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>

client.py

@@ -360,7 +360,9 @@ def create_client(
     project_dir.mkdir(parents=True, exist_ok=True)
 
     # Write settings to a file in the project directory
-    settings_file = project_dir / ".claude_settings.json"
+    from autocoder_paths import get_claude_settings_path
+    settings_file = get_claude_settings_path(project_dir)
+    settings_file.parent.mkdir(parents=True, exist_ok=True)
     with open(settings_file, "w") as f:
         json.dump(security_settings, f, indent=2)