fix(ui): improve React Query hooks and fix edge cases

- Update query keys to include all relevant parameters (branches, agents)
- Fix use-branches to pass includeRemote parameter to query key
- Fix use-settings to include sources in agents query key
- Update running-agents-view to use correct query key structure
- Update use-spec-loading to properly use spec query hooks
- Add missing queryClient invalidation in auto-mode mutations
- Add missing cache invalidation in spec mutations after creation

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

apps/ui/src/hooks/queries/use-worktrees.ts

@@ -162,7 +162,8 @@ interface BranchesResult {
  */
 export function useWorktreeBranches(worktreePath: string | undefined, includeRemote = false) {
   return useQuery({
-    queryKey: queryKeys.worktrees.branches(worktreePath ?? ''),
+    // Include includeRemote in query key so different configurations have separate caches
+    queryKey: queryKeys.worktrees.branches(worktreePath ?? '', includeRemote),
     queryFn: async (): Promise<BranchesResult> => {
       if (!worktreePath) throw new Error('No worktree path');
       const api = getElectronAPI();