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>

prompts.py

@@ -18,7 +18,8 @@ TEMPLATES_DIR = Path(__file__).parent / ".claude" / "templates"
 
 def get_project_prompts_dir(project_dir: Path) -> Path:
     """Get the prompts directory for a specific project."""
-    return project_dir / "prompts"
+    from autocoder_paths import get_prompts_dir
+    return get_prompts_dir(project_dir)
 
 
 def load_prompt(name: str, project_dir: Path | None = None) -> str:
@@ -190,9 +191,9 @@ def scaffold_project_prompts(project_dir: Path) -> Path:
     project_prompts = get_project_prompts_dir(project_dir)
     project_prompts.mkdir(parents=True, exist_ok=True)
 
-    # Create .autocoder directory for configuration files
-    autocoder_dir = project_dir / ".autocoder"
-    autocoder_dir.mkdir(parents=True, exist_ok=True)
+    # Create .autocoder directory with .gitignore for runtime files
+    from autocoder_paths import ensure_autocoder_dir
+    autocoder_dir = ensure_autocoder_dir(project_dir)
 
     # Define template mappings: (source_template, destination_name)
     templates = [