- Refactored CLI commands from nested Typer subapps to direct command functions
- Fixed main.py to use app.command() instead of app.add_typer_command()
- Fixed project_service.py to properly load projects from YAML
- Fixed file_storage.py to save session JSON files alongside markdown
- Added missing methods: write_file, read_file, extract_autogen_section, get_recent_sessions
- Fixed root_path and repo_path to use strings instead of Path objects
- Add complete CLI command implementations with Typer subcommands
- Implement utils/time.py with duration formatting and datetime utilities
- Implement utils/path.py with project path management utilities
- Wire up all commands to main CLI entry point
