fix: Prevent features from getting stuck in in_progress after server restart

- Add graceful shutdown handler that marks running features as 'interrupted'
  before server exit (SIGTERM/SIGINT)
- Add 30-second shutdown timeout to prevent hanging on exit
- Add orphan detection to identify features with missing branches
- Add isFeatureRunning() for idempotent resume checks
- Improve resumeInterruptedFeatures() to handle features without saved context
- Add 'interrupted' status to FeatureStatusWithPipeline type
- Replace console.log with proper logger in auto-mode-service
- Add comprehensive unit tests for all new functionality (15 new tests)

Fixes #696

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

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

@@ -5,6 +5,7 @@
 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 { EventEmitter } from '../../lib/events.js';
 import { validatePathParams } from '../../middleware/validate-paths.js';
 import { createListHandler } from './routes/list.js';
@@ -22,11 +23,16 @@ import { createImportHandler, createConflictCheckHandler } from './routes/import
 export function createFeaturesRoutes(
   featureLoader: FeatureLoader,
   settingsService?: SettingsService,
-  events?: EventEmitter
+  events?: EventEmitter,
+  autoModeService?: AutoModeService
 ): Router {
   const router = Router();
 
-  router.post('/list', validatePathParams('projectPath'), createListHandler(featureLoader));
+  router.post(
+    '/list',
+    validatePathParams('projectPath'),
+    createListHandler(featureLoader, autoModeService)
+  );
   router.post('/get', validatePathParams('projectPath'), createGetHandler(featureLoader));
   router.post(
     '/create',

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

@@ -1,12 +1,19 @@
 /**
  * POST /list endpoint - List all features for a project
+ *
+ * Also performs orphan detection when a project is loaded to identify
+ * features whose branches no longer exist. This runs on every project load/switch.
  */
 
 import type { Request, Response } from 'express';
 import { FeatureLoader } from '../../../services/feature-loader.js';
+import type { AutoModeService } from '../../../services/auto-mode-service.js';
 import { getErrorMessage, logError } from '../common.js';
+import { createLogger } from '@automaker/utils';
 
-export function createListHandler(featureLoader: FeatureLoader) {
+const logger = createLogger('FeaturesListRoute');
+
+export function createListHandler(featureLoader: FeatureLoader, autoModeService?: AutoModeService) {
   return async (req: Request, res: Response): Promise<void> => {
     try {
       const { projectPath } = req.body as { projectPath: string };
@@ -17,6 +24,31 @@ export function createListHandler(featureLoader: FeatureLoader) {
       }
 
       const features = await featureLoader.getAll(projectPath);
+
+      // Run orphan detection in background when project is loaded
+      // This detects features whose branches no longer exist (e.g., after merge/delete)
+      // We don't await this to keep the list response fast
+      if (autoModeService) {
+        autoModeService
+          .detectOrphanedFeatures(projectPath)
+          .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`
+                );
+              }
+            }
+          })
+          .catch((error: unknown) => {
+            const errorMessage = error instanceof Error ? error.message : String(error);
+            logger.warn(`[ProjectLoad] Failed to detect orphaned features: ${errorMessage}`);
+          });
+      }
+
       res.json({ success: true, features });
     } catch (error) {
       logError(error, 'List features failed');