+
+/// Record the current HEAD as the last indexed commit.
+fn stamp_index_commit(vault_path: &str) {
+    if let Some(commit) = get_head_commit(vault_path) {
+        let now = std::time::SystemTime::now()
+            .duration_since(std::time::UNIX_EPOCH)
+            .map(|d| d.as_secs())
+            .unwrap_or(0);
+        let meta = IndexMetadata {
+            last_indexed_commit: Some(commit),
+            last_indexed_at: Some(now),
+        };
+        let _ = save_index_metadata(vault_path, &meta);
+    }
 }
 
 /// Check whether the vault has a qmd index and its status.
 pub fn check_index_status(vault_path: &str) -> IndexStatus {
+    let meta = load_index_metadata(vault_path);
+
     let qmd = match find_qmd_binary() {
         Some(b) => b,
         None => {
@@ -237,6 +299,8 @@ pub fn check_index_status(vault_path: &str) -> IndexStatus {
                 indexed_count: 0,
                 embedded_count: 0,
                 pending_embed: 0,
+                last_indexed_commit: meta.last_indexed_commit,
+                last_indexed_at: meta.last_indexed_at,
             }
         }
     };
@@ -244,7 +308,7 @@ pub fn check_index_status(vault_path: &str) -> IndexStatus {
     let vault_name = vault_dir_name(vault_path);
     let output = qmd.command().args(["status"]).output();
 
-    match output {
+    let mut status = match output {
         Ok(o) if o.status.success() => {
             let stdout = String::from_utf8_lossy(&o.stdout);
             parse_status_for_vault(&stdout, &vault_name)
@@ -256,8 +320,14 @@ pub fn check_index_status(vault_path: &str) -> IndexStatus {
             indexed_count: 0,
             embedded_count: 0,
             pending_embed: 0,
+            last_indexed_commit: None,
+            last_indexed_at: None,
         },
-    }
+    };
+
+    status.last_indexed_commit = meta.last_indexed_commit;
+    status.last_indexed_at = meta.last_indexed_at;
+    status
 }
 
 fn vault_dir_name(vault_path: &str) -> String {
@@ -323,6 +393,8 @@ fn parse_status_for_vault(status_output: &str, vault_name: &str) -> IndexStatus
         indexed_count,
         embedded_count,
         pending_embed,
+        last_indexed_commit: None,
+        last_indexed_at: None,
     }
 }
 
@@ -451,6 +523,7 @@ where
         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}");
+        stamp_index_commit(vault_path);
         on_progress(IndexingProgress {
             phase: "complete".to_string(),
             current: total,
@@ -461,6 +534,8 @@ where
         return Ok(());
     }
 
+    stamp_index_commit(vault_path);
+
     on_progress(IndexingProgress {
         phase: "complete".to_string(),
         current: total,
@@ -513,9 +588,23 @@ pub fn run_incremental_update(vault_path: &str) -> Result<(), String> {
         return Err(format!("qmd update failed: {stderr}"));
     }
 
+    stamp_index_commit(vault_path);
+
     Ok(())
 }
 
+/// Check if HEAD has advanced past the last indexed commit.
+#[cfg(test)]
+fn needs_reindex_after_sync(vault_path: &str) -> bool {
+    let meta = load_index_metadata(vault_path);
+    let head = get_head_commit(vault_path);
+    match (meta.last_indexed_commit, head) {
+        (Some(last), Some(current)) => last != current,
+        (None, Some(_)) => true,
+        _ => false,
+    }
+}
+
 #[cfg(test)]
 mod tests {
     use super::*;
@@ -698,4 +787,126 @@ Collections
         // It verifies the function doesn't panic.
         let _ = find_bun();
     }
+
+    #[test]
+    fn index_metadata_roundtrip() {
+        let dir = tempfile::tempdir().unwrap();
+        let vault = dir.path().to_str().unwrap();
+
+        // Default when no file exists
+        let meta = load_index_metadata(vault);
+        assert!(meta.last_indexed_commit.is_none());
+        assert!(meta.last_indexed_at.is_none());
+
+        // Write and read back
+        let meta = IndexMetadata {
+            last_indexed_commit: Some("abc123def456".to_string()),
+            last_indexed_at: Some(1709000000),
+        };
+        save_index_metadata(vault, &meta).unwrap();
+
+        let loaded = load_index_metadata(vault);
+        assert_eq!(loaded.last_indexed_commit.as_deref(), Some("abc123def456"));
+        assert_eq!(loaded.last_indexed_at, Some(1709000000));
+    }
+
+    #[test]
+    fn index_metadata_survives_malformed_json() {
+        let dir = tempfile::tempdir().unwrap();
+        let vault = dir.path().to_str().unwrap();
+
+        // Write garbage
+        std::fs::write(dir.path().join(".laputa-index.json"), "not json").unwrap();
+
+        let meta = load_index_metadata(vault);
+        assert!(meta.last_indexed_commit.is_none());
+    }
+
+    #[test]
+    fn needs_reindex_after_sync_no_metadata() {
+        let dir = tempfile::tempdir().unwrap();
+        let vault = dir.path().to_str().unwrap();
+
+        // Init a git repo so get_head_commit works
+        Command::new("git")
+            .args(["init"])
+            .current_dir(dir.path())
+            .output()
+            .unwrap();
+        Command::new("git")
+            .args(["commit", "--allow-empty", "-m", "init"])
+            .current_dir(dir.path())
+            .output()
+            .unwrap();
+
+        // No metadata → needs reindex
+        assert!(needs_reindex_after_sync(vault));
+    }
+
+    #[test]
+    fn needs_reindex_after_sync_same_commit() {
+        let dir = tempfile::tempdir().unwrap();
+        let vault = dir.path().to_str().unwrap();
+
+        Command::new("git")
+            .args(["init"])
+            .current_dir(dir.path())
+            .output()
+            .unwrap();
+        Command::new("git")
+            .args(["commit", "--allow-empty", "-m", "init"])
+            .current_dir(dir.path())
+            .output()
+            .unwrap();
+
+        let head = get_head_commit(vault).unwrap();
+        let meta = IndexMetadata {
+            last_indexed_commit: Some(head),
+            last_indexed_at: Some(1709000000),
+        };
+        save_index_metadata(vault, &meta).unwrap();
+
+        assert!(!needs_reindex_after_sync(vault));
+    }
+
+    #[test]
+    fn needs_reindex_after_sync_different_commit() {
+        let dir = tempfile::tempdir().unwrap();
+        let vault = dir.path().to_str().unwrap();
+
+        Command::new("git")
+            .args(["init"])
+            .current_dir(dir.path())
+            .output()
+            .unwrap();
+        Command::new("git")
+            .args(["commit", "--allow-empty", "-m", "init"])
+            .current_dir(dir.path())
+            .output()
+            .unwrap();
+
+        let meta = IndexMetadata {
+            last_indexed_commit: Some("old_commit_hash".to_string()),
+            last_indexed_at: Some(1709000000),
+        };
+        save_index_metadata(vault, &meta).unwrap();
+
+        assert!(needs_reindex_after_sync(vault));
+    }
+
+    #[test]
+    fn check_index_status_includes_metadata() {
+        let dir = tempfile::tempdir().unwrap();
+        let vault = dir.path().to_str().unwrap();
+
+        let meta = IndexMetadata {
+            last_indexed_commit: Some("abc123".to_string()),
+            last_indexed_at: Some(1709000000),
+        };
+        save_index_metadata(vault, &meta).unwrap();
+
+        let status = check_index_status(vault);
+        assert_eq!(status.last_indexed_commit.as_deref(), Some("abc123"));
+        assert_eq!(status.last_indexed_at, Some(1709000000));
+    }
 }

src-tauri/src/menu.rs

@@ -32,7 +32,6 @@ 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";
@@ -49,6 +48,7 @@ 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 VAULT_REINDEX: &str = "vault-reindex";
 
 const CUSTOM_IDS: &[&str] = &[
     APP_SETTINGS,
@@ -75,7 +75,6 @@ const CUSTOM_IDS: &[&str] = &[
     VIEW_GO_BACK,
     VIEW_GO_FORWARD,
     GO_ALL_NOTES,
-    GO_FAVORITES,
     GO_ARCHIVED,
     GO_TRASH,
     GO_CHANGES,
@@ -90,6 +89,7 @@ const CUSTOM_IDS: &[&str] = &[
     VAULT_RESOLVE_CONFLICTS,
     VAULT_VIEW_CHANGES,
     VAULT_INSTALL_MCP,
+    VAULT_REINDEX,
 ];
 
 /// IDs of menu items that should be disabled when no note tab is active.
@@ -249,9 +249,6 @@ 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)?;
@@ -268,7 +265,6 @@ fn build_go_menu(app: &App) -> MenuResult {
 
     Ok(SubmenuBuilder::new(app, "Go")
         .item(&all_notes)
-        .item(&favorites)
         .item(&archived)
         .item(&trash)
         .item(&changes)
@@ -338,6 +334,9 @@ fn build_vault_menu(app: &App) -> MenuResult {
     let install_mcp = MenuItemBuilder::new("Install MCP Server")
         .id(VAULT_INSTALL_MCP)
         .build(app)?;
+    let reindex = MenuItemBuilder::new("Reindex Vault")
+        .id(VAULT_REINDEX)
+        .build(app)?;
 
     Ok(SubmenuBuilder::new(app, "Vault")
         .item(&open_vault)
@@ -351,6 +350,7 @@ fn build_vault_menu(app: &App) -> MenuResult {
         .item(&resolve_conflicts)
         .item(&view_changes)
         .separator()
+        .item(&reindex)
         .item(&install_mcp)
         .build()?)
 }
@@ -454,7 +454,6 @@ mod tests {
             VIEW_GO_BACK,
             VIEW_GO_FORWARD,
             GO_ALL_NOTES,
-            GO_FAVORITES,
             GO_ARCHIVED,
             GO_TRASH,
             GO_CHANGES,
@@ -469,6 +468,7 @@ mod tests {
             VAULT_RESOLVE_CONFLICTS,
             VAULT_VIEW_CHANGES,
             VAULT_INSTALL_MCP,
+            VAULT_REINDEX,
         ];
         for id in &expected {
             assert!(CUSTOM_IDS.contains(id), "missing custom ID: {id}");

src-tauri/src/vault/cache.rs

@@ -158,10 +158,7 @@ fn parse_files_at(vault: &Path, rel_paths: &[String]) -> Vec<VaultEntry> {
 
 /// Machine-local files that should never be git-tracked in any vault.
 /// These are either caches with absolute paths or per-machine settings.
-const UNTRACKED_FILES: &[&str] = &[
-    ".laputa-cache.json",
-    ".laputa/settings.json",
-];
+const UNTRACKED_FILES: &[&str] = &[".laputa-cache.json", ".laputa/settings.json"];
 
 /// Ensure machine-local files are excluded from git via `.git/info/exclude`
 /// and un-tracked if they were previously committed (git rm --cached).
@@ -184,7 +181,11 @@ fn ensure_cache_excluded(vault: &Path) {
 
     if !to_add.is_empty() {
         to_add.sort();
-        let separator = if existing.ends_with('\n') || existing.is_empty() { "" } else { "\n" };
+        let separator = if existing.ends_with('\n') || existing.is_empty() {
+            ""
+        } else {
+            "\n"
+        };
         let additions = to_add.join("\n");
         let _ = fs::write(&exclude_path, format!("{existing}{separator}{additions}\n"));
     }
@@ -645,4 +646,63 @@ mod tests {
         assert!(titles.contains(&"Default Theme"));
         assert!(titles.contains(&"Dark Theme"));
     }
+
+    #[test]
+    fn test_update_same_commit_visible_removed_from_type_note() {
+        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 with visible: false
+        create_test_file(
+            vault,
+            "type/topic.md",
+            "---\ntype: Type\nvisible: false\n---\n# Topic\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
+        let entries = scan_vault_cached(vault).unwrap();
+        assert_eq!(entries.len(), 1);
+        assert_eq!(
+            entries[0].visible,
+            Some(false),
+            "visible must be false initially"
+        );
+
+        // User removes visible field (uncommitted edit)
+        create_test_file(vault, "type/topic.md", "---\ntype: Type\n---\n# Topic\n");
+
+        // Reload — must reflect the removal (visible defaults to None)
+        let entries2 = scan_vault_cached(vault).unwrap();
+        assert_eq!(entries2.len(), 1);
+        assert_eq!(
+            entries2[0].visible, None,
+            "visible must be None after removing the field"
+        );
+    }
 }

src/App.test.tsx

@@ -179,7 +179,7 @@ describe('App', () => {
     await waitFor(() => {
       // "All Notes" should be rendered as the selected nav item
       expect(screen.getByText('All Notes')).toBeInTheDocument()
-      expect(screen.getByText('Favorites')).toBeInTheDocument()
+      expect(screen.getByText('Archive')).toBeInTheDocument()
     })
   })
 

src/App.tsx

@@ -48,10 +48,12 @@ import { filterEntries } from './utils/noteListHelpers'
 import { openLocalFile } from './utils/url'
 import './App.css'
 
-// Type declaration for mock content storage
+// Type declarations for mock content storage and test overrides
 declare global {
   interface Window {
     __mockContent?: Record<string, string>
+    // eslint-disable-next-line @typescript-eslint/no-explicit-any -- mock handler map for Playwright test overrides
+    __mockHandlers?: Record<string, (args: any) => any>
   }
 }
 
@@ -111,10 +113,13 @@ function App() {
 
   const { mcpStatus, installMcp } = useMcpStatus(resolvedPath, setToastMessage)
 
+  const indexing = useIndexing(resolvedPath)
+
   const autoSync = useAutoSync({
     vaultPath: resolvedPath,
     intervalMinutes: settings.auto_pull_interval_minutes,
     onVaultUpdated: vault.reloadVault,
+    onSyncUpdated: indexing.triggerIncrementalIndex,
     onConflict: (files) => {
       const names = files.map((f) => f.split('/').pop()).join(', ')
       setToastMessage(`Conflict in ${names} — click to resolve`)
@@ -125,8 +130,6 @@ function App() {
   // Ref bridges for conflict resolution callbacks (notes declared below)
   const openConflictFileRef = useRef<(relativePath: string) => void>(() => {})
 
-  const indexing = useIndexing(resolvedPath)
-
   const conflictResolver = useConflictResolver({
     vaultPath: resolvedPath,
     onResolved: () => {
@@ -230,19 +233,26 @@ function App() {
 
   useNavigationGestures({ onGoBack: handleGoBack, onGoForward: handleGoForward })
 
+  // O(1) path lookup map — rebuilt only when vault.entries changes
+  const entriesByPath = useMemo(() => {
+    const map = new Map<string, VaultEntry>()
+    for (const e of vault.entries) map.set(e.path, e)
+    return map
+  }, [vault.entries])
+
   // MCP UI bridge: react to AI-driven open/highlight/vault-change events
   const openNoteByPath = useCallback((path: string) => {
-    const entry = vault.entries.find(e => e.path === path || e.path === `${resolvedPath}/${path}`)
+    const entry = entriesByPath.get(path) ?? entriesByPath.get(`${resolvedPath}/${path}`)
     if (entry) {
       notes.handleSelectNote(entry)
     } else {
       // Entry not yet in vault (just created) — reload then open
       vault.reloadVault().then(freshEntries => {
-        const fresh = freshEntries.find((e: VaultEntry) => e.path === path || e.path === `${resolvedPath}/${path}`)
+        const fresh = (freshEntries as VaultEntry[]).find(e => e.path === path || e.path === `${resolvedPath}/${path}`)
         if (fresh) notes.handleSelectNote(fresh)
       })
     }
-  }, [vault, notes, resolvedPath])
+  }, [entriesByPath, vault, notes, resolvedPath])
 
   const aiActivity = useAiActivity({
     onOpenNote: openNoteByPath,
@@ -253,10 +263,18 @@ function App() {
     onVaultChanged: () => { vault.reloadVault() },
   })
 
+  // Stable callback for Pulse "open note" — never triggers reloadVault.
+  // Pulse files always exist in the vault; if somehow not found, silently skip.
+  const handlePulseOpenNote = useCallback((relativePath: string) => {
+    const fullPath = `${resolvedPath}/${relativePath}`
+    const entry = entriesByPath.get(fullPath) ?? entriesByPath.get(relativePath)
+    if (entry) notes.handleSelectNote(entry)
+  }, [entriesByPath, resolvedPath, notes])
+
   // Agent file operation handlers: auto-open created notes, live-refresh modified notes
   const handleAgentFileCreated = useCallback((relativePath: string) => {
     vault.reloadVault().then(freshEntries => {
-      const entry = freshEntries.find((e: VaultEntry) => e.path === relativePath || e.path === `${resolvedPath}/${relativePath}`)
+      const entry = (freshEntries as VaultEntry[]).find(e => e.path === relativePath || e.path === `${resolvedPath}/${relativePath}`)
       if (entry) notes.handleSelectNote(entry)
     })
   }, [vault, notes, resolvedPath])
@@ -315,6 +333,7 @@ function App() {
     handleUpdateFrontmatter: notes.handleUpdateFrontmatter,
     handleDeleteProperty: notes.handleDeleteProperty, setToastMessage,
     createTypeEntry: notes.createTypeEntrySilent,
+    onFrontmatterPersisted: vault.loadModifiedFiles,
   })
 
   const handleDeleteNote = useCallback(async (path: string) => {
@@ -448,6 +467,7 @@ function App() {
     vaultCount: vaultSwitcher.allVaults.length,
     mcpStatus,
     onInstallMcp: installMcp,
+    onReindexVault: indexing.triggerFullReindex,
   })
 
   const activeTab = notes.tabs.find((t) => t.entry.path === notes.activeTabPath) ?? null
@@ -509,11 +529,7 @@ function App() {
           <>
             <div className={`app__note-list${aiActivity.highlightElement === 'notelist' ? ' ai-highlight' : ''}`} style={{ width: layout.noteListWidth }}>
               {selection.kind === 'filter' && selection.filter === 'pulse' ? (
-                <PulseView vaultPath={resolvedPath} onOpenNote={(relativePath) => {
-                  const fullPath = `${resolvedPath}/${relativePath}`
-                  const entry = vault.entries.find(e => e.path === fullPath || e.path === relativePath)
-                  if (entry) notes.handleSelectNote(entry)
-                }} sidebarCollapsed={!sidebarVisible} onExpandSidebar={() => setViewMode('all')} />
+                <PulseView vaultPath={resolvedPath} onOpenNote={handlePulseOpenNote} sidebarCollapsed={!sidebarVisible} onExpandSidebar={() => setViewMode('all')} />
               ) : (
                 <NoteList entries={vault.entries} selection={selection} selectedNote={activeTab?.entry ?? null} allContent={vault.allContent} modifiedFiles={vault.modifiedFiles} modifiedFilesError={vault.modifiedFilesError} getNoteStatus={vault.getNoteStatus} sidebarCollapsed={!sidebarVisible} onSelectNote={notes.handleSelectNote} onReplaceActiveTab={notes.handleReplaceActiveTab} onCreateNote={notes.handleCreateNoteImmediate} onBulkArchive={bulkActions.handleBulkArchive} onBulkTrash={bulkActions.handleBulkTrash} onUpdateTypeSort={notes.handleUpdateFrontmatter} updateEntry={vault.updateEntry} />
               )}
@@ -573,7 +589,7 @@ function App() {
         </div>
       </div>
       <UpdateBanner status={updateStatus} actions={updateActions} />
-      <StatusBar noteCount={vault.entries.length} modifiedCount={vault.modifiedFiles.length} vaultPath={vaultSwitcher.vaultPath} vaults={vaultSwitcher.allVaults} onSwitchVault={vaultSwitcher.switchVault} onOpenSettings={dialogs.openSettings} onOpenLocalFolder={vaultSwitcher.handleOpenLocalFolder} onConnectGitHub={dialogs.openGitHubVault} onClickPending={() => setSelection({ kind: 'filter', filter: 'changes' })} hasGitHub={!!settings.github_token} syncStatus={autoSync.syncStatus} lastSyncTime={autoSync.lastSyncTime} conflictCount={autoSync.conflictFiles.length} lastCommitInfo={autoSync.lastCommitInfo} onTriggerSync={autoSync.triggerSync} onOpenConflictResolver={handleOpenConflictResolver} zoomLevel={zoom.zoomLevel} onZoomReset={zoom.zoomReset} buildNumber={buildNumber} onCheckForUpdates={handleCheckForUpdates} indexingProgress={indexing.progress} onRetryIndexing={indexing.retryIndexing} onRemoveVault={vaultSwitcher.removeVault} mcpStatus={mcpStatus} onInstallMcp={installMcp} />
+      <StatusBar noteCount={vault.entries.length} modifiedCount={vault.modifiedFiles.length} vaultPath={vaultSwitcher.vaultPath} vaults={vaultSwitcher.allVaults} onSwitchVault={vaultSwitcher.switchVault} onOpenSettings={dialogs.openSettings} onOpenLocalFolder={vaultSwitcher.handleOpenLocalFolder} onConnectGitHub={dialogs.openGitHubVault} onClickPending={() => setSelection({ kind: 'filter', filter: 'changes' })} hasGitHub={!!settings.github_token} syncStatus={autoSync.syncStatus} lastSyncTime={autoSync.lastSyncTime} conflictCount={autoSync.conflictFiles.length} lastCommitInfo={autoSync.lastCommitInfo} onTriggerSync={autoSync.triggerSync} onOpenConflictResolver={handleOpenConflictResolver} zoomLevel={zoom.zoomLevel} onZoomReset={zoom.zoomReset} buildNumber={buildNumber} onCheckForUpdates={handleCheckForUpdates} indexingProgress={indexing.progress} lastIndexedTime={indexing.lastIndexedTime} onRetryIndexing={indexing.retryIndexing} onReindexVault={indexing.triggerFullReindex} onRemoveVault={vaultSwitcher.removeVault} mcpStatus={mcpStatus} onInstallMcp={installMcp} />
       <Toast message={toastMessage} onDismiss={() => setToastMessage(null)} />
       <QuickOpenPalette open={dialogs.showQuickOpen} entries={vault.entries} onSelect={notes.handleSelectNote} onClose={dialogs.closeQuickOpen} />
       <CommandPalette open={dialogs.showCommandPalette} commands={commands} onClose={dialogs.closeCommandPalette} />

src/components/AIChatPanel.tsx

@@ -18,6 +18,7 @@ interface AIChatPanelProps {
   allContent: Record<string, string>
   entries?: VaultEntry[]
   onClose: () => void
+  onNavigateWikilink?: (target: string) => void
 }
 
 function TypingIndicator() {
@@ -99,10 +100,10 @@ function ContextSearchDropdown({
   )
 }
 
-function AssistantMessage({ msg, onRetry }: { msg: ChatMessage; onRetry: () => void }) {
+function AssistantMessage({ msg, onRetry, onNavigateWikilink }: { msg: ChatMessage; onRetry: () => void; onNavigateWikilink?: (target: string) => void }) {
   return (
     <div>
-      <MarkdownContent content={msg.content} />
+      <MarkdownContent content={msg.content} onWikilinkClick={onNavigateWikilink} />
       <div className="flex items-center gap-3" style={{ marginTop: 4 }}>
         <button className="border-none bg-transparent p-0 text-muted-foreground cursor-pointer hover:underline"
           style={{ fontSize: 11 }} onClick={() => navigator.clipboard.writeText(msg.content)}>
@@ -121,10 +122,10 @@ function AssistantMessage({ msg, onRetry }: { msg: ChatMessage; onRetry: () => v
   )
 }
 
-function StreamingContent({ content }: { content: string }) {
+function StreamingContent({ content, onNavigateWikilink }: { content: string; onNavigateWikilink?: (target: string) => void }) {
   return (
     <div style={{ marginBottom: 12 }}>
-      <MarkdownContent content={content} />
+      <MarkdownContent content={content} onWikilinkClick={onNavigateWikilink} />
     </div>
   )
 }
@@ -176,7 +177,7 @@ function useContextNotes(entry: VaultEntry | null) {
 
 // --- Main component ---
 
-export function AIChatPanel({ entry, allContent, entries = [], onClose }: AIChatPanelProps) {
+export function AIChatPanel({ entry, allContent, entries = [], onClose, onNavigateWikilink }: AIChatPanelProps) {
   const [input, setInput] = useState('')
   const [showSearch, setShowSearch] = useState(false)
   const messagesEndRef = useRef<HTMLDivElement>(null)
@@ -213,7 +214,7 @@ export function AIChatPanel({ entry, allContent, entries = [], onClose }: AIChat
       <MessageList
         messages={chat.messages} isStreaming={chat.isStreaming}
         streamingContent={chat.streamingContent} onRetry={chat.retryMessage}
-        messagesEndRef={messagesEndRef}
+        messagesEndRef={messagesEndRef} onNavigateWikilink={onNavigateWikilink}
       />
 
       <QuickActionsBar actions={QUICK_ACTIONS} disabled={chat.isStreaming}
@@ -284,10 +285,11 @@ function ContextBar({
 }
 
 function MessageList({
-  messages, isStreaming, streamingContent, onRetry, messagesEndRef,
+  messages, isStreaming, streamingContent, onRetry, messagesEndRef, onNavigateWikilink,
 }: {
   messages: ChatMessage[]; isStreaming: boolean; streamingContent: string
   onRetry: (idx: number) => void; messagesEndRef: React.RefObject<HTMLDivElement | null>
+  onNavigateWikilink?: (target: string) => void
 }) {
   return (
     <div className="flex-1 overflow-y-auto" style={{ padding: 12 }}>
@@ -302,10 +304,10 @@ function MessageList({
         <div key={msg.id} style={{ marginBottom: 12 }}>
           {msg.role === 'user'
             ? <UserBubble content={msg.content} />
-            : <AssistantMessage msg={msg} onRetry={() => onRetry(idx)} />}
+            : <AssistantMessage msg={msg} onRetry={() => onRetry(idx)} onNavigateWikilink={onNavigateWikilink} />}
         </div>
       ))}
-      {isStreaming && streamingContent && <StreamingContent content={streamingContent} />}
+      {isStreaming && streamingContent && <StreamingContent content={streamingContent} onNavigateWikilink={onNavigateWikilink} />}
       {isStreaming && !streamingContent && <TypingIndicator />}
       <div ref={messagesEndRef} />
     </div>

src/components/AiMessage.tsx

@@ -24,6 +24,7 @@ export interface AiMessageProps {
   response?: string
   isStreaming?: boolean
   onOpenNote?: (path: string) => void
+  onNavigateWikilink?: (target: string) => void
 }
 
 function ReferencePill({ reference, onClick }: {
@@ -147,10 +148,10 @@ function ActionCardsList({ actions, onOpenNote, expandedIds, onToggleExpand }: {
   )
 }
 
-function ResponseBlock({ text }: { text: string }) {
+function ResponseBlock({ text, onNavigateWikilink }: { text: string; onNavigateWikilink?: (target: string) => void }) {
   return (
     <div style={{ marginBottom: 4 }}>
-      <MarkdownContent content={text} />
+      <MarkdownContent content={text} onWikilinkClick={onNavigateWikilink} />
       <button
         className="flex items-center gap-1 border-none bg-transparent p-0 text-muted-foreground cursor-pointer hover:text-foreground transition-colors"
         style={{ fontSize: 11, marginTop: 4 }}
@@ -175,7 +176,7 @@ function StreamingIndicator() {
   )
 }
 
-export function AiMessage({ userMessage, references, reasoning, reasoningDone, actions, response, isStreaming, onOpenNote }: AiMessageProps) {
+export function AiMessage({ userMessage, references, reasoning, reasoningDone, actions, response, isStreaming, onOpenNote, onNavigateWikilink }: AiMessageProps) {
   // Manual override: null = follow auto behavior, true/false = user forced
   const [userOverride, setUserOverride] = useState(false)
   const [expandedActions, setExpandedActions] = useState<Set<string>>(new Set())
@@ -212,7 +213,7 @@ export function AiMessage({ userMessage, references, reasoning, reasoningDone, a
           onToggleExpand={toggleAction}
         />
       )}
-      {response && <ResponseBlock text={response} />}
+      {response && <ResponseBlock text={response} onNavigateWikilink={onNavigateWikilink} />}
       {isStreaming && !response && <StreamingIndicator />}
     </div>
   )

src/components/AiPanel.tsx

@@ -4,6 +4,7 @@ import { AiMessage } from './AiMessage'
 import { WikilinkChatInput } from './WikilinkChatInput'
 import { useAiAgent, type AiAgentMessage, type AgentFileCallbacks } from '../hooks/useAiAgent'
 import { collectLinkedEntries, buildContextSnapshot, type NoteReference, type NoteListItem } from '../utils/ai-context'
+import { findEntryByTarget } from '../utils/wikilinkColors'
 import type { VaultEntry } from '../types'
 
 export type { AiAgentMessage } from '../hooks/useAiAgent'
@@ -89,8 +90,8 @@ function EmptyState({ hasContext }: { hasContext: boolean }) {
   )
 }
 
-function MessageHistory({ messages, isActive, onOpenNote, hasContext }: {
-  messages: AiAgentMessage[]; isActive: boolean; onOpenNote?: (path: string) => void; hasContext: boolean
+function MessageHistory({ messages, isActive, onOpenNote, onNavigateWikilink, hasContext }: {
+  messages: AiAgentMessage[]; isActive: boolean; onOpenNote?: (path: string) => void; onNavigateWikilink?: (target: string) => void; hasContext: boolean
 }) {
   const endRef = useRef<HTMLDivElement>(null)
 
@@ -102,7 +103,7 @@ function MessageHistory({ messages, isActive, onOpenNote, hasContext }: {
     <div className="flex-1 overflow-y-auto" style={{ padding: 12 }}>
       {messages.length === 0 && !isActive && <EmptyState hasContext={hasContext} />}
       {messages.map((msg, i) => (
-        <AiMessage key={msg.id ?? i} {...msg} onOpenNote={onOpenNote} />
+        <AiMessage key={msg.id ?? i} {...msg} onOpenNote={onOpenNote} onNavigateWikilink={onNavigateWikilink} />
       ))}
       <div ref={endRef} />
     </div>
@@ -167,6 +168,12 @@ export function AiPanel({ onClose, onOpenNote, onFileCreated, onFileModified, va
     return () => window.removeEventListener('keydown', handleEscape)
   }, [handleEscape])
 
+  const handleNavigateWikilink = useCallback((target: string) => {
+    if (!entries) return
+    const entry = findEntryByTarget(entries, target)
+    if (entry) onOpenNote?.(entry.path)
+  }, [entries, onOpenNote])
+
   const handleSend = useCallback((text: string, references: NoteReference[]) => {
     if (!text.trim() || isActive) return
     setPendingRefs(references)
@@ -198,6 +205,7 @@ export function AiPanel({ onClose, onOpenNote, onFileCreated, onFileModified, va
         messages={agent.messages}
         isActive={isActive}
         onOpenNote={onOpenNote}
+        onNavigateWikilink={handleNavigateWikilink}
         hasContext={hasContext}
       />
       <div

src/components/MarkdownContent.test.tsx

@@ -1,6 +1,7 @@
-import { describe, it, expect } from 'vitest'
-import { render, screen } from '@testing-library/react'
+import { describe, it, expect, vi } from 'vitest'
+import { render, screen, fireEvent } from '@testing-library/react'
 import { MarkdownContent } from './MarkdownContent'
+import { preprocessWikilinks } from '../utils/chatWikilinks'
 
 describe('MarkdownContent', () => {
   it('renders bold text', () => {
@@ -72,4 +73,110 @@ describe('MarkdownContent', () => {
     expect(bq).toBeTruthy()
     expect(bq!.textContent).toContain('A quote')
   })
+
+  describe('wikilinks', () => {
+    it('preprocessWikilinks converts [[Target]] to markdown links', () => {
+      expect(preprocessWikilinks('See [[My Note]]')).toBe('See [My Note](wikilink://My%20Note)')
+      expect(preprocessWikilinks('[[A]] and [[B]]')).toBe('[A](wikilink://A) and [B](wikilink://B)')
+      expect(preprocessWikilinks('`[[code]]`')).toBe('`[[code]]`')
+    })
+
+    it('renders [[Note Title]] as a clickable wikilink chip', () => {
+      const onClick = vi.fn()
+      const { container } = render(
+        <MarkdownContent content="Check out [[My Note]]" onWikilinkClick={onClick} />,
+      )
+      const wikilink = container.querySelector('.chat-wikilink')
+      expect(wikilink).toBeTruthy()
+      expect(wikilink!.textContent).toBe('My Note')
+      expect(wikilink!.getAttribute('data-wikilink-target')).toBe('My Note')
+    })
+
+    it('fires onWikilinkClick when a wikilink is clicked', () => {
+      const onClick = vi.fn()
+      const { container } = render(
+        <MarkdownContent content="See [[Daily Log]]" onWikilinkClick={onClick} />,
+      )
+      const wikilink = container.querySelector('.chat-wikilink')!
+      fireEvent.click(wikilink)
+      expect(onClick).toHaveBeenCalledWith('Daily Log')
+    })
+
+    it('renders multiple wikilinks in the same paragraph', () => {
+      const onClick = vi.fn()
+      const { container } = render(
+        <MarkdownContent content="See [[Note A]] and [[Note B]]" onWikilinkClick={onClick} />,
+      )
+      const wikilinks = container.querySelectorAll('.chat-wikilink')
+      expect(wikilinks).toHaveLength(2)
+      expect(wikilinks[0].textContent).toBe('Note A')
+      expect(wikilinks[1].textContent).toBe('Note B')
+    })
+
+    it('handles pipe syntax [[target|display]]', () => {
+      const onClick = vi.fn()
+      const { container } = render(
+        <MarkdownContent content="See [[path/to/note|My Display]]" onWikilinkClick={onClick} />,
+      )
+      const wikilink = container.querySelector('.chat-wikilink')!
+      expect(wikilink.textContent).toBe('My Display')
+      expect(wikilink.getAttribute('data-wikilink-target')).toBe('path/to/note')
+      fireEvent.click(wikilink)
+      expect(onClick).toHaveBeenCalledWith('path/to/note')
+    })
+
+    it('does not render wikilinks inside inline code', () => {
+      const onClick = vi.fn()
+      const { container } = render(
+        <MarkdownContent content="Use `[[Not a link]]` syntax" onWikilinkClick={onClick} />,
+      )
+      expect(container.querySelector('.chat-wikilink')).toBeNull()
+    })
+
+    it('does not render wikilinks inside code blocks', () => {
+      const onClick = vi.fn()
+      const { container } = render(
+        <MarkdownContent content={'```\n[[Not a link]]\n```'} onWikilinkClick={onClick} />,
+      )
+      expect(container.querySelector('.chat-wikilink')).toBeNull()
+    })
+
+    it('handles notes with special characters in title', () => {
+      const onClick = vi.fn()
+      const { container } = render(
+        <MarkdownContent content="Check [[Meeting — 2024/01/15]]" onWikilinkClick={onClick} />,
+      )
+      const wikilink = container.querySelector('.chat-wikilink')!
+      expect(wikilink.textContent).toBe('Meeting — 2024/01/15')
+      fireEvent.click(wikilink)
+      expect(onClick).toHaveBeenCalledWith('Meeting — 2024/01/15')
+    })
+
+    it('does not transform wikilinks when onWikilinkClick is not provided', () => {
+      const { container } = render(
+        <MarkdownContent content="See [[Some Note]]" />,
+      )
+      expect(container.querySelector('.chat-wikilink')).toBeNull()
+      expect(container.textContent).toContain('[[Some Note]]')
+    })
+
+    it('renders wikilinks inside list items', () => {
+      const onClick = vi.fn()
+      const { container } = render(
+        <MarkdownContent content={'- First [[Note A]]\n- Second [[Note B]]'} onWikilinkClick={onClick} />,
+      )
+      const wikilinks = container.querySelectorAll('.chat-wikilink')
+      expect(wikilinks).toHaveLength(2)
+    })
+
+    it('has role="link" and tabIndex for accessibility', () => {
+      const onClick = vi.fn()
+      const { container } = render(
+        <MarkdownContent content="See [[Accessible Note]]" onWikilinkClick={onClick} />,
+      )
+      const wikilink = container.querySelector('.chat-wikilink')!
+      expect(wikilink.getAttribute('role')).toBe('link')
+      expect(wikilink.getAttribute('tabindex')).toBe('0')
+    })
+  })
 })

src/components/MarkdownContent.tsx

@@ -1,18 +1,63 @@
-import { memo, useMemo } from 'react'
-import Markdown from 'react-markdown'
+import { memo, useMemo, useCallback, type MouseEvent } from 'react'
+import Markdown, { defaultUrlTransform } from 'react-markdown'
 import remarkGfm from 'remark-gfm'
 import rehypeHighlight from 'rehype-highlight'
+import { preprocessWikilinks, WIKILINK_SCHEME } from '../utils/chatWikilinks'
 
 const REMARK_PLUGINS = [remarkGfm]
 const REHYPE_PLUGINS = [rehypeHighlight]
 
-export const MarkdownContent = memo(function MarkdownContent({ content }: { content: string }) {
-  const rendered = useMemo(() => (
-    <div className="ai-markdown">
-      <Markdown remarkPlugins={REMARK_PLUGINS} rehypePlugins={REHYPE_PLUGINS}>
-        {content}
+function wikilinkUrlTransform(url: string): string {
+  if (url.startsWith(WIKILINK_SCHEME)) return url
+  return defaultUrlTransform(url)
+}
+
+interface MarkdownContentProps {
+  content: string
+  onWikilinkClick?: (target: string) => void
+}
+
+export const MarkdownContent = memo(function MarkdownContent({ content, onWikilinkClick }: MarkdownContentProps) {
+  const processedContent = useMemo(
+    () => onWikilinkClick ? preprocessWikilinks(content) : content,
+    [content, onWikilinkClick],
+  )
+
+  const handleClick = useCallback((e: MouseEvent) => {
+    const el = (e.target as HTMLElement).closest<HTMLElement>('[data-wikilink-target]')
+    if (el) {
+      e.preventDefault()
+      onWikilinkClick?.(el.dataset.wikilinkTarget!)
+    }
+  }, [onWikilinkClick])
+
+  const components = useMemo(() => {
+    if (!onWikilinkClick) return undefined
+    return {
+      a: ({ href, children }: { href?: string; children?: React.ReactNode }) => {
+        if (href?.startsWith(WIKILINK_SCHEME)) {
+          const target = decodeURIComponent(href.slice(WIKILINK_SCHEME.length))
+          return (
+            <span className="chat-wikilink" data-wikilink-target={target} role="link" tabIndex={0}>
+              {children}
+            </span>
+          )
+        }
+        return <a href={href}>{children}</a>
+      },
+    }
+  }, [onWikilinkClick])
+
+  return (
+    <div className="ai-markdown" onClick={onWikilinkClick ? handleClick : undefined} role="presentation">
+      <Markdown
+        remarkPlugins={REMARK_PLUGINS}
+        rehypePlugins={REHYPE_PLUGINS}
+        components={components}
+        urlTransform={onWikilinkClick ? wikilinkUrlTransform : undefined}
+      >
+        {processedContent}
       </Markdown>
     </div>
-  ), [content])
-  return rendered
+  )
 })

src/components/Sidebar.test.tsx

@@ -233,10 +233,10 @@ const mockEntries: VaultEntry[] = [
 const defaultSelection: SidebarSelection = { kind: 'filter', filter: 'all' }
 
 describe('Sidebar', () => {
-  it('renders top nav items (All Notes and Favorites)', () => {
+  it('renders top nav items (All Notes)', () => {
     render(<Sidebar entries={[]} selection={defaultSelection} onSelect={() => {}} />)
     expect(screen.getByText('All Notes')).toBeInTheDocument()
-    expect(screen.getByText('Favorites')).toBeInTheDocument()
+    expect(screen.queryByText('Favorites')).not.toBeInTheDocument()
   })
 
   it('renders section group headers only for types present in entries', () => {
@@ -764,7 +764,7 @@ describe('Sidebar', () => {
       ]
       render(<Sidebar entries={entries} selection={defaultSelection} onSelect={() => {}} />)
       expect(screen.getByText('All Notes')).toBeInTheDocument()
-      expect(screen.getByText('Favorites')).toBeInTheDocument()
+      expect(screen.queryByText('Favorites')).not.toBeInTheDocument()
     })
 
     it('renders a "Customize sections" button', () => {

src/components/Sidebar.tsx

@@ -13,8 +13,8 @@ import {
 } from '@dnd-kit/sortable'
 import { CSS } from '@dnd-kit/utilities'
 import {
-  FileText, Star, Wrench, Flask, Target, ArrowsClockwise,
-  Users, CalendarBlank, Tag, TagSimple, Trash, StackSimple, Archive, CaretLeft, GitDiff, Pulse,
+  FileText, Wrench, Flask, Target, ArrowsClockwise,
+  Users, CalendarBlank, Tag, Trash, StackSimple, Archive, CaretLeft, GitDiff, Pulse,
 } from '@phosphor-icons/react'
 import { GitCommitHorizontal, SlidersHorizontal } from 'lucide-react'
 import {
@@ -356,9 +356,7 @@ export const Sidebar = memo(function Sidebar({
         {/* Top nav */}
         <div className="border-b border-border" style={{ padding: '4px 6px' }}>
           <NavItem icon={FileText} label="All Notes" count={activeCount} isActive={isSelectionActive(selection, { kind: 'filter', filter: 'all' })} badgeClassName="bg-primary text-primary-foreground" onClick={() => onSelect({ kind: 'filter', filter: 'all' })} />
-          <NavItem icon={Star} label="Favorites" isActive={isSelectionActive(selection, { kind: 'filter', filter: 'favorites' })} onClick={() => onSelect({ kind: 'filter', filter: 'favorites' })} />
           <NavItem icon={Archive} label="Archive" count={archivedCount} isActive={isSelectionActive(selection, { kind: 'filter', filter: 'archived' })} badgeClassName="text-muted-foreground" badgeStyle={{ background: 'var(--muted)' }} onClick={() => onSelect({ kind: 'filter', filter: 'archived' })} />
-          <NavItem icon={TagSimple} label="Untagged" disabled />
           <NavItem icon={Trash} label="Trash" count={trashedCount} isActive={isSelectionActive(selection, { kind: 'filter', filter: 'trash' })} activeClassName="bg-destructive/10 text-destructive" badgeClassName="text-muted-foreground" badgeStyle={{ background: 'var(--muted)' }} onClick={() => onSelect({ kind: 'filter', filter: 'trash' })} />
           {modifiedCount > 0 && (
             <NavItem icon={GitDiff} label="Changes" count={modifiedCount} isActive={isSelectionActive(selection, { kind: 'filter', filter: 'changes' })} activeClassName="bg-[color:var(--accent-orange)]/10 text-[var(--accent-orange)]" badgeClassName="text-white" badgeStyle={{ background: 'var(--accent-orange)' }} onClick={() => onSelect({ kind: 'filter', filter: 'changes' })} />

src/components/StatusBar.test.tsx

@@ -2,6 +2,7 @@ import { describe, it, expect, vi, beforeEach } from 'vitest'
 import { render, screen, fireEvent } from '@testing-library/react'
 import { StatusBar } from './StatusBar'
 import type { VaultOption } from './StatusBar'
+import { formatIndexedElapsed } from '../utils/indexingHelpers'
 
 vi.mock('../utils/url', async () => {
   const actual = await vi.importActual('../utils/url')
@@ -394,4 +395,71 @@ describe('StatusBar', () => {
     fireEvent.click(screen.getByTestId('status-mcp'))
     expect(onInstallMcp).not.toHaveBeenCalled()
   })
+
+  it('shows "Indexed just now" when lastIndexedTime is recent and phase is idle', () => {
+    render(
+      <StatusBar
+        noteCount={100}
+        vaultPath="/Users/luca/Laputa"
+        vaults={vaults}
+        onSwitchVault={vi.fn()}
+        indexingProgress={{ phase: 'idle', current: 0, total: 0, done: false, error: null }}
+        lastIndexedTime={Date.now() - 5000}
+      />
+    )
+    expect(screen.getByText(/Indexed just now/)).toBeInTheDocument()
+    expect(screen.getByTestId('status-indexed-time')).toBeInTheDocument()
+  })
+
+  it('calls onReindexVault when clicking the indexed time badge', () => {
+    const onReindexVault = vi.fn()
+    render(
+      <StatusBar
+        noteCount={100}
+        vaultPath="/Users/luca/Laputa"
+        vaults={vaults}
+        onSwitchVault={vi.fn()}
+        indexingProgress={{ phase: 'idle', current: 0, total: 0, done: false, error: null }}
+        lastIndexedTime={Date.now() - 5000}
+        onReindexVault={onReindexVault}
+      />
+    )
+    fireEvent.click(screen.getByTestId('status-indexed-time'))
+    expect(onReindexVault).toHaveBeenCalledOnce()
+  })
+
+  it('hides indexed time badge when no lastIndexedTime', () => {
+    render(
+      <StatusBar
+        noteCount={100}
+        vaultPath="/Users/luca/Laputa"
+        vaults={vaults}
+        onSwitchVault={vi.fn()}
+        indexingProgress={{ phase: 'idle', current: 0, total: 0, done: false, error: null }}
+      />
+    )
+    expect(screen.queryByTestId('status-indexed-time')).not.toBeInTheDocument()
+  })
+})
+
+describe('formatIndexedElapsed', () => {
+  it('returns empty string for null', () => {
+    expect(formatIndexedElapsed(null)).toBe('')
+  })
+
+  it('returns "Indexed just now" for < 60s', () => {
+    expect(formatIndexedElapsed(Date.now() - 30_000)).toBe('Indexed just now')
+  })
+
+  it('returns minutes for < 60min', () => {
+    expect(formatIndexedElapsed(Date.now() - 5 * 60_000)).toBe('Indexed 5m ago')
+  })
+
+  it('returns hours for < 24h', () => {
+    expect(formatIndexedElapsed(Date.now() - 3 * 3600_000)).toBe('Indexed 3h ago')
+  })
+
+  it('returns days for >= 24h', () => {
+    expect(formatIndexedElapsed(Date.now() - 48 * 3600_000)).toBe('Indexed 2d ago')
+  })
 })

src/components/StatusBar.tsx

@@ -4,6 +4,7 @@ import type { LastCommitInfo, SyncStatus } from '../types'
 import type { IndexingProgress } from '../hooks/useIndexing'
 import type { McpStatus } from '../hooks/useMcpStatus'
 import { openExternalUrl } from '../utils/url'
+import { formatIndexedElapsed } from '../utils/indexingHelpers'
 
 export interface VaultOption {
   label: string
@@ -33,7 +34,9 @@ interface StatusBarProps {
   buildNumber?: string
   onCheckForUpdates?: () => void
   indexingProgress?: IndexingProgress
+  lastIndexedTime?: number | null
   onRetryIndexing?: () => void
+  onReindexVault?: () => void
   onRemoveVault?: (path: string) => void
   mcpStatus?: McpStatus
   onInstallMcp?: () => void
@@ -245,8 +248,32 @@ const INDEXING_LABELS: Record<string, string> = {
   unavailable: 'Search unavailable',
 }
 
-function IndexingBadge({ progress, onRetry }: { progress: IndexingProgress; onRetry?: () => void }) {
-  if (progress.phase === 'idle' || progress.phase === 'unavailable') return null
+function IndexingBadge({ progress, lastIndexedTime, onRetry, onReindex }: { progress: IndexingProgress; lastIndexedTime?: number | null; onRetry?: () => void; onReindex?: () => void }) {
+  const isIdle = progress.phase === 'idle' || progress.phase === 'unavailable'
+
+  // When idle, show "Indexed Xm ago" if we have a timestamp
+  if (isIdle) {
+    if (!lastIndexedTime) return null
+    const elapsed = formatIndexedElapsed(lastIndexedTime)
+    if (!elapsed) return null
+    return (
+      <>
+        <span style={SEP_STYLE}>|</span>
+        <span
+          role={onReindex ? 'button' : undefined}
+          onClick={onReindex}
+          style={{ ...ICON_STYLE, color: 'var(--muted-foreground)', cursor: onReindex ? 'pointer' : 'default', padding: '2px 4px', borderRadius: 3, background: 'transparent' }}
+          title={onReindex ? 'Click to reindex vault' : undefined}
+          data-testid="status-indexed-time"
+          onMouseEnter={onReindex ? (e) => { e.currentTarget.style.background = 'var(--hover)' } : undefined}
+          onMouseLeave={onReindex ? (e) => { e.currentTarget.style.background = 'transparent' } : undefined}
+        >
+          <Search size={13} />{elapsed}
+        </span>
+      </>
+    )
+  }
+
   const label = INDEXING_LABELS[progress.phase] ?? progress.phase
   const isActive = !progress.done
   const isError = progress.phase === 'error'
@@ -329,7 +356,7 @@ function McpBadge({ status, onInstall }: { status: McpStatus; onInstall?: () =>
   )
 }
 
-export function StatusBar({ noteCount, modifiedCount = 0, vaultPath, vaults, onSwitchVault, onOpenSettings, onOpenLocalFolder, onConnectGitHub, onClickPending, hasGitHub, syncStatus = 'idle', lastSyncTime = null, conflictCount = 0, lastCommitInfo, onTriggerSync, onOpenConflictResolver, zoomLevel = 100, onZoomReset, buildNumber, onCheckForUpdates, indexingProgress, onRetryIndexing, onRemoveVault, mcpStatus, onInstallMcp }: StatusBarProps) {
+export function StatusBar({ noteCount, modifiedCount = 0, vaultPath, vaults, onSwitchVault, onOpenSettings, onOpenLocalFolder, onConnectGitHub, onClickPending, hasGitHub, syncStatus = 'idle', lastSyncTime = null, conflictCount = 0, lastCommitInfo, onTriggerSync, onOpenConflictResolver, zoomLevel = 100, onZoomReset, buildNumber, onCheckForUpdates, indexingProgress, lastIndexedTime, onRetryIndexing, onReindexVault, onRemoveVault, mcpStatus, onInstallMcp }: StatusBarProps) {
   const [, setTick] = useState(0)
   useEffect(() => {
     const id = setInterval(() => setTick((t) => t + 1), 30_000)
@@ -355,7 +382,7 @@ export function StatusBar({ noteCount, modifiedCount = 0, vaultPath, vaults, onS
         {lastCommitInfo && <CommitBadge info={lastCommitInfo} />}
         <ConflictBadge count={conflictCount} onClick={onOpenConflictResolver} />
         <PendingBadge count={modifiedCount} onClick={onClickPending} />
-        {indexingProgress && <IndexingBadge progress={indexingProgress} onRetry={onRetryIndexing} />}
+        {indexingProgress && <IndexingBadge progress={indexingProgress} lastIndexedTime={lastIndexedTime} onRetry={onRetryIndexing} onReindex={onReindexVault} />}
         {mcpStatus && <McpBadge status={mcpStatus} onInstall={onInstallMcp} />}
       </div>
       <div style={{ display: 'flex', alignItems: 'center', gap: 12 }}>

src/hooks/useAIChat.test.ts

@@ -0,0 +1,130 @@
+import { describe, it, expect, vi, beforeEach, afterEach } from 'vitest'
+import { renderHook, act } from '@testing-library/react'
+
+// Capture what streamClaudeChat receives
+const streamClaudeChatMock = vi.fn<
+  Parameters<typeof import('../utils/ai-chat').streamClaudeChat>,
+  ReturnType<typeof import('../utils/ai-chat').streamClaudeChat>
+>()
+
+vi.mock('../utils/ai-chat', async () => {
+  const actual = await vi.importActual<typeof import('../utils/ai-chat')>('../utils/ai-chat')
+  return {
+    ...actual,
+    streamClaudeChat: (...args: Parameters<typeof actual.streamClaudeChat>) => {
+      streamClaudeChatMock(...args)
+      // Simulate async: call onDone after a tick
+      const callbacks = args[3]
+      setTimeout(() => {
+        callbacks.onInit?.('test-session')
+        callbacks.onText('mock response')
+        callbacks.onDone()
+      }, 10)
+      return Promise.resolve('test-session')
+    },
+  }
+})
+
+import { useAIChat } from './useAIChat'
+
+beforeEach(() => {
+  streamClaudeChatMock.mockClear()
+  vi.useFakeTimers()
+})
+
+afterEach(() => {
+  vi.useRealTimers()
+})
+
+describe('useAIChat', () => {
+  const emptyContent: Record<string, string> = {}
+
+  it('sends first message without history', async () => {
+    const { result } = renderHook(() => useAIChat(emptyContent, []))
+
+    act(() => { result.current.sendMessage('hello') })
+
+    expect(streamClaudeChatMock).toHaveBeenCalledTimes(1)
+    const message = streamClaudeChatMock.mock.calls[0][0]
+    // First message: no history, so just the plain text
+    expect(message).toBe('hello')
+  })
+
+  it('includes conversation history in second message', async () => {
+    const { result } = renderHook(() => useAIChat(emptyContent, []))
+
+    // Send first message
+    act(() => { result.current.sendMessage('What is Rust?') })
+    // Wait for mock response
+    await act(async () => { vi.advanceTimersByTime(50) })
+
+    // Now messages state has: [user: What is Rust?, assistant: mock response]
+    expect(result.current.messages).toHaveLength(2)
+
+    // Send second message
+    act(() => { result.current.sendMessage('Tell me more') })
+
+    expect(streamClaudeChatMock).toHaveBeenCalledTimes(2)
+    const secondMessage = streamClaudeChatMock.mock.calls[1][0]
+    // Should contain conversation history
+    expect(secondMessage).toContain('What is Rust?')
+    expect(secondMessage).toContain('mock response')
+    expect(secondMessage).toContain('Tell me more')
+  })
+
+  it('resets history on clearConversation', async () => {
+    const { result } = renderHook(() => useAIChat(emptyContent, []))
+
+    // Send a message and get response
+    act(() => { result.current.sendMessage('hello') })
+    await act(async () => { vi.advanceTimersByTime(50) })
+
+    // Clear conversation
+    act(() => { result.current.clearConversation() })
+    expect(result.current.messages).toHaveLength(0)
+
+    // Send new message — should have no history
+    act(() => { result.current.sendMessage('fresh start') })
+
+    const lastCall = streamClaudeChatMock.mock.calls[streamClaudeChatMock.mock.calls.length - 1]
+    expect(lastCall[0]).toBe('fresh start')
+  })
+
+  it('accumulates multiple exchanges in history', async () => {
+    const { result } = renderHook(() => useAIChat(emptyContent, []))
+
+    // Exchange 1
+    act(() => { result.current.sendMessage('Q1') })
+    await act(async () => { vi.advanceTimersByTime(50) })
+
+    // Exchange 2
+    act(() => { result.current.sendMessage('Q2') })
+    await act(async () => { vi.advanceTimersByTime(50) })
+
+    // Exchange 3
+    act(() => { result.current.sendMessage('Q3') })
+
+    expect(streamClaudeChatMock).toHaveBeenCalledTimes(3)
+    const thirdMessage = streamClaudeChatMock.mock.calls[2][0]
+    // Should contain all prior exchanges
+    expect(thirdMessage).toContain('Q1')
+    expect(thirdMessage).toContain('Q2')
+    expect(thirdMessage).toContain('Q3')
+  })
+
+  it('does not pass session_id to avoid --resume (history is in prompt)', async () => {
+    const { result } = renderHook(() => useAIChat(emptyContent, []))
+
+    // First message
+    act(() => { result.current.sendMessage('hello') })
+    await act(async () => { vi.advanceTimersByTime(50) })
+
+    // Second message — session_id should still be undefined (no --resume)
+    act(() => { result.current.sendMessage('follow up') })
+
+    expect(streamClaudeChatMock).toHaveBeenCalledTimes(2)
+    // Third argument is sessionId — must be undefined for both calls
+    expect(streamClaudeChatMock.mock.calls[0][2]).toBeUndefined()
+    expect(streamClaudeChatMock.mock.calls[1][2]).toBeUndefined()
+  })
+})

src/hooks/useAIChat.ts

@@ -7,6 +7,7 @@ import type { VaultEntry } from '../types'
 import {
   type ChatMessage, nextMessageId,
   buildSystemPrompt, streamClaudeChat,
+  trimHistory, formatMessageWithHistory, MAX_HISTORY_TOKENS,
 } from '../utils/ai-chat'
 
 export function useAIChat(
@@ -17,7 +18,6 @@ export function useAIChat(
   const [isStreaming, setIsStreaming] = useState(false)
   const [streamingContent, setStreamingContent] = useState('')
   const abortRef = useRef(false)
-  const sessionIdRef = useRef<string | undefined>(undefined)
 
   const sendMessage = useCallback((text: string) => {
     if (!text.trim() || isStreaming) return
@@ -29,11 +29,14 @@ export function useAIChat(
     abortRef.current = false
 
     const { prompt: systemPrompt } = buildSystemPrompt(contextNotes, allContent)
+    const history = trimHistory(messages, MAX_HISTORY_TOKENS)
+    const messageWithHistory = formatMessageWithHistory(history, text.trim())
     let accumulated = ''
 
-    streamClaudeChat(text.trim(), systemPrompt || undefined, sessionIdRef.current, {
-      onInit: (sid) => { sessionIdRef.current = sid },
-
+    // No session_id: each call is independent. Context is provided via
+    // formatted history in the prompt, avoiding --resume which causes
+    // double-context confusion when combined with in-prompt history.
+    streamClaudeChat(messageWithHistory, systemPrompt || undefined, undefined, {
       onText: (chunk) => {
         if (abortRef.current) return
         accumulated += chunk
@@ -55,17 +58,14 @@ export function useAIChat(
         setStreamingContent('')
         setIsStreaming(false)
       },
-    }).then(sid => {
-      if (sid) sessionIdRef.current = sid
     })
-  }, [isStreaming, allContent, contextNotes])
+  }, [isStreaming, allContent, contextNotes, messages])
 
   const clearConversation = useCallback(() => {
     abortRef.current = true
     setMessages([])
     setIsStreaming(false)
     setStreamingContent('')
-    sessionIdRef.current = undefined
   }, [])
 
   const retryMessage = useCallback((msgIndex: number) => {

src/hooks/useAppCommands.ts

@@ -66,6 +66,7 @@ interface AppCommandsConfig {
   vaultCount?: number
   mcpStatus?: string
   onInstallMcp?: () => void
+  onReindexVault?: () => void
 }
 
 /** Sets up keyboard shortcuts, command registry, menu events, and keyboard navigation. */
@@ -86,7 +87,7 @@ export function useAppCommands(config: AppCommandsConfig): CommandAction[] {
 
   const { onSelect } = config
 
-  const selectFilter = useCallback((filter: 'all' | 'favorites' | 'archived' | 'trash' | 'changes' | 'pulse') => {
+  const selectFilter = useCallback((filter: 'all' | 'archived' | 'trash' | 'changes' | 'pulse') => {
     onSelect({ kind: 'filter', filter })
   }, [onSelect])
 
@@ -148,6 +149,7 @@ export function useAppCommands(config: AppCommandsConfig): CommandAction[] {
     onResolveConflicts: config.onResolveConflicts,
     onViewChanges: viewChanges,
     onInstallMcp: config.onInstallMcp,
+    onReindexVault: config.onReindexVault,
     activeTabPathRef: config.activeTabPathRef,
     handleCloseTabRef: config.handleCloseTabRef,
     activeTabPath: config.activeTabPath,
@@ -201,6 +203,7 @@ export function useAppCommands(config: AppCommandsConfig): CommandAction[] {
     vaultCount: config.vaultCount,
     mcpStatus: config.mcpStatus,
     onInstallMcp: config.onInstallMcp,
+    onReindexVault: config.onReindexVault,
   })
 
   useKeyboardNavigation({

src/hooks/useAutoSync.test.ts

@@ -255,6 +255,47 @@ describe('useAutoSync', () => {
     expect(pullCalls).toHaveLength(0)
   })
 
+  it('calls onSyncUpdated when pull has updates', async () => {
+    const onSyncUpdated = vi.fn()
+    mockInvokeFn.mockImplementation((cmd: string) => {
+      if (cmd === 'get_last_commit_info') return Promise.resolve(MOCK_COMMIT_INFO)
+      return Promise.resolve(updated(['note.md']))
+    })
+    renderHook(() =>
+      useAutoSync({
+        vaultPath: '/Users/luca/Laputa',
+        intervalMinutes: 5,
+        onVaultUpdated,
+        onSyncUpdated,
+        onConflict,
+        onToast,
+      }),
+    )
+
+    await waitFor(() => {
+      expect(onSyncUpdated).toHaveBeenCalledOnce()
+    })
+  })
+
+  it('does not call onSyncUpdated when pull is up_to_date', async () => {
+    const onSyncUpdated = vi.fn()
+    renderHook(() =>
+      useAutoSync({
+        vaultPath: '/Users/luca/Laputa',
+        intervalMinutes: 5,
+        onVaultUpdated,
+        onSyncUpdated,
+        onConflict,
+        onToast,
+      }),
+    )
+
+    await waitFor(() => {
+      expect(onVaultUpdated).not.toHaveBeenCalled()
+    })
+    expect(onSyncUpdated).not.toHaveBeenCalled()
+  })
+
   it('detects conflicts when git_pull returns error with unresolved conflicts', async () => {
     mockInvokeFn.mockImplementation((cmd: string) => {
       if (cmd === 'get_conflict_files') return Promise.resolve(['conflict.md'])

src/hooks/useAutoSync.ts

@@ -13,6 +13,7 @@ interface UseAutoSyncOptions {
   vaultPath: string
   intervalMinutes: number | null
   onVaultUpdated: () => void
+  onSyncUpdated?: () => void
   onConflict: (files: string[]) => void
   onToast: (msg: string) => void
 }
@@ -33,6 +34,7 @@ export function useAutoSync({
   vaultPath,
   intervalMinutes,
   onVaultUpdated,
+  onSyncUpdated,
   onConflict,
   onToast,
 }: UseAutoSyncOptions): AutoSyncState {
@@ -42,8 +44,8 @@ export function useAutoSync({
   const [lastCommitInfo, setLastCommitInfo] = useState<LastCommitInfo | null>(null)
   const syncingRef = useRef(false)
   const pauseRef = useRef(false)
-  const callbacksRef = useRef({ onVaultUpdated, onConflict, onToast })
-  callbacksRef.current = { onVaultUpdated, onConflict, onToast }
+  const callbacksRef = useRef({ onVaultUpdated, onSyncUpdated, onConflict, onToast })
+  callbacksRef.current = { onVaultUpdated, onSyncUpdated, onConflict, onToast }
 
   /** Check for pre-existing conflicts (e.g. from a prior session or interrupted rebase). */
   const checkExistingConflicts = useCallback(async (): Promise<boolean> => {
@@ -77,6 +79,7 @@ export function useAutoSync({
         setSyncStatus('idle')
         setConflictFiles([])
         callbacksRef.current.onVaultUpdated()
+        callbacksRef.current.onSyncUpdated?.()
         callbacksRef.current.onToast(`Pulled ${result.updatedFiles.length} update(s) from remote`)
       } else if (result.status === 'conflict') {
         setSyncStatus('conflict')

src/hooks/useCommandRegistry.test.ts

@@ -95,6 +95,46 @@ describe('useCommandRegistry', () => {
     expect(cmd!.enabled).toBe(false)
   })
 
+  it('includes reindex-vault command in Settings group', () => {
+    const config = makeConfig({ onReindexVault: vi.fn() })
+    const { result } = renderHook(() => useCommandRegistry(config))
+    const cmd = findCommand(result.current, 'reindex-vault')
+    expect(cmd).toBeDefined()
+    expect(cmd!.group).toBe('Settings')
+    expect(cmd!.label).toBe('Reindex Vault')
+  })
+
+  it('reindex-vault is enabled when onReindexVault is provided', () => {
+    const config = makeConfig({ onReindexVault: vi.fn() })
+    const { result } = renderHook(() => useCommandRegistry(config))
+    const cmd = findCommand(result.current, 'reindex-vault')
+    expect(cmd!.enabled).toBe(true)
+  })
+
+  it('reindex-vault is disabled when onReindexVault is not provided', () => {
+    const config = makeConfig()
+    const { result } = renderHook(() => useCommandRegistry(config))
+    const cmd = findCommand(result.current, 'reindex-vault')
+    expect(cmd!.enabled).toBe(false)
+  })
+
+  it('reindex-vault executes onReindexVault callback', () => {
+    const onReindexVault = vi.fn()
+    const config = makeConfig({ onReindexVault })
+    const { result } = renderHook(() => useCommandRegistry(config))
+    const cmd = findCommand(result.current, 'reindex-vault')
+    cmd!.execute()
+    expect(onReindexVault).toHaveBeenCalled()
+  })
+
+  it('reindex-vault has searchable keywords', () => {
+    const config = makeConfig({ onReindexVault: vi.fn() })
+    const { result } = renderHook(() => useCommandRegistry(config))
+    const cmd = findCommand(result.current, 'reindex-vault')
+    expect(cmd!.keywords).toContain('reindex')
+    expect(cmd!.keywords).toContain('search')
+  })
+
   it('resolve-conflicts stays enabled across rerenders', () => {
     const config = makeConfig()
     const { result, rerender } = renderHook(

src/hooks/useCommandRegistry.ts

@@ -20,6 +20,7 @@ interface CommandRegistryConfig {
   modifiedCount: number
   mcpStatus?: string
   onInstallMcp?: () => void
+  onReindexVault?: () => void
 
   onQuickOpen: () => void
   onCreateNote: () => void
@@ -196,6 +197,7 @@ export function useCommandRegistry(config: CommandRegistryConfig): CommandAction
     onCreateType,
     onRemoveActiveVault, onRestoreGettingStarted, onRestoreDefaultThemes, isGettingStartedHidden, vaultCount,
     mcpStatus, onInstallMcp,
+    onReindexVault,
   } = config
 
   const hasActiveNote = activeTabPath !== null
@@ -214,7 +216,6 @@ export function useCommandRegistry(config: CommandRegistryConfig): CommandAction
       // Navigation
       { id: 'search-notes', label: 'Search Notes', group: 'Navigation', shortcut: '⌘P', keywords: ['find', 'open', 'quick'], enabled: true, execute: onQuickOpen },
       { id: 'go-all', label: 'Go to All Notes', group: 'Navigation', keywords: ['filter'], enabled: true, execute: () => onSelect({ kind: 'filter', filter: 'all' }) },
-      { id: 'go-favorites', label: 'Go to Favorites', group: 'Navigation', keywords: ['starred'], enabled: true, execute: () => onSelect({ kind: 'filter', filter: 'favorites' }) },
       { id: 'go-archived', label: 'Go to Archived', group: 'Navigation', keywords: [], enabled: true, execute: () => onSelect({ kind: 'filter', filter: 'archived' }) },
       { id: 'go-trash', label: 'Go to Trash', group: 'Navigation', keywords: ['deleted'], enabled: true, execute: () => onSelect({ kind: 'filter', filter: 'trash' }) },
       { id: 'go-changes', label: 'Go to Changes', group: 'Navigation', keywords: ['git', 'modified', 'pending'], enabled: true, execute: () => onSelect({ kind: 'filter', filter: 'changes' }) },
@@ -258,6 +259,7 @@ export function useCommandRegistry(config: CommandRegistryConfig): CommandAction
       { id: 'restore-getting-started', label: 'Restore Getting Started Vault', group: 'Settings', keywords: ['vault', 'restore', 'demo', 'getting started', 'reset'], enabled: !!isGettingStartedHidden && !!onRestoreGettingStarted, execute: () => onRestoreGettingStarted?.() },
       { id: 'check-updates', label: 'Check for Updates', group: 'Settings', keywords: ['update', 'version', 'upgrade', 'release'], enabled: true, execute: () => onCheckForUpdates?.() },
       { id: 'install-mcp', label: 'Install MCP Server', group: 'Settings', keywords: ['mcp', 'claude', 'ai', 'tools', 'install'], enabled: mcpStatus === 'not_installed' && !!onInstallMcp, execute: () => onInstallMcp?.() },
+      { id: 'reindex-vault', label: 'Reindex Vault', group: 'Settings', keywords: ['reindex', 'index', 'search', 'rebuild', 'refresh'], enabled: !!onReindexVault, execute: () => onReindexVault?.() },
 
       // Type-aware: "New [Type]" and "List [Type]"
       ...buildTypeCommands(vaultTypes, onCreateNoteOfType, onSelect),
@@ -276,5 +278,6 @@ export function useCommandRegistry(config: CommandRegistryConfig): CommandAction
     vaultTypes, themes, activeThemeId, onSwitchTheme, onCreateTheme, onOpenTheme, onRestoreDefaultThemes,
     onRemoveActiveVault, onRestoreGettingStarted, isGettingStartedHidden, vaultCount,
     mcpStatus, onInstallMcp,
+    onReindexVault,
   ])
 }

src/hooks/useEntryActions.test.ts

@@ -25,8 +25,8 @@ const makeEntry = (overrides: Partial<VaultEntry> = {}): VaultEntry => ({
   relationships: {},
   icon: null,
   color: null,
-  order: null,
-  template: null, sort: null,
+  order: null, sidebarLabel: null,
+  template: null, sort: null, view: null, visible: null,
   outgoingLinks: [],
   properties: {},
   ...overrides,
@@ -50,10 +50,13 @@ describe('useEntryActions', () => {
         handleDeleteProperty,
         setToastMessage,
         createTypeEntry,
+        onFrontmatterPersisted,
       })
     )
   }
 
+  const onFrontmatterPersisted = vi.fn()
+
   beforeEach(() => {
     vi.clearAllMocks()
   })
@@ -73,6 +76,7 @@ describe('useEntryActions', () => {
         trashedAt: expect.any(Number),
       })
       expect(setToastMessage).toHaveBeenCalledWith('Note moved to trash')
+      expect(onFrontmatterPersisted).toHaveBeenCalledTimes(1)
     })
   })
 
@@ -91,6 +95,7 @@ describe('useEntryActions', () => {
         trashedAt: null,
       })
       expect(setToastMessage).toHaveBeenCalledWith('Note restored from trash')
+      expect(onFrontmatterPersisted).toHaveBeenCalledTimes(1)
     })
   })
 
@@ -105,6 +110,7 @@ describe('useEntryActions', () => {
       expect(handleUpdateFrontmatter).toHaveBeenCalledWith('/vault/note/test.md', 'archived', true)
       expect(updateEntry).toHaveBeenCalledWith('/vault/note/test.md', { archived: true })
       expect(setToastMessage).toHaveBeenCalledWith('Note archived')
+      expect(onFrontmatterPersisted).toHaveBeenCalledTimes(1)
     })
   })
 
@@ -119,6 +125,7 @@ describe('useEntryActions', () => {
       expect(handleUpdateFrontmatter).toHaveBeenCalledWith('/vault/note/test.md', 'archived', false)
       expect(updateEntry).toHaveBeenCalledWith('/vault/note/test.md', { archived: false })
       expect(setToastMessage).toHaveBeenCalledWith('Note unarchived')
+      expect(onFrontmatterPersisted).toHaveBeenCalledTimes(1)
     })
   })
 

src/hooks/useEntryActions.ts

@@ -8,6 +8,7 @@ interface EntryActionsConfig {
   handleDeleteProperty: (path: string, key: string) => Promise<void>
   setToastMessage: (msg: string | null) => void
   createTypeEntry: (typeName: string) => Promise<VaultEntry>
+  onFrontmatterPersisted?: () => void
 }
 
 function findTypeEntry(entries: VaultEntry[], typeName: string): VaultEntry | undefined {
@@ -15,7 +16,7 @@ function findTypeEntry(entries: VaultEntry[], typeName: string): VaultEntry | un
 }
 
 export function useEntryActions({
-  entries, updateEntry, handleUpdateFrontmatter, handleDeleteProperty, setToastMessage, createTypeEntry,
+  entries, updateEntry, handleUpdateFrontmatter, handleDeleteProperty, setToastMessage, createTypeEntry, onFrontmatterPersisted,
 }: EntryActionsConfig) {
   const handleTrashNote = useCallback(async (path: string) => {
     const now = new Date().toISOString().slice(0, 10)
@@ -23,26 +24,30 @@ export function useEntryActions({
     await handleUpdateFrontmatter(path, 'Trashed at', now)
     updateEntry(path, { trashed: true, trashedAt: Date.now() / 1000 })
     setToastMessage('Note moved to trash')
-  }, [handleUpdateFrontmatter, updateEntry, setToastMessage])
+    onFrontmatterPersisted?.()
+  }, [handleUpdateFrontmatter, updateEntry, setToastMessage, onFrontmatterPersisted])
 
   const handleRestoreNote = useCallback(async (path: string) => {
     await handleUpdateFrontmatter(path, 'Trashed', false)
     await handleDeleteProperty(path, 'Trashed at')
     updateEntry(path, { trashed: false, trashedAt: null })
     setToastMessage('Note restored from trash')
-  }, [handleUpdateFrontmatter, handleDeleteProperty, updateEntry, setToastMessage])
+    onFrontmatterPersisted?.()
+  }, [handleUpdateFrontmatter, handleDeleteProperty, updateEntry, setToastMessage, onFrontmatterPersisted])
 
   const handleArchiveNote = useCallback(async (path: string) => {
     await handleUpdateFrontmatter(path, 'archived', true)
     updateEntry(path, { archived: true })
     setToastMessage('Note archived')
-  }, [handleUpdateFrontmatter, updateEntry, setToastMessage])
+    onFrontmatterPersisted?.()
+  }, [handleUpdateFrontmatter, updateEntry, setToastMessage, onFrontmatterPersisted])
 
   const handleUnarchiveNote = useCallback(async (path: string) => {
     await handleUpdateFrontmatter(path, 'archived', false)
     updateEntry(path, { archived: false })
     setToastMessage('Note unarchived')
-  }, [handleUpdateFrontmatter, updateEntry, setToastMessage])
+    onFrontmatterPersisted?.()
+  }, [handleUpdateFrontmatter, updateEntry, setToastMessage, onFrontmatterPersisted])
 
   const handleCustomizeType = useCallback(async (typeName: string, icon: string, color: string) => {
     let typeEntry = findTypeEntry(entries, typeName)

src/hooks/useIndexing.test.ts

@@ -84,4 +84,62 @@ describe('useIndexing', () => {
     const { result } = renderHook(() => useIndexing('/test/vault'))
     expect(typeof result.current.retryIndexing).toBe('function')
   })
+
+  it('exposes triggerFullReindex function', () => {
+    const { result } = renderHook(() => useIndexing('/test/vault'))
+    expect(typeof result.current.triggerFullReindex).toBe('function')
+  })
+
+  it('retryIndexing is the same reference as triggerFullReindex', () => {
+    const { result } = renderHook(() => useIndexing('/test/vault'))
+    expect(result.current.retryIndexing).toBe(result.current.triggerFullReindex)
+  })
+
+  it('triggerFullReindex sets scanning phase then completes', async () => {
+    const { result } = renderHook(() => useIndexing('/test/vault'))
+
+    await act(async () => { await result.current.triggerFullReindex() })
+    // In non-Tauri mode, it goes to 'complete' then auto-dismisses
+    expect(result.current.progress.phase).toBe('complete')
+  })
+
+  it('triggerFullReindex sets lastIndexedTime on success', async () => {
+    const { result } = renderHook(() => useIndexing('/test/vault'))
+
+    expect(result.current.lastIndexedTime).toBeNull()
+    await act(async () => { await result.current.triggerFullReindex() })
+    expect(result.current.lastIndexedTime).toBeGreaterThan(0)
+  })
+
+  it('triggerFullReindex sets error phase on failure', async () => {
+    const { result } = renderHook(() => useIndexing('/test/vault'))
+
+    mockInvoke.mockRejectedValueOnce(new Error('indexing failed'))
+    await act(async () => { await result.current.triggerFullReindex() })
+    expect(result.current.progress.phase).toBe('error')
+  })
+
+  it('populates lastIndexedTime from backend metadata on mount', async () => {
+    mockInvoke.mockResolvedValue({
+      available: true,
+      qmd_installed: true,
+      collection_exists: true,
+      indexed_count: 100,
+      embedded_count: 80,
+      pending_embed: 0,
+      last_indexed_commit: 'abc123',
+      last_indexed_at: 1709800000,
+    })
+
+    const { result } = renderHook(() => useIndexing('/test/vault'))
+
+    // Wait for the effect to run
+    await act(async () => { await vi.advanceTimersByTimeAsync(10) })
+    expect(result.current.lastIndexedTime).toBe(1709800000000) // seconds → ms
+  })
+
+  it('starts with lastIndexedTime as null', () => {
+    const { result } = renderHook(() => useIndexing('/test/vault'))
+    expect(result.current.lastIndexedTime).toBeNull()
+  })
 })

src/hooks/useIndexing.ts

@@ -17,6 +17,8 @@ interface IndexStatus {
   indexed_count: number
   embedded_count: number
   pending_embed: number
+  last_indexed_commit: string | null
+  last_indexed_at: number | null
 }
 
 const IDLE: IndexingProgress = { phase: 'idle', current: 0, total: 0, done: false, error: null }
@@ -27,6 +29,7 @@ function invokeCmd<T>(cmd: string, args?: Record<string, unknown>): Promise<T> {
 
 export function useIndexing(vaultPath: string) {
   const [progress, setProgress] = useState<IndexingProgress>(IDLE)
+  const [lastIndexedTime, setLastIndexedTime] = useState<number | null>(null)
   const indexingRef = useRef(false)
   const vaultPathRef = useRef(vaultPath)
 
@@ -43,6 +46,9 @@ export function useIndexing(vaultPath: string) {
         setProgress(event.payload)
         if (event.payload.done) {
           indexingRef.current = false
+          if (event.payload.phase === 'complete') {
+            setLastIndexedTime(Date.now())
+          }
         }
       })
       cleanup = () => { unlisten.then(fn => fn()) }
@@ -61,6 +67,11 @@ export function useIndexing(vaultPath: string) {
         const status = await invokeCmd<IndexStatus>('get_index_status', { vaultPath })
         if (cancelled) return
 
+        // Populate last indexed time from backend metadata
+        if (status.last_indexed_at) {
+          setLastIndexedTime(status.last_indexed_at * 1000) // seconds → ms
+        }
+
         // If qmd not installed or no collection or pending embeds, trigger indexing
         const needsIndexing = !status.qmd_installed || !status.collection_exists || status.pending_embed > 0
         if (needsIndexing && !indexingRef.current) {
@@ -116,17 +127,23 @@ export function useIndexing(vaultPath: string) {
     if (indexingRef.current) return
     try {
       await invokeCmd('trigger_incremental_index', { vaultPath: vaultPathRef.current })
+      setLastIndexedTime(Date.now())
     } catch {
       // Incremental update failure is non-fatal
     }
   }, [])
 
-  const retryIndexing = useCallback(async () => {
+  const triggerFullReindex = useCallback(async () => {
     if (indexingRef.current || !vaultPathRef.current) return
     indexingRef.current = true
     setProgress({ phase: 'scanning', current: 0, total: 0, done: false, error: null })
     try {
       await invokeCmd('start_indexing', { vaultPath: vaultPathRef.current })
+      // In non-Tauri mode, mark complete immediately
+      if (!isTauri()) {
+        setProgress({ phase: 'complete', current: 0, total: 0, done: true, error: null })
+        setLastIndexedTime(Date.now())
+      }
     } catch (err) {
       const msg = String(err)
       const isUnavailable = msg.includes('not installed') || msg.includes('not available')
@@ -136,5 +153,7 @@ export function useIndexing(vaultPath: string) {
     }
   }, [])
 
-  return { progress, triggerIncrementalIndex, retryIndexing }
+  const retryIndexing = triggerFullReindex
+
+  return { progress, lastIndexedTime, triggerIncrementalIndex, triggerFullReindex, retryIndexing }
 }

src/hooks/useMenuEvents.test.ts

@@ -34,6 +34,7 @@ function makeHandlers(): MenuEventHandlers {
     onResolveConflicts: vi.fn(),
     onViewChanges: vi.fn(),
     onInstallMcp: vi.fn(),
+    onReindexVault: vi.fn(),
     activeTabPathRef: { current: '/vault/test.md' } as React.MutableRefObject<string | null>,
     handleCloseTabRef: { current: vi.fn() } as React.MutableRefObject<(path: string) => void>,
     activeTabPath: '/vault/test.md',
@@ -226,12 +227,6 @@ describe('dispatchMenuEvent', () => {
     expect(h.onSelectFilter).toHaveBeenCalledWith('all')
   })
 
-  it('go-favorites selects favorites filter', () => {
-    const h = makeHandlers()
-    dispatchMenuEvent('go-favorites', h)
-    expect(h.onSelectFilter).toHaveBeenCalledWith('favorites')
-  })
-
   it('go-archived selects archived filter', () => {
     const h = makeHandlers()
     dispatchMenuEvent('go-archived', h)
@@ -305,6 +300,12 @@ describe('dispatchMenuEvent', () => {
     expect(h.onInstallMcp).toHaveBeenCalled()
   })
 
+  it('vault-reindex triggers reindex vault', () => {
+    const h = makeHandlers()
+    dispatchMenuEvent('vault-reindex', h)
+    expect(h.onReindexVault).toHaveBeenCalled()
+  })
+
   // Edge cases
   it('unknown event ID does nothing', () => {
     const h = makeHandlers()

src/hooks/useMenuEvents.ts

@@ -35,6 +35,7 @@ export interface MenuEventHandlers {
   onResolveConflicts?: () => void
   onViewChanges?: () => void
   onInstallMcp?: () => void
+  onReindexVault?: () => void
   activeTabPathRef: React.MutableRefObject<string | null>
   handleCloseTabRef: React.MutableRefObject<(path: string) => void>
   activeTabPath: string | null
@@ -67,7 +68,6 @@ const SIMPLE_EVENT_MAP: Record<string, SimpleHandler> = {
 
 const FILTER_MAP: Record<string, SidebarFilter> = {
   'go-all-notes': 'all',
-  'go-favorites': 'favorites',
   'go-archived': 'archived',
   'go-trash': 'trash',
   'go-changes': 'changes',
@@ -78,7 +78,7 @@ type OptionalHandler =
   | 'onCreateType' | 'onToggleRawEditor' | 'onToggleDiff' | 'onToggleAIChat'
   | 'onOpenVault' | 'onRemoveActiveVault' | 'onRestoreGettingStarted'
   | 'onCreateTheme' | 'onRestoreDefaultThemes'
-  | 'onCommitPush' | 'onResolveConflicts' | 'onViewChanges' | 'onInstallMcp'
+  | 'onCommitPush' | 'onResolveConflicts' | 'onViewChanges' | 'onInstallMcp' | 'onReindexVault'
 
 const OPTIONAL_EVENT_MAP: Record<string, OptionalHandler> = {
   'view-go-back': 'onGoBack',
@@ -97,6 +97,7 @@ const OPTIONAL_EVENT_MAP: Record<string, OptionalHandler> = {
   'vault-resolve-conflicts': 'onResolveConflicts',
   'vault-view-changes': 'onViewChanges',
   'vault-install-mcp': 'onInstallMcp',
+  'vault-reindex': 'onReindexVault',
 }
 
 function dispatchActiveTabEvent(id: string, h: MenuEventHandlers): boolean {

src/hooks/useNoteActions.test.ts

@@ -28,6 +28,7 @@ vi.mock('../mock-tauri', () => ({
   isTauri: vi.fn(() => false),
   addMockEntry: vi.fn(),
   updateMockContent: vi.fn(),
+  trackMockChange: vi.fn(),
   mockInvoke: vi.fn().mockResolvedValue(''),
 }))
 vi.mock('./mockFrontmatterHelpers', () => ({
@@ -289,6 +290,8 @@ describe('frontmatterToEntryPatch', () => {
     ['trashed', true, { trashed: true }],
     ['order', 5, { order: 5 }],
     ['template', '## Heading\n\n', { template: '## Heading\n\n' }],
+    ['visible', false, { visible: false }],
+    ['visible', true, { visible: null }],
   ] as [string, unknown, Partial<VaultEntry>][])(
     'maps %s update to correct entry field',
     (key, value, expected) => {
@@ -320,6 +323,7 @@ describe('frontmatterToEntryPatch', () => {
     ['archived', { archived: false }],
     ['order', { order: null }],
     ['template', { template: null }],
+    ['visible', { visible: null }],
   ] as [string, Partial<VaultEntry>][])(
     'maps delete of %s to null/default',
     (key, expected) => {

src/hooks/useNoteActions.ts

@@ -1,6 +1,6 @@
 import { useCallback, useEffect, useRef } from 'react'
 import { invoke } from '@tauri-apps/api/core'
-import { isTauri, mockInvoke, addMockEntry, updateMockContent } from '../mock-tauri'
+import { isTauri, mockInvoke, addMockEntry, updateMockContent, trackMockChange } from '../mock-tauri'
 import type { VaultEntry } from '../types'
 import type { FrontmatterValue } from '../components/Inspector'
 import { useTabManagement } from './useTabManagement'
@@ -111,12 +111,14 @@ async function invokeFrontmatter(command: string, args: Record<string, unknown>)
 function applyMockFrontmatterUpdate(path: string, key: string, value: FrontmatterValue): string {
   const content = updateMockFrontmatter(path, key, value)
   updateMockContent(path, content)
+  trackMockChange(path)
   return content
 }
 
 function applyMockFrontmatterDelete(path: string, key: string): string {
   const content = deleteMockFrontmatterProperty(path, key)
   updateMockContent(path, content)
+  trackMockChange(path)
   return content
 }
 
@@ -148,7 +150,7 @@ const ENTRY_DELETE_MAP: Record<string, Partial<VaultEntry>> = {
   icon: { icon: null }, owner: { owner: null }, cadence: { cadence: null },
   aliases: { aliases: [] }, belongs_to: { belongsTo: [] }, related_to: { relatedTo: [] },
   archived: { archived: false }, trashed: { trashed: false }, order: { order: null },
-  template: { template: null }, sort: { sort: null },
+  template: { template: null }, sort: { sort: null }, visible: { visible: null },
 }
 
 /** Map a frontmatter key+value to the corresponding VaultEntry field(s). */
@@ -168,6 +170,7 @@ export function frontmatterToEntryPatch(
     template: { template: str },
     sort: { sort: str },
     view: { view: str },
+    visible: { visible: value === false ? false : null },
   }
   return updates[k] ?? {}
 }

src/hooks/useVaultLoader.test.ts

@@ -34,7 +34,7 @@ function defaultMockInvoke(cmd: string, args?: Record<string, unknown>) {
   if (cmd === 'get_file_diff') return Promise.resolve('--- a/note.md\n+++ b/note.md')
   if (cmd === 'get_file_diff_at_commit') return Promise.resolve(`diff for ${(args as Record<string, string>)?.commitHash}`)
   if (cmd === 'git_commit') return Promise.resolve('committed')
-  if (cmd === 'git_push') return Promise.resolve('pushed')
+  if (cmd === 'git_push') return Promise.resolve({ status: 'ok', message: 'Pushed to remote' })
   return Promise.resolve(null)
 }
 
@@ -382,6 +382,49 @@ describe('useVaultLoader', () => {
 
       expect(response).toBe('Committed and pushed')
     })
+
+    it('returns actionable message when push is rejected', async () => {
+      mockInvokeFn.mockImplementation(((cmd: string) => {
+        if (cmd === 'list_vault') return Promise.resolve(mockEntries)
+        if (cmd === 'get_all_content') return Promise.resolve(mockContent)
+        if (cmd === 'get_modified_files') return Promise.resolve([])
+        if (cmd === 'git_commit') return Promise.resolve('committed')
+        if (cmd === 'git_push') return Promise.resolve({ status: 'rejected', message: 'Push rejected: remote has new commits. Pull first, then push.' })
+        return Promise.resolve(null)
+      }) as typeof defaultMockInvoke)
+
+      const { result } = renderHook(() => useVaultLoader('/vault'))
+      await waitFor(() => { expect(result.current.entries).toHaveLength(1) })
+
+      let response = ''
+      await act(async () => {
+        response = await result.current.commitAndPush('test commit')
+      })
+
+      expect(response).toContain('Pull first')
+      expect(response).not.toBe('Committed and pushed')
+    })
+
+    it('returns network error message on network failure', async () => {
+      mockInvokeFn.mockImplementation(((cmd: string) => {
+        if (cmd === 'list_vault') return Promise.resolve(mockEntries)
+        if (cmd === 'get_all_content') return Promise.resolve(mockContent)
+        if (cmd === 'get_modified_files') return Promise.resolve([])
+        if (cmd === 'git_commit') return Promise.resolve('committed')
+        if (cmd === 'git_push') return Promise.resolve({ status: 'network_error', message: 'Push failed: network error. Check your connection and try again.' })
+        return Promise.resolve(null)
+      }) as typeof defaultMockInvoke)
+
+      const { result } = renderHook(() => useVaultLoader('/vault'))
+      await waitFor(() => { expect(result.current.entries).toHaveLength(1) })
+
+      let response = ''
+      await act(async () => {
+        response = await result.current.commitAndPush('test commit')
+      })
+
+      expect(response).toContain('network error')
+    })
   })
 
   describe('loadModifiedFiles', () => {

src/hooks/useVaultLoader.ts

@@ -1,7 +1,7 @@
 import { useCallback, useEffect, useState, startTransition } from 'react'
 import { invoke } from '@tauri-apps/api/core'
 import { isTauri, mockInvoke } from '../mock-tauri'
-import type { VaultEntry, GitCommit, ModifiedFile, NoteStatus } from '../types'
+import type { VaultEntry, GitCommit, ModifiedFile, NoteStatus, GitPushResult } from '../types'
 
 function tauriCall<T>(command: string, tauriArgs: Record<string, unknown>, mockArgs?: Record<string, unknown>): Promise<T> {
   return isTauri() ? invoke<T>(command, tauriArgs) : mockInvoke<T>(command, mockArgs ?? tauriArgs)
@@ -18,16 +18,12 @@ async function loadVaultData(vaultPath: string) {
 async function commitWithPush(vaultPath: string, message: string): Promise<string> {
   if (!isTauri()) {
     await mockInvoke<string>('git_commit', { message })
-    await mockInvoke<string>('git_push', {})
-    return 'Committed and pushed'
+    const pushResult = await mockInvoke<GitPushResult>('git_push', {})
+    return pushResult.status === 'ok' ? 'Committed and pushed' : pushResult.message
   }
   await invoke<string>('git_commit', { vaultPath, message })
-  try {
-    await invoke<string>('git_push', { vaultPath })
-    return 'Committed and pushed'
-  } catch {
-    return 'Committed (push failed)'
-  }
+  const pushResult = await invoke<GitPushResult>('git_push', { vaultPath })
+  return pushResult.status === 'ok' ? 'Committed and pushed' : pushResult.message
 }
 
 function useNewNoteTracker() {

src/index.css

@@ -246,6 +246,22 @@
 }
 .ai-markdown a:hover { text-decoration: underline; }
 
+.ai-markdown .chat-wikilink {
+  display: inline;
+  color: var(--primary);
+  background: color-mix(in srgb, var(--primary) 10%, transparent);
+  border-radius: 4px;
+  padding: 0 4px;
+  cursor: pointer;
+  font-weight: 500;
+  text-decoration: none;
+  transition: background 0.15s ease;
+}
+.ai-markdown .chat-wikilink:hover {
+  background: color-mix(in srgb, var(--primary) 20%, transparent);
+  text-decoration: underline;
+}
+
 .ai-markdown hr {
   border: none;
   border-top: 1px solid var(--border);

src/mock-tauri/index.ts

@@ -5,18 +5,19 @@
  */
 
 import { MOCK_CONTENT } from './mock-content'
-import { mockHandlers, addMockEntry, updateMockContent } from './mock-handlers'
+import { mockHandlers, addMockEntry, updateMockContent, trackMockChange } from './mock-handlers'
 import { tryVaultApi } from './vault-api'
 
-export { addMockEntry, updateMockContent }
+export { addMockEntry, updateMockContent, trackMockChange }
 
 export function isTauri(): boolean {
   return typeof window !== 'undefined' && ('__TAURI__' in window || '__TAURI_INTERNALS__' in window)
 }
 
-// Initialize window.__mockContent for browser testing
+// Initialize window globals for browser testing and Playwright overrides
 if (typeof window !== 'undefined') {
   window.__mockContent = MOCK_CONTENT
+  window.__mockHandlers = mockHandlers
 }
 
 export async function mockInvoke<T>(cmd: string, args?: Record<string, unknown>): Promise<T> {

src/mock-tauri/mock-handlers.ts

@@ -3,7 +3,7 @@
  * Each handler simulates a Tauri backend command.
  */
 
-import type { VaultEntry, VaultConfig, ModifiedFile, Settings, DeviceFlowStart, DeviceFlowPollResult, GitHubUser, GitPullResult, LastCommitInfo, ThemeFile, VaultSettings, PulseCommit } from '../types'
+import type { VaultEntry, VaultConfig, ModifiedFile, Settings, DeviceFlowStart, DeviceFlowPollResult, GitHubUser, GitPullResult, GitPushResult, LastCommitInfo, ThemeFile, VaultSettings, PulseCommit } from '../types'
 import { MOCK_CONTENT } from './mock-content'
 import { MOCK_ENTRIES } from './mock-entries'
 
@@ -172,7 +172,7 @@ export const mockHandlers: Record<string, (args: any) => any> = {
   get_build_number: () => 'bDEV',
   get_last_commit_info: (): LastCommitInfo => ({ shortHash: 'a1b2c3d', commitUrl: 'https://github.com/lucaong/laputa-vault/commit/a1b2c3d4e5f6a7b8c9d0e1f2a3b4c5d6e7f8a9b0' }),
   git_pull: (): GitPullResult => ({ status: 'up_to_date', message: 'Already up to date', updatedFiles: [], conflictFiles: [] }),
-  git_push: () => 'Everything up-to-date',
+  git_push: (): GitPushResult => ({ status: 'ok', message: 'Pushed to remote' }),
   get_vault_pulse: (args: { limit?: number }): PulseCommit[] => {
     const limit = args.limit ?? 30
     const ts = Math.floor(Date.now() / 1000)
@@ -277,7 +277,7 @@ export const mockHandlers: Record<string, (args: any) => any> = {
   create_getting_started_vault: () => '/Users/mock/Documents/Getting Started',
   register_mcp_tools: () => 'registered',
   check_mcp_status: () => 'installed',
-  get_index_status: () => ({ available: true, qmd_installed: true, collection_exists: true, indexed_count: 100, embedded_count: 80, pending_embed: 0 }),
+  get_index_status: () => ({ available: true, qmd_installed: true, collection_exists: true, indexed_count: 100, embedded_count: 80, pending_embed: 0, last_indexed_commit: 'abc123', last_indexed_at: Math.floor(Date.now() / 1000) - 3600 }),
   start_indexing: () => null,
   trigger_incremental_index: () => null,
   list_themes: (): ThemeFile[] => [...mockThemes],
@@ -347,3 +347,7 @@ export function updateMockContent(path: string, content: string): void {
   MOCK_CONTENT[path] = content
   syncWindowContent()
 }
+
+export function trackMockChange(path: string): void {
+  mockSavedSinceCommit.add(path)
+}

src/types.ts

@@ -78,6 +78,11 @@ export interface GitPullResult {
   conflictFiles: string[]
 }
 
+export interface GitPushResult {
+  status: 'ok' | 'rejected' | 'auth_error' | 'network_error' | 'error'
+  message: string
+}
+
 export type SyncStatus = 'idle' | 'syncing' | 'error' | 'conflict'
 
 export interface DeviceFlowStart {
@@ -170,7 +175,7 @@ export interface PulseCommit {
   deleted: number
 }
 
-export type SidebarFilter = 'all' | 'favorites' | 'archived' | 'trash' | 'changes' | 'pulse'
+export type SidebarFilter = 'all' | 'archived' | 'trash' | 'changes' | 'pulse'
 
 export type SidebarSelection =
   | { kind: 'filter'; filter: SidebarFilter }

src/utils/ai-agent.test.ts

@@ -23,6 +23,12 @@ describe('buildAgentSystemPrompt', () => {
     expect(prompt).toContain('Vault context:')
     expect(prompt).toContain('Recent notes: foo, bar')
   })
+
+  it('instructs AI to use wikilink syntax', () => {
+    const prompt = buildAgentSystemPrompt()
+    expect(prompt).toContain('[[')
+    expect(prompt).toMatch(/wikilink/i)
+  })
 })
 
 // --- streamClaudeAgent ---
@@ -44,7 +50,7 @@ describe('streamClaudeAgent', () => {
     // Wait for the setTimeout mock response
     await new Promise(r => setTimeout(r, 400))
 
-    expect(onText).toHaveBeenCalledWith(expect.stringContaining('Claude CLI'))
+    expect(onText).toHaveBeenCalledWith(expect.stringContaining('Build Laputa App'))
     expect(onDone).toHaveBeenCalled()
     expect(onError).not.toHaveBeenCalled()
     expect(onToolStart).not.toHaveBeenCalled()

src/utils/ai-agent.ts

@@ -17,6 +17,7 @@ You have full shell access. Use bash for file operations, search, bulk edits.
 Use the provided MCP tools for: full-text search (search_notes), vault orientation (get_vault_context), parsed note reading (get_note), and opening notes in the UI (open_note).
 
 When you create or edit a note, call open_note(path) so the user sees it in Laputa.
+When you mention or reference a note by name, always use [[Note Title]] wikilink syntax so the user can click to open it.
 Be concise and helpful. When you've completed a task, briefly summarize what you did.`
 
 export function buildAgentSystemPrompt(vaultContext?: string): string {
@@ -57,7 +58,7 @@ export async function streamClaudeAgent(
 ): Promise<void> {
   if (!isTauri()) {
     setTimeout(() => {
-      callbacks.onText('AI Agent requires the Claude CLI. Install it and run the native app.')
+      callbacks.onText('This note is related to [[Build Laputa App]] and [[Matteo Cellini]]. The AI Agent requires the Claude CLI for full functionality.')
       callbacks.onDone()
     }, 300)
     return

src/utils/ai-chat.test.ts

@@ -8,6 +8,8 @@ vi.mock('../mock-tauri', () => ({
 import {
   estimateTokens, buildSystemPrompt,
   nextMessageId, checkClaudeCli, streamClaudeChat,
+  trimHistory, formatMessageWithHistory,
+  type ChatMessage, MAX_HISTORY_TOKENS,
 } from './ai-chat'
 import type { VaultEntry } from '../types'
 
@@ -50,6 +52,14 @@ describe('buildSystemPrompt', () => {
     expect(result.prompt).toContain('Hello world')
     expect(result.totalTokens).toBeGreaterThan(0)
   })
+
+  it('instructs AI to use wikilink syntax', () => {
+    const notes = [makeEntry('/test.md', 'Test Note')]
+    const content = { '/test.md': 'content' }
+    const result = buildSystemPrompt(notes, content)
+    expect(result.prompt).toContain('[[')
+    expect(result.prompt).toMatch(/wikilink/i)
+  })
 })
 
 // --- nextMessageId ---
@@ -73,6 +83,107 @@ describe('checkClaudeCli', () => {
   })
 })
 
+// --- trimHistory ---
+
+describe('trimHistory', () => {
+  const msg = (role: 'user' | 'assistant', content: string): ChatMessage => ({
+    role, content, id: `msg-${content}`,
+  })
+
+  it('returns empty array for empty history', () => {
+    expect(trimHistory([], 1000)).toEqual([])
+  })
+
+  it('returns all messages when under token limit', () => {
+    const history = [msg('user', 'hi'), msg('assistant', 'hello')]
+    expect(trimHistory(history, 1000)).toEqual(history)
+  })
+
+  it('drops oldest messages when over token limit', () => {
+    const history = [
+      msg('user', 'a'.repeat(400)),      // 100 tokens
+      msg('assistant', 'b'.repeat(400)),  // 100 tokens
+      msg('user', 'c'.repeat(400)),       // 100 tokens
+    ]
+    const result = trimHistory(history, 200)
+    // Should keep the two most recent messages (200 tokens)
+    expect(result).toHaveLength(2)
+    expect(result[0].content).toBe('b'.repeat(400))
+    expect(result[1].content).toBe('c'.repeat(400))
+  })
+
+  it('keeps at least one message if it fits', () => {
+    const history = [
+      msg('user', 'a'.repeat(2000)),  // 500 tokens
+      msg('assistant', 'b'.repeat(80)), // 20 tokens
+    ]
+    const result = trimHistory(history, 30)
+    expect(result).toHaveLength(1)
+    expect(result[0].content).toBe('b'.repeat(80))
+  })
+
+  it('returns empty when single message exceeds limit', () => {
+    const history = [msg('user', 'a'.repeat(4000))] // 1000 tokens
+    expect(trimHistory(history, 10)).toEqual([])
+  })
+})
+
+// --- formatMessageWithHistory ---
+
+describe('formatMessageWithHistory', () => {
+  const msg = (role: 'user' | 'assistant', content: string): ChatMessage => ({
+    role, content, id: `msg-${content}`,
+  })
+
+  it('returns bare message when no history', () => {
+    expect(formatMessageWithHistory([], 'hello')).toBe('hello')
+  })
+
+  it('includes conversation history before the new message', () => {
+    const history = [msg('user', 'What is Rust?'), msg('assistant', 'A systems language.')]
+    const result = formatMessageWithHistory(history, 'How does it compare to Go?')
+    expect(result).toContain('What is Rust?')
+    expect(result).toContain('A systems language.')
+    expect(result).toContain('How does it compare to Go?')
+  })
+
+  it('labels user and assistant messages correctly', () => {
+    const history = [msg('user', 'Q1'), msg('assistant', 'A1')]
+    const result = formatMessageWithHistory(history, 'Q2')
+    expect(result).toContain('[user]: Q1')
+    expect(result).toContain('[assistant]: A1')
+    expect(result).toContain('[user]: Q2')
+  })
+
+  it('preserves message order', () => {
+    const history = [
+      msg('user', 'first'),
+      msg('assistant', 'second'),
+      msg('user', 'third'),
+      msg('assistant', 'fourth'),
+    ]
+    const result = formatMessageWithHistory(history, 'fifth')
+    const firstIdx = result.indexOf('first')
+    const secondIdx = result.indexOf('second')
+    const thirdIdx = result.indexOf('third')
+    const fourthIdx = result.indexOf('fourth')
+    const fifthIdx = result.indexOf('fifth')
+    expect(firstIdx).toBeLessThan(secondIdx)
+    expect(secondIdx).toBeLessThan(thirdIdx)
+    expect(thirdIdx).toBeLessThan(fourthIdx)
+    expect(fourthIdx).toBeLessThan(fifthIdx)
+  })
+})
+
+// --- MAX_HISTORY_TOKENS ---
+
+describe('MAX_HISTORY_TOKENS', () => {
+  it('is a reasonable token limit', () => {
+    expect(MAX_HISTORY_TOKENS).toBeGreaterThan(10_000)
+    expect(MAX_HISTORY_TOKENS).toBeLessThan(200_000)
+  })
+})
+
 // --- streamClaudeChat ---
 
 describe('streamClaudeChat', () => {

src/utils/ai-chat.ts

@@ -34,6 +34,7 @@ export function buildSystemPrompt(
   const preamble = [
     'You are a helpful AI assistant integrated into Laputa, a personal knowledge management app.',
     'The user has selected the following notes as context. Use them to answer questions accurately.',
+    'When you mention or reference a note by name, always use [[Note Title]] wikilink syntax so the user can click to open it.',
     '',
   ].join('\n')
 
@@ -76,6 +77,34 @@ export function nextMessageId(): string {
   return `msg-${++msgIdCounter}-${Date.now()}`
 }
 
+// --- Conversation history ---
+
+/** Max tokens of history to include in each request. */
+export const MAX_HISTORY_TOKENS = 100_000
+
+/** Keep the most recent messages that fit within `maxTokens`. Drops oldest first. */
+export function trimHistory(history: ChatMessage[], maxTokens: number): ChatMessage[] {
+  let tokenCount = 0
+  const result: ChatMessage[] = []
+  for (let i = history.length - 1; i >= 0; i--) {
+    const tokens = estimateTokens(history[i].content)
+    if (tokenCount + tokens > maxTokens) break
+    result.unshift(history[i])
+    tokenCount += tokens
+  }
+  return result
+}
+
+/** Format conversation history + new message into a single prompt for the CLI. */
+export function formatMessageWithHistory(history: ChatMessage[], newMessage: string): string {
+  if (history.length === 0) return newMessage
+
+  const lines = history.map(m => `[${m.role}]: ${m.content}`)
+  lines.push(`[user]: ${newMessage}`)
+
+  return `<conversation_history>\n${lines.join('\n\n')}\n</conversation_history>\n\nContinue the conversation. Respond only to the latest [user] message.`
+}
+
 // --- Claude CLI status ---
 
 export interface ClaudeCliStatus {

src/utils/chatWikilinks.ts

@@ -0,0 +1,35 @@
+const WIKILINK_SCHEME = 'wikilink://'
+
+export { WIKILINK_SCHEME }
+
+function encodeTarget(target: string): string {
+  return encodeURIComponent(target).replace(/\(/g, '%28').replace(/\)/g, '%29')
+}
+
+function escapeLinkText(text: string): string {
+  return text.replace(/[[\]]/g, '\\$&')
+}
+
+function replaceWikilinksInText(text: string): string {
+  return text.replace(/\[\[([^\]]+)\]\]/g, (_, inner: string) => {
+    const pipeIdx = inner.indexOf('|')
+    const target = pipeIdx !== -1 ? inner.slice(0, pipeIdx) : inner
+    const display = pipeIdx !== -1 ? inner.slice(pipeIdx + 1) : inner
+    return `[${escapeLinkText(display)}](${WIKILINK_SCHEME}${encodeTarget(target)})`
+  })
+}
+
+/** Convert [[Target]] to markdown links, but skip code blocks and inline code. */
+export function preprocessWikilinks(md: string): string {
+  const segments: string[] = []
+  const codeRegex = /(```[\s\S]*?```|`[^`\n]+`)/g
+  let lastIndex = 0
+  let match
+  while ((match = codeRegex.exec(md)) !== null) {
+    segments.push(replaceWikilinksInText(md.slice(lastIndex, match.index)))
+    segments.push(match[0])
+    lastIndex = match.index + match[0].length
+  }
+  segments.push(replaceWikilinksInText(md.slice(lastIndex)))
+  return segments.join('')
+}

src/utils/indexingHelpers.ts

@@ -0,0 +1,10 @@
+export function formatIndexedElapsed(lastIndexedTime: number | null): string {
+  if (!lastIndexedTime) return ''
+  const secs = Math.round((Date.now() - lastIndexedTime) / 1000)
+  if (secs < 60) return 'Indexed just now'
+  const mins = Math.floor(secs / 60)
+  if (mins < 60) return `Indexed ${mins}m ago`
+  const hrs = Math.floor(mins / 60)
+  if (hrs < 24) return `Indexed ${hrs}h ago`
+  return `Indexed ${Math.floor(hrs / 24)}d ago`
+}

tests/smoke/ai-chat-wikilink-clickable.spec.ts

@@ -0,0 +1,46 @@
+import { test, expect } from '@playwright/test'
+import { sendShortcut } from './helpers'
+
+test.describe('AI chat wikilink rendering', () => {
+  test.beforeEach(async ({ page }) => {
+    await page.goto('/')
+    await page.waitForTimeout(500)
+  })
+
+  test('[[Note]] in AI response renders as clickable wikilink', async ({ page }) => {
+    // Select a note first so the AI panel has context
+    const noteItem = page.locator('.app__note-list .cursor-pointer').first()
+    await noteItem.click()
+    await page.waitForTimeout(500)
+
+    // Open AI Chat with Ctrl+I
+    await sendShortcut(page, 'i', ['Control'])
+    await expect(page.getByTestId('ai-panel')).toBeVisible({ timeout: 3000 })
+
+    // Send a message to get a mock response containing wikilinks
+    const input = page.locator('input[placeholder*="Ask"]')
+    await input.fill('Tell me about this note')
+    await page.getByTestId('agent-send').click()
+
+    // Wait for mock response (contains [[Build Laputa App]] and [[Matteo Cellini]])
+    const wikilink = page.locator('.chat-wikilink').first()
+    await expect(wikilink).toBeVisible({ timeout: 5000 })
+
+    // Verify wikilink text and attributes
+    await expect(wikilink).toHaveText('Build Laputa App')
+    await expect(wikilink).toHaveAttribute('data-wikilink-target', 'Build Laputa App')
+    await expect(wikilink).toHaveAttribute('role', 'link')
+
+    // Verify second wikilink
+    const secondWikilink = page.locator('.chat-wikilink').nth(1)
+    await expect(secondWikilink).toHaveText('Matteo Cellini')
+
+    // Verify multiple wikilinks rendered
+    const allWikilinks = page.locator('.chat-wikilink')
+    await expect(allWikilinks).toHaveCount(2)
+
+    // Verify wikilink has pointer cursor (is styled as clickable)
+    const cursor = await wikilink.evaluate(el => getComputedStyle(el).cursor)
+    expect(cursor).toBe('pointer')
+  })
+})

tests/smoke/better-sync-error-ux.spec.ts

@@ -0,0 +1,71 @@
+import { test, expect } from '@playwright/test'
+import { openCommandPalette, executeCommand } from './helpers'
+
+test.describe('Sync error UX — actionable push error messages', () => {
+  test.beforeEach(async ({ page }) => {
+    await page.goto('/')
+    await page.waitForLoadState('networkidle')
+  })
+
+  test('rejected push shows actionable "Pull first" message in toast', async ({ page }) => {
+    // Override git_push mock to return a rejected result
+    await page.evaluate(() => {
+      window.__mockHandlers!.git_push = () => ({
+        status: 'rejected',
+        message: 'Push rejected: remote has new commits. Pull first, then push.',
+      })
+    })
+
+    // Open commit dialog via command palette
+    await openCommandPalette(page)
+    await executeCommand(page, 'Commit & Push')
+
+    // Wait for the CommitDialog textarea
+    const textarea = page.locator('textarea[placeholder="Commit message..."]')
+    await textarea.waitFor({ timeout: 5000 })
+    await textarea.fill('test commit')
+
+    // Click the "Commit & Push" button in the dialog
+    const commitButton = page.getByRole('button', { name: 'Commit & Push' })
+    await commitButton.click()
+
+    // Verify the toast shows the actionable rejection message
+    const toast = page.locator('.fixed.bottom-8')
+    await expect(toast).toContainText('Pull first', { timeout: 5000 })
+  })
+
+  test('auth error push shows authentication message in toast', async ({ page }) => {
+    await page.evaluate(() => {
+      window.__mockHandlers!.git_push = () => ({
+        status: 'auth_error',
+        message: 'Push failed: authentication error. Check your credentials.',
+      })
+    })
+
+    await openCommandPalette(page)
+    await executeCommand(page, 'Commit & Push')
+
+    const textarea = page.locator('textarea[placeholder="Commit message..."]')
+    await textarea.waitFor({ timeout: 5000 })
+    await textarea.fill('test commit')
+
+    await page.getByRole('button', { name: 'Commit & Push' }).click()
+
+    const toast = page.locator('.fixed.bottom-8')
+    await expect(toast).toContainText('authentication error', { timeout: 5000 })
+  })
+
+  test('successful push shows normal success message', async ({ page }) => {
+    await openCommandPalette(page)
+    await executeCommand(page, 'Commit & Push')
+
+    const textarea = page.locator('textarea[placeholder="Commit message..."]')
+    await textarea.waitFor({ timeout: 5000 })
+    await textarea.fill('test commit')
+
+    await page.getByRole('button', { name: 'Commit & Push' }).click()
+
+    const toast = page.locator('.fixed.bottom-8')
+    await expect(toast).toContainText('Committed and pushed', { timeout: 5000 })
+  })
+})

tests/smoke/indexing-reindex-status.spec.ts

@@ -0,0 +1,28 @@
+import { test, expect } from '@playwright/test'
+import {
+  openCommandPalette,
+  findCommand,
+  executeCommand,
+} from './helpers'
+
+test.describe('Reindex Vault smoke tests', () => {
+  test.beforeEach(async ({ page }) => {
+    await page.goto('/')
+    await page.waitForLoadState('networkidle')
+  })
+
+  test('Reindex Vault command appears in command palette', async ({ page }) => {
+    await openCommandPalette(page)
+    const found = await findCommand(page, 'Reindex Vault')
+    expect(found).toBe(true)
+  })
+
+  test('Reindex Vault command triggers indexing progress', async ({ page }) => {
+    await openCommandPalette(page)
+    await executeCommand(page, 'Reindex Vault')
+
+    // After triggering reindex, the indexing badge should appear in the status bar
+    const indexingBadge = page.locator('[data-testid="status-indexing"], [data-testid="status-indexed-time"]')
+    await expect(indexingBadge.first()).toBeVisible({ timeout: 5_000 })
+  })
+})

tests/smoke/trashed-archived-not-saved.spec.ts

@@ -0,0 +1,39 @@
+import { test, expect } from '@playwright/test'
+import { openCommandPalette, executeCommand } from './helpers'
+
+test.describe('Trash/archive notes appear in Changes', () => {
+  test.beforeEach(async ({ page }) => {
+    await page.goto('/')
+    await page.waitForLoadState('networkidle')
+  })
+
+  test('trashing a note increments the Changes badge', async ({ page }) => {
+    const sidebar = page.locator('.app__sidebar')
+
+    // Wait for Changes nav item (mock starts with 3 modified files)
+    const changesRow = sidebar.locator('div', { hasText: /^Changes/ }).first()
+    await changesRow.waitFor({ timeout: 5000 })
+
+    // Read the initial badge count from the Changes row
+    const badge = changesRow.locator('span').last()
+    const initialCount = Number(await badge.textContent())
+    expect(initialCount).toBeGreaterThan(0)
+
+    // Click the first note in the list to select it
+    const noteListContainer = page.locator('[data-testid="note-list-container"]')
+    await noteListContainer.waitFor({ timeout: 5000 })
+    // Click on the first visible note item (border-b items inside the list)
+    const firstNote = noteListContainer.locator('.cursor-pointer').first()
+    await firstNote.click()
+
+    // Trash the active note via command palette
+    await openCommandPalette(page)
+    await executeCommand(page, 'Trash Note')
+
+    // Wait for the badge count to increase
+    await expect(async () => {
+      const text = await badge.textContent()
+      expect(Number(text)).toBeGreaterThan(initialCount)
+    }).toPass({ timeout: 5000 })
+  })
+})