refactor: require working_directory in init-agent and separate state/working dirs

- Make init-agent require absolute working_directory parameter
- Add optional agent_id parameter for state directory naming
- Use CLAUDE_AGENT_BASE_DIR exclusively for state storage
- Fix transcript path to point to Claude Code's native transcripts
- Update all tests to use new parameter structure
- Remove transcript resource (state now contains transcript path)

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

Author: tadasant