fix: resolve type errors after merging upstream v0.12.0rc

- Fix ThemeMode type casting in __root.tsx
- Use specRegeneration.create() instead of non-existent generateAppSpec
- Add missing keyboard shortcut entries for projectSettings and notifications
- Fix lucide-react type casts with intermediate unknown cast
- Remove unused pipelineConfig prop from ListRow component
- Align SettingsProject interface with Project type
- Fix defaultDeleteBranchWithWorktree property name

apps/ui/src/routes/__root.tsx

@@ -8,7 +8,7 @@ import {
   useFileBrowser,
   setGlobalFileBrowser,
 } from '@/contexts/file-browser-context';
-import { useAppStore, getStoredTheme } from '@/store/app-store';
+import { useAppStore, getStoredTheme, type ThemeMode } from '@/store/app-store';
 import { useSetupStore } from '@/store/setup-store';
 import { useAuthStore } from '@/store/auth-store';
 import { getElectronAPI, isElectron } from '@/lib/electron';
@@ -681,7 +681,7 @@ function RootLayoutContent() {
           upsertAndSetCurrentProject(
             autoOpenCandidate.path,
             autoOpenCandidate.name,
-            autoOpenCandidate.theme
+            autoOpenCandidate.theme as ThemeMode | undefined
           );
         }