# Documentation

Welcome to the project documentation. This folder contains comprehensive documentation organized by category.

## Documentation Structure

### [Infrastructure](./infrastructure/)
DevOps, CI/CD, and self-hosted infrastructure setup
- [Self-Hosted Runner](./infrastructure/self-hosted-runner.md)
- [GitHub Environments](./infrastructure/github-environments.md)
- [Containerization](./infrastructure/containerization.md)
- [Git Hooks](./infrastructure/git-hooks.md)

### [Hardware](./hardware/)
Physical hardware systems for secure field deployment and biological automation
- [Secure Terminal Briefcase](./hardware/secure-terminal-briefcase.md) -- Tamper-responsive Pi briefcase with dual-sensor detection, LUKS2 wipe, and PQC recovery
- [BioForge CRISPR Automation](./hardware/bioforge-crispr-automation.md) -- Agent-driven biological automation with Pi 5, MCP tools, and closed-loop experiment orchestration

### [AI Agents](./agents/)
Comprehensive AI agent system documentation
- [Overview](./agents/README.md)
- [Security](./agents/security.md)
- [Claude Authentication](./agents/claude-auth.md)
- [Agent Matrix](./agents/agent-matrix.md)
- [PR Monitoring](./agents/pr-monitoring.md)

### [MCP](./mcp/)
Model Context Protocol servers and architecture
- [Architecture Overview](./mcp/README.md)
- [Servers Reference](./mcp/servers.md)
- [Tools Reference](./mcp/tools.md)
- [STDIO vs HTTP Modes](./mcp/architecture/stdio-vs-http.md)

### [Integrations](./integrations/)
External service integrations
- **AI Services**
  - [Gemini Setup](./integrations/ai-services/gemini-setup.md)
  - [AI Code Agents](./integrations/ai-services/ai-code-agents.md)
  - [OpenRouter Setup](./integrations/ai-services/openrouter-setup.md)
- **Creative Tools**
  - [AI Toolkit & ComfyUI](./integrations/creative-tools/ai-toolkit-comfyui.md)
  - [LoRA Transfer](./integrations/creative-tools/lora-transfer.md)

### [Developer](./developer/)
Developer tools and configuration
- [Claude Code Hooks](./developer/claude-code-hooks.md)

## Quick Start

### **[Template Quickstart Guide](./QUICKSTART.md)**
**Start here!** Step-by-step guide to customize this template for your specific needs:
- Choose from 4 pre-configured setup paths
- Enable/disable features based on your requirements
- Get running in 15 minutes

### Additional Resources
1. **New to the project?** Start with [AI Agents Overview](./agents/README.md)
2. **Setting up infrastructure?** See [Infrastructure Setup](./infrastructure/)
3. **Working with MCP servers?** Check [MCP Architecture](./mcp/README.md)
4. **Integrating services?** Browse [Integrations](./integrations/)

## Additional Resources

- [Main README](../README.md) - Project overview
- [AGENTS.md](../AGENTS.md) - Universal AI agent configuration
- [CLAUDE.md](../CLAUDE.md) - Claude Code instructions
- [SECURITY.md](../SECURITY.md) - Security policies
