This index provides navigation to all documentation in the GNN repository, organized by category.
| Getting Started | Core Reference | Frameworks |
|---|---|---|
| README | GNN Syntax | PyMDP |
| Setup Guide | Architecture | RxInfer.jl |
| CLAUDE.md | Pipeline Steps | ActiveInference.jl |
| CHANGELOG.md | Version history & release notes | Contributing |
| QUICK_REFERENCE.md | Commands & GNN syntax quick ref | GNN Spec |
- GNN Overview - High-level introduction to GNN
- About GNN - Background and motivation
- GNN Syntax Reference - Complete syntax specification
- GNN DSL Manual - Domain-specific language guide
- GNN File Structure - File format specification
- GNN Examples - Example GNN files
- GNN Implementation - Implementation details
- Active Inference README - Overview and navigation
- FEP Foundations - Free Energy Principle
- Active Inference Theory - Core theory
- Expected Free Energy - EFE computation
- Generative Models - Model structures
- Computational Patterns - Algorithm patterns
- Glossary - Terminology reference
- Architecture Reference - System architecture
- Advanced Modeling Patterns - Design patterns
- GNN Ontology - Ontological foundations
- LLM Neurosymbolic Integration - AI integration
- PyMDP README - Overview
- PyMDP POMDP - POMDP implementation
- JAX Integration - JAX execution documentation
- DisCoPy Integration - Category theory diagrams
- RxInfer README - Reactive inference
- Multiagent Planning - Multi-agent systems
- ActiveInference.jl README - Julia implementation
- Implementation Guide - Integration details
- Pipeline README - Pipeline overview
- Step 0: Template initialization
- Step 1: Environment setup
- Step 2: Test execution
- Step 3: GNN parsing
- Step 4: Model registry
- Step 5: Type checking
- Step 6: Validation
- Step 7: Export
- Step 8: Visualization
- Step 9: Advanced visualization
- Step 10: Ontology
- Step 11: Render (code generation)
- Step 12: Execute (simulation)
- Step 13: LLM analysis
- Step 14: ML integration
- Step 15: Audio
- Step 16: Analysis
- Step 17: Integration
- Step 18: Security
- Step 19: Research
- Step 20: Website
- Step 21: MCP
- Step 22: GUI
- Step 23: Report
- Step 24: Intelligent Analysis
- Framework Integration Guide - Connecting frameworks
- GNN Export - Export formats
- Visualization README - Visualization tools
- D2 Diagrams - D2 diagram generation
- GUI OxDraw - Interactive diagrams
- LLM Integration - Language model integration
- MCP Protocol - Model Context Protocol
- Audio Processing - Audio/SAPF integration
- DSPy - DSPy integration guide
- Development Guide - Contributing guide
- Testing - Test documentation
- Performance - Performance optimization
- Troubleshooting - Common issues
- Deployment - Deployment guide
- Security Guide - Security documentation
- Cognitive Phenomena - Cognitive modeling
- Axiom - Axiom integration
- CatColab - Category theory
- Cerebrum - Neural modeling
- Petri Nets - Petri net formalism
- SymPy - Symbolic computation
- NTQR - Quantum-inspired reasoning
- Quadray - Coordinate systems
- Research - Research documentation
- SPM - Statistical Parametric Mapping
- POMDP - POMDP theory
- Type Inference - Type systems
- Configuration - Configuration options
- Templates - Template files
- Dependencies - Dependency management
doc/
├── active_inference/ # Active Inference theory
├── activeinference_jl/ # ActiveInference.jl framework
├── advanced_visualization/
├── api/ # API documentation
├── arc-agi/ # ARC-AGI integration
├── archive/ # Archived docs
├── audio/ # Audio processing
├── axiom/ # Axiom integration
├── catcolab/ # Category theory
├── cerebrum/ # Neural modeling
├── cognitive_phenomena/ # Cognitive science models
├── configuration/ # Config docs
├── d2/ # D2 diagrams
├── dependencies/ # Dependency info
├── deployment/ # Deployment guides
├── development/ # Dev guides
├── discopy/ # DisCoPy integration
├── dspy/ # DSPy integration
├── execution/ # Execution docs
├── export/ # Export formats
├── glowstick/ # Glowstick tool
├── gnn/ # Core GNN docs
├── gui_oxdraw/ # GUI/OxDraw
├── iroh/ # Iroh integration
├── kit/ # GNN Kit
├── klong/ # Klong language
├── llm/ # LLM integration
├── mcp/ # MCP protocol
├── muscle-mem/ # Muscle memory
├── nock/ # Nock/Nockchain
├── ntqr/ # NTQR framework
├── onefilellm/ # OneFileLLM
├── other/ # Miscellaneous
├── pedalboard/ # Audio effects
├── performance/ # Performance docs
├── petri_nets/ # Petri nets
├── pkl/ # PKL format
├── poe-world/ # PoE World
├── pomdp/ # POMDP theory
├── pymdp/ # PyMDP framework
├── quadray/ # Coordinate systems
├── releases/ # Release notes
├── research/ # Research docs
├── rxinfer/ # RxInfer.jl
├── sapf/ # SAPF audio
├── security/ # Security docs
├── spm/ # SPM integration
├── sympy/ # SymPy integration
├── templates/ # Templates
├── testing/ # Test docs
├── timep/ # Time processing
├── troubleshooting/ # Troubleshooting
├── tutorials/ # Tutorials
├── type-inference-zoo/ # Type inference
├── vec2text/ # Vector-to-text
├── visualization/ # Visualization
└── x402/ # X402 protocol
Last updated: February 2026