diff --git a/src/renderer/src/components/settings/Settings.tsx b/src/renderer/src/components/settings/Settings.tsx
index eeffdeedea7..9678967f2c6 100644
--- a/src/renderer/src/components/settings/Settings.tsx
+++ b/src/renderer/src/components/settings/Settings.tsx
@@ -213,6 +213,18 @@ function Settings(): React.JSX.Element {
   const repoHooksRuntimeIdentityRef = useRef<string>('local')
   const shortcutsEscapeConfirmUntilRef = useRef(0)
 
+  const setSettingsRootNode = useCallback(
+    (node: HTMLDivElement | null): void => {
+      if (node) {
+        return
+      }
+      // Why: the settings search is a transient in-page filter. Leaving it behind makes the next
+      // visit look partially broken because whole sections stay hidden before the user types again.
+      setSettingsSearchQuery('')
+    },
+    [setSettingsSearchQuery]
+  )
+
   const confirmDiscardCommitPromptChanges = useCallback(async (): Promise<boolean> => {
     if (!hasUnsavedCommitPromptChanges) {
       return true
@@ -339,15 +351,6 @@ function Settings(): React.JSX.Element {
     return () => document.removeEventListener('keydown', handleFindShortcut)
   }, [keybindings])
 
-  useEffect(
-    () => () => {
-      // Why: the settings search is a transient in-page filter. Leaving it behind makes the next
-      // visit look partially broken because whole sections stay hidden before the user types again.
-      setSettingsSearchQuery('')
-    },
-    [setSettingsSearchQuery]
-  )
-
   useEffect(() => {
     if (!settings || !settingsNavigationTarget) {
       return
@@ -694,8 +697,13 @@ function Settings(): React.JSX.Element {
 
   if (!settings) {
     return (
-      <div className="flex flex-1 items-center justify-center text-muted-foreground">
-        Loading settings...
+      <div
+        ref={setSettingsRootNode}
+        className="settings-view-shell flex min-h-0 flex-1 overflow-hidden bg-background"
+      >
+        <div className="flex flex-1 items-center justify-center text-muted-foreground">
+          Loading settings...
+        </div>
       </div>
     )
   }
@@ -721,7 +729,10 @@ function Settings(): React.JSX.Element {
     activeSectionId === 'shortcuts' && settingsSearchQuery.trim() === ''
 
   return (
-    <div className="settings-view-shell flex min-h-0 flex-1 overflow-hidden bg-background">
+    <div
+      ref={setSettingsRootNode}
+      className="settings-view-shell flex min-h-0 flex-1 overflow-hidden bg-background"
+    >
       <SettingsSidebar
         activeSectionId={activeSectionId}
         generalGroups={generalNavGroups}
diff --git a/src/renderer/src/components/sidebar/AddRepoDialog.tsx b/src/renderer/src/components/sidebar/AddRepoDialog.tsx
index 8c423cc448c..f6178b5cc16 100644
--- a/src/renderer/src/components/sidebar/AddRepoDialog.tsx
+++ b/src/renderer/src/components/sidebar/AddRepoDialog.tsx
@@ -118,6 +118,9 @@ const AddRepoDialog = React.memo(function AddRepoDialog() {
   // Why: nested group import can create many repos; resetState must prevent
   // stale import completions from reopening setup UI after Back/close.
   const nestedImportGenRef = useRef(0)
+  // Why: setup actions can await settings/worktree refreshes; resetState
+  // cancels stale continuations when the setup step is dismissed.
+  const setupActionGenRef = useRef(0)
   // Why: a dropped path is modal data, so ordinary state updates must not
   // re-run the import while the Add Project dialog advances through steps.
   const droppedLocalPathHandledRef = useRef<string | null>(null)
@@ -252,6 +255,7 @@ const AddRepoDialog = React.memo(function AddRepoDialog() {
     localAddGenRef.current++
     serverAddGenRef.current++
     nestedImportGenRef.current++
+    setupActionGenRef.current++
     // Why: kill the git clone process if one is running, so backing out
     // or closing the dialog doesn't leave a clone running on disk.
     void window.api.repos.cloneAbort()
@@ -736,13 +740,20 @@ const AddRepoDialog = React.memo(function AddRepoDialog() {
     if (!projectId) {
       return
     }
+    const gen = ++setupActionGenRef.current
     trackSetupAction('open_existing')
     if (!otherWorktreesVisible) {
       const updated = await updateRepo(projectId, { externalWorktreeVisibility: 'show' })
+      if (gen !== setupActionGenRef.current) {
+        return
+      }
       if (updated && addedRepo) {
         setAddedRepo({ ...addedRepo, externalWorktreeVisibility: 'show' })
       }
       await fetchWorktrees(projectId)
+      if (gen !== setupActionGenRef.current) {
+        return
+      }
     }
     await finishImportedRepoWithoutOpening()
   }, [
diff --git a/src/renderer/src/components/sidebar/CommentMarkdown.test.tsx b/src/renderer/src/components/sidebar/CommentMarkdown.test.tsx
index 0c632615285..e39f528552a 100644
--- a/src/renderer/src/components/sidebar/CommentMarkdown.test.tsx
+++ b/src/renderer/src/components/sidebar/CommentMarkdown.test.tsx
@@ -1,6 +1,6 @@
 import { renderToStaticMarkup } from 'react-dom/server'
 import { describe, expect, it } from 'vitest'
-import CommentMarkdown from './CommentMarkdown'
+import CommentMarkdown, { remarkGitHubReferences } from './CommentMarkdown'
 
 describe('CommentMarkdown', () => {
   it('autolinks same-repo GitHub issue references when repo context is provided', () => {
@@ -42,6 +42,33 @@ describe('CommentMarkdown', () => {
     expect(markup).not.toContain('href="https://github.com/stablyai/orca/issues/2317"')
   })
 
+  it('autolinks very large generated GitHub reference comments', () => {
+    const referenceCount = 130_000
+    const tree = {
+      type: 'root',
+      children: [
+        {
+          type: 'paragraph',
+          children: [
+            {
+              type: 'text',
+              value: Array.from({ length: referenceCount }, (_, index) => `#${index + 1}`).join(' ')
+            }
+          ]
+        }
+      ]
+    }
+
+    const transform = remarkGitHubReferences({ owner: 'stablyai', repo: 'orca' })()
+
+    expect(() => transform(tree)).not.toThrow()
+    expect(tree.children[0]?.children).toHaveLength(referenceCount * 2 - 1)
+    expect(tree.children[0]?.children[0]).toMatchObject({
+      type: 'link',
+      url: 'https://github.com/stablyai/orca/issues/1'
+    })
+  })
+
   it('contains long PR body markdown inside its available width', () => {
     const markup = renderToStaticMarkup(
       <CommentMarkdown
diff --git a/src/renderer/src/components/sidebar/CommentMarkdown.tsx b/src/renderer/src/components/sidebar/CommentMarkdown.tsx
index 132f435aee2..5655889462d 100644
--- a/src/renderer/src/components/sidebar/CommentMarkdown.tsx
+++ b/src/renderer/src/components/sidebar/CommentMarkdown.tsx
@@ -265,7 +265,11 @@ function transformGitHubReferenceChildren(
   const nextChildren: MarkdownNode[] = []
   for (const child of node.children) {
     if (child.type === 'text' && child.value !== undefined) {
-      nextChildren.push(...splitGitHubReferenceText(child.value, defaultRepo))
+      // Why: generated agent comments can contain thousands of issue refs;
+      // appending iteratively avoids V8's argument-list limit.
+      for (const part of splitGitHubReferenceText(child.value, defaultRepo)) {
+        nextChildren.push(part)
+      }
     } else {
       transformGitHubReferenceChildren(child, defaultRepo)
       nextChildren.push(child)