Version: v1.2.7 | Status: Active | Last Updated: March 2026
Comprehensive documentation for the Codomyrmex modular coding workspace — a production-grade ecosystem with 128 top-level modules, 600 production @mcp_tool decorators (see reference/inventory.md), and 39 agent packages under src/codomyrmex/agents/ (see agents/).
| Document | Description |
|---|---|
| ARCHITECTURE.md | System architecture, layers, module graph (448 lines) |
| DEPENDENCIES.md | Dependency compatibility, version constraints |
| PAI.md | Personal AI Infrastructure documentation hub |
| PAI_DASHBOARD.md | Dashboard functionality matrix (Admin :8787, PM :8888) |
| SPEC.md | Functional specification |
| index.md | Documentation site entry point |
| reference/inventory.md | Repo metrics (modules, MCP tools, tests) — refresh via scripts/doc_inventory.py |
| Section | Purpose | Files |
|---|---|---|
| agents/ | 39 agent packages — Claude, Gemini, Jules, Hermes (skill preload / registry), and 35 more | 121 |
| agi/ | AGI theory, perspectives, emergence models | 14 |
| bio/ | Biological simulation documentation | 15 |
| cognitive/ | Cognitive architecture, Bayesian inference, active inference | 11 |
| compliance/ | Regulatory compliance, audit frameworks | 5 |
| deployment/ | Deployment guides, CI/CD, containerization | 5 |
| development/ | Developer guides, environment setup, testing strategy | 10 |
| examples/ | Executable examples and tutorials | 8 |
| getting-started/ | Quick start, installation, first steps | 9 |
| integration/ | Cross-module integration patterns | 11 |
| modules/ | Module-level documentation (128 top-level packages under src/codomyrmex/) |
9+ |
| pai/ | PAI infrastructure, dashboard, skills, memory | 11 |
| plans/ | Project roadmap and release plans | 6 |
| project/ | Project standards, contributing, architecture | 9 |
| project_orchestration/ | Workflow orchestration, multi-agent coordination | 11 |
| reference/ | API reference, CLI tools, configuration | 16 |
| security/ | Security policies, threat models, audit guides | 11 |
| skills/ | Agent skill creation and management | 9 |
| assets/ | Static assets (images, diagrams) | 2 |
- Start Here: getting-started/quickstart.md
- Architecture: ARCHITECTURE.md
- API Reference: reference/api.md
- Examples: examples/
- Environment Setup: development/environment-setup.md
- Testing Strategy: development/testing-strategy.md
- Code Review & SARIF: development/code-review-and-sarif.md — local
scripts/review/helpers and Bandit SARIF triage - Contributing: project/contributing.md
- Agent Coordination: AGENTS.md
- Agent Integrations: agents/
- PAI Infrastructure: pai/
- Module Documentation: modules/
- Project Root: README.md
- Root AGENTS.md: AGENTS.md
- Source Code: src/codomyrmex/