# Codomyrmex Agents — scripts

**Version**: v0.1.0 | **Status**: Active | **Last Updated**: April 2026

## Purpose
Maintenance and automation utilities for project management.

## Metrics and doc audits
- `doc_inventory.py` — counts aligned with [docs/reference/inventory.md](../docs/reference/inventory.md) (top-level modules, `@mcp_tool`, `mcp_tools.py`, `.github/workflows/*.yml`; optional `--pytest`, `--manifest`).
- `rasp_gap_report.py` — writes [docs/plans/agents-readme-gap-report.md](../docs/plans/agents-readme-gap-report.md) for scoped `AGENTS.md` / `README.md` gaps.
- `src_structure_audit.py` — read-only `src/codomyrmex` structure gate for module docs/API/MCP/test parity, PEP 561 `py.typed` markers, docs/modules counterparts, stale docs/modules directories, support-surface docs, and retired module names.

## Active Components
- `PAI.md` – Project file
- `README.md` – Project file
- `SPEC.md` – Project file
- `__init__.py` – Project file
- `agentic_memory/` – Directory containing agentic_memory components
- `agents/` – Directory containing agents components
- `api/` – Directory containing api components
- `audio/` – Directory containing audio components
- `audits/` – Directory containing audits components
- `auth/` – Directory containing auth components
- `bio_simulation/` – Directory containing bio_simulation components
- `build_synthesis/` – Directory containing build_synthesis components
- `cache/` – Directory containing cache components
- `cerebrum/` – Directory containing cerebrum components
- `ci_cd_automation/` – Directory containing ci_cd_automation components
- `cli/` – Directory containing cli components
- `cloud/` – Directory containing cloud components
- `coding/` – Directory containing coding components
- `collaboration/` – Directory containing collaboration components
- `compression/` – Directory containing compression components
- `concurrency/` – Directory containing concurrency components
- `config.yaml` – Project file
- `config_audits/` – Directory containing config_audits components
- `config_management/` – Directory containing config_management components
- `config_monitoring/` – Directory containing config_monitoring components
- `container_optimization/` – Directory containing container_optimization components
- `containerization/` – Directory containing containerization components
- `cost_management/` – Directory containing cost_management components
- `dark/` – Directory containing dark components
- `data_lineage/` – Directory containing data_lineage components
- `data_visualization/` – Directory containing data_visualization components
- `database_management/` – Directory containing database_management components
- `defense/` – Directory containing defense components
- `demos/` – Directory containing demos components
- `dependency_injection/` – Directory containing dependency_injection components
- `deployment/` – Directory containing deployment components
- `docs/` – Directory containing docs components
- `docs_gen/` – Directory containing docs_gen components
- `documentation/` – Directory containing documentation components
- `documents/` – Directory containing documents components
- `edge_computing/` – Directory containing edge_computing components
- `email/` – Directory containing email components
- `embodiment/` – Directory containing embodiment components
- `encryption/` – Directory containing encryption components
- `environment_setup/` – Directory containing environment_setup components
- `events/` – Directory containing events components
- `evolutionary_ai/` – Directory containing evolutionary_ai components
- `examples/` – Directory containing examples components
- `exceptions/` – Directory containing exceptions components
- `exploration/` – Directory containing exploration components
- `feature_flags/` – Directory containing feature_flags components
- `feature_store/` – Directory containing feature_store components
- `file_system/` – Directory containing file_system components
- `finance/` – Directory containing finance components
- `fix_ty_ast.py` – Project file
- `fix_ty_imports.py` – Project file
- `fix_ty_stubborn.py` – Project file
- `formal_verification/` – Directory containing formal_verification components
- `fpf/` – Directory containing fpf components
- `git_analysis/` – Directory containing git_analysis components
- `git_operations/` – Directory containing git_operations components
- `graph_rag/` – Directory containing graph_rag components
- `ide/` – Directory containing ide components
- `identity/` – Directory containing identity components
- `index.html` – Project file
- `inference_optimization/` – Directory containing inference_optimization components
- `llm/` – Directory containing llm components
- `logging_monitoring/` – Directory containing logging_monitoring components
- `logistics/` – Directory containing logistics components
- `maintenance/` – Directory containing maintenance components
- `metrics/` – Directory containing metrics components
- `migration/` – Directory containing migration components
- `model_context_protocol/` – Directory containing model_context_protocol components
- `model_ops/` – Directory containing model_ops components
- `model_registry/` – Directory containing model_registry components
- `module_template/` – Directory containing module_template components
- `multimodal/` – Directory containing multimodal components
- `networking/` – Directory containing networking components
- `notification/` – Directory containing notification components
- `observability_dashboard/` – Directory containing observability_dashboard components
- `orchestrator/` – Directory containing orchestrator components
- `pai/` – Directory containing pai components
- `pattern_matching/` – Directory containing pattern_matching components
- `performance/` – Directory containing performance components
- `physical_management/` – Directory containing physical_management components
- `plugin_system/` – Directory containing plugin_system components
- `prompt_testing/` – Directory containing prompt_testing components
- `reports/` – Directory containing reports components
- `review/` – PR diff heuristics, Python structural checks, Bandit JSON→SARIF, SARIF merge/summary (`pr_analyzer.py`, `code_quality_checker.py`, `review_report_generator.py`, `sarif_merge.py`, `bandit_json_to_sarif.py`, `sarif_utils.py`); see [review/README.md](review/README.md), [review/AGENTS.md](review/AGENTS.md)
- `rna/` – Directory containing rna components
- `run_all_scripts.py` – Project file
- `scrape/` – Directory containing scrape components
- `security/` – Directory containing security components
- `serialization/` – Directory containing serialization components
- `setup_submodules.sh` – Project file
- `skills/` – Directory containing skills components
- `spatial/` – Directory containing spatial components
- `static_analysis/` – Directory containing static_analysis components
- `system_discovery/` – Directory containing system_discovery components
- `telemetry/` – Directory containing telemetry components
- `templating/` – Directory containing templating components
- `terminal_interface/` – Directory containing terminal_interface components
- `tools/` – Directory containing tools components
- `tree_sitter/` – Directory containing tree_sitter components
- `utils/` – Directory containing utils components
- `validation/` – Directory containing validation components
- `verification/` – Directory containing verification components
- `video/` – Directory containing video components
- `website/` – Directory containing website components
- `workflow_execution/` – Directory containing workflow_execution components
- `workflow_testing/` – Directory containing workflow_testing components
- `src_structure_audit.py` – Project file

## Operating Contracts
- Maintain alignment between code, documentation, and configured workflows.
- Ensure Model Context Protocol interfaces remain available for sibling agents.
- Record outcomes in shared telemetry and update TODO queues when necessary.

## Key Files
- `AGENTS.md` - Agent coordination and navigation
- `README.md` - Directory overview
- `PAI.md`
- `README.md`
- `SPEC.md`
- `__init__.py`
- `config.yaml`
- `fix_ty_ast.py`
- `fix_ty_imports.py`
- `fix_ty_stubborn.py`
- `index.html`
- `run_all_scripts.py`
- `setup_submodules.sh`
- `src_structure_audit.py`

## Dependencies
- Inherits dependencies from the parent module. See `pyproject.toml` or `package.json` for global dependencies.

## Development Guidelines
- Follow the universal agent protocols defined in the root `AGENTS.md`.
- Adhere to the Python PEP 8 style guide and project-specific linting rules.
- Ensure all new features are accompanied by corresponding tests (zero-mock policy).

## Navigation Links
- **🏠 Project Root**: ../README.md - Main project documentation
