feat: move autocoder runtime files into .autocoder/ subdirectory

Add centralized path resolution module (autocoder_paths.py) that
consolidates all autocoder-generated file paths behind a dual-path
strategy: check .autocoder/X first, fall back to root-level X for
backward compatibility, default to .autocoder/X for new projects.

Key changes:
- New autocoder_paths.py with dual-path resolution for features.db,
  assistant.db, lock files, settings, prompts dir, and progress cache
- migrate_project_layout() safely moves old-layout projects to new
  layout with SQLite WAL flush and integrity verification
- Updated 22 files to delegate path construction to autocoder_paths
- Reset/delete logic cleans both old and new file locations
- Orphan lock cleanup checks both locations per project
- Migration called automatically at agent start in autonomous_agent_demo.py
- Updated markdown commands/skills to reference .autocoder/prompts/
- CLAUDE.md documentation updated with new project structure

Files at project root that remain unchanged:
- CLAUDE.md (Claude SDK reads from cwd via setting_sources=["project"])
- app_spec.txt root copy (agent templates reference it via cat)

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

server/services/scheduler_service.py

@@ -92,8 +92,9 @@ class SchedulerService:
     async def _load_project_schedules(self, project_name: str, project_dir: Path) -> int:
         """Load schedules for a single project. Returns count of schedules loaded."""
         from api.database import Schedule, create_database
+        from autocoder_paths import get_features_db_path
 
-        db_path = project_dir / "features.db"
+        db_path = get_features_db_path(project_dir)
         if not db_path.exists():
             return 0
 
@@ -567,8 +568,9 @@ class SchedulerService:
     ):
         """Check if a project should be started on server startup."""
         from api.database import Schedule, ScheduleOverride, create_database
+        from autocoder_paths import get_features_db_path
 
-        db_path = project_dir / "features.db"
+        db_path = get_features_db_path(project_dir)
         if not db_path.exists():
             return