fix: use git ls-files --unmerged for reliable conflict detection

git diff --name-only --diff-filter=U only works during an active merge
(while MERGE_HEAD exists). When the vault has stale conflict state —
e.g. after a reboot — git diff returns empty, causing conflictFiles=[]
and making the StatusBar click handler, command palette entry, and
conflict resolver modal all non-functional.

Switch to git ls-files --unmerged which reads unmerged index entries
directly and works regardless of MERGE_HEAD state.

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

src-tauri/src/git.rs

@@ -427,20 +427,28 @@ pub fn git_pull(vault_path: &str) -> Result<GitPullResult, String> {
 }
 
 /// List files with merge conflicts (unmerged paths).
+///
+/// Uses `git ls-files --unmerged` instead of `git diff --diff-filter=U` because
+/// ls-files reliably detects unmerged index entries even when the merge state is
+/// stale (e.g. after a reboot or when MERGE_HEAD is missing).
 pub fn get_conflict_files(vault_path: &str) -> Result<Vec<String>, String> {
     let vault = Path::new(vault_path);
     let output = Command::new("git")
-        .args(["diff", "--name-only", "--diff-filter=U"])
+        .args(["ls-files", "--unmerged"])
         .current_dir(vault)
         .output()
         .map_err(|e| format!("Failed to check conflicts: {}", e))?;
 
     let stdout = String::from_utf8_lossy(&output.stdout);
-    Ok(stdout
+    // Each unmerged file appears multiple times (once per stage: base/ours/theirs).
+    // Format: "<mode> <hash> <stage>\t<path>"
+    let mut files: Vec<String> = stdout
         .lines()
-        .filter(|l| !l.is_empty())
-        .map(|l| l.to_string())
-        .collect())
+        .filter_map(|line| line.split('\t').nth(1).map(|s| s.to_string()))
+        .collect();
+    files.sort();
+    files.dedup();
+    Ok(files)
 }
 
 /// Parse `git pull` output to extract updated file paths.

src/App.tsx

@@ -24,7 +24,7 @@ import { useAppCommands } from './hooks/useAppCommands'
 import { useDialogs } from './hooks/useDialogs'
 import { useVaultSwitcher } from './hooks/useVaultSwitcher'
 import { useGitHistory } from './hooks/useGitHistory'
-import { useUpdater } from './hooks/useUpdater'
+import { useUpdater, restartApp } from './hooks/useUpdater'
 import { useNavigationHistory } from './hooks/useNavigationHistory'
 import { useAutoSync } from './hooks/useAutoSync'
 import { useConflictResolver } from './hooks/useConflictResolver'
@@ -280,6 +280,14 @@ function App() {
   const { status: updateStatus, actions: updateActions } = useUpdater()
 
   const handleCheckForUpdates = useCallback(async () => {
+    if (updateStatus.state === 'downloading') {
+      setToastMessage('Update is downloading…')
+      return
+    }
+    if (updateStatus.state === 'ready') {
+      await restartApp()
+      return
+    }
     const result = await updateActions.checkForUpdates()
     if (result === 'up-to-date') {
       setToastMessage("You're on the latest version")
@@ -287,7 +295,7 @@ function App() {
       setToastMessage('Could not check for updates')
     }
     // 'available' → UpdateBanner handles it automatically
-  }, [updateActions, setToastMessage])
+  }, [updateActions, updateStatus.state, setToastMessage])
 
   const commands = useAppCommands({
     activeTabPath: notes.activeTabPath, activeTabPathRef: notes.activeTabPathRef,
@@ -322,9 +330,13 @@ function App() {
     themes: themeManager.themes, activeThemeId: themeManager.activeThemeId,
     onSwitchTheme: themeManager.switchTheme,
     onCreateTheme: async () => {
-      await themeManager.createTheme()
-      await vault.reloadVault()
+      const path = await themeManager.createTheme()
+      const freshEntries = await vault.reloadVault()
       setSelection({ kind: 'sectionGroup', type: 'Theme' })
+      if (path) {
+        const entry = freshEntries.find(e => e.path === path)
+        if (entry) notes.handleSelectNote(entry)
+      }
     },
     onOpenTheme: (themeId: string) => {
       const entry = vault.entries.find(e => e.path === themeId)
@@ -334,7 +346,6 @@ function App() {
     onCreateType: dialogs.openCreateType,
     onToggleAIChat: dialogs.toggleAIChat,
     onCheckForUpdates: handleCheckForUpdates,
-    isUpdating: updateStatus.state === 'downloading' || updateStatus.state === 'ready',
     onRemoveActiveVault: () => vaultSwitcher.removeVault(vaultSwitcher.vaultPath),
     onRestoreGettingStarted: vaultSwitcher.restoreGettingStarted,
     isGettingStartedHidden: vaultSwitcher.isGettingStartedHidden,

src/components/AiPanel.test.tsx

@@ -1,5 +1,5 @@
 import { describe, it, expect, vi } from 'vitest'
-import { render, screen, fireEvent } from '@testing-library/react'
+import { render, screen, fireEvent, act } from '@testing-library/react'
 import { AiPanel } from './AiPanel'
 import type { VaultEntry } from '../types'
 
@@ -133,4 +133,33 @@ describe('AiPanel', () => {
     const input = screen.getByTestId('agent-input') as HTMLInputElement
     expect(input.placeholder).toBe('Ask the AI agent...')
   })
+
+  it('auto-focuses input on mount', async () => {
+    vi.useFakeTimers()
+    render(<AiPanel onClose={vi.fn()} vaultPath="/tmp/vault" />)
+    await act(() => { vi.advanceTimersByTime(1) })
+    const input = screen.getByTestId('agent-input')
+    expect(document.activeElement).toBe(input)
+    vi.useRealTimers()
+  })
+
+  it('calls onClose when Escape is pressed while panel has focus', async () => {
+    vi.useFakeTimers()
+    const onClose = vi.fn()
+    render(<AiPanel onClose={onClose} vaultPath="/tmp/vault" />)
+    await act(() => { vi.advanceTimersByTime(1) })
+    // Input is focused inside the panel, so Escape should trigger onClose
+    fireEvent.keyDown(document.activeElement!, { key: 'Escape' })
+    expect(onClose).toHaveBeenCalledOnce()
+    vi.useRealTimers()
+  })
+
+  it('calls onClose when Escape is pressed on panel element', () => {
+    const onClose = vi.fn()
+    render(<AiPanel onClose={onClose} vaultPath="/tmp/vault" />)
+    const panel = screen.getByTestId('ai-panel')
+    panel.focus()
+    fireEvent.keyDown(panel, { key: 'Escape' })
+    expect(onClose).toHaveBeenCalledOnce()
+  })
 })

src/components/AiPanel.tsx

@@ -1,4 +1,4 @@
-import { useState, useRef, useEffect, useMemo } from 'react'
+import { useState, useRef, useEffect, useCallback, useMemo } from 'react'
 import { Robot, X, PaperPlaneRight, Plus, Link } from '@phosphor-icons/react'
 import { AiMessage } from './AiMessage'
 import { useAiAgent, type AiAgentMessage } from '../hooks/useAiAgent'
@@ -103,10 +103,10 @@ function MessageHistory({ messages, isActive, onOpenNote, hasContext }: {
   )
 }
 
-function InputBar({ input, onInputChange, onSend, onKeyDown, isActive, hasContext }: {
+function InputBar({ input, onInputChange, onSend, onKeyDown, isActive, hasContext, inputRef }: {
   input: string; onInputChange: (v: string) => void
   onSend: () => void; onKeyDown: (e: React.KeyboardEvent) => void
-  isActive: boolean; hasContext: boolean
+  isActive: boolean; hasContext: boolean; inputRef: React.RefObject<HTMLInputElement | null>
 }) {
   const sendDisabled = isActive || !input.trim()
   return (
@@ -116,6 +116,7 @@ function InputBar({ input, onInputChange, onSend, onKeyDown, isActive, hasContex
     >
       <div className="flex items-end gap-2">
         <input
+          ref={inputRef}
           value={input}
           onChange={e => onInputChange(e.target.value)}
           onKeyDown={onKeyDown}
@@ -150,6 +151,8 @@ function InputBar({ input, onInputChange, onSend, onKeyDown, isActive, hasContex
 
 export function AiPanel({ onClose, onOpenNote, vaultPath, activeEntry, entries, allContent }: AiPanelProps) {
   const [input, setInput] = useState('')
+  const inputRef = useRef<HTMLInputElement>(null)
+  const panelRef = useRef<HTMLElement>(null)
 
   const linkedEntries = useMemo(() => {
     if (!activeEntry || !entries) return []
@@ -163,9 +166,33 @@ export function AiPanel({ onClose, onOpenNote, vaultPath, activeEntry, entries,
 
   const agent = useAiAgent(vaultPath, contextPrompt)
   const hasContext = !!activeEntry
-
   const isActive = agent.status === 'thinking' || agent.status === 'tool-executing'
 
+  useEffect(() => {
+    const timer = setTimeout(() => inputRef.current?.focus(), 0)
+    return () => clearTimeout(timer)
+  }, [])
+
+  useEffect(() => {
+    if (isActive) {
+      panelRef.current?.focus()
+    } else {
+      inputRef.current?.focus()
+    }
+  }, [isActive])
+
+  const handleEscape = useCallback((e: KeyboardEvent) => {
+    if (e.key === 'Escape' && panelRef.current?.contains(document.activeElement)) {
+      e.preventDefault()
+      onClose()
+    }
+  }, [onClose])
+
+  useEffect(() => {
+    window.addEventListener('keydown', handleEscape)
+    return () => window.removeEventListener('keydown', handleEscape)
+  }, [handleEscape])
+
   const handleSend = () => {
     if (!input.trim() || isActive) return
     agent.sendMessage(input)
@@ -181,7 +208,10 @@ export function AiPanel({ onClose, onOpenNote, vaultPath, activeEntry, entries,
 
   return (
     <aside
+      ref={panelRef}
+      tabIndex={-1}
       className="flex flex-1 flex-col overflow-hidden border-l border-border bg-background text-foreground"
+      style={{ outline: 'none' }}
       data-testid="ai-panel"
     >
       <PanelHeader onClose={onClose} onClear={agent.clearConversation} />
@@ -201,6 +231,7 @@ export function AiPanel({ onClose, onOpenNote, vaultPath, activeEntry, entries,
         onKeyDown={handleKeyDown}
         isActive={isActive}
         hasContext={hasContext}
+        inputRef={inputRef}
       />
     </aside>
   )

src/components/StatusBar.tsx

@@ -1,5 +1,5 @@
 import { useState, useRef, useEffect } from 'react'
-import { Package, RefreshCw, Sparkles, FileText, Bell, Settings, FolderOpen, Check, Github, CircleDot, AlertTriangle, Loader2, GitCommitHorizontal, Search, X } from 'lucide-react'
+import { Package, RefreshCw, FileText, Bell, Settings, FolderOpen, Check, Github, CircleDot, AlertTriangle, Loader2, GitCommitHorizontal, Search, X } from 'lucide-react'
 import type { LastCommitInfo, SyncStatus } from '../types'
 import type { IndexingProgress } from '../hooks/useIndexing'
 import { openExternalUrl } from '../utils/url'
@@ -302,7 +302,6 @@ export function StatusBar({ noteCount, modifiedCount = 0, vaultPath, vaults, onS
         {indexingProgress && <IndexingBadge progress={indexingProgress} />}
       </div>
       <div style={{ display: 'flex', alignItems: 'center', gap: 12 }}>
-        <span style={ICON_STYLE}><Sparkles size={13} style={{ color: 'var(--accent-purple)' }} />Claude Sonnet 4</span>
         <span style={ICON_STYLE}><FileText size={13} />{noteCount.toLocaleString()} notes</span>
         {zoomLevel !== 100 && (
           <span

src/hooks/useAppCommands.ts

@@ -60,7 +60,6 @@ interface AppCommandsConfig {
   onCreateType?: () => void
   onToggleAIChat?: () => void
   onCheckForUpdates?: () => void
-  isUpdating?: boolean
   onRemoveActiveVault?: () => void
   onRestoreGettingStarted?: () => void
   isGettingStartedHidden?: boolean
@@ -169,7 +168,6 @@ export function useAppCommands(config: AppCommandsConfig): CommandAction[] {
     onCreateType: config.onCreateType,
     onToggleAIChat: config.onToggleAIChat,
     onCheckForUpdates: config.onCheckForUpdates,
-    isUpdating: config.isUpdating,
     onRemoveActiveVault: config.onRemoveActiveVault,
     onRestoreGettingStarted: config.onRestoreGettingStarted,
     isGettingStartedHidden: config.isGettingStartedHidden,

src/hooks/useCommandRegistry.test.ts

@@ -369,20 +369,11 @@ describe('useCommandRegistry', () => {
       expect(cmd!.keywords).toContain('version')
     })
 
-    it('is enabled when not updating', () => {
-      const { result } = renderHook(() =>
-        useCommandRegistry(makeConfig({ isUpdating: false })),
-      )
+    it('is always enabled', () => {
+      const { result } = renderHook(() => useCommandRegistry(makeConfig()))
       expect(result.current.find(c => c.id === 'check-updates')!.enabled).toBe(true)
     })
 
-    it('is disabled when updating', () => {
-      const { result } = renderHook(() =>
-        useCommandRegistry(makeConfig({ isUpdating: true })),
-      )
-      expect(result.current.find(c => c.id === 'check-updates')!.enabled).toBe(false)
-    })
-
     it('calls onCheckForUpdates when executed', () => {
       const onCheckForUpdates = vi.fn()
       const { result } = renderHook(() =>

src/hooks/useCommandRegistry.ts

@@ -40,7 +40,6 @@ interface CommandRegistryConfig {
   onToggleAIChat?: () => void
   activeNoteModified: boolean
   onCheckForUpdates?: () => void
-  isUpdating?: boolean
   onZoomIn: () => void
   onZoomOut: () => void
   onZoomReset: () => void
@@ -191,7 +190,7 @@ export function useCommandRegistry(config: CommandRegistryConfig): CommandAction
     onSelect, onOpenDailyNote, onCloseTab,
     onGoBack, onGoForward, canGoBack, canGoForward,
     themes, activeThemeId, onSwitchTheme, onCreateTheme, onOpenTheme,
-    onCheckForUpdates, isUpdating,
+    onCheckForUpdates,
     onCreateType,
     onRemoveActiveVault, onRestoreGettingStarted, isGettingStartedHidden, vaultCount,
   } = config
@@ -252,7 +251,7 @@ export function useCommandRegistry(config: CommandRegistryConfig): CommandAction
       { id: 'open-vault', label: 'Open Vault…', group: 'Settings', keywords: ['vault', 'folder', 'switch', 'open', 'workspace'], enabled: true, execute: () => onOpenVault?.() },
       { id: 'remove-vault', label: 'Remove Vault from List', group: 'Settings', keywords: ['vault', 'remove', 'disconnect', 'hide'], enabled: (vaultCount ?? 0) > 1 && !!onRemoveActiveVault, execute: () => onRemoveActiveVault?.() },
       { 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: !isUpdating, execute: () => onCheckForUpdates?.() },
+      { id: 'check-updates', label: 'Check for Updates', group: 'Settings', keywords: ['update', 'version', 'upgrade', 'release'], enabled: true, execute: () => onCheckForUpdates?.() },
 
       // Type-aware: "New [Type]" and "List [Type]"
       ...buildTypeCommands(vaultTypes, onCreateNoteOfType, onSelect),
@@ -264,7 +263,7 @@ export function useCommandRegistry(config: CommandRegistryConfig): CommandAction
     onQuickOpen, onCreateNote, onCreateNoteOfType, onCreateType, onSave, onOpenSettings,
     onTrashNote, onRestoreNote, onArchiveNote, onUnarchiveNote,
     onCommitPush, onResolveConflicts, onSetViewMode, onToggleInspector, onToggleDiff, onToggleRawEditor, onToggleAIChat, onOpenVault,
-    onCheckForUpdates, isUpdating,
+    onCheckForUpdates,
     onZoomIn, onZoomOut, onZoomReset, zoomLevel,
     onSelect, onOpenDailyNote, onCloseTab,
     onGoBack, onGoForward, canGoBack, canGoForward,

src/hooks/useVaultLoader.ts

@@ -172,8 +172,8 @@ export function useVaultLoader(vaultPath: string) {
 
   const reloadVault = useCallback(
     () => loadVaultData(vaultPath)
-      .then((data) => { setEntries(data.entries); setAllContent((prev) => ({ ...prev, ...data.allContent })); loadModifiedFiles() })
-      .catch((err) => console.warn('Vault reload failed:', err)),
+      .then((data) => { setEntries(data.entries); setAllContent((prev) => ({ ...prev, ...data.allContent })); loadModifiedFiles(); return data.entries })
+      .catch((err) => { console.warn('Vault reload failed:', err); return [] as VaultEntry[] }),
     [vaultPath, loadModifiedFiles],
   )