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# DeepBoner Documentation
Welcome to the DeepBoner documentation. This directory contains comprehensive documentation for developers, contributors, and operators.
## Quick Navigation
| Need to... | Go to... |
|------------|----------|
| Get started quickly | [Getting Started](getting-started/installation.md) |
| Understand the architecture | [Architecture Overview](architecture/overview.md) |
| Assess production readiness | [Production Readiness](architecture/production-readiness.md) |
| Set up for development | [Development Guide](development/testing.md) |
| Deploy the application | [Deployment Guide](deployment/docker.md) |
| Look up configuration | [Reference](reference/configuration.md) |
| Track technical debt | [Technical Debt](technical-debt/index.md) |
## Documentation Structure
```
docs/
├── README.md # This file - documentation index
│
├── getting-started/ # Onboarding documentation
│ ├── installation.md # Installation guide
│ ├── quickstart.md # 5-minute quickstart
│ ├── configuration.md # Configuration guide
│ └── troubleshooting.md # Common issues and solutions
│
├── architecture/ # System design documentation
│ ├── overview.md # High-level architecture
│ ├── agent-tool-state-contracts.md # Agent/Tool/State contracts (CRITICAL)
│ ├── production-readiness.md # Enterprise gap analysis (HONEST)
│ ├── system-registry.md # Service registry (canonical wiring)
│ ├── workflow-diagrams.md # Visual workflow diagrams
│ ├── component-inventory.md # Complete component catalog
│ ├── data-models.md # Pydantic model documentation
│ └── exception-hierarchy.md # Exception types and handling
│
├── development/ # Developer guides
│ ├── testing.md # Testing strategy and patterns
│ ├── code-style.md # Code style and conventions
│ └── release-process.md # Release workflow
│
├── deployment/ # Deployment documentation
│ ├── docker.md # Docker deployment
│ ├── huggingface-spaces.md # HuggingFace Spaces deployment
│ └── mcp-integration.md # MCP server setup
│
├── technical-debt/ # Known issues and improvements
│ ├── index.md # Technical debt overview
│ └── debt-registry.md # Itemized debt tracking
│
├── reference/ # API and configuration reference
│ ├── configuration.md # All configuration options
│ └── environment-variables.md # Environment variable reference
│
├── bugs/ # Bug tracking (existing)
│ ├── active-bugs.md
│ └── p3-progress-bar-positioning.md
│
├── decisions/ # Architecture Decision Records (existing)
│ └── 2025-11-27-pr55-evaluation.md
│
└── future-roadmap/ # Future feature specs (existing)
└── 16-pubmed-fulltext.md
```
## Documentation Standards
### File Naming
- Use **kebab-case** for all filenames (e.g., `getting-started.md`)
- Keep names descriptive but concise
### Content Guidelines
- Start each document with a clear title and purpose
- Include a table of contents for longer documents
- Use Mermaid diagrams for visual documentation
- Link to related documentation
- Keep content current - update when code changes
### Markdown Conventions
- Use ATX-style headers (`#`, `##`, etc.)
- Code blocks with language specification
- Tables for structured data
- Admonitions for warnings/notes (where supported)
## Key Documents
### For New Developers
1. [Installation](getting-started/installation.md) - Set up your environment
2. [Quickstart](getting-started/quickstart.md) - Run your first query
3. [Architecture Overview](architecture/overview.md) - Understand the system
4. [Testing](development/testing.md) - Run and write tests
### For Contributors
1. [CONTRIBUTING.md](../CONTRIBUTING.md) - Contribution guidelines
2. [Code Style](development/code-style.md) - Style conventions
3. [Testing](development/testing.md) - Testing requirements
### For Operators
1. [Docker Deployment](deployment/docker.md) - Container deployment
2. [HuggingFace Spaces](deployment/huggingface-spaces.md) - Cloud deployment
3. [Configuration Reference](reference/configuration.md) - All options
### For Understanding the Codebase
1. [Agent-Tool-State Contracts](architecture/agent-tool-state-contracts.md) - **CRITICAL** - Agent coordination contracts
2. [Component Inventory](architecture/component-inventory.md) - All modules
3. [Data Models](architecture/data-models.md) - Core types
4. [System Registry](architecture/system-registry.md) - Service wiring
5. [Technical Debt](technical-debt/index.md) - Known issues
## Related Documentation
- **[README.md](../README.md)** - Project overview and quick start
- **[CLAUDE.md](../CLAUDE.md)** - AI agent developer reference
- **[CHANGELOG.md](../CHANGELOG.md)** - Release history
- **[SECURITY.md](../SECURITY.md)** - Security policy
- **[CODE_OF_CONDUCT.md](../CODE_OF_CONDUCT.md)** - Community guidelines
## Contributing to Documentation
Documentation is code. Please:
1. Keep docs updated when changing related code
2. Follow the naming and style conventions
3. Test links before committing
4. Add new documents to this index
See [CONTRIBUTING.md](../CONTRIBUTING.md) for full guidelines.
---
*"Well-documented boners only. We take evidence-based documentation very seriously."* 📚
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