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-settings.ts

@@ -107,7 +107,8 @@ export function useDiscoveredAgents(
   sources?: Array<'user' | 'project'>
 ) {
   return useQuery({
-    queryKey: queryKeys.settings.agents(projectPath ?? ''),
+    // Include sources in query key so different source combinations have separate caches
+    queryKey: queryKeys.settings.agents(projectPath ?? '', sources),
     queryFn: async () => {
       const api = getElectronAPI();
       const result = await api.settings.discoverAgents(projectPath, sources);