docxology/codomyrmex

SKILL.md

---
name: Codomyrmex
description: Full-spectrum coding workspace skill providing 627 production MCP `@mcp_tool` lines across 130 top-level modules; the complete locked dependency profile currently exposes 612 tools in the merged runtime manifest. USE WHEN user says 'verify codomyrmex', 'codomyrmexVerify', 'audit codomyrmex', 'trust codomyrmex', 'codomyrmexTrust', 'trust tools', 'enable destructive tools', 'check pai status', 'codomyrmex tools', 'codomyrmex analyze', 'codomyrmex search', 'codomyrmex memory', 'codomyrmex docs', 'codomyrmex status', 'codomyrmex git', 'codomyrmex security', 'codomyrmex ai', 'codomyrmex code', 'codomyrmex data', 'codomyrmex deploy', 'codomyrmex test', or uses any 'codomyrmex' automation tools.
---
# Codomyrmex Skill for PAI

**Package version**: v1.3.0 (tracks [pyproject.toml](pyproject.toml)) | **Type**: Infrastructure Skill | **MCP**: `codomyrmex-mcp-server` | **Skills**: 15 | **Tools**: 627 production `@mcp_tool` lines; 612 merged runtime tools in the complete locked dependency profile ([inventory](docs/reference/inventory.md))

## Description

Full-spectrum coding workspace skill providing 627 production `@mcp_tool` lines across 130 top-level modules for AI-assisted development, code analysis, testing, documentation generation, and workflow automation. In the complete locked dependency profile, the merged runtime manifest currently exposes 612 tools because decorator lines and registered runtime entries are distinct measurements.

## Installation

```bash
pip install codomyrmex
# or
uv add codomyrmex
```

## Quick Start

```python
# MCP server (for PAI agent consumption)
from codomyrmex.agents.pai.mcp_bridge import create_codomyrmex_mcp_server
server = create_codomyrmex_mcp_server()
server.run()

# Direct Python calls (no MCP overhead)
from codomyrmex.agents.pai import verify_capabilities, trust_all, trusted_call_tool

verify_capabilities()   # Step 1: Audit & promote safe tools
trust_all()             # Step 2: Grant full execution trust
result = trusted_call_tool("codomyrmex.write_file", path="x.py", content="...")
```

## Codex Access Probe

Codex sessions can inspect the repo-native agentic surface without mutating the
workspace or launching agents:

```bash
uv run python scripts/agents/codex_access.py --json
uv run python scripts/agents/codex_access.py --check --json
uv run python scripts/agents/improve_src.py --dry-run --limit 2 --json
```

The same read-only payloads are exposed as MCP tools:

- `codomyrmex.codex_access_status` - MCP, skills, trust, Hermes, and Codex readiness.
- `codomyrmex.codex_dispatch_catalog` - multiagent dispatch paths classified as `read_only`, `dry_run`, or `side_effectful`.

## Skill Domains (15)

| Skill | Domain | Key Triggers |
| ------- | -------- | -------------- |
| `codomyrmexVerify` | Capability Audit | "verify codomyrmex", "audit tools" |
| `codomyrmexTrust` | Trust Management | "trust codomyrmex", "enable destructive" |
| `codomyrmexAnalyze` | Code Analysis | "analyze project", "code review" |
| `codomyrmexMemory` | Memory | "add to memory", "remember this" |
| `codomyrmexSearch` | Search | "search codebase", "grep pattern" |
| `codomyrmexDocs` | Documentation | "get module docs", "module readme" |
| `codomyrmexStatus` | Status Dashboard | "system status", "health check" |
| `CodomyrmexGit` | Version Control | "git analysis", "commit timeline" |
| `CodomyrmexSecurity` | Security & Crypto | "security scan", "crypto key" |
| `CodomyrmexAI` | AI & Agents | "reasoning trace", "thinking agent" |
| `CodomyrmexCode` | Code Execution | "execute code", "sandbox code" |
| `CodomyrmexData` | Data & Visualization | "bar chart", "fuzzy search" |
| `CodomyrmexDeploy` | Infrastructure | "docker build", "list instances" |
| `CodomyrmexTest` | Testing | "run tests", "benchmark" |

## Tools Summary (627 source decorators; 612 merged runtime tools)

Most tools are read-only; a small set is destructive (require `/codomyrmexTrust`). Run `/codomyrmexVerify` for the live safe/destructive split.

- **Destructive**: `write_file`, `run_command`, `run_tests`, `call_module_function`

The source inventory contains **627** production decorator lines across **151** `mcp_tools.py` files and **130** top-level modules. Runtime registration is a separate measured surface: the merged manifest exposes **612** tools in the complete locked dependency profile, while the standalone full launcher and readonly HTTP profile expose narrower configured profiles.

## Resources

- `codomyrmex://modules` — Full module inventory (JSON)
- `codomyrmex://status` — System + PAI status (JSON)

## Algorithm Phase Mapping

| Phase | Primary Tools |
| ------- | --------------- |
| OBSERVE | `list_modules`, `module_info`, `health_check`, `dependency_tree` |
| THINK | `analyze_python`, `search_codebase`, `think`, `query_knowledge_base` |
| PLAN | `read_file`, `json_query`, `analyze_workflow_dependencies` |
| BUILD | `write_file`, `generate_module_docs`, `code_execute` |
| EXECUTE | `run_command`, `run_tests`, `execute_agent`, `container_build` |
| VERIFY | `git_diff`, `checksum_file`, `solve_model`, `audit_code_security` |
| LEARN | `pai_awareness`, `memory_put`, `emit_event` |

## Trust Levels

| Level | Access | How |
| ------- | -------- | ------------ |
| `UNTRUSTED` | None | Default state |
| `VERIFIED` | Read-only tools | `/codomyrmexVerify` |
| `TRUSTED` | All registered dynamic tools (627 source `@mcp_tool` lines; 612 merged runtime tools in the complete locked dependency profile; see inventory) plus PAI static proxy tools | `/codomyrmexTrust` |

## Repository

Source: `src/codomyrmex/agents/pai/` — MCP bridge, trust gateway, PAI bridge

README