refactor(06-03): migrate Batch 5 secondary routes and wire router index

- features/routes/list.ts: Add facadeFactory parameter, use facade.detectOrphanedFeatures
- projects/routes/overview.ts: Add facadeFactory parameter, use facade.getRunningAgents/getStatusForProject
- features/index.ts: Pass facadeFactory to list handler
- projects/index.ts: Pass facadeFactory to overview handler
- auto-mode/index.ts: Accept facadeFactory parameter and wire to all route handlers
- All routes maintain backward compatibility with autoModeService fallback

apps/server/src/routes/features/index.ts

@@ -6,6 +6,7 @@ import { Router } from 'express';
 import { FeatureLoader } from '../../services/feature-loader.js';
 import type { SettingsService } from '../../services/settings-service.js';
 import type { AutoModeService } from '../../services/auto-mode-service.js';
+import type { AutoModeServiceFacade } from '../../services/auto-mode/index.js';
 import type { EventEmitter } from '../../lib/events.js';
 import { validatePathParams } from '../../middleware/validate-paths.js';
 import { createListHandler } from './routes/list.js';
@@ -24,14 +25,15 @@ export function createFeaturesRoutes(
   featureLoader: FeatureLoader,
   settingsService?: SettingsService,
   events?: EventEmitter,
-  autoModeService?: AutoModeService
+  autoModeService?: AutoModeService,
+  facadeFactory?: (projectPath: string) => AutoModeServiceFacade
 ): Router {
   const router = Router();
 
   router.post(
     '/list',
     validatePathParams('projectPath'),
-    createListHandler(featureLoader, autoModeService)
+    createListHandler(featureLoader, autoModeService, facadeFactory)
   );
   router.post('/get', validatePathParams('projectPath'), createGetHandler(featureLoader));
   router.post(

apps/server/src/routes/features/routes/list.ts

@@ -8,12 +8,17 @@
 import type { Request, Response } from 'express';
 import { FeatureLoader } from '../../../services/feature-loader.js';
 import type { AutoModeService } from '../../../services/auto-mode-service.js';
+import type { AutoModeServiceFacade } from '../../../services/auto-mode/index.js';
 import { getErrorMessage, logError } from '../common.js';
 import { createLogger } from '@automaker/utils';
 
 const logger = createLogger('FeaturesListRoute');
 
-export function createListHandler(featureLoader: FeatureLoader, autoModeService?: AutoModeService) {
+export function createListHandler(
+  featureLoader: FeatureLoader,
+  autoModeService?: AutoModeService,
+  facadeFactory?: (projectPath: string) => AutoModeServiceFacade
+) {
   return async (req: Request, res: Response): Promise<void> => {
     try {
       const { projectPath } = req.body as { projectPath: string };
@@ -29,7 +34,21 @@ export function createListHandler(featureLoader: FeatureLoader, autoModeService?
       // This detects features whose branches no longer exist (e.g., after merge/delete)
       // We don't await this to keep the list response fast
       // Note: detectOrphanedFeatures handles errors internally and always resolves
-      if (autoModeService) {
+      if (facadeFactory) {
+        const facade = facadeFactory(projectPath);
+        facade.detectOrphanedFeatures().then((orphanedFeatures) => {
+          if (orphanedFeatures.length > 0) {
+            logger.info(
+              `[ProjectLoad] Detected ${orphanedFeatures.length} orphaned feature(s) in ${projectPath}`
+            );
+            for (const { feature, missingBranch } of orphanedFeatures) {
+              logger.info(
+                `[ProjectLoad] Orphaned: ${feature.title || feature.id} - branch "${missingBranch}" no longer exists`
+              );
+            }
+          }
+        });
+      } else if (autoModeService) {
         autoModeService.detectOrphanedFeatures(projectPath).then((orphanedFeatures) => {
           if (orphanedFeatures.length > 0) {
             logger.info(