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>

api/database.py

@@ -183,7 +183,8 @@ class ScheduleOverride(Base):
 
 def get_database_path(project_dir: Path) -> Path:
     """Return the path to the SQLite database for a project."""
-    return project_dir / "features.db"
+    from autocoder_paths import get_features_db_path
+    return get_features_db_path(project_dir)
 
 
 def get_database_url(project_dir: Path) -> str:
@@ -384,6 +385,10 @@ def create_database(project_dir: Path) -> tuple:
 
     db_url = get_database_url(project_dir)
 
+    # Ensure parent directory exists (for .autocoder/ layout)
+    db_path = get_database_path(project_dir)
+    db_path.parent.mkdir(parents=True, exist_ok=True)
+
     # Choose journal mode based on filesystem type
     # WAL mode doesn't work reliably on network filesystems and can cause corruption
     is_network = _is_network_path(project_dir)