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/mutations/use-auto-mode-mutations.ts

@@ -99,21 +99,36 @@ export function useResumeFeature(projectPath: string) {
  * Stop a running feature
  *
  * @returns Mutation for stopping a feature
+ *
+ * @example
+ * ```tsx
+ * const stopFeature = useStopFeature();
+ * // Simple stop
+ * stopFeature.mutate('feature-id');
+ * // Stop with project path for cache invalidation
+ * stopFeature.mutate({ featureId: 'feature-id', projectPath: '/path/to/project' });
+ * ```
  */
 export function useStopFeature() {
   const queryClient = useQueryClient();
 
   return useMutation({
-    mutationFn: async (featureId: string) => {
+    mutationFn: async (input: string | { featureId: string; projectPath?: string }) => {
+      const featureId = typeof input === 'string' ? input : input.featureId;
       const api = getElectronAPI();
       const result = await api.autoMode.stopFeature(featureId);
       if (!result.success) {
         throw new Error(result.error || 'Failed to stop feature');
       }
-      return result;
+      // Return projectPath for use in onSuccess
+      return { ...result, projectPath: typeof input === 'string' ? undefined : input.projectPath };
     },
-    onSuccess: () => {
+    onSuccess: (data) => {
       queryClient.invalidateQueries({ queryKey: queryKeys.runningAgents.all() });
+      // Also invalidate features cache if projectPath is provided
+      if (data.projectPath) {
+        queryClient.invalidateQueries({ queryKey: queryKeys.features.all(data.projectPath) });
+      }
       toast.success('Feature stopped');
     },
     onError: (error: Error) => {

apps/ui/src/hooks/mutations/use-github-mutations.ts

@@ -9,6 +9,7 @@ import { getElectronAPI, GitHubIssue, GitHubComment } from '@/lib/electron';
 import { queryKeys } from '@/lib/query-keys';
 import { toast } from 'sonner';
 import type { LinkedPRInfo, ModelId } from '@automaker/types';
+import { resolveModelString } from '@automaker/model-resolver';
 
 /**
  * Input for validating a GitHub issue
@@ -64,10 +65,13 @@ export function useValidateIssue(projectPath: string) {
         linkedPRs,
       };
 
+      // Resolve model alias to canonical model identifier
+      const resolvedModel = model ? resolveModelString(model) : undefined;
+
       const result = await api.github.validateIssue(
         projectPath,
         validationInput,
-        model,
+        resolvedModel,
         thinkingLevel,
         reasoningEffort
       );

apps/ui/src/hooks/mutations/use-spec-mutations.ts

@@ -157,6 +157,11 @@ export function useSaveSpec(projectPath: string) {
 
   return useMutation({
     mutationFn: async (content: string) => {
+      // Guard against empty projectPath to prevent writing to invalid locations
+      if (!projectPath || projectPath.trim() === '') {
+        throw new Error('Invalid project path: cannot save spec without a valid project');
+      }
+
       const api = getElectronAPI();
 
       await api.writeFile(`${projectPath}/.automaker/app_spec.txt`, content);

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);

apps/ui/src/hooks/queries/use-worktrees.ts

@@ -162,7 +162,8 @@ interface BranchesResult {
  */
 export function useWorktreeBranches(worktreePath: string | undefined, includeRemote = false) {
   return useQuery({
-    queryKey: queryKeys.worktrees.branches(worktreePath ?? ''),
+    // Include includeRemote in query key so different configurations have separate caches
+    queryKey: queryKeys.worktrees.branches(worktreePath ?? '', includeRemote),
     queryFn: async (): Promise<BranchesResult> => {
       if (!worktreePath) throw new Error('No worktree path');
       const api = getElectronAPI();