diff --git a/packages/desktop/src-tauri/src/commands/settings.rs b/packages/desktop/src-tauri/src/commands/settings.rs
index 69ffec5f..65de2e85 100644
--- a/packages/desktop/src-tauri/src/commands/settings.rs
+++ b/packages/desktop/src-tauri/src/commands/settings.rs
@@ -289,6 +289,18 @@ fn sanitize_settings_update(payload: &Value) -> Value {
         if let Some(Value::Bool(b)) = obj.get("showReasoningTraces") {
             result_obj.insert("showReasoningTraces".to_string(), json!(b));
         }
+        if let Some(Value::Bool(b)) = obj.get("showTextJustificationActivity") {
+            result_obj.insert("showTextJustificationActivity".to_string(), json!(b));
+        }
+        if let Some(Value::Bool(b)) = obj.get("nativeNotificationsEnabled") {
+            result_obj.insert("nativeNotificationsEnabled".to_string(), json!(b));
+        }
+        if let Some(Value::String(s)) = obj.get("notificationMode") {
+            let trimmed = s.trim();
+            if trimmed == "always" || trimmed == "hidden-only" {
+                result_obj.insert("notificationMode".to_string(), json!(trimmed));
+            }
+        }
         if let Some(Value::Bool(b)) = obj.get("autoDeleteEnabled") {
             result_obj.insert("autoDeleteEnabled".to_string(), json!(b));
         }
@@ -298,6 +310,12 @@ fn sanitize_settings_update(payload: &Value) -> Value {
         if let Some(Value::Bool(b)) = obj.get("autoCreateWorktree") {
             result_obj.insert("autoCreateWorktree".to_string(), json!(b));
         }
+        if let Some(Value::String(s)) = obj.get("toolCallExpansion") {
+            let trimmed = s.trim();
+            if trimmed == "collapsed" || trimmed == "activity" || trimmed == "detailed" {
+                result_obj.insert("toolCallExpansion".to_string(), json!(trimmed));
+            }
+        }
 
         // Number fields
         if let Some(Value::Number(n)) = obj.get("autoDeleteAfterDays") {
@@ -314,6 +332,47 @@ fn sanitize_settings_update(payload: &Value) -> Value {
             }
         }
 
+        if let Some(Value::Number(n)) = obj.get("fontSize") {
+            let parsed = n
+                .as_u64()
+                .or_else(|| n.as_i64().and_then(|v| if v >= 0 { Some(v as u64) } else { None }))
+                .or_else(|| n.as_f64().map(|v| v.round().max(0.0) as u64));
+            if let Some(value) = parsed {
+                let clamped = value.max(50).min(200);
+                result_obj.insert("fontSize".to_string(), json!(clamped));
+            }
+        }
+        if let Some(Value::Number(n)) = obj.get("padding") {
+            let parsed = n
+                .as_u64()
+                .or_else(|| n.as_i64().and_then(|v| if v >= 0 { Some(v as u64) } else { None }))
+                .or_else(|| n.as_f64().map(|v| v.round().max(0.0) as u64));
+            if let Some(value) = parsed {
+                let clamped = value.max(50).min(200);
+                result_obj.insert("padding".to_string(), json!(clamped));
+            }
+        }
+        if let Some(Value::Number(n)) = obj.get("cornerRadius") {
+            let parsed = n
+                .as_u64()
+                .or_else(|| n.as_i64().and_then(|v| if v >= 0 { Some(v as u64) } else { None }))
+                .or_else(|| n.as_f64().map(|v| v.round().max(0.0) as u64));
+            if let Some(value) = parsed {
+                let clamped = value.max(0).min(32);
+                result_obj.insert("cornerRadius".to_string(), json!(clamped));
+            }
+        }
+        if let Some(Value::Number(n)) = obj.get("inputBarOffset") {
+            let parsed = n
+                .as_u64()
+                .or_else(|| n.as_i64().and_then(|v| if v >= 0 { Some(v as u64) } else { None }))
+                .or_else(|| n.as_f64().map(|v| v.round().max(0.0) as u64));
+            if let Some(value) = parsed {
+                let clamped = value.max(0).min(100);
+                result_obj.insert("inputBarOffset".to_string(), json!(clamped));
+            }
+        }
+
         // Memory limit fields
         if let Some(Value::Number(n)) = obj.get("memoryLimitHistorical") {
             let parsed = n
@@ -355,6 +414,25 @@ fn sanitize_settings_update(payload: &Value) -> Value {
             }
         }
 
+        if let Some(Value::String(s)) = obj.get("diffLayoutPreference") {
+            let trimmed = s.trim();
+            if trimmed == "dynamic" || trimmed == "inline" || trimmed == "side-by-side" {
+                result_obj.insert("diffLayoutPreference".to_string(), json!(trimmed));
+            }
+        }
+        if let Some(Value::String(s)) = obj.get("diffViewMode") {
+            let trimmed = s.trim();
+            if trimmed == "single" || trimmed == "stacked" {
+                result_obj.insert("diffViewMode".to_string(), json!(trimmed));
+            }
+        }
+        if let Some(Value::Bool(b)) = obj.get("directoryShowHidden") {
+            result_obj.insert("directoryShowHidden".to_string(), json!(b));
+        }
+        if let Some(Value::Bool(b)) = obj.get("filesViewShowGitignored") {
+            result_obj.insert("filesViewShowGitignored".to_string(), json!(b));
+        }
+
         // Array fields
         if let Some(arr) = obj.get("approvedDirectories") {
             result_obj.insert(
diff --git a/packages/ui/src/components/chat/FileAttachment.tsx b/packages/ui/src/components/chat/FileAttachment.tsx
index a4e9ca44..15d8886e 100644
--- a/packages/ui/src/components/chat/FileAttachment.tsx
+++ b/packages/ui/src/components/chat/FileAttachment.tsx
@@ -6,6 +6,7 @@ import { toast } from '@/components/ui';
 import { cn } from '@/lib/utils';
 import { Tooltip, TooltipTrigger, TooltipContent } from '@/components/ui/tooltip';
 import { useIsVSCodeRuntime } from '@/hooks/useRuntimeAPIs';
+import { useIsTextTruncated } from '@/hooks/useIsTextTruncated';
 import type { ToolPopupContent } from './message/types';
 
 export const FileAttachmentButton = memo(() => {
@@ -125,6 +126,21 @@ interface FileChipProps {
   onRemove: () => void;
 }
 
+const TruncatedMarquee = memo(({ text, title }: { text: string; title?: string }) => {
+  const labelRef = useRef<HTMLSpanElement>(null);
+  const isTruncated = useIsTextTruncated(labelRef, [text]);
+
+  return (
+    <span
+      ref={labelRef}
+      className={cn('marquee-text', isTruncated && 'marquee-text--active')}
+      title={title ?? text}
+    >
+      {text}
+    </span>
+  );
+});
+
 const FileChip = memo(({ file, onRemove }: FileChipProps) => {
   const getFileIcon = () => {
     if (file.mimeType.startsWith('image/')) {
@@ -169,9 +185,7 @@ const FileChip = memo(({ file, onRemove }: FileChipProps) => {
       </div>
       {getFileIcon()}
       <div className="overflow-hidden max-w-[200px]">
-        <span className="marquee-text" title={file.serverPath || displayName}>
-          {displayName}
-        </span>
+        <TruncatedMarquee text={displayName} title={file.serverPath || displayName} />
       </div>
       <span className="text-muted-foreground flex-shrink-0">
         ({formatFileSize(file.size)})
@@ -292,9 +306,7 @@ export const MessageFilesDisplay = memo(({ files, onShowPopup }: MessageFilesDis
             >
               {getFileIcon(file.mime)}
               <div className="overflow-hidden max-w-[200px]">
-                <span className="marquee-text">
-                  {extractFilename(file.filename)}
-                </span>
+                <TruncatedMarquee text={extractFilename(file.filename)} />
               </div>
             </div>
           ))}
diff --git a/packages/ui/src/components/chat/ModelControls.tsx b/packages/ui/src/components/chat/ModelControls.tsx
index 90e83e9d..65bfa57c 100644
--- a/packages/ui/src/components/chat/ModelControls.tsx
+++ b/packages/ui/src/components/chat/ModelControls.tsx
@@ -47,6 +47,7 @@ import { useConfigStore } from '@/stores/useConfigStore';
 import { useSessionStore } from '@/stores/useSessionStore';
 import { useUIStore } from '@/stores/useUIStore';
 import { useModelLists } from '@/hooks/useModelLists';
+import { useIsTextTruncated } from '@/hooks/useIsTextTruncated';
 
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 type IconComponent = ComponentType<any>;
@@ -1083,6 +1084,10 @@ export const ModelControls: React.FC<ModelControlsProps> = ({ className }) => {
         return getModelDisplayName(currentModel);
     };
 
+    const currentModelDisplayName = getCurrentModelDisplayName();
+    const modelLabelRef = React.useRef<HTMLSpanElement>(null);
+    const isModelLabelTruncated = useIsTextTruncated(modelLabelRef, [currentModelDisplayName, isCompact]);
+
     const getAgentDisplayName = () => {
         if (!uiAgentName) {
             const primaryAgents = agents.filter(agent => isPrimaryMode(agent.mode));
@@ -2122,19 +2127,20 @@ export const ModelControls: React.FC<ModelControlsProps> = ({ className }) => {
                                     ) : (
                                         <RiPencilAiLine className={cn(controlIconSize, 'text-muted-foreground')} />
                                     )}
-                                    <span
-                                        key={`${currentProviderId}-${currentModelId}`}
-                                        className={cn(
-                                            'model-controls__model-label overflow-hidden',
-                                            controlTextSize,
-                                            'font-medium whitespace-nowrap text-foreground min-w-0',
-                                            'max-w-[260px]'
-                                        )}
-                                    >
-                                        <span className="marquee-text">
-                                            {getCurrentModelDisplayName()}
+                                        <span
+                                            ref={modelLabelRef}
+                                            key={`${currentProviderId}-${currentModelId}`}
+                                            className={cn(
+                                                'model-controls__model-label overflow-hidden',
+                                                controlTextSize,
+                                                'font-medium whitespace-nowrap text-foreground min-w-0',
+                                                'max-w-[260px]'
+                                            )}
+                                        >
+                                            <span className={cn('marquee-text', isModelLabelTruncated && 'marquee-text--active')}>
+                                                {currentModelDisplayName}
+                                            </span>
                                         </span>
-                                    </span>
                                 </div>
                             </DropdownMenuTrigger>
                         </TooltipTrigger>
@@ -2246,13 +2252,14 @@ export const ModelControls: React.FC<ModelControlsProps> = ({ className }) => {
                             <RiPencilAiLine className={cn(controlIconSize, 'text-muted-foreground')} />
                         )}
                         <span
+                            ref={modelLabelRef}
                             className={cn(
                                 'model-controls__model-label typography-micro font-medium overflow-hidden min-w-0',
                                 isMobile ? 'max-w-[120px]' : 'max-w-[220px]',
                             )}
                         >
-                            <span className="marquee-text">
-                                {getCurrentModelDisplayName()}
+                            <span className={cn('marquee-text', isModelLabelTruncated && 'marquee-text--active')}>
+                                {currentModelDisplayName}
                             </span>
                         </span>
                     </button>
diff --git a/packages/ui/src/components/terminal/TerminalViewport.tsx b/packages/ui/src/components/terminal/TerminalViewport.tsx
index bb5b1f98..0a949afe 100644
--- a/packages/ui/src/components/terminal/TerminalViewport.tsx
+++ b/packages/ui/src/components/terminal/TerminalViewport.tsx
@@ -122,6 +122,55 @@ const TerminalViewport = React.forwardRef<TerminalController, TerminalViewportPr
       }
     }, []);
 
+    const copySelectionToClipboard = React.useCallback(async () => {
+      if (typeof window === 'undefined' || typeof document === 'undefined') {
+        return;
+      }
+      const selection = window.getSelection();
+      if (!selection) {
+        return;
+      }
+      const text = selection.toString();
+      if (!text.trim()) {
+        return;
+      }
+      const container = containerRef.current;
+      if (!container) {
+        return;
+      }
+      const anchorNode = selection.anchorNode;
+      const focusNode = selection.focusNode;
+      if (anchorNode && !container.contains(anchorNode)) {
+        return;
+      }
+      if (focusNode && !container.contains(focusNode)) {
+        return;
+      }
+
+      try {
+        if (navigator.clipboard?.writeText) {
+          await navigator.clipboard.writeText(text);
+          return;
+        }
+      } catch {
+        // fall through to execCommand
+      }
+
+      try {
+        const textarea = document.createElement('textarea');
+        textarea.value = text;
+        textarea.style.position = 'fixed';
+        textarea.style.opacity = '0';
+        document.body.appendChild(textarea);
+        textarea.focus();
+        textarea.select();
+        document.execCommand('copy');
+        document.body.removeChild(textarea);
+      } catch {
+        // ignore
+      }
+    }, []);
+
     const resetWriteState = React.useCallback(() => {
       pendingWriteRef.current = '';
       if (writeScheduledRef.current !== null && typeof window !== 'undefined') {
@@ -782,6 +831,12 @@ const TerminalViewport = React.forwardRef<TerminalController, TerminalViewportPr
             terminalRef.current?.focus();
           }
         }}
+        onMouseUp={() => {
+          void copySelectionToClipboard();
+        }}
+        onTouchEnd={() => {
+          void copySelectionToClipboard();
+        }}
       >
         {enableTouchScroll ? (
           <textarea
diff --git a/packages/ui/src/components/views/GitView.tsx b/packages/ui/src/components/views/GitView.tsx
index 4ece2ef5..fca9642b 100644
--- a/packages/ui/src/components/views/GitView.tsx
+++ b/packages/ui/src/components/views/GitView.tsx
@@ -49,6 +49,7 @@ type GitViewSnapshot = {
   directory?: string;
   selectedPaths: string[];
   commitMessage: string;
+  generatedHighlights: string[];
 };
 
 type GitmojiEntry = {
@@ -179,7 +180,7 @@ const matchGitmojiFromSubject = (subject: string, gitmojis: GitmojiEntry[]): Git
   return null;
 };
 
-let gitViewSnapshot: GitViewSnapshot | null = null;
+const gitViewSnapshots = new Map<string, GitViewSnapshot>();
 
 const useEffectiveDirectory = () => {
   const { currentSessionId, sessions, worktreeMetadata: worktreeMap } = useSessionStore();
@@ -226,9 +227,8 @@ export const GitView: React.FC = () => {
   } = useGitStore();
 
   const initialSnapshot = React.useMemo(() => {
-    if (!gitViewSnapshot) return null;
-    if (gitViewSnapshot.directory !== currentDirectory) return null;
-    return gitViewSnapshot;
+    if (!currentDirectory) return null;
+    return gitViewSnapshots.get(currentDirectory) ?? null;
   }, [currentDirectory]);
 
   const settingsGitmojiEnabled = useConfigStore((state) => state.settingsGitmojiEnabled);
@@ -273,7 +273,9 @@ export const GitView: React.FC = () => {
   const [hasUserAdjustedSelection, setHasUserAdjustedSelection] = React.useState(false);
   const [revertingPaths, setRevertingPaths] = React.useState<Set<string>>(new Set());
   const [isGeneratingMessage, setIsGeneratingMessage] = React.useState(false);
-  const [generatedHighlights, setGeneratedHighlights] = React.useState<string[]>([]);
+  const [generatedHighlights, setGeneratedHighlights] = React.useState<string[]>(
+    initialSnapshot?.generatedHighlights ?? []
+  );
   const clearGeneratedHighlights = React.useCallback(() => {
     setGeneratedHighlights([]);
   }, []);
@@ -346,19 +348,14 @@ export const GitView: React.FC = () => {
   }, [expandedCommitHashes, currentDirectory, git, commitFilesMap, loadingCommitHashes]);
 
   React.useEffect(() => {
-    return () => {
-      if (!currentDirectory) {
-        gitViewSnapshot = null;
-        return;
-      }
-
-      gitViewSnapshot = {
-        directory: currentDirectory,
-        selectedPaths: Array.from(selectedPaths),
-        commitMessage,
-      };
-    };
-  }, [commitMessage, currentDirectory, selectedPaths]);
+    if (!currentDirectory) return;
+    gitViewSnapshots.set(currentDirectory, {
+      directory: currentDirectory,
+      selectedPaths: Array.from(selectedPaths),
+      commitMessage,
+      generatedHighlights,
+    });
+  }, [commitMessage, currentDirectory, selectedPaths, generatedHighlights]);
 
   React.useEffect(() => {
     loadProfiles();
diff --git a/packages/ui/src/components/views/TerminalView.tsx b/packages/ui/src/components/views/TerminalView.tsx
index ab938895..aaeb628e 100644
--- a/packages/ui/src/components/views/TerminalView.tsx
+++ b/packages/ui/src/components/views/TerminalView.tsx
@@ -44,6 +44,7 @@ const MODIFIER_ARROW_SUFFIX: Record<Modifier, string> = {
     cmd: '3',
 };
 
+
 const STREAM_OPTIONS = {
     retry: {
         maxRetries: 3,
@@ -429,6 +430,7 @@ export const TerminalView: React.FC = () => {
         }
     }, [clearBuffer, effectiveDirectory, setConnectionError, terminal]);
 
+
     const handleViewportInput = React.useCallback(
         (data: string) => {
             if (!data) {
diff --git a/packages/ui/src/components/views/git/PullRequestSection.tsx b/packages/ui/src/components/views/git/PullRequestSection.tsx
index 0a942536..cd5bf1f1 100644
--- a/packages/ui/src/components/views/git/PullRequestSection.tsx
+++ b/packages/ui/src/components/views/git/PullRequestSection.tsx
@@ -60,6 +60,15 @@ const branchToTitle = (branch: string): string => {
     .replace(/\b\w/g, (c) => c.toUpperCase());
 };
 
+type PullRequestDraftSnapshot = {
+  title: string;
+  body: string;
+  draft: boolean;
+  isOpen: boolean;
+};
+
+const pullRequestDraftSnapshots = new Map<string, PullRequestDraftSnapshot>();
+
 const openExternal = async (url: string) => {
   if (typeof window === 'undefined') return;
   const desktop = (window as typeof window & { opencodeDesktop?: { openExternal?: (url: string) => Promise<unknown> } }).opencodeDesktop;
@@ -96,14 +105,20 @@ export const PullRequestSection: React.FC<{
     setSettingsDialogOpen(true);
   }, [setSettingsDialogOpen, setSidebarSection]);
 
-  const [isOpen, setIsOpen] = React.useState(true);
+  const snapshotKey = React.useMemo(() => `${directory}::${branch}`, [directory, branch]);
+  const initialSnapshot = React.useMemo(
+    () => pullRequestDraftSnapshots.get(snapshotKey) ?? null,
+    [snapshotKey]
+  );
+
+  const [isOpen, setIsOpen] = React.useState(initialSnapshot?.isOpen ?? true);
   const [isLoading, setIsLoading] = React.useState(false);
   const [status, setStatus] = React.useState<GitHubPullRequestStatus | null>(null);
   const [error, setError] = React.useState<string | null>(null);
 
-  const [title, setTitle] = React.useState(() => branchToTitle(branch));
-  const [body, setBody] = React.useState('');
-  const [draft, setDraft] = React.useState(false);
+  const [title, setTitle] = React.useState(() => initialSnapshot?.title ?? branchToTitle(branch));
+  const [body, setBody] = React.useState(() => initialSnapshot?.body ?? '');
+  const [draft, setDraft] = React.useState(() => initialSnapshot?.draft ?? false);
   const [mergeMethod, setMergeMethod] = React.useState<MergeMethod>('squash');
 
   const [isGenerating, setIsGenerating] = React.useState(false);
@@ -359,11 +374,25 @@ export const PullRequestSection: React.FC<{
   }, [branch, canShow, directory, github]);
 
   React.useEffect(() => {
-    setTitle(branchToTitle(branch));
-    setBody('');
-    setDraft(false);
+    const snapshot = pullRequestDraftSnapshots.get(snapshotKey) ?? null;
+    setTitle(snapshot?.title ?? branchToTitle(branch));
+    setBody(snapshot?.body ?? '');
+    setDraft(snapshot?.draft ?? false);
+    setIsOpen(snapshot?.isOpen ?? true);
     void refresh();
-  }, [branch, refresh]);
+  }, [branch, refresh, snapshotKey]);
+
+  React.useEffect(() => {
+    if (!directory || !branch) {
+      return;
+    }
+    pullRequestDraftSnapshots.set(snapshotKey, {
+      title,
+      body,
+      draft,
+      isOpen,
+    });
+  }, [snapshotKey, title, body, draft, isOpen, directory, branch]);
 
   const generateDescription = React.useCallback(async () => {
     if (isGenerating) return;
diff --git a/packages/ui/src/hooks/useIsTextTruncated.ts b/packages/ui/src/hooks/useIsTextTruncated.ts
new file mode 100644
index 00000000..d2a46582
--- /dev/null
+++ b/packages/ui/src/hooks/useIsTextTruncated.ts
@@ -0,0 +1,46 @@
+import React from 'react';
+
+const useIsomorphicLayoutEffect = typeof window !== 'undefined' ? React.useLayoutEffect : React.useEffect;
+
+export const useIsTextTruncated = <T extends HTMLElement>(
+  ref: React.RefObject<T | null>,
+  deps: React.DependencyList = []
+): boolean => {
+  const [isTruncated, setIsTruncated] = React.useState(false);
+
+  const checkTruncation = React.useCallback(() => {
+    const element = ref.current;
+    if (!element) {
+      return;
+    }
+    const next = element.scrollWidth > element.clientWidth + 1;
+    setIsTruncated(next);
+  }, [ref]);
+
+  useIsomorphicLayoutEffect(() => {
+    checkTruncation();
+  }, [checkTruncation, ...deps]);
+
+  React.useEffect(() => {
+    const element = ref.current;
+    if (!element || typeof ResizeObserver === 'undefined') {
+      return;
+    }
+    const observer = new ResizeObserver(() => {
+      checkTruncation();
+    });
+    observer.observe(element);
+    return () => observer.disconnect();
+  }, [checkTruncation, ref]);
+
+  React.useEffect(() => {
+    if (typeof window === 'undefined') {
+      return;
+    }
+    const handleResize = () => checkTruncation();
+    window.addEventListener('resize', handleResize);
+    return () => window.removeEventListener('resize', handleResize);
+  }, [checkTruncation]);
+
+  return isTruncated;
+};
diff --git a/packages/ui/src/index.css b/packages/ui/src/index.css
index 7b4aacf3..9f301dc5 100644
--- a/packages/ui/src/index.css
+++ b/packages/ui/src/index.css
@@ -644,7 +644,7 @@ html:not(.dark) .chat-scroll {
   white-space: nowrap;
 }
 
-.group:hover .marquee-text,
-.marquee-text:hover {
+.group:hover .marquee-text--active,
+.marquee-text--active:hover {
   animation: marquee-scroll 5s linear infinite alternate;
 }
diff --git a/packages/ui/src/lib/api/types.ts b/packages/ui/src/lib/api/types.ts
index b8033c98..883fe266 100644
--- a/packages/ui/src/lib/api/types.ts
+++ b/packages/ui/src/lib/api/types.ts
@@ -395,10 +395,22 @@ export interface SettingsPayload {
   securityScopedBookmarks?: string[];
   pinnedDirectories?: string[];
   showReasoningTraces?: boolean;
+  showTextJustificationActivity?: boolean;
+  nativeNotificationsEnabled?: boolean;
+  notificationMode?: 'always' | 'hidden-only';
   autoDeleteEnabled?: boolean;
   autoDeleteAfterDays?: number;
   queueModeEnabled?: boolean;
   gitmojiEnabled?: boolean;
+  toolCallExpansion?: 'collapsed' | 'activity' | 'detailed';
+  fontSize?: number;
+  padding?: number;
+  cornerRadius?: number;
+  inputBarOffset?: number;
+  diffLayoutPreference?: 'dynamic' | 'inline' | 'side-by-side';
+  diffViewMode?: 'single' | 'stacked';
+  directoryShowHidden?: boolean;
+  filesViewShowGitignored?: boolean;
 
   [key: string]: unknown;
 }
diff --git a/packages/ui/src/lib/appearanceAutoSave.ts b/packages/ui/src/lib/appearanceAutoSave.ts
index 6ac79ad7..531dd70a 100644
--- a/packages/ui/src/lib/appearanceAutoSave.ts
+++ b/packages/ui/src/lib/appearanceAutoSave.ts
@@ -4,8 +4,18 @@ import type { DesktopSettings } from '@/lib/desktop';
 
 type AppearanceSlice = {
   showReasoningTraces: boolean;
+  showTextJustificationActivity: boolean;
+  nativeNotificationsEnabled: boolean;
+  notificationMode: 'always' | 'hidden-only';
   autoDeleteEnabled: boolean;
   autoDeleteAfterDays: number;
+  toolCallExpansion: 'collapsed' | 'activity' | 'detailed';
+  fontSize: number;
+  padding: number;
+  cornerRadius: number;
+  inputBarOffset: number;
+  diffLayoutPreference: 'dynamic' | 'inline' | 'side-by-side';
+  diffViewMode: 'single' | 'stacked';
 };
 
 let initialized = false;
@@ -19,8 +29,18 @@ export const startAppearanceAutoSave = (): void => {
 
   let previous: AppearanceSlice = {
     showReasoningTraces: useUIStore.getState().showReasoningTraces,
+    showTextJustificationActivity: useUIStore.getState().showTextJustificationActivity,
+    nativeNotificationsEnabled: useUIStore.getState().nativeNotificationsEnabled,
+    notificationMode: useUIStore.getState().notificationMode,
     autoDeleteEnabled: useUIStore.getState().autoDeleteEnabled,
     autoDeleteAfterDays: useUIStore.getState().autoDeleteAfterDays,
+    toolCallExpansion: useUIStore.getState().toolCallExpansion,
+    fontSize: useUIStore.getState().fontSize,
+    padding: useUIStore.getState().padding,
+    cornerRadius: useUIStore.getState().cornerRadius,
+    inputBarOffset: useUIStore.getState().inputBarOffset,
+    diffLayoutPreference: useUIStore.getState().diffLayoutPreference,
+    diffViewMode: useUIStore.getState().diffViewMode,
   };
 
   let pending: Partial<DesktopSettings> | null = null;
@@ -46,8 +66,18 @@ export const startAppearanceAutoSave = (): void => {
   useUIStore.subscribe((state) => {
     const current: AppearanceSlice = {
       showReasoningTraces: state.showReasoningTraces,
+      showTextJustificationActivity: state.showTextJustificationActivity,
+      nativeNotificationsEnabled: state.nativeNotificationsEnabled,
+      notificationMode: state.notificationMode,
       autoDeleteEnabled: state.autoDeleteEnabled,
       autoDeleteAfterDays: state.autoDeleteAfterDays,
+      toolCallExpansion: state.toolCallExpansion,
+      fontSize: state.fontSize,
+      padding: state.padding,
+      cornerRadius: state.cornerRadius,
+      inputBarOffset: state.inputBarOffset,
+      diffLayoutPreference: state.diffLayoutPreference,
+      diffViewMode: state.diffViewMode,
     };
 
     const diff: Partial<DesktopSettings> = {};
@@ -55,12 +85,42 @@ export const startAppearanceAutoSave = (): void => {
     if (current.showReasoningTraces !== previous.showReasoningTraces) {
       diff.showReasoningTraces = current.showReasoningTraces;
     }
+    if (current.showTextJustificationActivity !== previous.showTextJustificationActivity) {
+      diff.showTextJustificationActivity = current.showTextJustificationActivity;
+    }
+    if (current.nativeNotificationsEnabled !== previous.nativeNotificationsEnabled) {
+      diff.nativeNotificationsEnabled = current.nativeNotificationsEnabled;
+    }
+    if (current.notificationMode !== previous.notificationMode) {
+      diff.notificationMode = current.notificationMode;
+    }
     if (current.autoDeleteEnabled !== previous.autoDeleteEnabled) {
       diff.autoDeleteEnabled = current.autoDeleteEnabled;
     }
     if (current.autoDeleteAfterDays !== previous.autoDeleteAfterDays) {
       diff.autoDeleteAfterDays = current.autoDeleteAfterDays;
     }
+    if (current.toolCallExpansion !== previous.toolCallExpansion) {
+      diff.toolCallExpansion = current.toolCallExpansion;
+    }
+    if (current.fontSize !== previous.fontSize) {
+      diff.fontSize = current.fontSize;
+    }
+    if (current.padding !== previous.padding) {
+      diff.padding = current.padding;
+    }
+    if (current.cornerRadius !== previous.cornerRadius) {
+      diff.cornerRadius = current.cornerRadius;
+    }
+    if (current.inputBarOffset !== previous.inputBarOffset) {
+      diff.inputBarOffset = current.inputBarOffset;
+    }
+    if (current.diffLayoutPreference !== previous.diffLayoutPreference) {
+      diff.diffLayoutPreference = current.diffLayoutPreference;
+    }
+    if (current.diffViewMode !== previous.diffViewMode) {
+      diff.diffViewMode = current.diffViewMode;
+    }
 
     previous = current;
 
diff --git a/packages/ui/src/lib/desktop.ts b/packages/ui/src/lib/desktop.ts
index f1864e92..2450a1e2 100644
--- a/packages/ui/src/lib/desktop.ts
+++ b/packages/ui/src/lib/desktop.ts
@@ -52,6 +52,8 @@ export type DesktopSettings = {
   pinnedDirectories?: string[];
   showReasoningTraces?: boolean;
   showTextJustificationActivity?: boolean;
+  nativeNotificationsEnabled?: boolean;
+  notificationMode?: 'always' | 'hidden-only';
   autoDeleteEnabled?: boolean;
   autoDeleteAfterDays?: number;
   defaultModel?: string; // format: "provider/model"
@@ -61,6 +63,15 @@ export type DesktopSettings = {
   autoCreateWorktree?: boolean;
   queueModeEnabled?: boolean;
   gitmojiEnabled?: boolean;
+  toolCallExpansion?: 'collapsed' | 'activity' | 'detailed';
+  fontSize?: number;
+  padding?: number;
+  cornerRadius?: number;
+  inputBarOffset?: number;
+  diffLayoutPreference?: 'dynamic' | 'inline' | 'side-by-side';
+  diffViewMode?: 'single' | 'stacked';
+  directoryShowHidden?: boolean;
+  filesViewShowGitignored?: boolean;
 
   // Memory limits for message viewport management
   memoryLimitHistorical?: number;   // Default fetch limit when loading/syncing (default: 90)
@@ -320,4 +331,3 @@ export const restartToApplyUpdate = async (): Promise<boolean> => {
     return false;
   }
 };
-
diff --git a/packages/ui/src/lib/directoryShowHidden.ts b/packages/ui/src/lib/directoryShowHidden.ts
index 05539619..bca1492d 100644
--- a/packages/ui/src/lib/directoryShowHidden.ts
+++ b/packages/ui/src/lib/directoryShowHidden.ts
@@ -1,18 +1,22 @@
 import React from 'react';
 import { getSafeStorage } from '@/stores/utils/safeStorage';
+import { updateDesktopSettings } from '@/lib/persistence';
 
 const SHOW_HIDDEN_STORAGE_KEY = 'directoryTreeShowHidden';
 const SHOW_HIDDEN_EVENT = 'directory-show-hidden-change';
 
 const readStoredShowHidden = (): boolean => {
   if (typeof window === 'undefined') {
-    return false;
+    return true;
   }
   try {
     const stored = getSafeStorage().getItem(SHOW_HIDDEN_STORAGE_KEY);
+    if (stored === null) {
+      return true;
+    }
     return stored === 'true';
   } catch {
-    return false;
+    return true;
   }
 };
 
@@ -23,7 +27,10 @@ export const notifyDirectoryShowHiddenChanged = () => {
   window.dispatchEvent(new Event(SHOW_HIDDEN_EVENT));
 };
 
-export const setDirectoryShowHidden = (value: boolean) => {
+export const setDirectoryShowHidden = (
+  value: boolean,
+  options: { persist?: boolean } = {}
+) => {
   if (typeof window === 'undefined') {
     return;
   }
@@ -33,6 +40,10 @@ export const setDirectoryShowHidden = (value: boolean) => {
   } catch {
     // ignore storage errors
   }
+
+  if (options.persist !== false) {
+    void updateDesktopSettings({ directoryShowHidden: value });
+  }
 };
 
 export const useDirectoryShowHidden = (): boolean => {
diff --git a/packages/ui/src/lib/filesViewShowGitignored.ts b/packages/ui/src/lib/filesViewShowGitignored.ts
index 34557210..cceea748 100644
--- a/packages/ui/src/lib/filesViewShowGitignored.ts
+++ b/packages/ui/src/lib/filesViewShowGitignored.ts
@@ -1,6 +1,7 @@
 import React from 'react';
 
 import { getSafeStorage } from '@/stores/utils/safeStorage';
+import { updateDesktopSettings } from '@/lib/persistence';
 
 const SHOW_GITIGNORED_STORAGE_KEY = 'filesViewShowGitignored';
 const SHOW_GITIGNORED_EVENT = 'files-view-show-gitignored-change';
@@ -24,7 +25,10 @@ export const notifyFilesViewShowGitignoredChanged = () => {
   window.dispatchEvent(new Event(SHOW_GITIGNORED_EVENT));
 };
 
-export const setFilesViewShowGitignored = (value: boolean) => {
+export const setFilesViewShowGitignored = (
+  value: boolean,
+  options: { persist?: boolean } = {}
+) => {
   if (typeof window === 'undefined') {
     return;
   }
@@ -34,6 +38,10 @@ export const setFilesViewShowGitignored = (value: boolean) => {
   } catch {
     // ignore storage errors
   }
+
+  if (options.persist !== false) {
+    void updateDesktopSettings({ filesViewShowGitignored: value });
+  }
 };
 
 export const useFilesViewShowGitignored = (): boolean => {
diff --git a/packages/ui/src/lib/persistence.ts b/packages/ui/src/lib/persistence.ts
index 79e7aae0..71989d0f 100644
--- a/packages/ui/src/lib/persistence.ts
+++ b/packages/ui/src/lib/persistence.ts
@@ -2,6 +2,8 @@ import { getDesktopSettings, updateDesktopSettings as updateDesktopSettingsApi,
 import type { DesktopSettings } from '@/lib/desktop';
 import { useUIStore } from '@/stores/useUIStore';
 import { useMessageQueueStore } from '@/stores/messageQueueStore';
+import { setDirectoryShowHidden } from '@/lib/directoryShowHidden';
+import { setFilesViewShowGitignored } from '@/lib/filesViewShowGitignored';
 import { loadAppearancePreferences, applyAppearancePreferences } from '@/lib/appearancePersistence';
 import { getRegisteredRuntimeAPIs } from '@/contexts/runtimeAPIRegistry';
 
@@ -52,6 +54,12 @@ const persistToLocalStorage = (settings: DesktopSettings) => {
   } else {
     localStorage.removeItem('gitmojiEnabled');
   }
+  if (typeof settings.directoryShowHidden === 'boolean') {
+    localStorage.setItem('directoryTreeShowHidden', settings.directoryShowHidden ? 'true' : 'false');
+  }
+  if (typeof settings.filesViewShowGitignored === 'boolean') {
+    localStorage.setItem('filesViewShowGitignored', settings.filesViewShowGitignored ? 'true' : 'false');
+  }
 };
 
 type PersistApi = {
@@ -199,6 +207,54 @@ const applyDesktopUiPreferences = (settings: DesktopSettings) => {
   if (typeof settings.queueModeEnabled === 'boolean' && settings.queueModeEnabled !== queueStore.queueModeEnabled) {
     queueStore.setQueueMode(settings.queueModeEnabled);
   }
+
+  if (typeof settings.showTextJustificationActivity === 'boolean' && settings.showTextJustificationActivity !== store.showTextJustificationActivity) {
+    store.setShowTextJustificationActivity(settings.showTextJustificationActivity);
+  }
+  if (typeof settings.nativeNotificationsEnabled === 'boolean' && settings.nativeNotificationsEnabled !== store.nativeNotificationsEnabled) {
+    store.setNativeNotificationsEnabled(settings.nativeNotificationsEnabled);
+  }
+  if (typeof settings.notificationMode === 'string' && (settings.notificationMode === 'always' || settings.notificationMode === 'hidden-only')) {
+    if (settings.notificationMode !== store.notificationMode) {
+      store.setNotificationMode(settings.notificationMode);
+    }
+  }
+  if (typeof settings.toolCallExpansion === 'string'
+    && (settings.toolCallExpansion === 'collapsed' || settings.toolCallExpansion === 'activity' || settings.toolCallExpansion === 'detailed')) {
+    if (settings.toolCallExpansion !== store.toolCallExpansion) {
+      store.setToolCallExpansion(settings.toolCallExpansion);
+    }
+  }
+  if (typeof settings.fontSize === 'number' && Number.isFinite(settings.fontSize) && settings.fontSize !== store.fontSize) {
+    store.setFontSize(settings.fontSize);
+  }
+  if (typeof settings.padding === 'number' && Number.isFinite(settings.padding) && settings.padding !== store.padding) {
+    store.setPadding(settings.padding);
+  }
+  if (typeof settings.cornerRadius === 'number' && Number.isFinite(settings.cornerRadius) && settings.cornerRadius !== store.cornerRadius) {
+    store.setCornerRadius(settings.cornerRadius);
+  }
+  if (typeof settings.inputBarOffset === 'number' && Number.isFinite(settings.inputBarOffset) && settings.inputBarOffset !== store.inputBarOffset) {
+    store.setInputBarOffset(settings.inputBarOffset);
+  }
+  if (typeof settings.diffLayoutPreference === 'string'
+    && (settings.diffLayoutPreference === 'dynamic' || settings.diffLayoutPreference === 'inline' || settings.diffLayoutPreference === 'side-by-side')) {
+    if (settings.diffLayoutPreference !== store.diffLayoutPreference) {
+      store.setDiffLayoutPreference(settings.diffLayoutPreference);
+    }
+  }
+  if (typeof settings.diffViewMode === 'string'
+    && (settings.diffViewMode === 'single' || settings.diffViewMode === 'stacked')) {
+    if (settings.diffViewMode !== store.diffViewMode) {
+      store.setDiffViewMode(settings.diffViewMode);
+    }
+  }
+  if (typeof settings.directoryShowHidden === 'boolean') {
+    setDirectoryShowHidden(settings.directoryShowHidden, { persist: false });
+  }
+  if (typeof settings.filesViewShowGitignored === 'boolean') {
+    setFilesViewShowGitignored(settings.filesViewShowGitignored, { persist: false });
+  }
 };
 
 const sanitizeWebSettings = (payload: unknown): DesktopSettings | null => {
@@ -283,6 +339,55 @@ const sanitizeWebSettings = (payload: unknown): DesktopSettings | null => {
   if (typeof candidate.queueModeEnabled === 'boolean') {
     result.queueModeEnabled = candidate.queueModeEnabled;
   }
+  if (typeof candidate.showTextJustificationActivity === 'boolean') {
+    result.showTextJustificationActivity = candidate.showTextJustificationActivity;
+  }
+  if (typeof candidate.nativeNotificationsEnabled === 'boolean') {
+    result.nativeNotificationsEnabled = candidate.nativeNotificationsEnabled;
+  }
+  if (typeof candidate.notificationMode === 'string' && (candidate.notificationMode === 'always' || candidate.notificationMode === 'hidden-only')) {
+    result.notificationMode = candidate.notificationMode;
+  }
+  if (
+    typeof candidate.toolCallExpansion === 'string'
+    && (candidate.toolCallExpansion === 'collapsed'
+      || candidate.toolCallExpansion === 'activity'
+      || candidate.toolCallExpansion === 'detailed')
+  ) {
+    result.toolCallExpansion = candidate.toolCallExpansion;
+  }
+  if (typeof candidate.fontSize === 'number' && Number.isFinite(candidate.fontSize)) {
+    result.fontSize = candidate.fontSize;
+  }
+  if (typeof candidate.padding === 'number' && Number.isFinite(candidate.padding)) {
+    result.padding = candidate.padding;
+  }
+  if (typeof candidate.cornerRadius === 'number' && Number.isFinite(candidate.cornerRadius)) {
+    result.cornerRadius = candidate.cornerRadius;
+  }
+  if (typeof candidate.inputBarOffset === 'number' && Number.isFinite(candidate.inputBarOffset)) {
+    result.inputBarOffset = candidate.inputBarOffset;
+  }
+  if (
+    typeof candidate.diffLayoutPreference === 'string'
+    && (candidate.diffLayoutPreference === 'dynamic'
+      || candidate.diffLayoutPreference === 'inline'
+      || candidate.diffLayoutPreference === 'side-by-side')
+  ) {
+    result.diffLayoutPreference = candidate.diffLayoutPreference;
+  }
+  if (
+    typeof candidate.diffViewMode === 'string'
+    && (candidate.diffViewMode === 'single' || candidate.diffViewMode === 'stacked')
+  ) {
+    result.diffViewMode = candidate.diffViewMode;
+  }
+  if (typeof candidate.directoryShowHidden === 'boolean') {
+    result.directoryShowHidden = candidate.directoryShowHidden;
+  }
+  if (typeof candidate.filesViewShowGitignored === 'boolean') {
+    result.filesViewShowGitignored = candidate.filesViewShowGitignored;
+  }
 
   if (typeof candidate.memoryLimitHistorical === 'number' && Number.isFinite(candidate.memoryLimitHistorical)) {
     result.memoryLimitHistorical = candidate.memoryLimitHistorical;
diff --git a/packages/ui/src/stores/messageQueueStore.ts b/packages/ui/src/stores/messageQueueStore.ts
index 386500c1..7c22a80b 100644
--- a/packages/ui/src/stores/messageQueueStore.ts
+++ b/packages/ui/src/stores/messageQueueStore.ts
@@ -33,7 +33,7 @@ export const useMessageQueueStore = create<MessageQueueStore>()(
         persist(
             (set, get) => ({
                 queuedMessages: {},
-                queueModeEnabled: false,
+                queueModeEnabled: true,
 
                 addToQueue: (sessionId, message) => {
                     const id = `queued-${Date.now()}-${Math.random().toString(36).substring(2, 9)}`;
diff --git a/packages/ui/src/stores/useUIStore.ts b/packages/ui/src/stores/useUIStore.ts
index 1c43b89d..26da7228 100644
--- a/packages/ui/src/stores/useUIStore.ts
+++ b/packages/ui/src/stores/useUIStore.ts
@@ -145,7 +145,7 @@ export const useUIStore = create<UIStore>()(
         sidebarSection: 'sessions',
         eventStreamStatus: 'idle',
         eventStreamHint: null,
-        showReasoningTraces: false,
+        showReasoningTraces: true,
         showTextJustificationActivity: false,
         autoDeleteEnabled: false,
         autoDeleteAfterDays: 30,
@@ -160,10 +160,10 @@ export const useUIStore = create<UIStore>()(
         inputBarOffset: 0,
         favoriteModels: [],
         recentModels: [],
-        diffLayoutPreference: 'dynamic',
+        diffLayoutPreference: 'inline',
         diffFileLayout: {},
         diffWrapLines: false,
-        diffViewMode: 'single',
+        diffViewMode: 'stacked',
         isTimelineDialogOpen: false,
         nativeNotificationsEnabled: false,
         notificationMode: 'hidden-only',
diff --git a/packages/web/server/index.js b/packages/web/server/index.js
index a45eee30..9a4a8eac 100644
--- a/packages/web/server/index.js
+++ b/packages/web/server/index.js
@@ -736,6 +736,18 @@ const sanitizeSettingsUpdate = (payload) => {
   if (typeof candidate.showReasoningTraces === 'boolean') {
     result.showReasoningTraces = candidate.showReasoningTraces;
   }
+  if (typeof candidate.showTextJustificationActivity === 'boolean') {
+    result.showTextJustificationActivity = candidate.showTextJustificationActivity;
+  }
+  if (typeof candidate.nativeNotificationsEnabled === 'boolean') {
+    result.nativeNotificationsEnabled = candidate.nativeNotificationsEnabled;
+  }
+  if (typeof candidate.notificationMode === 'string') {
+    const mode = candidate.notificationMode.trim();
+    if (mode === 'always' || mode === 'hidden-only') {
+      result.notificationMode = mode;
+    }
+  }
   if (typeof candidate.autoDeleteEnabled === 'boolean') {
     result.autoDeleteEnabled = candidate.autoDeleteEnabled;
   }
@@ -774,6 +786,42 @@ const sanitizeSettingsUpdate = (payload) => {
   if (typeof candidate.gitmojiEnabled === 'boolean') {
     result.gitmojiEnabled = candidate.gitmojiEnabled;
   }
+  if (typeof candidate.toolCallExpansion === 'string') {
+    const mode = candidate.toolCallExpansion.trim();
+    if (mode === 'collapsed' || mode === 'activity' || mode === 'detailed') {
+      result.toolCallExpansion = mode;
+    }
+  }
+  if (typeof candidate.fontSize === 'number' && Number.isFinite(candidate.fontSize)) {
+    result.fontSize = Math.max(50, Math.min(200, Math.round(candidate.fontSize)));
+  }
+  if (typeof candidate.padding === 'number' && Number.isFinite(candidate.padding)) {
+    result.padding = Math.max(50, Math.min(200, Math.round(candidate.padding)));
+  }
+  if (typeof candidate.cornerRadius === 'number' && Number.isFinite(candidate.cornerRadius)) {
+    result.cornerRadius = Math.max(0, Math.min(32, Math.round(candidate.cornerRadius)));
+  }
+  if (typeof candidate.inputBarOffset === 'number' && Number.isFinite(candidate.inputBarOffset)) {
+    result.inputBarOffset = Math.max(0, Math.min(100, Math.round(candidate.inputBarOffset)));
+  }
+  if (typeof candidate.diffLayoutPreference === 'string') {
+    const mode = candidate.diffLayoutPreference.trim();
+    if (mode === 'dynamic' || mode === 'inline' || mode === 'side-by-side') {
+      result.diffLayoutPreference = mode;
+    }
+  }
+  if (typeof candidate.diffViewMode === 'string') {
+    const mode = candidate.diffViewMode.trim();
+    if (mode === 'single' || mode === 'stacked') {
+      result.diffViewMode = mode;
+    }
+  }
+  if (typeof candidate.directoryShowHidden === 'boolean') {
+    result.directoryShowHidden = candidate.directoryShowHidden;
+  }
+  if (typeof candidate.filesViewShowGitignored === 'boolean') {
+    result.filesViewShowGitignored = candidate.filesViewShowGitignored;
+  }
 
   // Memory limits for message viewport management
   if (typeof candidate.memoryLimitHistorical === 'number' && Number.isFinite(candidate.memoryLimitHistorical)) {