refactor(config): restructure configuration with unified LLM and enhanced documentation

- Replace indexer section with unified llm configuration containing summary,
  retrieval, and pilot subsections
- Add comprehensive LLM configuration with default API key, retry, throttle,
  and fallback mechanisms
- Introduce metrics section with LLM, pilot, and retrieval specific metrics
- Add detailed pilot configuration with budget, intervention, and feedback
  settings
- Enhance retrieval configuration with multiturn and reference following
  capabilities
- Update storage configuration with compression and atomic write options
- Restructure example TOML with clear sections and improved comments
- Update test assertions to reflect new configuration structure

Author: zTgx