fix: restore React hook dep arrays and harden biome rules

Reverts unsafe biome lint --write --unsafe changes that modified React
hook dependency arrays, potentially introducing stale closures and
infinite re-render bugs. Promotes useExhaustiveDependencies,
noAssignInExpressions, and noInvalidUseBeforeDeclaration from off/warn
to error with targeted inline suppressions. Reverts _onUpdate rename
in pi-extension.

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

Author: backnotprop

apps/pi-extension/index.ts

@@ -286,7 +286,7 @@ export default function plannotator(pi: ExtensionAPI): void {
       ),
     }),
 
-    async execute(_toolCallId, _params, _signal, _update, ctx) {
+    async execute(_toolCallId, _params, _signal, _onUpdate, ctx) {
       // Guard: must be in planning phase
       if (phase !== 'planning') {
         return {

biome.jsonc

@@ -19,13 +19,13 @@
       "suspicious": {
         "noArrayIndexKey": "warn",
         "noExplicitAny": "warn",
-        "noAssignInExpressions": "off",
+        "noAssignInExpressions": "error",
         "useIterableCallbackReturn": "warn"
       },
       "correctness": {
-        "useExhaustiveDependencies": "warn",
+        "useExhaustiveDependencies": "error",
         "noUnusedFunctionParameters": "warn",
-        "noInvalidUseBeforeDeclaration": "off"
+        "noInvalidUseBeforeDeclaration": "error"
       },
       "security": {
         "noDangerouslySetInnerHtml": "warn"

packages/editor/App.tsx

@@ -420,20 +420,22 @@ const App: React.FC = () => {
   const sidebar = useSidebar(getUIPreferences().tocEnabled);
 
   // Sync sidebar open state when preference changes in Settings
+  // biome-ignore lint/correctness/useExhaustiveDependencies: sidebar methods are stable
   useEffect(() => {
     if (uiPrefs.tocEnabled) {
       sidebar.open('toc');
     } else {
       sidebar.close();
     }
-  }, [uiPrefs.tocEnabled, sidebar.close, sidebar.open]);
+  }, [uiPrefs.tocEnabled]);
 
   // Clear diff view when switching away from versions tab
+  // biome-ignore lint/correctness/useExhaustiveDependencies: isPlanDiffActive is read, not a trigger
   useEffect(() => {
     if (sidebar.activeTab === 'toc' && isPlanDiffActive) {
       setIsPlanDiffActive(false);
     }
-  }, [sidebar.activeTab, isPlanDiffActive]);
+  }, [sidebar.activeTab]);
 
   // Clear diff view on Escape key
   useEffect(() => {
@@ -467,19 +469,23 @@ const App: React.FC = () => {
   // Obsidian vault browser
   const vaultBrowser = useVaultBrowser();
 
-  const showVaultTab = useMemo(() => isVaultBrowserEnabled(), []);
+  // biome-ignore lint/correctness/useExhaustiveDependencies: recompute when user changes settings
+  const showVaultTab = useMemo(() => isVaultBrowserEnabled(), [uiPrefs]);
+  // biome-ignore lint/correctness/useExhaustiveDependencies: recompute when user changes settings
   const vaultPath = useMemo(() => {
     if (!showVaultTab) return '';
     const settings = getObsidianSettings();
     return getEffectiveVaultPath(settings);
-  }, [showVaultTab]);
+  }, [showVaultTab, uiPrefs]);
 
   // Clear active file when vault browser is disabled
+  // biome-ignore lint/correctness/useExhaustiveDependencies: vaultBrowser.setActiveFile is stable
   useEffect(() => {
     if (!showVaultTab) vaultBrowser.setActiveFile(null);
-  }, [showVaultTab, vaultBrowser.setActiveFile]);
+  }, [showVaultTab]);
 
   // Auto-fetch vault tree when vault tab is first opened
+  // biome-ignore lint/correctness/useExhaustiveDependencies: vaultBrowser methods/state are read inside, not triggers
   useEffect(() => {
     if (
       sidebar.activeTab === 'vault' &&
@@ -490,14 +496,7 @@ const App: React.FC = () => {
     ) {
       vaultBrowser.fetchTree(vaultPath);
     }
-  }, [
-    sidebar.activeTab,
-    showVaultTab,
-    vaultPath,
-    vaultBrowser.fetchTree,
-    vaultBrowser.isLoading,
-    vaultBrowser.tree.length,
-  ]);
+  }, [sidebar.activeTab, showVaultTab, vaultPath]);
 
   const buildVaultDocUrl = React.useCallback(
     (vp: string) => (path: string) =>
@@ -842,6 +841,7 @@ const App: React.FC = () => {
   };
 
   // Global keyboard shortcuts (Cmd/Ctrl+Enter to submit)
+  // biome-ignore lint/correctness/useExhaustiveDependencies: handler functions are stable enough — wrapping in useCallback would be a larger refactor
   useEffect(() => {
     const handleKeyDown = (e: KeyboardEvent) => {
       // Only handle Cmd/Ctrl+Enter
@@ -923,9 +923,6 @@ const App: React.FC = () => {
     annotateMode,
     origin,
     getAgentWarning,
-    handleAnnotateFeedback,
-    handleApprove,
-    handleDeny,
   ]);
 
   const handleAddAnnotation = (ann: Annotation) => {
@@ -1042,6 +1039,7 @@ const App: React.FC = () => {
   };
 
   // Cmd/Ctrl+S keyboard shortcut — save to default notes app
+  // biome-ignore lint/correctness/useExhaustiveDependencies: handler functions are stable enough
   useEffect(() => {
     const handleSaveShortcut = (e: KeyboardEvent) => {
       if (e.key !== 's' || !(e.metaKey || e.ctrlKey)) return;
@@ -1094,8 +1092,6 @@ const App: React.FC = () => {
     pendingPasteImage,
     submitted,
     isApiMode,
-    handleDownloadAnnotations,
-    handleQuickSaveToNotes,
   ]);
 
   // Close export dropdown on click outside

packages/review-editor/App.tsx

@@ -173,6 +173,7 @@ const ReviewApp: React.FC = () => {
   const isResizing = panelResize.isDragging || fileTreeResize.isDragging;
 
   // Global keyboard shortcuts
+  // biome-ignore lint/correctness/useExhaustiveDependencies: handleCopyDiff is stable enough
   useEffect(() => {
     const handleKeyDown = (e: KeyboardEvent) => {
       // Escape closes modals
@@ -190,8 +191,7 @@ const ReviewApp: React.FC = () => {
 
     window.addEventListener('keydown', handleKeyDown);
     return () => window.removeEventListener('keydown', handleKeyDown);
-    // eslint-disable-next-line react-hooks/exhaustive-deps
-  }, [showExportModal, handleCopyDiff]);
+  }, [showExportModal]);
 
   // Get annotations for active file
   const activeFileAnnotations = useMemo(() => {

packages/review-editor/utils/renderInlineMarkdown.tsx

@@ -41,6 +41,7 @@ function renderInline(text: string, startKey: number): React.ReactNode[] {
   let lastIndex = 0;
   let match: RegExpExecArray | null;
 
+  // biome-ignore lint/suspicious/noAssignInExpressions: standard regex exec loop pattern
   while ((match = regex.exec(text)) !== null) {
     // Text before match
     if (match.index > lastIndex) {

packages/ui/components/AnnotationToolbar.tsx

@@ -73,6 +73,7 @@ export const AnnotationToolbar: React.FC<AnnotationToolbarProps> = ({
   };
 
   // Focus input when entering input step (including on mount with initialStep='input')
+  // biome-ignore lint/correctness/useExhaustiveDependencies: element triggers refocus on new selection
   useEffect(() => {
     if (step === 'input') {
       // Use setTimeout to ensure DOM is fully ready (portals can have timing issues)
@@ -86,16 +87,17 @@ export const AnnotationToolbar: React.FC<AnnotationToolbarProps> = ({
       }, 0);
       return () => clearTimeout(timeoutId);
     }
-  }, [step]); // Also re-run when element changes (new selection)
+  }, [step, element]);
 
   // Reset state when element changes
+  // biome-ignore lint/correctness/useExhaustiveDependencies: element triggers reset on new selection
   useEffect(() => {
     setStep(initialStep);
     setActiveType(initialType ?? null);
     setInputValue('');
     setImages([]);
     setCopied(false);
-  }, [initialStep, initialType]);
+  }, [element, initialStep, initialType]);
 
   // Notify parent when locked (in input mode)
   useEffect(() => {

packages/ui/components/ImageAnnotator/index.tsx

@@ -37,6 +37,7 @@ export const ImageAnnotator: React.FC<ImageAnnotatorProps> = ({
   }, [isOpen, initialName]);
 
   // Keyboard shortcuts
+  // biome-ignore lint/correctness/useExhaustiveDependencies: handlers are stable useCallbacks with empty deps
   useEffect(() => {
     if (!isOpen) return;
 
@@ -74,7 +75,7 @@ export const ImageAnnotator: React.FC<ImageAnnotatorProps> = ({
 
     window.addEventListener('keydown', handleKeyDown);
     return () => window.removeEventListener('keydown', handleKeyDown);
-  }, [isOpen, handleAccept, handleUndo]);
+  }, [isOpen, state.strokes]);
 
   const handleStrokeStart = useCallback((point: Point) => {
     const id = crypto.randomUUID();

packages/ui/components/MermaidBlock.tsx

@@ -117,11 +117,12 @@ export const MermaidBlock: React.FC<{ block: Block }> = ({ block }) => {
   }, [block.content, block.id]);
 
   // Reset zoom and pan when content changes
+  // biome-ignore lint/correctness/useExhaustiveDependencies: block.content triggers zoom reset
   useEffect(() => {
     zoomLevelRef.current = 1.0;
     baseViewBoxRef.current = null;
     panOffsetRef.current = { x: 0, y: 0 };
-  }, []);
+  }, [block.content]);
 
   // Reset zoom and pan when switching from source back to diagram
   useEffect(() => {

packages/ui/components/Settings.tsx

@@ -96,6 +96,7 @@ export const Settings: React.FC<SettingsProps> = ({
     return t;
   }, [mode]);
 
+  // biome-ignore lint/correctness/useExhaustiveDependencies: re-read settings when availableAgents loads
   useEffect(() => {
     if (showDialog) {
       setIdentity(getIdentity());
@@ -113,7 +114,7 @@ export const Settings: React.FC<SettingsProps> = ({
         setAgentWarning(getAgentWarning());
       }
     }
-  }, [showDialog, origin, getAgentWarning]);
+  }, [showDialog, availableAgents, origin, getAgentWarning]);
 
   // Fetch detected vaults when Obsidian is enabled
   useEffect(() => {
@@ -125,6 +126,7 @@ export const Settings: React.FC<SettingsProps> = ({
           setDetectedVaults(data.vaults || []);
           // Auto-select first vault if none set
           if (data.vaults?.length > 0 && !obsidian.vaultPath) {
+            // biome-ignore lint/correctness/noInvalidUseBeforeDeclaration: handleObsidianChange defined after this effect but stable
             handleObsidianChange({ vaultPath: data.vaults[0] });
           }
         })
@@ -134,6 +136,8 @@ export const Settings: React.FC<SettingsProps> = ({
   }, [
     obsidian.enabled,
     detectedVaults.length,
+    // biome-ignore lint/correctness/useExhaustiveDependencies: handleObsidianChange is defined below but stable
+    // biome-ignore lint/correctness/noInvalidUseBeforeDeclaration: handleObsidianChange is defined below but stable
     handleObsidianChange,
     obsidian.vaultPath,
     vaultsLoading,

packages/ui/components/Viewer.tsx

@@ -279,6 +279,7 @@ export const Viewer = forwardRef<ViewerHandle, ViewerProps>(
       const walker = document.createTreeWalker(containerRef.current, NodeFilter.SHOW_TEXT, null);
 
       let node: Text | null;
+      // biome-ignore lint/suspicious/noAssignInExpressions: standard TreeWalker loop pattern
       while ((node = walker.nextNode() as Text | null)) {
         const text = node.textContent || '';
         const index = text.indexOf(searchText);
@@ -308,6 +309,7 @@ export const Viewer = forwardRef<ViewerHandle, ViewerProps>(
       let endNode: Text | null = null;
       let endOffset = 0;
 
+      // biome-ignore lint/suspicious/noAssignInExpressions: standard TreeWalker loop pattern
       while ((node = walker2.nextNode() as Text | null)) {
         const nodeLength = node.textContent?.length || 0;
 
@@ -335,6 +337,7 @@ export const Viewer = forwardRef<ViewerHandle, ViewerProps>(
       return null;
     }, []);
 
+    // biome-ignore lint/correctness/useExhaustiveDependencies: blocks.find changes every render, blocks is stable enough
     useImperativeHandle(
       ref,
       () => ({
@@ -435,6 +438,7 @@ export const Viewer = forwardRef<ViewerHandle, ViewerProps>(
               let node: Text | null;
               let inRange = false;
 
+              // biome-ignore lint/suspicious/noAssignInExpressions: standard TreeWalker loop pattern
               while ((node = walker.nextNode() as Text | null)) {
                 // Check if this node is the start container
                 if (node === range.startContainer) {
@@ -505,7 +509,7 @@ export const Viewer = forwardRef<ViewerHandle, ViewerProps>(
           });
         },
       }),
-      [findTextInDOM, onSelectAnnotation, blocks.find],
+      [findTextInDOM, onSelectAnnotation],
     );
 
     useEffect(() => {
@@ -565,6 +569,7 @@ export const Viewer = forwardRef<ViewerHandle, ViewerProps>(
       return () => highlighter.dispose();
     }, [
       onSelectAnnotation, // Auto-delete in redline mode
+      // biome-ignore lint/correctness/useExhaustiveDependencies: createAnnotationFromSource is stable (only depends on refs and props)
       createAnnotationFromSource,
     ]);
 
@@ -1322,14 +1327,15 @@ const CodeBlock: React.FC<CodeBlockProps> = ({ block, onHover, onLeave, isHovere
   const codeRef = useRef<HTMLElement>(null);
 
   // Highlight code block on mount and when content/language changes
+  // biome-ignore lint/correctness/useExhaustiveDependencies: block.content triggers re-highlight when code changes
   useEffect(() => {
     if (codeRef.current) {
       // Reset any previous highlighting
       codeRef.current.removeAttribute('data-highlighted');
       codeRef.current.className = `hljs font-mono${block.language ? ` language-${block.language}` : ''}`;
       hljs.highlightElement(codeRef.current);
     }
-  }, [block.language]);
+  }, [block.content, block.language]);
 
   const handleCopy = useCallback(async () => {
     try {