docs: add comprehensive reference documentation (Phase 4) (#255)

- API Reference: Complete guide to raw API access
  - All Cloud and Enterprise endpoints documented
  - Request/response formats
  - Error handling and status codes
  - Pagination and rate limiting

- Troubleshooting Guide: Solutions for common issues
  - Installation and authentication problems
  - Connection and SSL/TLS issues
  - API errors and debugging techniques
  - Performance optimization tips

- Best Practices: Production-ready patterns
  - Profile management strategies
  - Security recommendations
  - Error handling and retries
  - Automation and GitOps patterns
  - Monitoring and auditing

- Configuration File Reference: Complete TOML format guide
  - All profile options for Cloud and Enterprise
  - Environment variable expansion
  - Security considerations
  - Example configurations

Part of #247

Author: joshrotenberg