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(