Fix concurrency limits and remote branch fetching issues (#788)

* Changes from fix/bug-fixes

* feat: Refactor worktree iteration and improve error logging across services

* feat: Extract URL/port patterns to module level and fix abort condition

* fix: Improve IPv6 loopback handling, select component layout, and terminal UI

* feat: Add thinking level defaults and adjust list row padding

* Update apps/ui/src/store/app-store.ts

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

* feat: Add worktree-aware terminal creation and split options, fix npm security issues from audit

* feat: Add tracked remote detection to pull dialog flow

* feat: Add merge state tracking to git operations

* feat: Improve merge detection and add post-merge action preferences

* Update apps/ui/src/components/views/board-view/dialogs/git-pull-dialog.tsx

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

* Update apps/ui/src/components/views/board-view/dialogs/git-pull-dialog.tsx

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

* fix: Pass merge detection info to stash reapplication and handle merge state consistently

* fix: Call onPulled callback in merge handlers and add validation checks

---------

Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>

apps/ui/src/components/views/board-view/dialogs/git-pull-dialog.tsx

@@ -1,4 +1,4 @@
-import { useState, useEffect, useCallback } from 'react';
+import { useState, useEffect, useCallback, useRef } from 'react';
 import {
   Dialog,
   DialogContent,
@@ -17,11 +17,17 @@ import {
   FileWarning,
   Wrench,
   Sparkles,
+  GitMerge,
+  GitCommitHorizontal,
+  FileText,
+  Settings,
 } from 'lucide-react';
 import { Spinner } from '@/components/ui/spinner';
+import { Checkbox } from '@/components/ui/checkbox';
 import { getElectronAPI } from '@/lib/electron';
 import { toast } from 'sonner';
 import { cn } from '@/lib/utils';
+import { useAppStore } from '@/store/app-store';
 import type { MergeConflictInfo } from '../worktree-panel/types';
 
 interface WorktreeInfo {
@@ -37,6 +43,7 @@ type PullPhase =
   | 'local-changes' // Local changes detected, asking user what to do
   | 'pulling' // Actively pulling (with or without stash)
   | 'success' // Pull completed successfully
+  | 'merge-complete' // Pull resulted in a merge (not fast-forward, no conflicts)
   | 'conflict' // Merge conflicts detected
   | 'error'; // Something went wrong
 
@@ -53,6 +60,9 @@ interface PullResult {
   stashed?: boolean;
   stashRestored?: boolean;
   stashRecoveryFailed?: boolean;
+  isMerge?: boolean;
+  isFastForward?: boolean;
+  mergeAffectedFiles?: string[];
 }
 
 interface GitPullDialogProps {
@@ -62,6 +72,8 @@ interface GitPullDialogProps {
   remote?: string;
   onPulled?: () => void;
   onCreateConflictResolutionFeature?: (conflictInfo: MergeConflictInfo) => void;
+  /** Called when user chooses to commit the merge — opens the commit dialog */
+  onCommitMerge?: (worktree: { path: string; branch: string; isMain: boolean }) => void;
 }
 
 export function GitPullDialog({
@@ -71,10 +83,54 @@ export function GitPullDialog({
   remote,
   onPulled,
   onCreateConflictResolutionFeature,
+  onCommitMerge,
 }: GitPullDialogProps) {
   const [phase, setPhase] = useState<PullPhase>('checking');
   const [pullResult, setPullResult] = useState<PullResult | null>(null);
   const [errorMessage, setErrorMessage] = useState<string | null>(null);
+  const [rememberChoice, setRememberChoice] = useState(false);
+  const [showMergeFiles, setShowMergeFiles] = useState(false);
+
+  const mergePostAction = useAppStore((s) => s.mergePostAction);
+  const setMergePostAction = useAppStore((s) => s.setMergePostAction);
+
+  /**
+   * Determine the appropriate phase after a successful pull.
+   * If the pull resulted in a merge (not fast-forward) and no conflicts,
+   * check user preference before deciding whether to show merge prompt.
+   */
+  const handleSuccessfulPull = useCallback(
+    (result: PullResult) => {
+      setPullResult(result);
+
+      if (result.isMerge && !result.hasConflicts) {
+        // Merge happened — check user preference
+        if (mergePostAction === 'commit') {
+          // User preference: auto-commit
+          setPhase('success');
+          onPulled?.();
+          // Auto-trigger commit dialog
+          if (worktree && onCommitMerge) {
+            onCommitMerge(worktree);
+            onOpenChange(false);
+          }
+        } else if (mergePostAction === 'manual') {
+          // User preference: manual review
+          setPhase('success');
+          onPulled?.();
+        } else {
+          // No preference — show merge prompt; onPulled will be called from the
+          // user-action handlers (handleCommitMerge / handleMergeManually) once
+          // the user makes their choice, consistent with the conflict phase.
+          setPhase('merge-complete');
+        }
+      } else {
+        setPhase('success');
+        onPulled?.();
+      }
+    },
+    [mergePostAction, worktree, onCommitMerge, onPulled, onOpenChange]
+  );
 
   const checkForLocalChanges = useCallback(async () => {
     if (!worktree) return;
@@ -103,9 +159,7 @@ export function GitPullDialog({
         setPhase('local-changes');
       } else if (result.result?.pulled !== undefined) {
         // No local changes, pull went through (or already up to date)
-        setPullResult(result.result);
-        setPhase('success');
-        onPulled?.();
+        handleSuccessfulPull(result.result);
       } else {
         // Unexpected response: success but no recognizable fields
         setPullResult(result.result ?? null);
@@ -116,18 +170,33 @@ export function GitPullDialog({
       setErrorMessage(err instanceof Error ? err.message : 'Failed to check for changes');
       setPhase('error');
     }
-  }, [worktree, remote, onPulled]);
+  }, [worktree, remote, handleSuccessfulPull]);
 
-  // Reset state when dialog opens
+  // Keep a ref to the latest checkForLocalChanges to break the circular dependency
+  // between the "reset/start" effect and the callback chain. Without this, any
+  // change in onPulled (passed from the parent) would recreate handleSuccessfulPull
+  // → checkForLocalChanges → re-trigger the effect while the dialog is already open,
+  // causing the pull flow to restart unintentionally.
+  const checkForLocalChangesRef = useRef(checkForLocalChanges);
+  useEffect(() => {
+    checkForLocalChangesRef.current = checkForLocalChanges;
+  });
+
+  // Reset state when dialog opens and start the initial pull check.
+  // Depends only on `open` and `worktree` — NOT on `checkForLocalChanges` —
+  // so that parent callback re-creations don't restart the pull flow mid-flight.
   useEffect(() => {
     if (open && worktree) {
       setPhase('checking');
       setPullResult(null);
       setErrorMessage(null);
-      // Start the initial check
-      checkForLocalChanges();
+      setRememberChoice(false);
+      setShowMergeFiles(false);
+      // Start the initial check using the ref so we always call the latest version
+      // without making it a dependency of this effect.
+      checkForLocalChangesRef.current();
     }
-  }, [open, worktree, checkForLocalChanges]);
+  }, [open, worktree]);
 
   const handlePullWithStash = useCallback(async () => {
     if (!worktree) return;
@@ -155,8 +224,7 @@ export function GitPullDialog({
       if (result.result?.hasConflicts) {
         setPhase('conflict');
       } else if (result.result?.pulled) {
-        setPhase('success');
-        onPulled?.();
+        handleSuccessfulPull(result.result);
       } else {
         // Unrecognized response: no pulled flag and no conflicts
         console.warn('handlePullWithStash: unrecognized response', result.result);
@@ -167,7 +235,7 @@ export function GitPullDialog({
       setErrorMessage(err instanceof Error ? err.message : 'Failed to pull');
       setPhase('error');
     }
-  }, [worktree, remote, onPulled]);
+  }, [worktree, remote, handleSuccessfulPull]);
 
   const handleResolveWithAI = useCallback(() => {
     if (!worktree || !pullResult || !onCreateConflictResolutionFeature) return;
@@ -186,6 +254,35 @@ export function GitPullDialog({
     onOpenChange(false);
   }, [worktree, pullResult, remote, onCreateConflictResolutionFeature, onOpenChange]);
 
+  const handleCommitMerge = useCallback(() => {
+    if (!worktree || !onCommitMerge) {
+      // No handler available — show feedback and bail without persisting preference
+      toast.error('Commit merge is not available', {
+        description: 'The commit merge action is not configured for this context.',
+        duration: 4000,
+      });
+      return;
+    }
+    if (rememberChoice) {
+      setMergePostAction('commit');
+    }
+    onPulled?.();
+    onCommitMerge(worktree);
+    onOpenChange(false);
+  }, [rememberChoice, setMergePostAction, worktree, onCommitMerge, onPulled, onOpenChange]);
+
+  const handleMergeManually = useCallback(() => {
+    if (rememberChoice) {
+      setMergePostAction('manual');
+    }
+    toast.info('Merge left for manual review', {
+      description: 'Review the merged files and commit when ready.',
+      duration: 5000,
+    });
+    onPulled?.();
+    onOpenChange(false);
+  }, [rememberChoice, setMergePostAction, onPulled, onOpenChange]);
+
   const handleClose = useCallback(() => {
     onOpenChange(false);
   }, [onOpenChange]);
@@ -336,6 +433,137 @@ export function GitPullDialog({
           </>
         )}
 
+        {/* Merge Complete Phase — post-merge prompt */}
+        {phase === 'merge-complete' && (
+          <>
+            <DialogHeader>
+              <DialogTitle className="flex items-center gap-2">
+                <GitMerge className="w-5 h-5 text-purple-500" />
+                Merge Complete
+              </DialogTitle>
+              <DialogDescription asChild>
+                <div className="space-y-3">
+                  <span className="block">
+                    Pull resulted in a merge on{' '}
+                    <code className="font-mono bg-muted px-1 rounded">{worktree.branch}</code>
+                    {pullResult?.mergeAffectedFiles && pullResult.mergeAffectedFiles.length > 0 && (
+                      <span>
+                        {' '}
+                        affecting {pullResult.mergeAffectedFiles.length} file
+                        {pullResult.mergeAffectedFiles.length !== 1 ? 's' : ''}
+                      </span>
+                    )}
+                    . How would you like to proceed?
+                  </span>
+
+                  {pullResult?.mergeAffectedFiles && pullResult.mergeAffectedFiles.length > 0 && (
+                    <div>
+                      <button
+                        onClick={() => setShowMergeFiles(!showMergeFiles)}
+                        className="text-xs text-muted-foreground hover:text-foreground transition-colors inline-flex items-center gap-1"
+                      >
+                        <FileText className="w-3 h-3" />
+                        {showMergeFiles ? 'Hide' : 'Show'} affected files (
+                        {pullResult.mergeAffectedFiles.length})
+                      </button>
+                      {showMergeFiles && (
+                        <div className="mt-1.5 border border-border rounded-lg overflow-hidden max-h-[150px] overflow-y-auto scrollbar-visible">
+                          {pullResult.mergeAffectedFiles.map((file) => (
+                            <div
+                              key={file}
+                              className="flex items-center gap-2 px-3 py-1.5 text-xs font-mono border-b border-border last:border-b-0 hover:bg-accent/30"
+                            >
+                              <GitMerge className="w-3 h-3 text-purple-500 flex-shrink-0" />
+                              <span className="truncate">{file}</span>
+                            </div>
+                          ))}
+                        </div>
+                      )}
+                    </div>
+                  )}
+
+                  {pullResult?.stashed &&
+                    pullResult?.stashRestored &&
+                    !pullResult?.stashRecoveryFailed && (
+                      <div className="flex items-start gap-2 p-3 rounded-md bg-green-500/10 border border-green-500/20">
+                        <Archive className="w-4 h-4 text-green-500 mt-0.5 flex-shrink-0" />
+                        <span className="text-green-600 dark:text-green-400 text-sm">
+                          Your stashed changes have been restored successfully.
+                        </span>
+                      </div>
+                    )}
+
+                  <div className="mt-2 p-3 rounded-md bg-muted/50 border border-border">
+                    <p className="text-sm text-muted-foreground font-medium mb-2">
+                      Choose how to proceed:
+                    </p>
+                    <ul className="text-sm text-muted-foreground list-disc list-inside space-y-1">
+                      <li>
+                        <strong>Commit Merge</strong> &mdash; Open the commit dialog with a merge
+                        commit message
+                      </li>
+                      <li>
+                        <strong>Review Manually</strong> &mdash; Leave the working tree as-is for
+                        manual review
+                      </li>
+                    </ul>
+                  </div>
+                </div>
+              </DialogDescription>
+            </DialogHeader>
+
+            {/* Remember choice option */}
+            <div className="flex items-center gap-2 px-1">
+              <label className="flex items-center gap-2 text-xs text-muted-foreground cursor-pointer">
+                <Checkbox
+                  checked={rememberChoice}
+                  onCheckedChange={(checked) => setRememberChoice(checked === true)}
+                  className="rounded border-border"
+                />
+                <Settings className="w-3 h-3" />
+                Remember my choice for future merges
+              </label>
+              {(rememberChoice || mergePostAction) && (
+                <span className="text-xs text-muted-foreground ml-auto flex items-center gap-2">
+                  <span className="opacity-70">
+                    Current:{' '}
+                    {mergePostAction === 'commit'
+                      ? 'auto-commit'
+                      : mergePostAction === 'manual'
+                        ? 'manual review'
+                        : 'ask every time'}
+                  </span>
+                  <button
+                    onClick={() => {
+                      setMergePostAction(null);
+                      setRememberChoice(false);
+                    }}
+                    className="text-xs text-muted-foreground hover:text-foreground transition-colors"
+                  >
+                    Reset preference
+                  </button>
+                </span>
+              )}
+            </div>
+
+            <DialogFooter className={cn('flex-col sm:flex-row gap-2')}>
+              <Button variant="outline" onClick={handleMergeManually} className="w-full sm:w-auto">
+                <FileText className="w-4 h-4 mr-2" />
+                Review Manually
+              </Button>
+              {worktree && onCommitMerge && (
+                <Button
+                  onClick={handleCommitMerge}
+                  className="w-full sm:w-auto bg-purple-600 hover:bg-purple-700 text-white"
+                >
+                  <GitCommitHorizontal className="w-4 h-4 mr-2" />
+                  Commit Merge
+                </Button>
+              )}
+            </DialogFooter>
+          </>
+        )}
+
         {/* Conflict Phase */}
         {phase === 'conflict' && (
           <>