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/lib/query-keys.ts

@@ -40,7 +40,8 @@ export const queryKeys = {
     single: (projectPath: string, featureId: string) =>
       ['worktrees', projectPath, featureId] as const,
     /** Branches for a worktree */
-    branches: (worktreePath: string) => ['worktrees', 'branches', worktreePath] as const,
+    branches: (worktreePath: string, includeRemote = false) =>
+      ['worktrees', 'branches', worktreePath, { includeRemote }] as const,
     /** Worktree status */
     status: (projectPath: string, featureId: string) =>
       ['worktrees', projectPath, featureId, 'status'] as const,
@@ -86,7 +87,8 @@ export const queryKeys = {
     /** Credentials (API keys) */
     credentials: () => ['settings', 'credentials'] as const,
     /** Discovered agents */
-    agents: (projectPath: string) => ['settings', 'agents', projectPath] as const,
+    agents: (projectPath: string, sources?: Array<'user' | 'project'>) =>
+      ['settings', 'agents', projectPath, sources ?? []] as const,
   },
 
   // ============================================