Add orphaned features management routes and UI integration (#819)

* test(copilot): add edge case test for error with code field

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

* Changes from fix/bug-fixes-1-0

* refactor(auto-mode): enhance orphaned feature detection and improve project initialization

- Updated detectOrphanedFeatures method to accept preloaded features, reducing redundant disk reads.
- Improved project initialization by creating required directories and files in parallel for better performance.
- Adjusted planning mode handling in UI components to clarify approval requirements for different modes.
- Added refresh functionality for file editor tabs to ensure content consistency with disk state.

These changes enhance performance, maintainability, and user experience across the application.

* feat(orphaned-features): add orphaned features management routes and UI integration

- Introduced new routes for managing orphaned features, including listing, resolving, and bulk resolving.
- Updated the UI to include an Orphaned Features section in project settings and navigation.
- Enhanced the execution service to support new orphaned feature functionalities.

These changes improve the application's capability to handle orphaned features effectively, enhancing user experience and project management.

* fix: Normalize line endings and resolve stale dirty states in file editor

* chore: Update .gitignore and enhance orphaned feature handling

- Added a blank line in .gitignore for better readability.
- Introduced a hash to worktree paths in orphaned feature resolution to prevent conflicts.
- Added validation for target branch existence during orphaned feature resolution.
- Improved prompt formatting in execution service for clarity.
- Enhanced error handling in project selector for project initialization failures.
- Refactored orphaned features section to improve state management and UI responsiveness.

These changes improve code maintainability and user experience when managing orphaned features.

---------

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

apps/ui/src/hooks/use-auto-mode.ts

@@ -288,12 +288,51 @@ export function useAutoMode(worktree?: WorktreeInfo) {
 
     try {
       const sessionData = readAutoModeSession();
-      const currentBranchName = branchNameRef.current;
-      const currentKey = getWorktreeSessionKey(currentProject.path, currentBranchName);
+      const projectPath = currentProject.path;
 
-      if (sessionData[currentKey] === true) {
-        setAutoModeRunning(currentProject.id, currentBranchName, true);
-        logger.debug(`Restored auto mode state from session storage for key: ${currentKey}`);
+      // Track restored worktrees to avoid redundant state updates
+      const restoredKeys = new Set<string>();
+
+      // Find all session storage keys that match this project
+      Object.entries(sessionData).forEach(([sessionKey, isRunning]) => {
+        if (!isRunning) return;
+
+        // Parse the session key: "projectPath::branchName" or "projectPath::__main__"
+        // Use lastIndexOf to split from the right, since projectPath may contain the delimiter
+        const delimiterIndex = sessionKey.lastIndexOf(SESSION_KEY_DELIMITER);
+        if (delimiterIndex === -1) {
+          // Malformed session key - skip it
+          logger.warn(`Malformed session storage key: ${sessionKey}`);
+          return;
+        }
+
+        const keyProjectPath = sessionKey.slice(0, delimiterIndex);
+        const keyBranchName = sessionKey.slice(delimiterIndex + SESSION_KEY_DELIMITER.length);
+        if (keyProjectPath !== projectPath) return;
+
+        // Validate branch name: __main__ means null (main worktree)
+        if (keyBranchName !== MAIN_WORKTREE_MARKER && !keyBranchName) {
+          logger.warn(`Invalid branch name in session key: ${sessionKey}`);
+          return;
+        }
+
+        const branchName = keyBranchName === MAIN_WORKTREE_MARKER ? null : keyBranchName;
+
+        // Skip if we've already restored this worktree (prevents duplicates)
+        const worktreeKey = getWorktreeSessionKey(projectPath, branchName);
+        if (restoredKeys.has(worktreeKey)) {
+          return;
+        }
+        restoredKeys.add(worktreeKey);
+
+        // Restore the auto mode running state in the store
+        setAutoModeRunning(currentProject.id, branchName, true);
+      });
+
+      if (restoredKeys.size > 0) {
+        logger.debug(
+          `Restored auto mode state for ${restoredKeys.size} worktree(s) from session storage`
+        );
       }
     } catch (error) {
       logger.error('Error restoring auto mode state from session storage:', error);