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>

progress.py

@@ -46,7 +46,8 @@ def has_features(project_dir: Path) -> bool:
         return True
 
     # Check SQLite database
-    db_file = project_dir / "features.db"
+    from autocoder_paths import get_features_db_path
+    db_file = get_features_db_path(project_dir)
     if not db_file.exists():
         return False
 
@@ -71,7 +72,8 @@ def count_passing_tests(project_dir: Path) -> tuple[int, int, int]:
     Returns:
         (passing_count, in_progress_count, total_count)
     """
-    db_file = project_dir / "features.db"
+    from autocoder_paths import get_features_db_path
+    db_file = get_features_db_path(project_dir)
     if not db_file.exists():
         return 0, 0, 0
 
@@ -120,7 +122,8 @@ def get_all_passing_features(project_dir: Path) -> list[dict]:
     Returns:
         List of dicts with id, category, name for each passing feature
     """
-    db_file = project_dir / "features.db"
+    from autocoder_paths import get_features_db_path
+    db_file = get_features_db_path(project_dir)
     if not db_file.exists():
         return []
 
@@ -144,7 +147,8 @@ def send_progress_webhook(passing: int, total: int, project_dir: Path) -> None:
     if not WEBHOOK_URL:
         return  # Webhook not configured
 
-    cache_file = project_dir / PROGRESS_CACHE_FILE
+    from autocoder_paths import get_progress_cache_path
+    cache_file = get_progress_cache_path(project_dir)
     previous = 0
     previous_passing_ids = set()