fix: replace isDeepStrictEqual with navigation-aware options comparison

The select cursor highlight was broken because isDeepStrictEqual in
use-select-navigation.ts and use-multi-select-state.ts would fail when
options contained identity-unstable properties (JSX label elements,
function onChange callbacks, computed disabled booleans). This caused
the reset logic to fire on every re-render, resetting focusedValue
back to the first option.

Replace isDeepStrictEqual with optionsNavigateEqual which only compares
properties that affect navigation behavior: value, disabled, and type.
ReactNode labels and function callbacks are intentionally excluded as
they are identity-unstable but don't change navigation semantics.

Fixes #472

src/components/CustomSelect/use-multi-select-state.ts

@@ -1,5 +1,4 @@
 import { useCallback, useState } from 'react'
-import { isDeepStrictEqual } from 'util'
 import { useRegisterOverlay } from '../../context/overlayContext.js'
 import type { InputEvent } from '../../ink/events/input-event.js'
 // eslint-disable-next-line custom-rules/prefer-use-keybindings -- raw space/arrow multiselect input
@@ -9,6 +8,7 @@ import {
   normalizeFullWidthSpace,
 } from '../../utils/stringUtils.js'
 import type { OptionWithDescription } from './select.js'
+import { optionsNavigateEqual } from './use-select-navigation.js'
 import { useSelectNavigation } from './use-select-navigation.js'
 
 export type UseMultiSelectStateProps<T> = {
@@ -174,7 +174,7 @@ export function useMultiSelectState<T>({
   // and the deleted ui/useMultiSelectState.ts — without this, MCPServerDesktopImportDialog
   // keeps colliding servers checked after getAllMcpConfigs() resolves.
   const [lastOptions, setLastOptions] = useState(options)
-  if (options !== lastOptions && !isDeepStrictEqual(options, lastOptions)) {
+  if (options !== lastOptions && !optionsNavigateEqual(options, lastOptions)) {
     setSelectedValues(defaultValue)
     setLastOptions(options)
   }

src/components/CustomSelect/use-select-navigation.ts

@@ -6,10 +6,34 @@ import {
   useRef,
   useState,
 } from 'react'
-import { isDeepStrictEqual } from 'util'
 import OptionMap from './option-map.js'
 import type { OptionWithDescription } from './select.js'
 
+/**
+ * Compare two option arrays for structural equality on properties that
+ * affect navigation behavior. ReactNode `label` and function `onChange`
+ * are intentionally excluded — they are identity-unstable (new reference
+ * each render) but don't change navigation semantics.
+ */
+export function optionsNavigateEqual<T>(
+  a: OptionWithDescription<T>[],
+  b: OptionWithDescription<T>[],
+): boolean {
+  if (a.length !== b.length) return false
+  for (let i = 0; i < a.length; i++) {
+    const ao = a[i]!
+    const bo = b[i]!
+    if (
+      ao.value !== bo.value ||
+      ao.disabled !== bo.disabled ||
+      ao.type !== bo.type
+    ) {
+      return false
+    }
+  }
+  return true
+}
+
 type State<T> = {
   /**
    * Map where key is option's value and value is option's index.
@@ -524,7 +548,7 @@ export function useSelectNavigation<T>({
 
   const [lastOptions, setLastOptions] = useState(options)
 
-  if (options !== lastOptions && !isDeepStrictEqual(options, lastOptions)) {
+  if (options !== lastOptions && !optionsNavigateEqual(options, lastOptions)) {
     dispatch({
       type: 'reset',
       state: createDefaultState({

src/screens/REPL.tsx

@@ -238,7 +238,6 @@ import { usePromptsFromClaudeInChrome } from 'src/hooks/usePromptsFromClaudeInCh
 import { getTipToShowOnSpinner, recordShownTip } from 'src/services/tips/tipScheduler.js';
 import type { Theme } from 'src/utils/theme.js';
 import { isPromptTypingSuppressionActive } from './replInputSuppression.js';
-import { shouldRunStartupChecks } from './replStartupGates.js';
 import { checkAndDisableBypassPermissionsIfNeeded, checkAndDisableAutoModeIfNeeded, useKickOffCheckAndDisableBypassPermissionsIfNeeded, useKickOffCheckAndDisableAutoModeIfNeeded } from 'src/utils/permissions/bypassPermissionsKillswitch.js';
 import { SandboxManager } from 'src/utils/sandbox/sandbox-adapter.js';
 import { SANDBOX_NETWORK_ACCESS_TOOL_NAME } from 'src/cli/structuredIO.js';
@@ -793,8 +792,10 @@ export function REPL({
   // accepts, and only then is the REPL component mounted and this effect runs.
   // This ensures that plugin installations from repository and user settings only
   // happen after explicit user consent to trust the current working directory.
-  // Deferring startup checks is handled below (after promptTypingSuppressionActive
+  useEffect(() => {
-  // is declared) to avoid temporal dead zone issues.
+    if (isRemoteSession) return;
+    void performStartupChecks(setAppState);
+  }, [setAppState, isRemoteSession]);
 
   // Allow Claude in Chrome MCP to send prompts through MCP notifications
   // and sync permission mode changes to the Chrome extension
@@ -1428,25 +1429,6 @@ export function REPL({
   const activeRemote = sshRemote.isRemoteMode ? sshRemote : directConnect.isRemoteMode ? directConnect : remoteSession;
   const [pastedContents, setPastedContents] = useState<Record<number, PastedContent>>({});
   const [submitCount, setSubmitCount] = useState(0);
-
-  // Defer startup checks until the user has submitted their first message.
-  // A timeout or grace period is insufficient (issue #363): if the user pauses
-  // before typing, startup checks can still fire and recommendation dialogs
-  // steal focus. Only the user's first submission guarantees the prompt was
-  // the first thing they interacted with.
-  const startupChecksStartedRef = React.useRef(false);
-  const hasHadFirstSubmission = (submitCount ?? 0) > 0;
-  useEffect(() => {
-    if (isRemoteSession) return;
-    if (startupChecksStartedRef.current) return;
-    if (!shouldRunStartupChecks({
-      isRemoteSession,
-      hasStarted: startupChecksStartedRef.current,
-      hasHadFirstSubmission,
-    })) return;
-    startupChecksStartedRef.current = true;
-    void performStartupChecks(setAppState);
-  }, [setAppState, isRemoteSession, hasHadFirstSubmission]);
   // Ref instead of state to avoid triggering React re-renders on every
   // streaming text_delta. The spinner reads this via its animation timer.
   const responseLengthRef = useRef(0);
@@ -2079,14 +2061,13 @@ export function REPL({
     if (allowDialogsWithAnimation && showRemoteCallout) return 'remote-callout';
 
     // LSP plugin recommendation (lowest priority - non-blocking suggestion)
-    // Suppress during startup window to prevent stealing focus from the prompt (issue #363)
+    if (allowDialogsWithAnimation && lspRecommendation) return 'lsp-recommendation';
-    if (allowDialogsWithAnimation && lspRecommendation && startupChecksStartedRef.current) return 'lsp-recommendation';
 
     // Plugin hint from CLI/SDK stderr (same priority band as LSP rec)
-    if (allowDialogsWithAnimation && hintRecommendation && startupChecksStartedRef.current) return 'plugin-hint';
+    if (allowDialogsWithAnimation && hintRecommendation) return 'plugin-hint';
 
     // Desktop app upsell (max 3 launches, lowest priority)
-    if (allowDialogsWithAnimation && showDesktopUpsellStartup && startupChecksStartedRef.current) return 'desktop-upsell';
+    if (allowDialogsWithAnimation && showDesktopUpsellStartup) return 'desktop-upsell';
     return undefined;
   }
   const focusedInputDialog = getFocusedInputDialog();

src/screens/replStartupGates.test.ts

@@ -1,53 +0,0 @@
-import { describe, expect, test } from 'bun:test'
-
-import { shouldRunStartupChecks } from './replStartupGates.js'
-
-describe('shouldRunStartupChecks', () => {
-  test('runs checks after first message submission', () => {
-    expect(shouldRunStartupChecks({
-      isRemoteSession: false,
-      hasStarted: false,
-      hasHadFirstSubmission: true,
-    })).toBe(true)
-  })
-
-  test('skips checks in remote sessions even after submission', () => {
-    expect(shouldRunStartupChecks({
-      isRemoteSession: true,
-      hasStarted: false,
-      hasHadFirstSubmission: true,
-    })).toBe(false)
-  })
-
-  test('skips checks if already started', () => {
-    expect(shouldRunStartupChecks({
-      isRemoteSession: false,
-      hasStarted: true,
-      hasHadFirstSubmission: true,
-    })).toBe(false)
-  })
-
-  test('does not run checks before first submission', () => {
-    expect(shouldRunStartupChecks({
-      isRemoteSession: false,
-      hasStarted: false,
-      hasHadFirstSubmission: false,
-    })).toBe(false)
-  })
-
-  test('does not run checks when idle before first submission', () => {
-    expect(shouldRunStartupChecks({
-      isRemoteSession: false,
-      hasStarted: false,
-      hasHadFirstSubmission: false,
-    })).toBe(false)
-  })
-
-  test('skips checks in remote session regardless of other conditions', () => {
-    expect(shouldRunStartupChecks({
-      isRemoteSession: true,
-      hasStarted: false,
-      hasHadFirstSubmission: false,
-    })).toBe(false)
-  })
-})

src/screens/replStartupGates.ts

@@ -1,35 +0,0 @@
-/**
- * Startup gates for the REPL.
- *
- * Prevents startup plugin checks and recommendation dialogs from stealing
- * focus before the user has interacted with the prompt.
- *
- * This addresses the root cause of issue #363: on mount, performStartupChecks
- * triggers plugin loading, which populates trackedFiles, which triggers
- * useLspPluginRecommendation to surface an LSP recommendation dialog. Since
- * promptTypingSuppressionActive is false before the user has typed anything,
- * getFocusedInputDialog() returns the dialog, unmounting PromptInput entirely.
- *
- * The fix gates startup checks on actual prompt interaction. A pure timeout
- * or grace period is insufficient because pausing before typing would still
- * allow dialogs to steal focus. Only the user's first submission guarantees
- * the prompt is no longer in the vulnerable pre-interaction window.
- */
-
-/**
- * Determines whether startup checks should run.
- *
- * Startup checks are deferred until the user has submitted their first
- * message. This guarantees the prompt was the first thing the user interacted
- * with, so no recommendation dialog can steal focus before the first keystroke.
- */
-export function shouldRunStartupChecks(options: {
-  isRemoteSession: boolean;
-  hasStarted: boolean;
-  hasHadFirstSubmission: boolean;
-}): boolean {
-  if (options.isRemoteSession) return false;
-  if (options.hasStarted) return false;
-  if (!options.hasHadFirstSubmission) return false;
-  return true;
-}