fix: prevent orchestrator early exit due to stale session cache

The parallel orchestrator was exiting prematurely with "All features
complete!" while pending features remained. This was caused by SQLAlchemy
session caching not seeing commits made by agent subprocesses.

Changes:
- Add session.expire_all() to get_resumable_features() to force fresh reads
- Add session.expire_all() to get_ready_features() to force fresh reads
- Add session.expire_all() to get_all_complete() to force fresh reads
- Add defensive retry logic in run_loop() when no features are ready
  but nothing is running - now forces a fresh check before declaring blocked
- Add debug logging to get_all_complete() and get_ready_features() to
  track passing/pending/in_progress counts for easier diagnosis

The root cause was cross-process database visibility: when an agent
subprocess committed feature completion, the orchestrator's session
had cached the old state and didn't see the update.

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

parallel_orchestrator.py

@@ -140,6 +140,10 @@ class ParallelOrchestrator:
         """
         session = self.get_session()
         try:
+            # Force fresh read from database to avoid stale cached data
+            # This is critical when agent subprocesses have committed changes
+            session.expire_all()
+
             # Find features that are in_progress but not complete
             stale = session.query(Feature).filter(
                 Feature.in_progress == True,
@@ -169,6 +173,10 @@ class ParallelOrchestrator:
         """Get features with satisfied dependencies, not already running."""
         session = self.get_session()
         try:
+            # Force fresh read from database to avoid stale cached data
+            # This is critical when agent subprocesses have committed changes
+            session.expire_all()
+
             all_features = session.query(Feature).all()
             all_dicts = [f.to_dict() for f in all_features]
 
@@ -190,6 +198,15 @@ class ParallelOrchestrator:
             # Sort by scheduling score (higher = first), then priority, then id
             scores = compute_scheduling_scores(all_dicts)
             ready.sort(key=lambda f: (-scores.get(f["id"], 0), f["priority"], f["id"]))
+
+            # Debug logging
+            passing = sum(1 for f in all_features if f.passes)
+            in_progress = sum(1 for f in all_features if f.in_progress and not f.passes)
+            print(
+                f"[DEBUG] get_ready_features: {len(ready)} ready, "
+                f"{passing} passing, {in_progress} in_progress, {len(all_features)} total",
+                flush=True
+            )
             return ready
         finally:
             session.close()
@@ -198,14 +215,31 @@ class ParallelOrchestrator:
         """Check if all features are complete or permanently failed."""
         session = self.get_session()
         try:
+            # Force fresh read from database to avoid stale cached data
+            # This is critical when agent subprocesses have committed changes
+            session.expire_all()
+
             all_features = session.query(Feature).all()
+            passing_count = 0
+            failed_count = 0
+            pending_count = 0
             for f in all_features:
                 if f.passes:
+                    passing_count += 1
                     continue  # Completed successfully
                 if self._failure_counts.get(f.id, 0) >= MAX_FEATURE_RETRIES:
+                    failed_count += 1
                     continue  # Permanently failed, count as "done"
-                return False  # Still workable
-            return True
+                pending_count += 1
+
+            total = len(all_features)
+            is_complete = pending_count == 0
+            print(
+                f"[DEBUG] get_all_complete: {passing_count}/{total} passing, "
+                f"{failed_count} failed, {pending_count} pending -> {is_complete}",
+                flush=True
+            )
+            return is_complete
         finally:
             session.close()
 
@@ -429,7 +463,21 @@ class ParallelOrchestrator:
                         await asyncio.sleep(POLL_INTERVAL)
                         continue
                     else:
-                        # No ready features and nothing running - might be blocked
+                        # No ready features and nothing running
+                        # Force a fresh database check before declaring blocked
+                        # This handles the case where subprocess commits weren't visible yet
+                        session = self.get_session()
+                        try:
+                            session.expire_all()
+                        finally:
+                            session.close()
+
+                        # Recheck if all features are now complete
+                        if self.get_all_complete():
+                            print("\nAll features complete!", flush=True)
+                            break
+
+                        # Still have pending features but all are blocked by dependencies
                         print("No ready features available. All remaining features may be blocked by dependencies.", flush=True)
                         await asyncio.sleep(POLL_INTERVAL * 2)
                         continue