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/board-view/worktree-panel/hooks/use-branches.ts

@@ -22,9 +22,11 @@ export function useBranches() {
   const branches = branchData?.branches ?? [];
   const aheadCount = branchData?.aheadCount ?? 0;
   const behindCount = branchData?.behindCount ?? 0;
+  // Use conservative defaults (false) until data is confirmed
+  // This prevents the UI from assuming git capabilities before the query completes
   const gitRepoStatus: GitRepoStatus = {
-    isGitRepo: branchData?.isGitRepo ?? true,
-    hasCommits: branchData?.hasCommits ?? true,
+    isGitRepo: branchData?.isGitRepo ?? false,
+    hasCommits: branchData?.hasCommits ?? false,
   };
 
   const fetchBranches = useCallback(

apps/ui/src/components/views/running-agents-view.tsx

@@ -34,8 +34,8 @@ export function RunningAgentsView() {
   }, [refetch]);
 
   const handleStopAgent = useCallback(
-    (featureId: string) => {
-      stopFeature.mutate(featureId);
+    (featureId: string, projectPath: string) => {
+      stopFeature.mutate({ featureId, projectPath });
     },
     [stopFeature]
   );
@@ -168,7 +168,7 @@ export function RunningAgentsView() {
                   <Button
                     variant="destructive"
                     size="sm"
-                    onClick={() => handleStopAgent(agent.featureId)}
+                    onClick={() => handleStopAgent(agent.featureId, agent.projectPath)}
                     disabled={stopFeature.isPending}
                   >
                     <Square className="h-3.5 w-3.5 mr-1.5" />

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;
     }