# scripts

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

## Overview

Maintenance and automation utilities for project management.

## Code review and SARIF

- [`review/`](review/) — `pr_analyzer.py`, `code_quality_checker.py`, `review_report_generator.py`, `sarif_merge.py`, `bandit_json_to_sarif.py`, and `sarif_utils.py` for local diff heuristics, Python structural checks, Bandit JSON→SARIF, and SARIF merge/summary. See [review/README.md](review/README.md), [review/AGENTS.md](review/AGENTS.md), and [docs/development/code-review-and-sarif.md](../docs/development/code-review-and-sarif.md).

## Directory Contents
- `PAI.md` – File
- `README.md` – File
- `SPEC.md` – File
- `__init__.py` – File
- `agentic_memory/` – Subdirectory
- `agents/` – Subdirectory
- `api/` – Subdirectory
- `audio/` – Subdirectory
- `audits/` – Subdirectory
- `auth/` – Subdirectory
- `bio_simulation/` – Subdirectory
- `build_synthesis/` – Subdirectory
- `cache/` – Subdirectory
- `cerebrum/` – Subdirectory
- `ci_cd_automation/` – Subdirectory
- `cli/` – Subdirectory
- `cloud/` – Subdirectory
- `coding/` – Subdirectory
- `collaboration/` – Subdirectory
- `compression/` – Subdirectory
- `concurrency/` – Subdirectory
- `config.yaml` – File
- `config_audits/` – Subdirectory
- `config_management/` – Subdirectory
- `config_monitoring/` – Subdirectory
- `container_optimization/` – Subdirectory
- `containerization/` – Subdirectory
- `cost_management/` – Subdirectory
- `dark/` – Subdirectory
- `data_lineage/` – Subdirectory
- `data_visualization/` – Subdirectory
- `database_management/` – Subdirectory
- `defense/` – Subdirectory
- `demos/` – Subdirectory
- `dependency_injection/` – Subdirectory
- `deployment/` – Subdirectory
- `docs/` – Subdirectory
- `docs_gen/` – Subdirectory
- `documentation/` – Subdirectory
- `documents/` – Subdirectory
- `edge_computing/` – Subdirectory
- `email/` – Subdirectory
- `embodiment/` – Subdirectory
- `encryption/` – Subdirectory
- `environment_setup/` – Subdirectory
- `events/` – Subdirectory
- `evolutionary_ai/` – Subdirectory
- `examples/` – Subdirectory
- `exceptions/` – Subdirectory
- `exploration/` – Subdirectory
- `feature_flags/` – Subdirectory
- `feature_store/` – Subdirectory
- `file_system/` – Subdirectory
- `finance/` – Subdirectory
- `fix_ty_ast.py` – File
- `fix_ty_imports.py` – File
- `fix_ty_stubborn.py` – File
- `formal_verification/` – Subdirectory
- `fpf/` – Subdirectory
- `git_analysis/` – Subdirectory
- `git_operations/` – Subdirectory
- `graph_rag/` – Subdirectory
- `ide/` – Subdirectory
- `identity/` – Subdirectory
- `index.html` – File
- `inference_optimization/` – Subdirectory
- `llm/` – Subdirectory
- `logging_monitoring/` – Subdirectory
- `logistics/` – Subdirectory
- `maintenance/` – Subdirectory
- `metrics/` – Subdirectory
- `migration/` – Subdirectory
- `model_context_protocol/` – Subdirectory
- `model_ops/` – Subdirectory
- `model_registry/` – Subdirectory
- `module_template/` – Subdirectory
- `multimodal/` – Subdirectory
- `networking/` – Subdirectory
- `notification/` – Subdirectory
- `observability_dashboard/` – Subdirectory
- `orchestrator/` – Subdirectory
- `pai/` – Subdirectory
- `pattern_matching/` – Subdirectory
- `performance/` – Subdirectory
- `physical_management/` – Subdirectory
- `plugin_system/` – Subdirectory
- `prompt_testing/` – Subdirectory
- `reports/` – Subdirectory
- `review/` – Subdirectory (PR/SARIF helpers)
- `rna/` – Subdirectory
- `run_all_scripts.py` – File
- `scrape/` – Subdirectory
- `security/` – Subdirectory
- `serialization/` – Subdirectory
- `setup_submodules.sh` – File
- `skills/` – Subdirectory
- `spatial/` – Subdirectory
- `src_structure_audit.py` – File
- `static_analysis/` – Subdirectory
- `system_discovery/` – Subdirectory
- `telemetry/` – Subdirectory
- `templating/` – Subdirectory
- `terminal_interface/` – Subdirectory
- `tools/` – Subdirectory
- `tree_sitter/` – Subdirectory
- `utils/` – Subdirectory
- `validation/` – Subdirectory
- `verification/` – Subdirectory
- `video/` – Subdirectory
- `website/` – Subdirectory
- `workflow_execution/` – Subdirectory
- `workflow_testing/` – Subdirectory
- `sair/` – SAIR Mathematics Distillation submodule (Equational Theories)

## Documentation (Mermaid)

| Script | Purpose |
| :--- | :--- |
| `strip_mermaid_style_lines.py` | Remove `style … fill:…` lines from fenced `mermaid` blocks under `docs/` |
| `normalize_mermaid_subgraphs.py` | Rewrite `subgraph "Label"` → `subgraph sg_<hash> [Label]` in `docs/` |
| `doc_inventory.py` | Print module / `mcp_tools.py` / `@mcp_tool` counts; optional `--pytest`, `--manifest` (`get_skill_manifest` tool count). Canonical definitions: [docs/reference/inventory.md](../docs/reference/inventory.md) |
| `mcp_spec_gap.py` | List `mcp_tools.py` paths missing sibling `MCP_TOOL_SPECIFICATION.md`; see [docs/reference/mcp-tool-spec-coverage.md](../docs/reference/mcp-tool-spec-coverage.md) |
| `src_structure_audit.py` | Run the read-only source module structure gate (`--json` available); checks runtime 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 |

See [docs/development/documentation.md](../docs/development/documentation.md).

## Navigation
- **Project Root**: ../README.md
