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Codomyrmex Project Index

Version: v1.2.7 | Status: Active | Last Updated: April 2026

Tip

Master index for the Codomyrmex project. Use this as the entry point for navigating the entire repository.

Quick Access

What You Need Where to Go
Run the CLI codomyrmex --help → cli/
Understand PAI integration PAI.md — algorithm phase ↔ module mapping
Browse all 128 top-level modules src/codomyrmex/INDEX.md — full module catalog by layer
MCP tool reference docs/pai/tools-reference.md — 600 production @mcp_tool lines (inventory)
Check system health codomyrmex status or codomyrmex check
Run tests uv run pytest
Install dependencies uv sync
Trust PAI tools codomyrmex quick run /codomyrmexTrust

System Status Snapshot

Metric Value Source
Top-level packages 128 docs/reference/inventory.md
@mcp_tool decorators (production) 600 uv run python scripts/doc_inventory.py
mcp_tools.py files (non-test) 149 docs/reference/inventory.md
MCP resources 3 docs/pai/tools-reference.md
MCP prompts 10 docs/pai/tools-reference.md
Tests collected 34,593 uv run pytest --collect-only -q --no-cov
GitHub Actions workflows 37 .github/workflows/*.yml (see uv run python scripts/doc_inventory.py)
RASP doc coverage 100% (128/128) AGENTS.md
Version v1.2.7 pyproject.toml

Module Layer Browser

Layer Count Key Modules Entry Point
Foundation 6 logging_monitoring, model_context_protocol, environment_setup, terminal_interface Foundation →
Core 15 agents, git_operations, coding, search, llm, static_analysis, performance Core →
Service 10 ci_cd_automation, orchestrator, api, cloud, documentation, containerization Service →
Specialized 58 agentic_memory, formal_verification, collaboration, crypto, events, release Specialized →

Full module catalog with layer assignments: src/codomyrmex/INDEX.md

Project Structure

Key Documentation

Document Purpose
README.md Project overview, installation, quickstart
SPEC.md Project-level functional specification
AGENTS.md Agent coordination & capabilities
PAI.md Personal AI Infrastructure bridge
CHANGELOG.md Version history
TODO.md Future features & improvements
CONTRIBUTING.md Contribution guidelines
SECURITY.md Security policy
CODE_OF_CONDUCT.md Community standards
CLAUDE.md Claude Code integration notes

Source Code

Directory Description
src/ Source root — namespace package
src/codomyrmex/ Main package — 128 top-level modules across 4 layers

Infrastructure

Directory Description
config/ Configuration files (YAML, TOML)
docs/ Generated & authored documentation
scripts/ Utility & automation scripts
.github/ GitHub Actions CI/CD workflows

Development

Directory Description
projects/ Sub-projects & reference implementations
plugin_system Plugin registry and loading (src/codomyrmex/plugin_system)
examples/ Top-level examples

Build & Test

File Purpose
pyproject.toml Python project config (uv/pip), pytest and coverage ([tool.pytest.ini_options], [tool.coverage.*])
Makefile Primary dev tasks (make test, make lint, …)
justfile Optional just recipes mirroring common Makefile targets
index.html Root redirect to /output/website/index.html for static hosting / GitHub Pages entry
uv.lock Dependency lock file

Index Hierarchy

INDEX.md                           ← You are here
├── src/INDEX.md                   ← Source directory index
│   └── src/codomyrmex/INDEX.md    ← 128-module catalog by layer
└── docs/                          ← Documentation site

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