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/components/views/spec-view/hooks/use-spec-loading.ts

@@ -27,15 +27,13 @@ export function useSpecLoading() {
   const loadSpec = useCallback(async () => {
     if (!currentProject?.path) return;
 
-    // First check if generation is running
-    await queryClient.invalidateQueries({
+    // Fetch fresh status data to avoid stale cache issues
+    // Using fetchQuery ensures we get the latest data before checking
+    const statusData = await queryClient.fetchQuery<{ isRunning: boolean }>({
       queryKey: queryKeys.specRegeneration.status(currentProject.path),
+      staleTime: 0, // Force fresh fetch
     });
 
-    const statusData = queryClient.getQueryData<{ isRunning: boolean }>(
-      queryKeys.specRegeneration.status(currentProject.path)
-    );
-
     if (statusData?.isRunning) {
       return;
     }