Merge main into feat/terminal-diagnostics + address review feedback

Conflicts: OnLoaded restore loop and OnClosing teardown both diverged
from the staggered-shutdown work that landed in #37.

Resolutions:
- OnLoaded: keep main's launching-placeholder + sequential staggered
  launch flow; layer this PR's batched WebView2-access-denied dialog
  on top so a single consolidated message replaces the previous N
  per-session popups. Drop the duplicate dormant-loop tail (main now
  adds dormant entries up-front before launches start).
- OnClosing: keep main's claude-aware sequential disposal and
  DisposeAndWaitForExitAsync wait; layer this PR's try/catch around
  _db.Close()/_db.Dispose() in to swallow the SqliteConnection NRE
  observed during shutdown.

Review fixes (from PR self-review):
- OnClosing was async void with multiple awaits, which WPF doesn't
  wait for. Switched to the standard e.Cancel=true + reclose pattern
  gated by _shutdownComplete so async cleanup actually finishes before
  the window tears down.
- _lastOutputTickMs in TerminalBridge.OnPtyData was read-modify-written
  without a memory barrier. Replaced with Interlocked.Exchange — atomic
  read+write in one call, and gives the JIT a barrier even though the
  PTY read loop is currently single-threaded.

Author: AThraen

src/CodeShellManager/MainWindow.xaml.cs

@@ -33,6 +33,13 @@ public class AppSettings
 {
     public bool AutoRestoreSessions { get; set; } = true;
     public bool AutoResumeClaude { get; set; } = true;
+    /// <summary>
+    /// Milliseconds to wait between consecutive Claude session launches (and shutdowns).
+    /// The Claude CLI performs an unlocked read-modify-write on <c>~/.claude.json</c> on
+    /// startup and exit, so two claude.exe processes touching the file at the same time
+    /// can corrupt it. Spacing them out by ~2s avoids the race. 0 disables the stagger.
+    /// </summary>
+    public int ClaudeLaunchStaggerMs { get; set; } = 2000;
     public bool AutoFocusTerminalOnSelect { get; set; } = true;
     public bool ShowToastNotifications { get; set; } = false;
     public bool ShowNotificationSound { get; set; } = false;
@@ -43,6 +50,19 @@ public class AppSettings
     /// <summary>Authoritative grouping UI selector. Replaces the legacy <see cref="ShowGroupsTab"/> boolean.</summary>
     public GroupDisplayMode GroupDisplayMode { get; set; } = GroupDisplayMode.FilterStrip;
     /// <summary>
+    /// In FilterStrip mode with an active group filter, restrict the terminal grid
+    /// (multi-pane layouts) to sessions belonging to that group. The sidebar already
+    /// hides non-matching rows; with this on, the panes match. Off = the grid keeps
+    /// showing every live session regardless of group filter.
+    /// </summary>
+    public bool FilterGridByActiveGroup { get; set; } = true;
+    /// <summary>
+    /// Remember the grid layout (Single / TwoByTwo / etc.) separately per group so each
+    /// group restores its own layout when selected. See <see cref="AppState.GroupLayouts"/>
+    /// for the backing store.
+    /// </summary>
+    public bool PerGroupLayout { get; set; } = true;
+    /// <summary>
     /// Legacy flag — kept for back-compat with older state.json files. When deserialized
     /// as false on a state that still has GroupDisplayMode at its default, the loader
     /// migrates the mode to None. Newer code paths read GroupDisplayMode instead.
@@ -121,6 +141,13 @@ public class AppState
     public List<ShellSession> Sessions { get; set; } = [];
     public List<SessionGroup> Groups { get; set; } = [];
     public string LastLayout { get; set; } = "Single";
+    /// <summary>
+    /// Per-group grid layouts when <see cref="AppSettings.PerGroupLayout"/> is on.
+    /// Key = group Id, <c>GroupFilter.Ungrouped</c>, or <c>"__ALL__"</c> for the
+    /// no-filter view. Value = <see cref="ViewModels.LayoutMode"/> name. Missing
+    /// keys fall back to <see cref="LastLayout"/>.
+    /// </summary>
+    public Dictionary<string, string> GroupLayouts { get; set; } = new();
     public AppSettings Settings { get; set; } = new();
 
     // Window state persistence

src/CodeShellManager/Models/AppState.cs

@@ -182,8 +182,8 @@ private void OnPtyData(string rawData)
         if (DebugSettings?.DebugTerminalTrace == true)
         {
             long now = Environment.TickCount64;
-            long gap = _lastOutputTickMs == 0 ? 0 : now - _lastOutputTickMs;
-            _lastOutputTickMs = now;
+            long prev = System.Threading.Interlocked.Exchange(ref _lastOutputTickMs, now);
+            long gap = prev == 0 ? 0 : now - prev;
             Trace($"OUTPUT recv len={rawData.Length} gap-since-prev={gap}ms");
         }
 

src/CodeShellManager/Terminal/TerminalBridge.cs

@@ -16,6 +16,8 @@ public enum LayoutMode { Single, TwoColumn, ThreeColumn, TwoByTwo, TwoRow, FourC
 public static class GroupFilter
 {
     public const string Ungrouped = "__UNGROUPED__";
+    /// <summary>Key used in <see cref="Models.AppState.GroupLayouts"/> for the no-filter ("All") view.</summary>
+    public const string AllKey = "__ALL__";
 }
 
 public partial class MainViewModel : ObservableObject
@@ -38,6 +40,15 @@ public partial class MainViewModel : ObservableObject
     /// </summary>
     [ObservableProperty] private string? _activeGroupId;
 
+    /// <summary>Guard so layout assignments driven by state-load or per-group restore don't write back to GroupLayouts.</summary>
+    private bool _suppressLayoutPersist;
+
+    /// <summary>Tracks the previous effective group key so the per-group handler can save the old slot before switching.</summary>
+    private string _lastEffectiveLayoutKey = GroupFilter.AllKey;
+
+    /// <summary>Key used to look up the current view's layout in <see cref="AppState.GroupLayouts"/>.</summary>
+    private string CurrentLayoutKey => EffectiveActiveGroupId ?? GroupFilter.AllKey;
+
     /// <summary>IDs of sessions currently in the multi-select set (in addition to ActiveSession).</summary>
     public HashSet<string> SelectedSessionIds { get; } = new();
 
@@ -96,6 +107,36 @@ public bool SessionMatchesActiveGroup(SessionViewModel vm)
         return vm.GroupId == ActiveGroupId;
     }
 
+    /// <summary>
+    /// The group the main grid is currently scoped to, accounting for display mode:
+    /// FilterStrip = ActiveGroupId (explicit tab); InlineHeaders = the ActiveSession's
+    /// group (there's no tab strip, so the focused session is the implicit selector);
+    /// None = null (no group concept). Returns <see cref="GroupFilter.Ungrouped"/> for
+    /// sessions without a group, or the group id, or null for "no filter".
+    /// </summary>
+    public string? EffectiveActiveGroupId
+    {
+        get
+        {
+            var mode = Settings.GroupDisplayMode;
+            if (mode == Models.GroupDisplayMode.FilterStrip) return ActiveGroupId;
+            if (mode == Models.GroupDisplayMode.InlineHeaders && ActiveSession != null)
+                return string.IsNullOrEmpty(ActiveSession.GroupId)
+                    ? GroupFilter.Ungrouped
+                    : ActiveSession.GroupId;
+            return null;
+        }
+    }
+
+    /// <summary>Like <see cref="SessionMatchesActiveGroup"/> but uses <see cref="EffectiveActiveGroupId"/>.</summary>
+    public bool SessionMatchesEffectiveGroup(SessionViewModel vm)
+    {
+        var eff = EffectiveActiveGroupId;
+        if (eff == null) return true;
+        if (eff == GroupFilter.Ungrouped) return string.IsNullOrEmpty(vm.GroupId);
+        return vm.GroupId == eff;
+    }
+
     public bool IsSelected(string sessionId) => SelectedSessionIds.Contains(sessionId);
 
     public void ClearSelection()
@@ -160,7 +201,12 @@ public async Task LoadStateAsync()
     {
         _appState = await _stateService.LoadAsync();
         _sessionManager.LoadFromState(_appState);
-        Layout = Enum.TryParse<LayoutMode>(_appState.LastLayout, out var lm) ? lm : LayoutMode.Single;
+        _suppressLayoutPersist = true;
+        try
+        {
+            Layout = Enum.TryParse<LayoutMode>(_appState.LastLayout, out var lm) ? lm : LayoutMode.Single;
+        }
+        finally { _suppressLayoutPersist = false; }
 
         // Legacy migration: pre-enum installs persisted "ShowGroupsTab=false" to hide
         // the strip. Translate to the new enum on first load with the new code.
@@ -317,4 +363,58 @@ public void MoveSession(string sessionId, int newIndex)
         if (cur != newIndex) Sessions.Move(cur, newIndex);
         _ = SaveStateAsync();
     }
+
+    partial void OnLayoutChanged(LayoutMode value)
+    {
+        if (_suppressLayoutPersist) return;
+        if (!Settings.PerGroupLayout) return;
+        _appState.GroupLayouts[CurrentLayoutKey] = value.ToString();
+    }
+
+    partial void OnActiveGroupIdChanged(string? oldValue, string? newValue) => HandleEffectiveGroupChanged();
+
+    partial void OnActiveSessionChanged(SessionViewModel? oldValue, SessionViewModel? newValue)
+    {
+        // ActiveSession only contributes to the effective group in InlineHeaders mode —
+        // in other modes its change doesn't move us between groups.
+        if (Settings.GroupDisplayMode != Models.GroupDisplayMode.InlineHeaders) return;
+        HandleEffectiveGroupChanged();
+    }
+
+    /// <summary>
+    /// Called whenever the effective group filter may have changed (ActiveGroupId in
+    /// FilterStrip mode, or ActiveSession in InlineHeaders mode). Saves the old group's
+    /// layout if not already persisted, then restores the new group's saved layout if any.
+    /// </summary>
+    private void HandleEffectiveGroupChanged()
+    {
+        if (!Settings.PerGroupLayout) return;
+        string newKey = EffectiveActiveGroupId ?? GroupFilter.AllKey;
+        if (newKey == _lastEffectiveLayoutKey) return;
+        string oldKey = _lastEffectiveLayoutKey;
+        _lastEffectiveLayoutKey = newKey;
+
+        // Seed the old key with the current layout in case the user never explicitly
+        // changed it there — otherwise round-tripping back to that group would miss.
+        bool seeded = false;
+        if (!_appState.GroupLayouts.ContainsKey(oldKey))
+        {
+            _appState.GroupLayouts[oldKey] = Layout.ToString();
+            seeded = true;
+        }
+
+        bool layoutSwitched = false;
+        if (_appState.GroupLayouts.TryGetValue(newKey, out var s)
+            && Enum.TryParse<LayoutMode>(s, out var lm)
+            && lm != Layout)
+        {
+            _suppressLayoutPersist = true;
+            try { Layout = lm; }
+            finally { _suppressLayoutPersist = false; }
+            layoutSwitched = true;
+        }
+
+        if (seeded || layoutSwitched)
+            _ = SaveStateAsync();
+    }
 }

src/CodeShellManager/ViewModels/MainViewModel.cs

@@ -212,6 +212,13 @@
                           Margin="0,4,0,0"
                           ToolTip="When clicking a session in the sidebar (or cycling with Ctrl+Tab), move keyboard focus into the terminal so you can start typing immediately."/>
 
+                <StackPanel Margin="0,10,0,0">
+                    <TextBlock Text="Claude launch / shutdown stagger (ms)" Style="{StaticResource Label}"/>
+                    <TextBox x:Name="ClaudeLaunchStaggerBox" Width="100" HorizontalAlignment="Left"/>
+                    <TextBlock Text="Delay between consecutive Claude sessions during restore-on-startup and app shutdown. Claude's CLI rewrites ~/.claude.json on startup/exit without locking, so back-to-back Claude processes can corrupt it. 2000 ms is the safe default; set 0 to disable."
+                               Foreground="#6c7086" FontSize="10" Margin="0,4,0,0" TextWrapping="Wrap"/>
+                </StackPanel>
+
                 <!-- Appearance -->
                 <TextBlock Text="APPEARANCE" Style="{StaticResource SectionHeader}"/>
                 <Border BorderBrush="#313244" BorderThickness="0,0,0,1" Margin="0,4,0,0"/>
@@ -239,6 +246,12 @@
                         <TextBlock Text="Filter strip = one group view at a time, via a tab strip. Inline headers = all groups visible at once, expand/collapse per group."
                                    Foreground="#6c7086" FontSize="10" Margin="0,4,0,0" TextWrapping="Wrap"/>
                     </StackPanel>
+                    <CheckBox x:Name="FilterGridByActiveGroupCheck"
+                              Content="Limit terminal grid to active group"
+                              ToolTip="When a group filter is selected in the strip, the multi-pane grid only shows sessions from that group. Off = the grid keeps showing every live session regardless of which group is selected."/>
+                    <CheckBox x:Name="PerGroupLayoutCheck"
+                              Content="Remember layout per group"
+                              ToolTip="Switching to a group restores the grid layout (Single / 2×2 / etc.) you last used while that group was active. Off = a single global layout shared across groups."/>
                     <CheckBox x:Name="ShowWorktreeClustersCheck" Content="Group worktree siblings in sidebar"
                               ToolTip="When 2+ adjacent sessions share a git repo, render them under a small '📁 repo (N)' header so the worktree cluster is visible at a glance. Off = only the shared stripe color + subtitle line indicate worktree siblings."/>
                     <CheckBox x:Name="ImportWindowsTerminalProfilesCheck"

src/CodeShellManager/Views/SettingsWindow.xaml

@@ -24,6 +24,7 @@ public SettingsWindow(AppSettings current, SearchService? searchService = null)
         {
             AutoRestoreSessions = current.AutoRestoreSessions,
             AutoResumeClaude = current.AutoResumeClaude,
+            ClaudeLaunchStaggerMs = current.ClaudeLaunchStaggerMs,
             AutoFocusTerminalOnSelect = current.AutoFocusTerminalOnSelect,
             ShowToastNotifications = current.ShowToastNotifications,
             ShowNotificationSound = current.ShowNotificationSound,
@@ -33,6 +34,8 @@ public SettingsWindow(AppSettings current, SearchService? searchService = null)
             ShowGitBranch = current.ShowGitBranch,
             ShowGroupsTab = current.ShowGroupsTab,
             GroupDisplayMode = current.GroupDisplayMode,
+            FilterGridByActiveGroup = current.FilterGridByActiveGroup,
+            PerGroupLayout = current.PerGroupLayout,
             SidebarActionIconsMode = current.SidebarActionIconsMode,
             ShowWorktreeClusters = current.ShowWorktreeClusters,
             SearchCollapseAfterNavigate = current.SearchCollapseAfterNavigate,
@@ -56,6 +59,7 @@ public SettingsWindow(AppSettings current, SearchService? searchService = null)
         DefaultFolderBox.Text = _edited.DefaultWorkingFolder;
         AutoRestoreCheck.IsChecked = _edited.AutoRestoreSessions;
         AutoResumeClaudeCheck.IsChecked = _edited.AutoResumeClaude;
+        ClaudeLaunchStaggerBox.Text = _edited.ClaudeLaunchStaggerMs.ToString();
         AutoFocusTerminalOnSelectCheck.IsChecked = _edited.AutoFocusTerminalOnSelect;
         ShowToastCheck.IsChecked = _edited.ShowToastNotifications;
         ShowNotificationSoundCheck.IsChecked = _edited.ShowNotificationSound;
@@ -82,6 +86,8 @@ public SettingsWindow(AppSettings current, SearchService? searchService = null)
         }
         if (SidebarActionIconsModeCombo.SelectedIndex < 0)
             SidebarActionIconsModeCombo.SelectedIndex = 0; // OnHover default
+        FilterGridByActiveGroupCheck.IsChecked = _edited.FilterGridByActiveGroup;
+        PerGroupLayoutCheck.IsChecked = _edited.PerGroupLayout;
         ImportWindowsTerminalProfilesCheck.IsChecked = _edited.ImportWindowsTerminalProfiles;
         SearchCollapseAfterNavigateCheck.IsChecked = _edited.SearchCollapseAfterNavigate;
         MaxSearchResultsBox.Text = _edited.MaxSearchResults.ToString();
@@ -141,6 +147,8 @@ private void Save_Click(object sender, RoutedEventArgs e)
         _edited.DefaultWorkingFolder = DefaultFolderBox.Text.Trim();
         _edited.AutoRestoreSessions = AutoRestoreCheck.IsChecked == true;
         _edited.AutoResumeClaude = AutoResumeClaudeCheck.IsChecked == true;
+        if (int.TryParse(ClaudeLaunchStaggerBox.Text, out int staggerMs) && staggerMs >= 0)
+            _edited.ClaudeLaunchStaggerMs = staggerMs;
         _edited.AutoFocusTerminalOnSelect = AutoFocusTerminalOnSelectCheck.IsChecked == true;
         _edited.ShowToastNotifications = ShowToastCheck.IsChecked == true;
         _edited.ShowNotificationSound = ShowNotificationSoundCheck.IsChecked == true;
@@ -157,6 +165,8 @@ private void Save_Click(object sender, RoutedEventArgs e)
         var iconsModeTag = (SidebarActionIconsModeCombo.SelectedItem as ComboBoxItem)?.Tag?.ToString();
         if (System.Enum.TryParse<Models.SidebarActionIconsMode>(iconsModeTag, out var newIconsMode))
             _edited.SidebarActionIconsMode = newIconsMode;
+        _edited.FilterGridByActiveGroup = FilterGridByActiveGroupCheck.IsChecked == true;
+        _edited.PerGroupLayout = PerGroupLayoutCheck.IsChecked == true;
         _edited.ImportWindowsTerminalProfiles = ImportWindowsTerminalProfilesCheck.IsChecked == true;
         _edited.SearchCollapseAfterNavigate = SearchCollapseAfterNavigateCheck.IsChecked == true;
         _edited.AnthropicApiKey = ApiKeyBox.Password;