python -m scripts.ai vibe and the"
- },
{
"path": "scripts/ai/vibe/README.md",
"line": 9,
@@ -72,6 +66,12 @@
"line": 15,
"source_group": "scripts",
"text": "python -m scripts.ai vibe check"
+ },
+ {
+ "path": "scripts/ai/vibe/README.md",
+ "line": 16,
+ "source_group": "scripts",
+ "text": "python -m scripts.ai vibe setup"
}
]
},
@@ -131,7 +131,7 @@
"type": "sh",
"status": "active",
"agent_usage": [],
- "reference_count": 3,
+ "reference_count": 2,
"references": [
{
"path": "docs/00-project/ai/skills/_references/README.md",
@@ -139,12 +139,6 @@
"source_group": "docs",
"text": "| `scripts/ai/codex/check_skills_layout.sh` | Validates `_references` exists as a required subdirectory |"
},
- {
- "path": "docs/site/00-project/ai/skills/_references/index.html",
- "line": 23225,
- "source_group": "docs",
- "text": "scripts/ai/codex/check_skills_layout.shscripts/ai/codex/check_skills_mirror.shscript-codex/helper/test-basic.sh - Basic functionality testbash ./script-codex/helper/test-basic.shКогда запускаете launch-codex-wsl.ps1 start, Codex зависает потому что:
bash scripts/ai/mcp/check.sh"
- },
- {
- "path": "docs/site/05-operations/deployment/NEO4J-STARTUP-GUIDE/index.html",
- "line": 23595,
- "source_group": "docs",
- "text": "✅ Запустить тест: bash scripts/ai/mcp/check.sh "
+ "path": "scripts/ai/mcp/__main__.py",
+ "line": 29,
+ "source_group": "scripts",
+ "text": "\"check\": shell_command(\"check.sh\"),"
}
]
},
@@ -1727,7 +1685,7 @@
"type": "sh",
"status": "active",
"agent_usage": [],
- "reference_count": 69,
+ "reference_count": 39,
"references": [
{
"path": "docs/05-operations/deployment/NEO4J-COMPLETION-GUIDE.md",
@@ -1799,7 +1757,7 @@
"type": "sh",
"status": "active",
"agent_usage": [],
- "reference_count": 4,
+ "reference_count": 3,
"references": [
{
"path": "scripts/ai/.mcp.json",
@@ -1807,12 +1765,6 @@
"source_group": "scripts",
"text": "\"/mnt/wsl/docker-desktop-bind-mounts/Ubuntu/ccd98afae0adb4ee090bbfed89f354b31936eafe0874d43825bf3cb903f3bd1d/scripts/ai/mcp/github-mcp-wrapper.sh\""
},
- {
- "path": "scripts/ai/.vscode/mcp.json",
- "line": 61,
- "source_group": "scripts",
- "text": "\"/mnt/wsl/docker-desktop-bind-mounts/Ubuntu/ccd98afae0adb4ee090bbfed89f354b31936eafe0874d43825bf3cb903f3bd1d/scripts/ai/mcp/github-mcp-wrapper.sh\""
- },
{
"path": "scripts/ai/mcp/check.sh",
"line": 8,
@@ -1863,7 +1815,7 @@
"type": "sh",
"status": "active",
"agent_usage": [],
- "reference_count": 3,
+ "reference_count": 2,
"references": [
{
"path": "scripts/ai/.mcp.json",
@@ -1871,12 +1823,6 @@
"source_group": "scripts",
"text": "\"/mnt/wsl/docker-desktop-bind-mounts/Ubuntu/ccd98afae0adb4ee090bbfed89f354b31936eafe0874d43825bf3cb903f3bd1d/scripts/ai/mcp/mcp_brave_search_wrapper.sh\""
},
- {
- "path": "scripts/ai/.vscode/mcp.json",
- "line": 112,
- "source_group": "scripts",
- "text": "\"/mnt/wsl/docker-desktop-bind-mounts/Ubuntu/ccd98afae0adb4ee090bbfed89f354b31936eafe0874d43825bf3cb903f3bd1d/scripts/ai/mcp/mcp_brave_search_wrapper.sh\""
- },
{
"path": "scripts/ai/mcp/check.sh",
"line": 15,
@@ -1898,19 +1844,13 @@
"type": "sh",
"status": "active",
"agent_usage": [],
- "reference_count": 2,
+ "reference_count": 1,
"references": [
{
"path": "scripts/ai/.mcp.json",
"line": 142,
"source_group": "scripts",
"text": "\"/mnt/wsl/docker-desktop-bind-mounts/Ubuntu/ccd98afae0adb4ee090bbfed89f354b31936eafe0874d43825bf3cb903f3bd1d/scripts/ai/mcp/mcp_chembl_wrapper.sh\""
- },
- {
- "path": "scripts/ai/.vscode/mcp.json",
- "line": 142,
- "source_group": "scripts",
- "text": "\"/mnt/wsl/docker-desktop-bind-mounts/Ubuntu/ccd98afae0adb4ee090bbfed89f354b31936eafe0874d43825bf3cb903f3bd1d/scripts/ai/mcp/mcp_chembl_wrapper.sh\""
}
]
},
@@ -1950,7 +1890,7 @@
"type": "sh",
"status": "active",
"agent_usage": [],
- "reference_count": 3,
+ "reference_count": 2,
"references": [
{
"path": "scripts/ai/.mcp.json",
@@ -1958,12 +1898,6 @@
"source_group": "scripts",
"text": "\"/mnt/wsl/docker-desktop-bind-mounts/Ubuntu/ccd98afae0adb4ee090bbfed89f354b31936eafe0874d43825bf3cb903f3bd1d/scripts/ai/mcp/mcp_context7_wrapper.sh\""
},
- {
- "path": "scripts/ai/.vscode/mcp.json",
- "line": 82,
- "source_group": "scripts",
- "text": "\"/mnt/wsl/docker-desktop-bind-mounts/Ubuntu/ccd98afae0adb4ee090bbfed89f354b31936eafe0874d43825bf3cb903f3bd1d/scripts/ai/mcp/mcp_context7_wrapper.sh\""
- },
{
"path": "scripts/ai/mcp/check.sh",
"line": 10,
@@ -1985,7 +1919,7 @@
"type": "sh",
"status": "active",
"agent_usage": [],
- "reference_count": 5,
+ "reference_count": 3,
"references": [
{
"path": "docs/CODEX_WSL_SETUP.md",
@@ -1993,24 +1927,12 @@
"source_group": "docs",
"text": "\"args\": [\"exec\", \"-i\", \"bioetl-mcp-docker\", \"/mcp_docker_wrapper.sh\"]"
},
- {
- "path": "docs/site/CODEX_WSL_SETUP/index.html",
- "line": 23391,
- "source_group": "docs",
- "text": " "args": scripts/ai/mcp/support/load_repo_env.ps1 - PowerShell environment loader"
- },
{
"path": "scripts/ai/mcp/github-mcp-wrapper.ps1",
"line": 6,
@@ -2530,6 +2404,12 @@
"line": 6,
"source_group": "scripts",
"text": ". (Join-Path $PSScriptRoot \"support/load_repo_env.ps1\")"
+ },
+ {
+ "path": "scripts/ai/mcp/mcp_sonarqube_wrapper.ps1",
+ "line": 6,
+ "source_group": "scripts",
+ "text": ". (Join-Path $PSScriptRoot \"support/load_repo_env.ps1\")"
}
]
},
@@ -2538,7 +2418,7 @@
"type": "sh",
"status": "active",
"agent_usage": [],
- "reference_count": 5,
+ "reference_count": 3,
"references": [
{
"path": "docs/00-project/ai/memory/neo4j-project-memory-seed.json",
@@ -2552,18 +2432,6 @@
"source_group": "docs",
"text": "| `scripts/ai/mcp/support/load_repo_env.sh` | Env variable loader |"
},
- {
- "path": "docs/site/00-project/ai/memory/neo4j-project-memory-seed.json",
- "line": 76,
- "source_group": "docs",
- "text": "\"scripts/ai/mcp/support/load_repo_env.sh\","
- },
- {
- "path": "docs/site/05-operations/deployment/WSL-NEO4J-SETUP/index.html",
- "line": 23541,
- "source_group": "docs",
- "text": "scripts/ai/mcp/support/load_repo_env.shVibe setup helper: scripts/ai/vibe/helper/setup-env.sh "
- },
- {
- "path": "docs/site/03-guides/development/mistral-vibe-wsl2-setup/index.html",
- "line": 23258,
- "source_group": "docs",
- "text": "bash scripts/ai/vibe/helper/setup-env.sh"
- },
{
"path": "scripts/ai/vibe/helper/setup-env.ps1",
"line": 5,
@@ -2739,7 +2595,7 @@
"type": "ps1",
"status": "active",
"agent_usage": [],
- "reference_count": 12,
+ "reference_count": 9,
"references": [
{
"path": "docs/03-guides/development/mistral-vibe-wsl2-setup.md",
@@ -2772,22 +2628,22 @@
"text": "powershell -NoProfile -ExecutionPolicy Bypass -File .\\scripts\\ai\\vibe\\launch.ps1 \"inspect the failing architecture tests\""
},
{
- "path": "docs/site/03-guides/development/mistral-vibe-wsl2-setup/index.html",
- "line": 23242,
- "source_group": "docs",
- "text": "Canonical Windows PowerShell launcher: scripts/ai/vibe/launch.ps1 "
+ "path": "scripts/ai/__main__.py",
+ "line": 72,
+ "source_group": "scripts",
+ "text": "str(vibe_dir / \"launch.ps1\"),"
},
{
- "path": "docs/site/03-guides/development/mistral-vibe-wsl2-setup/index.html",
- "line": 23290,
- "source_group": "docs",
- "text": "powershell -NoProfile -ExecutionPolicy Bypass -File .\\scripts\\ai\\vibe\\launc"
+ "path": "scripts/ai/vibe/README.md",
+ "line": 18,
+ "source_group": "scripts",
+ "text": "pwsh -File scripts/ai/vibe/launch.ps1 --help"
},
{
- "path": "docs/site/03-guides/development/mistral-vibe-wsl2-setup/index.html",
- "line": 23291,
- "source_group": "docs",
- "text": "powershell -NoProfile -ExecutionPolicy Bypass -File .\\scripts\\ai\\vibe\\launch.ps1 "inspect the failing architecture te"
+ "path": "scripts/ai/vibe/README.md",
+ "line": 22,
+ "source_group": "scripts",
+ "text": "`launch.sh` / `launch.ps1` entrypoints and the local `helper/` setup/check"
}
]
},
@@ -2796,7 +2652,7 @@
"type": "sh",
"status": "active",
"agent_usage": [],
- "reference_count": 12,
+ "reference_count": 8,
"references": [
{
"path": "docs/03-guides/development/mistral-vibe-wsl2-setup.md",
@@ -2823,28 +2679,28 @@
"text": "bash scripts/ai/vibe/launch.sh --prompt \"fix the failing architecture test\" --max-turns 5"
},
{
- "path": "docs/site/03-guides/development/mistral-vibe-wsl2-setup/index.html",
- "line": 23241,
- "source_group": "docs",
- "text": "Canonical WSL launcher: scripts/ai/vibe/launch.sh "
+ "path": "scripts/ai/__main__.py",
+ "line": 80,
+ "source_group": "scripts",
+ "text": "return [\"bash\", str(vibe_dir / \"launch.sh\"), *rest]"
},
{
- "path": "docs/site/03-guides/development/mistral-vibe-wsl2-setup/index.html",
- "line": 23281,
- "source_group": "docs",
- "text": "bash scripts/ai/vibe/launch.sh"
+ "path": "scripts/ai/vibe/README.md",
+ "line": 17,
+ "source_group": "scripts",
+ "text": "bash scripts/ai/vibe/launch.sh --help"
},
{
- "path": "docs/site/03-guides/development/mistral-vibe-wsl2-setup/index.html",
- "line": 23282,
- "source_group": "docs",
- "text": "bash scripts/ai/vibe/launch.sh "inspect the failing ar"
+ "path": "scripts/ai/vibe/README.md",
+ "line": 22,
+ "source_group": "scripts",
+ "text": "`launch.sh` / `launch.ps1` entrypoints and the local `helper/` setup/check"
},
{
- "path": "docs/site/03-guides/development/mistral-vibe-wsl2-setup/index.html",
- "line": 23283,
- "source_group": "docs",
- "text": "bash scripts/ai/vibe/launch.sh --prompt uv run python scripts/check_entity_config_parity.py"
- },
- {
- "path": "docs/site/03-guides/docs-parity-gate/index.html",
- "line": 23760,
- "source_group": "docs",
- "text": "The active config/spec gate is located at scripts/check_entity_config_parity.py. It performs the following checks:
"
- },
{
"path": "scripts/ci_check_docs_parity.sh",
"line": 12,
@@ -2913,7 +2757,7 @@
"type": "sh",
"status": "active",
"agent_usage": [],
- "reference_count": 5,
+ "reference_count": 3,
"references": [
{
"path": "docs/03-guides/docs-parity-gate.md",
@@ -2927,18 +2771,6 @@
"source_group": "docs",
"text": "- bash scripts/ci_check_docs_parity.sh"
},
- {
- "path": "docs/site/03-guides/docs-parity-gate/index.html",
- "line": 23732,
- "source_group": "docs",
- "text": " run: - ./.venv/bin/python scripts/data_quality/export_chemb"
}
]
},
@@ -2973,7 +2799,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 14,
+ "reference_count": 8,
"references": [
{
"path": "docs/filters/README.md",
@@ -3018,10 +2844,10 @@
"text": "`scripts/data_quality/inventory_silver_filters_migration.py`."
},
{
- "path": "docs/site/filters/index.html",
- "line": 23339,
- "source_group": "docs",
- "text": "Generated by scripts/data_quality/inventory_silver_filters_migration.py.
"
+ "path": "tests/architecture/test_silver_filter_boundary_inventory.py",
+ "line": 349,
+ "source_group": "tests",
+ "text": "\"Run: python scripts/data_quality/inventory_silver_filters_migration.py\\n\""
}
]
},
@@ -3030,7 +2856,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 44,
+ "reference_count": 41,
"references": [
{
"path": ".pre-commit-config.yaml",
@@ -3087,7 +2913,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 16,
+ "reference_count": 10,
"references": [
{
"path": "docs/02-architecture/diagrams/governance/diagram-modernization-program.md",
@@ -3126,16 +2952,16 @@
"text": "if ! \"$PYTHON_BIN\" \"$REPO_ROOT/scripts/diagrams/add_svg_text_fallback.py\" --fix -f \"$temp_png_svg\" >/dev/null 2>&1; then"
},
{
- "path": "docs/site/02-architecture/diagrams/governance/diagram-modernization-program/index.html",
- "line": 23749,
- "source_group": "docs",
- "text": "scripts/diagrams/add_svg_text_fallback.pyadd_svg_text_fallback.py + checkpython scripts/diagrams/check_class_method_render_integrity.py --source-dir docs/02-architecture/diagrams/class-diagrams --svg-dir docs/02-architecture/diagrams/class-diagrams/svgscripts/diagrams/check_class_method_render_integrity.py"
- },
{
"path": "scripts/diagrams/README.md",
"line": 31,
@@ -3193,15 +3001,27 @@
"line": 65,
"source_group": "scripts",
"text": "\"check-class-methods\": python_command(\"check_class_method_render_integrity.py\"),"
- }
- ]
- },
- {
- "path": "scripts/diagrams/check_diagram_artifacts.py",
+ },
+ {
+ "path": "scripts/diagrams/run_diagram_checks.sh",
+ "line": 356,
+ "source_group": "scripts",
+ "text": "python3 \"$REPO_ROOT/scripts/diagrams/check_class_method_render_integrity.py\" \\"
+ },
+ {
+ "path": "scripts/diagrams/run_diagram_checks.sh",
+ "line": 369,
+ "source_group": "scripts",
+ "text": "python3 \"$REPO_ROOT/scripts/diagrams/check_class_method_render_integrity.py\" \\"
+ }
+ ]
+ },
+ {
+ "path": "scripts/diagrams/check_diagram_artifacts.py",
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 15,
+ "reference_count": 11,
"references": [
{
"path": ".github/workflows/diagram-nightly.yml",
@@ -3240,16 +3060,16 @@
"text": "- запуск `check_diagram_artifacts.py` (DIAG-T010/T011/T012);"
},
{
- "path": "docs/site/02-architecture/diagrams/governance/DIAGRAM-WORKFLOW-GUIDE/index.html",
- "line": 24790,
- "source_group": "docs",
- "text": "Проверить обязательные SVG-артефакты: python scripts/diagrams/check_diagram_artifacts.py --manifest docs/02-architecture/diagrams/manifests/visual-smoke.txt"
+ "path": "scripts/diagrams/README.md",
+ "line": 27,
+ "source_group": "scripts",
+ "text": "| `check-artifacts` | `check_diagram_artifacts.py` | Check required SVG artifacts and optional PNG compatibility artifacts |"
},
{
- "path": "docs/site/02-architecture/diagrams/governance/DIAGRAM-WORKFLOW-GUIDE/index.html",
- "line": 24791,
- "source_group": "docs",
- "text": "Для дополнительной compatibility-проверки PNG используйте curated manifest: python scripts/diagrams/check_diagram_artifacts.py --manifest docs/02-architecture/diagrams/manifests/png-compatibilit"
+ "path": "scripts/diagrams/__main__.py",
+ "line": 61,
+ "source_group": "scripts",
+ "text": "\"check-artifacts\": python_command(\"check_diagram_artifacts.py\"),"
}
]
},
@@ -3258,7 +3078,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 28,
+ "reference_count": 19,
"references": [
{
"path": ".github/workflows/diagram-nightly.yml",
@@ -3317,7 +3137,7 @@
"agent_usage": [
"technical-designer-mermaid"
],
- "reference_count": 13,
+ "reference_count": 10,
"references": [
{
"path": ".codex/skills/technical-designer-mermaid/SKILL.md",
@@ -3356,16 +3176,16 @@
"text": "| DIAG-T013 | Visual smoke manifest pass | Базовая читаемость эталонного пула | `check_diagram_visual_smoke.py` | Auto | PR | Ha"
},
{
- "path": "docs/site/00-project/ai/skills/local/technical-designer-mermaid/SKILL/index.html",
- "line": 23668,
- "source_group": "docs",
- "text": "python scripts/diagrams/check_diagram_visual_smoke.py --manifest docs/02-architecture/mmd-diagrams/visual-smoke-manifest.txt
"
+ "path": "scripts/diagrams/README.md",
+ "line": 29,
+ "source_group": "scripts",
+ "text": "| `check-visual-smoke` | `check_diagram_visual_smoke.py` | Visual smoke test for diagrams |"
},
{
- "path": "docs/site/02-architecture/diagrams/governance/diagram-modernization-program/index.html",
- "line": 23746,
- "source_group": "docs",
- "text": "scripts/diagrams/check_diagram_visual_smoke.pypost-check: scripts/diagrams/check_pdf_image_bounds.py "
- },
{
"path": "scripts/diagrams/README.md",
"line": 32,
@@ -3413,7 +3227,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 23,
+ "reference_count": 15,
"references": [
{
"path": ".github/workflows/diagram-nightly.yml",
@@ -3518,7 +3332,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 7,
+ "reference_count": 6,
"references": [
{
"path": ".github/workflows/diagram-nightly.yml",
@@ -3532,12 +3346,6 @@
"source_group": "docs",
"text": "`scripts/diagrams/enforce_diagram_quality_budget.py`."
},
- {
- "path": "docs/site/02-architecture/diagrams/index.html",
- "line": 24906,
- "source_group": "docs",
- "text": "scripts/diagrams/enforce_diagram_quality_budget.py."
- },
{
"path": "scripts/diagrams/README.md",
"line": 20,
@@ -3749,7 +3557,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 3,
+ "reference_count": 2,
"references": [
{
"path": "docs/02-architecture/diagrams/README.md",
@@ -3757,12 +3565,6 @@
"source_group": "docs",
"text": "- Supplemental generator: `scripts/diagrams/generate_package_family_class_diagrams.py`"
},
- {
- "path": "docs/site/02-architecture/diagrams/index.html",
- "line": 24232,
- "source_group": "docs",
- "text": "Supplemental generator: scripts/diagrams/generate_package_family_class_diagrams.py "
- },
{
"path": "scripts/diagrams/README.md",
"line": 100,
@@ -3776,7 +3578,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 9,
+ "reference_count": 7,
"references": [
{
"path": "docs/00-project/ai/agents/scripts/diagrams/py-doc-bot-2.py",
@@ -3790,18 +3592,6 @@
"source_group": "docs",
"text": "- `scripts/diagrams/generate_with_descriptions_docx.py`"
},
- {
- "path": "docs/site/00-project/ai/agents/scripts/diagrams/py-doc-bot-2.py",
- "line": 13,
- "source_group": "docs",
- "text": "return repo_root / \"scripts\" / \"diagrams\" / \"generate_with_descriptions_docx.py\""
- },
- {
- "path": "docs/site/02-architecture/diagrams/index.html",
- "line": 24828,
- "source_group": "docs",
- "text": "scripts/diagrams/generate_with_descriptions_docx.pyscripts/diagrams/generate_with_descriptions_pdf.pyrepo scripts now use scripts/diagrams/mmdc_wrapper.sh as the default mmdc entrypoint; "
- },
- {
- "path": "docs/site/02-architecture/diagrams/tooling/render.sh",
- "line": 46,
- "source_group": "docs",
- "text": "MMDC_BIN=\"${MMDC_BIN:-$REPO_ROOT/scripts/diagrams/mmdc_wrapper.sh}\""
- },
- {
- "path": "docs/site/02-architecture/diagrams/tooling/render.sh",
- "line": 294,
- "source_group": "docs",
- "text": "echo \" Provide MMDC_BIN=/path/to/mmdc or restore scripts/diagrams/mmdc_wrapper.sh\""
- },
{
"path": "scripts/diagrams/run_diagram_checks.sh",
"line": 237,
@@ -4051,7 +3811,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 39,
+ "reference_count": 21,
"references": [
{
"path": "docs/02-architecture/decisions/ADR-040-diagram-governance.md",
@@ -4129,7 +3889,7 @@
"type": "sh",
"status": "active",
"agent_usage": [],
- "reference_count": 34,
+ "reference_count": 21,
"references": [
{
"path": "docs/00-project/ai/agents/agents/py-doc-bot.md",
@@ -4186,7 +3946,7 @@
"type": "sh",
"status": "active",
"agent_usage": [],
- "reference_count": 8,
+ "reference_count": 6,
"references": [
{
"path": "docs/00-project/ai/agents/scripts/diagrams/py-doc-bot-4.sh",
@@ -4200,18 +3960,6 @@
"source_group": "docs",
"text": "- unified orchestrator: `scripts/diagrams/run_diagram_docs_agent.sh`"
},
- {
- "path": "docs/site/00-project/ai/agents/scripts/diagrams/py-doc-bot-4.sh",
- "line": 12,
- "source_group": "docs",
- "text": "exec bash \"$REPO_ROOT/scripts/diagrams/run_diagram_docs_agent.sh\" \"$@\""
- },
- {
- "path": "docs/site/02-architecture/diagrams/index.html",
- "line": 24829,
- "source_group": "docs",
- "text": "unified orchestrator: scripts/diagrams/run_diagram_docs_agent.sh "
- },
{
"path": "scripts/diagrams/README.md",
"line": 51,
@@ -4243,7 +3991,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 14,
+ "reference_count": 11,
"references": [
{
"path": ".github/workflows/diagram-nightly.yml",
@@ -4270,28 +4018,28 @@
"text": "- `run_diagram_nightly_suite.py` (DIAG-T024..T029);"
},
{
- "path": "docs/site/02-architecture/diagrams/governance/DIAGRAM-WORKFLOW-GUIDE/index.html",
- "line": 24860,
- "source_group": "docs",
- "text": "run_diagram_nightly_suite.py "
+ "path": "scripts/diagrams/README.md",
+ "line": 62,
+ "source_group": "scripts",
+ "text": "| `nightly` | `run_diagram_nightly_suite.py` | Run full diagram nightly suite |"
},
{
- "path": "docs/site/02-architecture/diagrams/governance/DIAGRAM-WORKFLOW-GUIDE/index.html",
- "line": 24879,
- "source_group": "docs",
- "text": "nightly — pr + DIAG-T024..T029 (run_diagram_nightly_suite.py).run_diagram_nightly_suite.py (DIAG-T024..T029);Примечание по size-normalization (scripts/diagrams/uniform_diagram_sizes.py):
"
+ "path": "scripts/diagrams/README.md",
+ "line": 44,
+ "source_group": "scripts",
+ "text": "| `fix-sizes` | `uniform_diagram_sizes.py` | Uniform diagram sizes |"
},
{
- "path": "docs/site/02-architecture/diagrams/governance/policy/index.html",
- "line": 23707,
- "source_group": "docs",
- "text": "uniform_diagram_sizes.py использовать только точечно и только после ручной проверки,"
+ "path": "scripts/diagrams/__main__.py",
+ "line": 74,
+ "source_group": "scripts",
+ "text": "\"fix-sizes\": python_command(\"uniform_diagram_sizes.py\"),"
},
{
- "path": "docs/site/02-architecture/diagrams/index.html",
- "line": 24941,
- "source_group": "docs",
- "text": "
Use scripts/diagrams/uniform_diagram_sizes.py to normalize class/flowchart object sizes:
"
+ "path": "tests/architecture/test_uniform_diagram_group_width.py",
+ "line": 12,
+ "source_group": "tests",
+ "text": "\"\"\"Load scripts/diagrams/uniform_diagram_sizes.py as a module.\"\"\""
}
]
},
@@ -4500,7 +4218,7 @@
"agent_usage": [
"technical-designer-mermaid"
],
- "reference_count": 24,
+ "reference_count": 16,
"references": [
{
"path": ".codex/skills/technical-designer-mermaid/SKILL.md",
@@ -4587,7 +4305,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 144,
+ "reference_count": 120,
"references": [
{
"path": ".github/workflows/docs-kpi-weekly.yml",
@@ -4889,7 +4607,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 46,
+ "reference_count": 30,
"references": [
{
"path": ".github/workflows/docs.yml",
@@ -5279,7 +4997,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 8,
+ "reference_count": 5,
"references": [
{
"path": "docs/05-engineering/normalization_plan_P0_P6.md",
@@ -5299,24 +5017,6 @@
"source_group": "docs",
"text": "- [generate_pipeline_normalization_field_matrix.py](../../scripts/docs/generate_pipeline_normalization_field_matrix.py) already generates deterministic multi-pipeline artifacts"
},
- {
- "path": "docs/site/05-engineering/normalization_plan_P0_P6/index.html",
- "line": 25751,
- "source_group": "docs",
- "text": "generate_pipeline_normalization_field_matrix.py "
- },
- {
- "path": "docs/site/05-engineering/normalization_plan_P0_P6/index.html",
- "line": 25849,
- "source_group": "docs",
- "text": "generate_pipeline_normalization_field_matrix.py "
- },
- {
- "path": "docs/site/05-engineering/normalization_plan_P0_P6/index.html",
- "line": 26264,
- "source_group": "docs",
- "text": "generate_pipeline_normalization_field_matrix.py already generates deterministic multi-pipeline artifacts "
- },
{
"path": "tests/architecture/test_docs_compat_shim_governance.py",
"line": 21,
@@ -5703,7 +5403,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 12,
+ "reference_count": 8,
"references": [
{
"path": "docs/00-project/DOCUMENTATION_GOVERNANCE.md",
@@ -5730,28 +5430,28 @@
"text": "The broader governance report path is implemented by `scripts/docs_parity_check.py`,"
},
{
- "path": "docs/site/00-project/DOCUMENTATION_GOVERNANCE/index.html",
- "line": 24428,
- "source_group": "docs",
- "text": "docs_parity_check.py "
+ "path": "scripts/documentation_governance_check.py",
+ "line": 84,
+ "source_group": "scripts",
+ "text": "# Check if docs_parity_check.py exists and is executable"
},
{
- "path": "docs/site/00-project/DOCUMENTATION_GOVERNANCE/index.html",
- "line": 24443,
- "source_group": "docs",
- "text": "scripts/docs_parity_check.py - Configuration parityThe broader governance report path is implemented by scripts/docs_parity_check.py,"
+ "path": "scripts/engineering/repo/catalog.yaml",
+ "line": 24,
+ "source_group": "scripts",
+ "text": "- docs_parity_check.py"
}
]
},
@@ -5775,7 +5475,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 7,
+ "reference_count": 5,
"references": [
{
"path": "docs/00-project/TOOLS.md",
@@ -5795,18 +5495,6 @@
"source_group": "docs",
"text": "uv run python -m scripts.engineering.baselines dq-baseline --dry-run"
},
- {
- "path": "docs/site/00-project/TOOLS/index.html",
- "line": 23572,
- "source_group": "docs",
- "text": "
uv run python -m scripts.engineering.baselines dq-baselineuv run python -m scripts.engineering.baselinesdq_baseline_update.pydq_baseline_update.py scripts/engineering/ci/run_pytest_resilient.py"
- },
{
"path": "scripts/engineering/ci/README.md",
"line": 16,
"source_group": "scripts",
"text": "| `run-tests` | `scripts/engineering/ci/run_pytest_resilient.py` | Run pytest with resilient retry logic |"
+ },
+ {
+ "path": "scripts/engineering/ci/__main__.py",
+ "line": 29,
+ "source_group": "scripts",
+ "text": "\"run-tests\": \"run_pytest_resilient.py\","
+ },
+ {
+ "path": "tests/architecture/test_generated_artifact_routing.py",
+ "line": 153,
+ "source_group": "tests",
+ "text": "ROOT / \"scripts\" / \"engineering\" / \"ci\" / \"run_pytest_resilient.py\""
}
]
},
@@ -6420,68 +6090,11 @@
"references": []
},
{
- "path": "scripts/engineering/dev/.setup_wsl_codex.sh",
- "type": "sh",
+ "path": "scripts/engineering/dev/.wsl-vpn-fix.ps1",
+ "type": "ps1",
"status": "active",
"agent_usage": [],
- "reference_count": 21,
- "references": [
- {
- "path": "docs/03-guides/development/codex-wsl2-setup.md",
- "line": 68,
- "source_group": "docs",
- "text": "| `.setup_wsl_codex.sh` | `scripts/engineering/dev/` | DNS resolver (dig + PowerShell fallback) |"
- },
- {
- "path": "docs/03-guides/development/codex-wsl2-setup.md",
- "line": 253,
- "source_group": "docs",
- "text": "**Layer 1: DNS** (`scripts/engineering/dev/.setup_wsl_codex.sh`)"
- },
- {
- "path": "docs/03-guides/development/codex-wsl2-setup.md",
- "line": 266,
- "source_group": "docs",
- "text": "bash \"$BIOETL_DIR/scripts/engineering/dev/.setup_wsl_codex.sh\""
- },
- {
- "path": "docs/03-guides/development/codex-wsl2-setup.md",
- "line": 292,
- "source_group": "docs",
- "text": "bash \"$BIOETL_DIR/scripts/engineering/dev/.setup_wsl_codex.sh\" 2>/dev/null"
- },
- {
- "path": "docs/03-guides/development/codex-wsl2-setup.md",
- "line": 348,
- "source_group": "docs",
- "text": "bash \"$BIOETL_DIR/scripts/engineering/dev/.setup_wsl_codex.sh\""
- },
- {
- "path": "docs/05-operations/tooling/scripts-ops/CODEX_QUICK_REF.md",
- "line": 7,
- "source_group": "docs",
- "text": ".\\scripts\\engineering\\dev\\.setup_wsl_codex.sh"
- },
- {
- "path": "docs/05-operations/tooling/scripts-ops/CODEX_QUICK_REF.md",
- "line": 71,
- "source_group": "docs",
- "text": "| `OpenAI timeout` | Run setup: `.\\scripts\\engineering\\dev\\.setup_wsl_codex.sh` |"
- },
- {
- "path": "docs/05-operations/tooling/scripts-ops/CODEX_SETUP.md",
- "line": 23,
- "source_group": "docs",
- "text": ".\\scripts\\engineering\\dev\\.setup_wsl_codex.sh"
- }
- ]
- },
- {
- "path": "scripts/engineering/dev/.wsl-vpn-fix.ps1",
- "type": "ps1",
- "status": "active",
- "agent_usage": [],
- "reference_count": 1,
+ "reference_count": 1,
"references": [
{
"path": "scripts/engineering/dev/README.md",
@@ -6496,7 +6109,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 40,
+ "reference_count": 30,
"references": [
{
"path": "docs/00-project/ai/agents/guides/AGENT.md",
@@ -6553,7 +6166,7 @@
"type": "sh",
"status": "active",
"agent_usage": [],
- "reference_count": 54,
+ "reference_count": 36,
"references": [
{
"path": "docs/03-guides/development/codex-wsl2-setup.md",
@@ -6795,7 +6408,7 @@
"agent_usage": [
"py-test-swarm"
],
- "reference_count": 43,
+ "reference_count": 32,
"references": [
{
"path": ".codex/agents/py-test-swarm.md",
@@ -6854,7 +6467,7 @@
"agent_usage": [
"py-test-swarm"
],
- "reference_count": 50,
+ "reference_count": 32,
"references": [
{
"path": ".codex/agents/py-test-swarm.md",
@@ -6911,7 +6524,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 23,
+ "reference_count": 22,
"references": [
{
"path": ".pre-commit-config.yaml",
@@ -6970,7 +6583,7 @@
"agent_usage": [
"py-test-swarm"
],
- "reference_count": 66,
+ "reference_count": 48,
"references": [
{
"path": ".codex/agents/py-test-swarm.md",
@@ -7029,7 +6642,7 @@
"agent_usage": [
"py-test-swarm"
],
- "reference_count": 94,
+ "reference_count": 62,
"references": [
{
"path": ".codex/agents/py-test-swarm.md",
@@ -7086,7 +6699,7 @@
"type": "sh",
"status": "active",
"agent_usage": [],
- "reference_count": 21,
+ "reference_count": 17,
"references": [
{
"path": "Makefile",
@@ -7119,22 +6732,22 @@
"text": "| 6 | `BIOETL_PYTEST_SHARDED_FORCE_COVERAGE=1 bash scripts/engineering/dev/run_pytest_sharded.sh --stream --keep-coverage-files --coverage-dir .coverage-sharded -- -vv --cov-report=term-missing` | В"
},
{
- "path": "docs/site/03-guides/testing/index.html",
- "line": 23998,
- "source_group": "docs",
- "text": "ignore/deselect inventory for run_pytest_sharded.sh lives in"
+ "path": "scripts/engineering/dev/README.md",
+ "line": 50,
+ "source_group": "scripts",
+ "text": "bash scripts/engineering/dev/run_pytest_sharded.sh"
},
{
- "path": "docs/site/03-guides/testing/index.html",
- "line": 24391,
- "source_group": "docs",
- "text": "bash scripts/engineering/dev/run_pytest_sharded.sh \\BIOETL_PYTEST_SHARDED_FORCE_COVERAGE=1 bash scripts/engineering/dev/run_pytest_sharded.sh --stream --keep-coverage-files --coverage-dir .coverage-sharded -- -vv --cov-report=term-missingaudit_structure.py"
- },
- {
- "path": "docs/site/00-project/TOOLS/index.html",
- "line": 23676,
- "source_group": "docs",
- "text": "audit_structure.py, create_pipeline.pycleanup_consolidate.py"
- },
{
"path": "scripts/engineering/diagnostics/README.md",
"line": 17,
@@ -7557,7 +7152,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 7,
+ "reference_count": 5,
"references": [
{
"path": "docs/00-project/TOOLS.md",
@@ -7571,18 +7166,6 @@
"source_group": "docs",
"text": "| [cleanup-policy.md](../03-guides/cleanup-policy.md) | `cleanup_project.py`, `cleanup_repository.py`, `vacuum_delta.py`, `verify_checksums.py` |"
},
- {
- "path": "docs/site/00-project/TOOLS/index.html",
- "line": 23537,
- "source_group": "docs",
- "text": "cleanup_project.pycleanup_project.py, cleanup_repository.py, vacuum_delta.py, verify_checksums.pyscripts/engineering/qa/check_generic_field_ownership.py --check validates that"
- },
- {
- "path": "docs/site/04-reference/contracts/canonical-field-registry/index.html",
- "line": 23645,
- "source_group": "docs",
- "text": "python3 scripts/engineering/qa/check_generic_field_ownership.py --check
"
- },
{
"path": "scripts/engineering/qa/__main__.py",
"line": 80,
@@ -7985,7 +7556,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 3,
+ "reference_count": 2,
"references": [
{
"path": "docs/04-reference/contracts/gold-schemas.md",
@@ -7993,12 +7564,6 @@
"source_group": "docs",
"text": "`python3 scripts/engineering/qa/check_gold_nullable_numeric_compatibility.py --check`."
},
- {
- "path": "docs/site/04-reference/contracts/gold-schemas/index.html",
- "line": 25615,
- "source_group": "docs",
- "text": "python3 scripts/engineering/qa/check_gold_nullable_numeric_compatibility.py --check."
- },
{
"path": "scripts/engineering/qa/__main__.py",
"line": 79,
@@ -8069,7 +7634,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 7,
+ "reference_count": 5,
"references": [
{
"path": ".github/workflows/semantic-governance.yml",
@@ -8095,18 +7660,6 @@
"source_group": "docs",
"text": "`python3 scripts/engineering/qa/check_ontology_unit_semantics.py --check`"
},
- {
- "path": "docs/site/04-reference/contracts/canonical-field-registry/index.html",
- "line": 23620,
- "source_group": "docs",
- "text": "scripts/engineering/qa/check_ontology_unit_semantics.py --check validates"
- },
- {
- "path": "docs/site/04-reference/contracts/canonical-field-registry/index.html",
- "line": 23647,
- "source_group": "docs",
- "text": "python3 scripts/engineering/qa/check_ontology_unit_semantics.py --check"
- },
{
"path": "scripts/engineering/qa/__main__.py",
"line": 81,
@@ -8120,7 +7673,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 6,
+ "reference_count": 4,
"references": [
{
"path": "docs/00-project/ai/prompts/architecture_metric_exemptions_tasks_json_prompt.md",
@@ -8134,18 +7687,6 @@
"source_group": "docs",
"text": "1. `scripts/engineering/qa/check_quality_exemptions.py --mode warn` passes."
},
- {
- "path": "docs/site/00-project/ai/prompts/architecture_metric_exemptions_tasks_json_prompt/index.html",
- "line": 23291,
- "source_group": "docs",
- "text": "
python scripts/engineering/qa/check_quality_exemptions.py --mode auto --growth-mode auto --trend-report offscripts/engineering/qa/check_quality_exemptions.py --mode warn passes.scripts/engineering/qa/check_semantic_anchor_parity.py --check is the"
- },
- {
- "path": "docs/site/04-reference/contracts/canonical-field-registry/index.html",
- "line": 23643,
- "source_group": "docs",
- "text": "python3 scripts/engineering/qa/check_semantic_anchor_parity.py --check"
- },
{
"path": "scripts/engineering/qa/__main__.py",
"line": 78,
@@ -8216,7 +7745,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 3,
+ "reference_count": 2,
"references": [
{
"path": "docs/04-reference/contracts/canonical-field-registry.md",
@@ -8224,12 +7753,6 @@
"source_group": "docs",
"text": "- QA check: `python3 scripts/engineering/qa/check_semantic_field_registry.py --check`"
},
- {
- "path": "docs/site/04-reference/contracts/canonical-field-registry/index.html",
- "line": 23637,
- "source_group": "docs",
- "text": "
QA check: python3 scripts/engineering/qa/check_semantic_field_registry.py --check "
- },
{
"path": "scripts/engineering/qa/__main__.py",
"line": 73,
@@ -8270,7 +7793,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 7,
+ "reference_count": 5,
"references": [
{
"path": ".github/workflows/semantic-governance.yml",
@@ -8296,18 +7819,6 @@
"source_group": "docs",
"text": "`python3 scripts/engineering/qa/check_semantic_pair_matrix_budget.py --check`"
},
- {
- "path": "docs/site/04-reference/contracts/canonical-field-registry/index.html",
- "line": 23591,
- "source_group": "docs",
- "text": "scripts/engineering/qa/check_semantic_pair_matrix_budget.py --check validates"
- },
- {
- "path": "docs/site/04-reference/contracts/canonical-field-registry/index.html",
- "line": 23641,
- "source_group": "docs",
- "text": "python3 scripts/engineering/qa/check_semantic_pair_matrix_budget.py --check"
- },
{
"path": "scripts/engineering/qa/__main__.py",
"line": 75,
@@ -8321,7 +7832,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 7,
+ "reference_count": 5,
"references": [
{
"path": ".github/workflows/semantic-governance.yml",
@@ -8347,18 +7858,6 @@
"source_group": "docs",
"text": "`python3 scripts/engineering/qa/check_semantic_registry_drift.py --check`"
},
- {
- "path": "docs/site/04-reference/contracts/canonical-field-registry/index.html",
- "line": 23554,
- "source_group": "docs",
- "text": "
scripts/engineering/qa/check_semantic_registry_drift.py --check regenerates"
- },
- {
- "path": "docs/site/04-reference/contracts/canonical-field-registry/index.html",
- "line": 23639,
- "source_group": "docs",
- "text": "python3 scripts/engineering/qa/check_semantic_registry_drift.py --check"
- },
{
"path": "scripts/engineering/qa/__main__.py",
"line": 74,
@@ -8372,21 +7871,8 @@
"type": "py",
"status": "supporting",
"agent_usage": [],
- "reference_count": 2,
- "references": [
- {
- "path": "docs/site/03-guides/testing/index.html",
- "line": 24025,
- "source_group": "docs",
- "text": "
python scripts/engineering/qa/check_test_audit_prefl"
- },
- {
- "path": "docs/site/03-guides/testing/index.html",
- "line": 24028,
- "source_group": "docs",
- "text": "check_test_audit_preflight.py --strict treats missing or unhealthy git-lfs,"
- }
- ]
+ "reference_count": 0,
+ "references": []
},
{
"path": "scripts/engineering/qa/check_xwalk_missing_backlog.py",
@@ -8426,7 +7912,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 3,
+ "reference_count": 2,
"references": [
{
"path": "docs/04-reference/normalization/pubchem-normalization.md",
@@ -8434,12 +7920,6 @@
"source_group": "docs",
"text": "fixtures by `scripts/engineering/qa/extract_pubchem_property_vocab.py`."
},
- {
- "path": "docs/site/04-reference/normalization/pubchem-normalization/index.html",
- "line": 23482,
- "source_group": "docs",
- "text": "fixtures by scripts/engineering/qa/extract_pubchem_property_vocab.py.
"
- },
{
"path": "scripts/engineering/qa/__main__.py",
"line": 91,
@@ -8453,7 +7933,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 3,
+ "reference_count": 2,
"references": [
{
"path": "docs/04-reference/normalization/publication-normalization.md",
@@ -8461,12 +7941,6 @@
"source_group": "docs",
"text": "and the extractor `scripts/engineering/qa/extract_publication_nested_vocab.py`."
},
- {
- "path": "docs/site/04-reference/normalization/publication-normalization/index.html",
- "line": 23648,
- "source_group": "docs",
- "text": "and the extractor scripts/engineering/qa/extract_publication_nested_vocab.py."
- },
{
"path": "scripts/engineering/qa/__main__.py",
"line": 92,
@@ -8535,7 +8009,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 31,
+ "reference_count": 26,
"references": [
{
"path": ".github/workflows/architecture-docs-nightly.yml",
@@ -8592,7 +8066,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 18,
+ "reference_count": 11,
"references": [
{
"path": "docs/00-project/ai/memory/memory-py-architecture-debt-bot.md",
@@ -8649,7 +8123,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 5,
+ "reference_count": 4,
"references": [
{
"path": ".github/workflows/tests.yml",
@@ -8663,12 +8137,6 @@
"source_group": "docs",
"text": "- `scripts/engineering/qa/generate_hotspot_degradation_report.py` (`uv run python -m scripts.engineering.qa report-hotspots`, rolling-window degradation report)"
},
- {
- "path": "docs/site/05-operations/performance-baselines/index.html",
- "line": 23485,
- "source_group": "docs",
- "text": "scripts/engineering/qa/generate_hotspot_degradation_report.py (uv run python -m scripts.engineering.qa report-hotspots, rolling-window degradation report)Generated by scripts/engineering/qa/generate_reproducibility_support_matrix.py."
}
]
},
@@ -8736,39 +8198,8 @@
"type": "py",
"status": "supporting",
"agent_usage": [],
- "reference_count": 5,
- "references": [
- {
- "path": "docs/site/fixes/test_dependency_fixes/index.html",
- "line": 23174,
- "source_group": "docs",
- "text": "2. Missing hotspot_family_metrics.py Module"
- },
- {
- "path": "docs/site/fixes/test_dependency_fixes/index.html",
- "line": 23318,
- "source_group": "docs",
- "text": "
2. Missing hotspot_family_metrics.py ModuleRoot Cause: The file scripts/engineering/qa/hotspot_family_metrics.py was missing from the current branch but existed in git history."
- },
- {
- "path": "docs/site/fixes/test_dependency_fixes/index.html",
- "line": 23326,
- "source_group": "docs",
- "text": "Command used: git show b4c2d5abb:scripts/engineering/qa/hotspot_family_metrics.py > scripts/engineering/qa/hotspot_family_metrics.py "
- },
- {
- "path": "docs/site/fixes/test_dependency_fixes/index.html",
- "line": 23363,
- "source_group": "docs",
- "text": "Restored: scripts/engineering/qa/hotspot_family_metrics.py (from git history) "
- }
- ]
+ "reference_count": 0,
+ "references": []
},
{
"path": "scripts/engineering/qa/import_graph_inventory.py",
@@ -8783,7 +8214,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 18,
+ "reference_count": 11,
"references": [
{
"path": "docs/00-project/TOOLS.md",
@@ -8828,10 +8259,10 @@
"text": "python scripts/engineering/qa/lint_terminology.py src/bioetl/"
},
{
- "path": "docs/site/00-project/TOOLS/index.html",
- "line": 23601,
- "source_group": "docs",
- "text": "lint_terminology.py --help`. Скрипты также доступны напрямую: `python scripts/engineering/qa/naming_audit.py`."
},
- {
- "path": "docs/site/00-project/TOOLS/index.html",
- "line": 23593,
- "source_group": "docs",
- "text": "naming_audit.pynaming_audit.pyКаждая группа поддерживает --help и <command> --help. Скрипты также доступны напрямую: python scripts/engineering/qa/naming_audit.py.
"
- },
{
"path": "scripts/engineering/qa/README.md",
"line": 16,
@@ -8889,6 +8302,24 @@
"line": 63,
"source_group": "scripts",
"text": "\"check-naming\": \"scripts.engineering.qa.naming_audit\","
+ },
+ {
+ "path": "scripts/engineering/qa/check_naming_package_consistency.py",
+ "line": 5,
+ "source_group": "scripts",
+ "text": "1) strict suffix-policy: delegated to ``scripts/engineering/qa/naming_audit.py --check``."
+ },
+ {
+ "path": "scripts/engineering/qa/check_naming_package_consistency.py",
+ "line": 31,
+ "source_group": "scripts",
+ "text": "CANONICAL_NAMING_AUDIT_PATH = Path(\"scripts/engineering/qa/naming_audit.py\")"
+ },
+ {
+ "path": "scripts/engineering/qa/check_naming_package_consistency.py",
+ "line": 244,
+ "source_group": "scripts",
+ "text": "location=\"scripts/engineering/qa/naming_audit.py --check\","
}
]
},
@@ -9141,7 +8572,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 6,
+ "reference_count": 4,
"references": [
{
"path": "docs/05-engineering/normalization_plan_P0_P6.md",
@@ -9156,22 +8587,10 @@
"text": "- fallback inventory report: [report_normalization_fallback_inventory.py](../../scripts/engineering/qa/report_normalization_fallback_inventory.py)"
},
{
- "path": "docs/site/05-engineering/normalization_plan_P0_P6/index.html",
- "line": 25756,
- "source_group": "docs",
- "text": "report_normalization_fallback_inventory.py "
- },
- {
- "path": "docs/site/05-engineering/normalization_plan_P0_P6/index.html",
- "line": 25873,
- "source_group": "docs",
- "text": "fallback inventory report: report_normalization_fallback_inventory.py "
- },
- {
- "path": "scripts/engineering/qa/__main__.py",
- "line": 98,
- "source_group": "scripts",
- "text": "\"report-normalization-fallback-inventory\": \"scripts.engineering.qa.report_normalization_fallback_inventory\","
+ "path": "scripts/engineering/qa/__main__.py",
+ "line": 98,
+ "source_group": "scripts",
+ "text": "\"report-normalization-fallback-inventory\": \"scripts.engineering.qa.report_normalization_fallback_inventory\","
},
{
"path": "tests/architecture/test_normalization_evidence_governance.py",
@@ -9246,28 +8665,15 @@
"type": "py",
"status": "supporting",
"agent_usage": [],
- "reference_count": 2,
- "references": [
- {
- "path": "docs/site/03-guides/testing/index.html",
- "line": 24026,
- "source_group": "docs",
- "text": "python scripts/engineering/qa/report_test_governance_audit.py --check"
- },
- {
- "path": "docs/site/03-guides/testing/index.html",
- "line": 24032,
- "source_group": "docs",
- "text": "report_test_governance_audit.py --check enforces the current ratcheting"
- }
- ]
+ "reference_count": 0,
+ "references": []
},
{
"path": "scripts/engineering/qa/report_vcr_metadata_catalog.py",
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 12,
+ "reference_count": 10,
"references": [
{
"path": "docs/02-architecture/decisions/ADR-042-testing-strategy-matrix.md",
@@ -9287,18 +8693,6 @@
"source_group": "docs",
"text": "- `scripts/engineering/qa/report_vcr_metadata_catalog.py --check`"
},
- {
- "path": "docs/site/02-architecture/decisions/ADR-042-testing-strategy-matrix/index.html",
- "line": 23815,
- "source_group": "docs",
- "text": "scripts/engineering/qa/report_vcr_metadata_catalog.py and"
- },
- {
- "path": "docs/site/03-guides/testing/index.html",
- "line": 24090,
- "source_group": "docs",
- "text": "canonical tooling paths активированы для enforced rollout: scripts/engineering/qa/report_vcr_metadata_catalog.py генерирует/проверяет catalog, а scripts/ops/migrations/active/ba"
- },
{
"path": "scripts/engineering/qa/README.md",
"line": 28,
@@ -9316,6 +8710,18 @@
"line": 87,
"source_group": "scripts",
"text": "python scripts/engineering/qa/report_vcr_metadata_catalog.py --update"
+ },
+ {
+ "path": "scripts/engineering/qa/__main__.py",
+ "line": 86,
+ "source_group": "scripts",
+ "text": "\"report-vcr-metadata\": \"scripts.engineering.qa.report_vcr_metadata_catalog\","
+ },
+ {
+ "path": "tests/architecture/test_integration_vcr_policy.py",
+ "line": 366,
+ "source_group": "tests",
+ "text": "\"scripts/engineering/qa/report_vcr_metadata_catalog.py\","
}
]
},
@@ -9324,7 +8730,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 9,
+ "reference_count": 5,
"references": [
{
"path": "docs/04-reference/contracts/run-manifest-ledger.md",
@@ -9351,28 +8757,10 @@
"text": "- `run_historical_replay_closure_campaign.py` is the deterministic batch path"
},
{
- "path": "docs/site/04-reference/contracts/run-manifest-ledger/index.html",
- "line": 24217,
- "source_group": "docs",
- "text": "scripts/engineering/qa/run_historical_replay_closure_campaign.py --require-global-claim"
- },
- {
- "path": "docs/site/05-operations/runbooks/run-manifest-inspection/index.html",
- "line": 23857,
- "source_group": "docs",
- "text": "./.venv/bin/python scripts/engineering/qa/run_historical_replay_closure_campaign.py"
- },
- {
- "path": "docs/site/05-operations/runbooks/run-manifest-inspection/index.html",
- "line": 23858,
- "source_group": "docs",
- "text": "./.venv/bin/python scripts/engineering/qa/run_historical_replay_closure_campaign.py"
- },
- {
- "path": "docs/site/05-operations/runbooks/run-manifest-inspection/index.html",
- "line": 23883,
- "source_group": "docs",
- "text": "run_historical_replay_closure_campaign.py is the deterministic batch path"
+ "path": "tests/architecture/test_reproducibility_docs_contract_drift.py",
+ "line": 217,
+ "source_group": "tests",
+ "text": "assert \"run_historical_replay_closure_campaign.py\" in runbook"
}
]
},
@@ -9381,7 +8769,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 13,
+ "reference_count": 8,
"references": [
{
"path": "docs/04-reference/contracts/run-manifest-ledger.md",
@@ -9420,16 +8808,16 @@
"text": "- `run_historical_replay_universe_campaign.py` is the full-universe path: it"
},
{
- "path": "docs/site/04-reference/contracts/run-manifest-ledger/index.html",
- "line": 24214,
- "source_group": "docs",
- "text": "scripts/engineering/qa/run_historical_replay_universe_campaign.py persists"
+ "path": "tests/architecture/test_reproducibility_docs_contract_drift.py",
+ "line": 130,
+ "source_group": "tests",
+ "text": "assert \"run_historical_replay_universe_campaign.py\" in text"
},
{
- "path": "docs/site/04-reference/contracts/run-manifest-ledger/index.html",
- "line": 24220,
- "source_group": "docs",
- "text": "scripts/engineering/qa/run_historical_replay_universe_campaign.py --require-universal-claim"
+ "path": "tests/architecture/test_reproducibility_docs_contract_drift.py",
+ "line": 224,
+ "source_group": "tests",
+ "text": "assert \"run_historical_replay_universe_campaign.py\" in runbook"
}
]
},
@@ -9501,7 +8889,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 30,
+ "reference_count": 24,
"references": [
{
"path": ".github/workflows/tests.yml",
@@ -9558,7 +8946,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 15,
+ "reference_count": 13,
"references": [
{
"path": ".github/workflows/tests.yml",
@@ -9597,16 +8985,16 @@
"text": "- `python -m scripts.engineering.qa.vcr check-placement`"
},
{
- "path": "docs/site/00-project/ai/memory/agent-memory/index.html",
- "line": 24510,
- "source_group": "docs",
- "text": "uv run python -m scripts.en"
+ "path": "scripts/engineering/qa/vcr/__main__.py",
+ "line": 9,
+ "source_group": "scripts",
+ "text": "check-placement Block VCR cassette anti-patterns"
},
{
- "path": "docs/site/03-guides/testing/index.html",
- "line": 24456,
- "source_group": "docs",
- "text": "python -m scripts.engineering.qa.vcr check-placementvcr_cassette_max_age_days: 90 является blocking stale-age threshold: CI теперь валидирует managed metadata inventory через scripts/engineering/qa/vcr/check_vcr_metadata_age.py -"
- },
{
"path": "scripts/engineering/qa/vcr/__main__.py",
"line": 12,
@@ -9721,6 +9103,12 @@
"line": 185,
"source_group": "tests",
"text": "\"python -m scripts.engineering.qa.vcr check-metadata-age --max-age-days 90\""
+ },
+ {
+ "path": "tests/architecture/test_vcr_metadata_inventory.py",
+ "line": 72,
+ "source_group": "tests",
+ "text": "== \"scripts/engineering/qa/vcr/check_vcr_metadata_age.py\""
}
]
},
@@ -9744,7 +9132,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 54,
+ "reference_count": 50,
"references": [
{
"path": ".github/workflows/compiled-artifacts-block.yml",
@@ -9809,7 +9197,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 26,
+ "reference_count": 19,
"references": [
{
"path": "docs/00-project/governance/03-file-policy.md",
@@ -9854,10 +9242,10 @@
"text": "- root placement: `python scripts/engineering/repo/audit_root_cleanliness.py`"
},
{
- "path": "docs/site/00-project/governance/03-file-policy/index.html",
- "line": 24045,
- "source_group": "docs",
- "text": "python3 scripts/engineering/repo/audit_root_cleanlin"
+ "path": "scripts/engineering/ci/apply_ci_fixes.py",
+ "line": 278,
+ "source_group": "scripts",
+ "text": "`scripts/engineering/repo/audit_root_cleanliness.py` enforces a root-directory allowlist and"
}
]
},
@@ -9893,7 +9281,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 3,
+ "reference_count": 2,
"references": [
{
"path": "docs/05-operations/runbooks/incident-response.md",
@@ -9901,12 +9289,6 @@
"source_group": "docs",
"text": "2. Replace failing references with vetted pinned SHAs from CI runtime policy (see `scripts/engineering/repo/check_github_actions_runtime_policy.py`)."
},
- {
- "path": "docs/site/05-operations/runbooks/incident-response/index.html",
- "line": 23721,
- "source_group": "docs",
- "text": "Replace failing references with vetted pinned SHAs from CI runtime policy (see scripts/engineering/repo/check_github_actions_runtime_policy.py). "
- },
{
"path": "scripts/engineering/repo/__main__.py",
"line": 45,
@@ -9998,7 +9380,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 24,
+ "reference_count": 21,
"references": [
{
"path": ".github/workflows/tests.yml",
@@ -10043,10 +9425,10 @@
"text": "python3 -m scripts.engineering.repo check-inventory --check"
},
{
- "path": "docs/site/00-project/TOOLS/index.html",
- "line": 23485,
- "source_group": "docs",
- "text": "uv run python"
+ "path": "scripts/engineering/README.md",
+ "line": 33,
+ "source_group": "scripts",
+ "text": "python -m scripts.engineering.repo check-inventory --check --manifest configs/quality/scripts_inventory_manifest.json"
}
]
},
@@ -10244,7 +9626,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 27,
+ "reference_count": 17,
"references": [
{
"path": "docs/02-architecture/04-interfaces-layer.md",
@@ -10301,7 +9683,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 5,
+ "reference_count": 4,
"references": [
{
"path": "docs/00-project/DOCUMENTATION_GOVERNANCE.md",
@@ -10321,12 +9703,6 @@
"source_group": "docs",
"text": "python3 scripts/generate_adr_registry.py"
},
- {
- "path": "docs/site/00-project/DOCUMENTATION_GOVERNANCE/index.html",
- "line": 24444,
- "source_group": "docs",
- "text": "scripts/generate_adr_registry.py - ADR metadata generationscripts/memory/prompts/print_seed.shscripts/memory/query.pyscripts/memory/sync.pyuv run python -m scripts.opsvacuum_delta.pycleanup_project.py, cleanup_repository.py, vacuum_delta.py, verify_checksums.pyvacuum_delta.pyverify_checksums.pycleanup_project.py, cleanup_repository.py, vacuum_delta.py, verify_checksums.py.\\scripts\\ops\\docker-setup.ps1 - Canonical интерактивная настройка Docker для Windows; .env создается только с -AllowEnvFileCreate"
- },
{
"path": "tests/architecture/test_docs_root_surface_governance_alignment.py",
"line": 271,
@@ -11011,7 +10333,7 @@
"type": "sh",
"status": "active",
"agent_usage": [],
- "reference_count": 4,
+ "reference_count": 3,
"references": [
{
"path": "docs/DOCKER_QUICKSTART.md",
@@ -11025,12 +10347,6 @@
"source_group": "docs",
"text": "`scripts/ops/docker-setup.sh` automatically ensure these shared external"
},
- {
- "path": "docs/site/DOCKER_QUICKSTART/index.html",
- "line": 23619,
- "source_group": "docs",
- "text": "- scripts/ops/docker-setup.sh - Canonical Bash версия для WSL/Linux; .env создается только с BIOETL_ALLOW_ENV_FILE_CREATE=1"
- },
{
"path": "tests/architecture/test_docs_root_surface_governance_alignment.py",
"line": 270,
@@ -11044,7 +10360,7 @@
"type": "bat",
"status": "active",
"agent_usage": [],
- "reference_count": 3,
+ "reference_count": 2,
"references": [
{
"path": "docs/03-guides/development/codex-wsl2-setup.md",
@@ -11052,12 +10368,6 @@
"source_group": "docs",
"text": "scripts\\ops\\install-codex-cmd.bat"
},
- {
- "path": "docs/site/03-guides/development/codex-wsl2-setup/index.html",
- "line": 24171,
- "source_group": "docs",
- "text": "scripts\\ops\\install-codex-cmd.bat"
- },
{
"path": "scripts/ai/codex/README.md",
"line": 42,
@@ -11079,7 +10389,7 @@
"type": "bat",
"status": "active",
"agent_usage": [],
- "reference_count": 11,
+ "reference_count": 8,
"references": [
{
"path": "docs/05-operations/tooling/scripts-ops/CODEX_SETUP.md",
@@ -11099,24 +10409,6 @@
"source_group": "docs",
"text": "- `scripts/ops/launchers/codex/codex-exec.bat` - WSL2-based auto-execution launcher"
},
- {
- "path": "docs/site/05-operations/tooling/scripts-ops/CODEX_SETUP/index.html",
- "line": 23559,
- "source_group": "docs",
- "text": "scripts/ops/launchers/codex/codex-exec.bat - Auto-execution launcherscripts/ops/launchers/codex/codex-exec.bat - Original auto-execscripts/ops/launchers/codex/codex-exec.bat - WSL2-based auto-execution launcherscripts/ops/launchers/codex/codex.bat - Main launcher (interactive & prompt modes)scripts/ops/launchers/codex/codex.bat - Original Windows launcherscripts/ops/launchers/codex/codex.bat - WSL2-based interactive launcherscripts/ops/launchers/codex/setup_plugins.sh --pytest-only перед запуском pytest."
- },
- {
- "path": "makefile",
- "line": 33,
- "source_group": "build",
- "text": "bash scripts/ops/launchers/codex/setup_plugins.sh --pytest-only"
- },
- {
- "path": "makefile",
- "line": 36,
- "source_group": "build",
- "text": "bash scripts/ops/launchers/codex/setup_plugins.sh"
- },
{
"path": "scripts/engineering/dev/README.md",
"line": 91,
@@ -11413,6 +10705,24 @@
"line": 522,
"source_group": "scripts",
"text": "if [[ -f \"scripts/ops/launchers/codex/setup_plugins.sh\" ]]; then"
+ },
+ {
+ "path": "scripts/engineering/dev/run_pytest.sh",
+ "line": 523,
+ "source_group": "scripts",
+ "text": "bash scripts/ops/launchers/codex/setup_plugins.sh --pytest-only"
+ },
+ {
+ "path": "scripts/engineering/dev/run_pytest.sh",
+ "line": 527,
+ "source_group": "scripts",
+ "text": "# setup_plugins.sh may provision a temporary pytest runtime under /tmp when"
+ },
+ {
+ "path": "scripts/engineering/repo/generate_scripts_wrapper_caller_matrix.py",
+ "line": 107,
+ "source_group": "scripts",
+ "text": "Candidate(\"scripts/ops/launchers/codex/setup_plugins.sh\", BOOTSTRAP_HELPER_ROLE),"
}
]
},
@@ -11421,7 +10731,7 @@
"type": "bat",
"status": "active",
"agent_usage": [],
- "reference_count": 7,
+ "reference_count": 4,
"references": [
{
"path": "docs/05-operations/tooling/scripts-ops/00_START_HERE.md",
@@ -11441,24 +10751,6 @@
"source_group": "docs",
"text": "| `start-codex.bat` | Existing quick launcher | PowerShell |"
},
- {
- "path": "docs/site/05-operations/tooling/scripts-ops/00_START_HERE/index.html",
- "line": 23533,
- "source_group": "docs",
- "text": "├── start-codex.bat ← Quick start wrapper"
- },
- {
- "path": "docs/site/05-operations/tooling/scripts-ops/WSL_SETUP_SUMMARY/index.html",
- "line": 23422,
- "source_group": "docs",
- "text": "scripts/ops/launchers/codex/start-codex.bat - Quick start wrapperstart-codex.batsalt_rotate.pysalt_rotate.pyscripts/ops/migrations/active/backfill_vcr_metadata_sidecars.py; workflow-level"
- },
- {
- "path": "docs/site/03-guides/testing/index.html",
- "line": 24090,
- "source_group": "docs",
- "text": "canonical tooling paths активированы для enforced rollout: scripts/engineering/qa/report_vcr_metadata_catalog.py генерирует/проверяет catalog, а scripts/ops/migrations/active/ba"
- },
{
"path": "scripts/engineering/qa/vcr/check_vcr_metadata_age.py",
"line": 100,
@@ -11665,6 +10933,18 @@
"line": 233,
"source_group": "tests",
"text": "\"uv run python scripts/ops/migrations/active/backfill_vcr_metadata_sidecars.py --check\""
+ },
+ {
+ "path": "tests/architecture/test_integration_vcr_policy.py",
+ "line": 367,
+ "source_group": "tests",
+ "text": "\"scripts/ops/migrations/active/backfill_vcr_metadata_sidecars.py\","
+ },
+ {
+ "path": "tests/architecture/test_integration_vcr_policy.py",
+ "line": 417,
+ "source_group": "tests",
+ "text": "assert \"backfill_vcr_metadata_sidecars.py\" in migrations_readme"
}
]
},
@@ -11766,7 +11046,7 @@
"type": "sh",
"status": "active",
"agent_usage": [],
- "reference_count": 7,
+ "reference_count": 4,
"references": [
{
"path": "docs/05-operations/deployment/deployment-guide.md",
@@ -11786,24 +11066,6 @@
"source_group": "docs",
"text": "1. Optionally use `scripts/ops/runtime/deploy/deploy-bioetl.sh`"
},
- {
- "path": "docs/site/05-operations/deployment/deployment-guide/index.html",
- "line": 24223,
- "source_group": "docs",
- "text": " scripts/ops/runtime/deploy/deploy-bioetl.sh deploy "
- },
- {
- "path": "docs/site/05-operations/deployment/k8s-summary/index.html",
- "line": 23529,
- "source_group": "docs",
- "text": "scripts/ops/runtime/deploy/deploy-bioetl.sh
"
- },
- {
- "path": "docs/site/05-operations/deployment/k8s-summary/index.html",
- "line": 23541,
- "source_group": "docs",
- "text": "Optionally use scripts/ops/runtime/deploy/deploy-bioetl.sh "
- },
{
"path": "scripts/ops/__main__.py",
"line": 61,
@@ -11817,7 +11079,7 @@
"type": "ps1",
"status": "active",
"agent_usage": [],
- "reference_count": 6,
+ "reference_count": 4,
"references": [
{
"path": "docs/05-operations/runbooks/neo4j-backend-recovery-quick-start.md",
@@ -11837,18 +11099,6 @@
"source_group": "docs",
"text": "| `scripts/ops/runtime/docker/restart-docker.ps1` | Docker Desktop restart helper |"
},
- {
- "path": "docs/site/05-operations/runbooks/neo4j-backend-recovery-quick-start/index.html",
- "line": 23483,
- "source_group": "docs",
- "text": "scripts/ops/runtime/docker/restart-docker.ps1scripts/ops/runtime/docker/restart-docker.ps1The neo4j-recovery-checklist.ps1 does:
"
- },
- {
- "path": "docs/site/05-operations/runbooks/neo4j-backend-recovery-quick-start/index.html",
- "line": 23479,
- "source_group": "docs",
- "text": "scripts/ops/runtime/neo4j/neo4j-recovery-checklist.ps1scripts/ops/runtime/neo4j/neo4j-recovery-checklist.ps1 reports backend"
+ "path": "scripts/engineering/repo/check_scripts_inventory.py",
+ "line": 220,
+ "source_group": "scripts",
+ "text": "\"scripts/ops/runtime/neo4j/neo4j-recovery-checklist.ps1\","
}
]
},
@@ -11919,7 +11157,7 @@
"type": "sh",
"status": "active",
"agent_usage": [],
- "reference_count": 13,
+ "reference_count": 7,
"references": [
{
"path": "docs/05-operations/deployment/NEO4J-MCP-INDEX.md",
@@ -11958,16 +11196,10 @@
"text": "| **Quick Start** | `bash scripts/ops/runtime/neo4j/neo4j_quick_start.sh` |"
},
{
- "path": "docs/site/05-operations/deployment/NEO4J-MCP-INDEX/index.html",
- "line": 23481,
- "source_group": "docs",
- "text": "bash scripts/ops/runtime/neo4j/neo4j_quick_start.sh"
- },
- {
- "path": "docs/site/05-operations/deployment/NEO4J-MCP-INDEX/index.html",
- "line": 23514,
- "source_group": "docs",
- "text": "neo4j_quick_start.sh "
+ "path": "scripts/engineering/repo/check_scripts_inventory.py",
+ "line": 221,
+ "source_group": "scripts",
+ "text": "\"scripts/ops/runtime/neo4j/neo4j_quick_start.sh\","
}
]
},
@@ -11976,7 +11208,7 @@
"type": "ps1",
"status": "active",
"agent_usage": [],
- "reference_count": 37,
+ "reference_count": 25,
"references": [
{
"path": "docs/05-operations/deployment/neo4j-audit-instance-guide.md",
@@ -12033,7 +11265,7 @@
"type": "sh",
"status": "active",
"agent_usage": [],
- "reference_count": 13,
+ "reference_count": 7,
"references": [
{
"path": "docs/05-operations/deployment/neo4j-audit-instance-implementation.md",
@@ -12072,16 +11304,10 @@
"text": "./scripts/ops/runtime/neo4j/start-neo4j-audit.sh --stop"
},
{
- "path": "docs/site/05-operations/deployment/neo4j-audit-instance-implementation/index.html",
- "line": 23505,
- "source_group": "docs",
- "text": "✅ scripts/ops/runtime/neo4j/start-neo4j-audit.sh
"
- },
- {
- "path": "docs/site/05-operations/deployment/neo4j-audit-instance-implementation/index.html",
- "line": 23727,
- "source_group": "docs",
- "text": "scripts/ops/runtime/neo4j/start-neo4j-audit.sh "
+ "path": "scripts/engineering/repo/check_scripts_inventory.py",
+ "line": 223,
+ "source_group": "scripts",
+ "text": "\"scripts/ops/runtime/neo4j/start-neo4j-audit.sh\","
}
]
},
@@ -12090,7 +11316,7 @@
"type": "bat",
"status": "active",
"agent_usage": [],
- "reference_count": 30,
+ "reference_count": 21,
"references": [
{
"path": "docs/03-guides/development/codex-wsl2-setup.md",
@@ -12147,7 +11373,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 22,
+ "reference_count": 13,
"references": [
{
"path": "docs/03-guides/development/codex-wsl2-setup.md",
@@ -12219,7 +11445,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 7,
+ "reference_count": 5,
"references": [
{
"path": ".github/workflows/root-hygiene.yml",
@@ -12239,18 +11465,6 @@
"source_group": "docs",
"text": "`scripts/ops/support/repo/cleanup_repository.py` больше не является broad"
},
- {
- "path": "docs/site/00-project/TOOLS/index.html",
- "line": 23680,
- "source_group": "docs",
- "text": "cleanup_project.py, cleanup_repository.py, vacuum_delta.py, verify_checksums.pyscripts/ops/support/repo/cleanup_repository.py больше не является broad"
- },
{
"path": "scripts/engineering/repo/check_scripts_inventory.py",
"line": 204,
@@ -12357,7 +11571,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 72,
+ "reference_count": 66,
"references": [
{
"path": ".github/workflows/quality-debt-weekly.yml",
@@ -12489,7 +11703,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 8,
+ "reference_count": 6,
"references": [
{
"path": "docs/00-project/TOOLS.md",
@@ -12515,18 +11729,6 @@
"source_group": "docs",
"text": "| Config gap analysis | `scripts/schema/config_gap_analysis.py` |"
},
- {
- "path": "docs/site/00-project/TOOLS/index.html",
- "line": 23609,
- "source_group": "docs",
- "text": "
config_gap_analysis.pyconfig_gap_analysis.py, validate_pipeline_configs.pysrc/tools/scripts/schema/generate_contracts.py),scripts/schema/generate_contracts.py."
- },
{
"path": "scripts/engineering/repo/check_scripts_inventory.py",
"line": 193,
@@ -12616,6 +11806,18 @@
"line": 30,
"source_group": "scripts",
"text": "| `generate-contracts` | `scripts/schema/generate_contracts.py` | Generate contracts |"
+ },
+ {
+ "path": "scripts/schema/__main__.py",
+ "line": 38,
+ "source_group": "scripts",
+ "text": "\"generate-contracts\": \"scripts.schema.generate_contracts\","
+ },
+ {
+ "path": "tests/unit/contracts/test_contracts_exports.py",
+ "line": 149,
+ "source_group": "tests",
+ "text": "# This method is used by generate_contracts.py"
}
]
},
@@ -12720,7 +11922,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 8,
+ "reference_count": 7,
"references": [
{
"path": ".github/workflows/schema-governance.yml",
@@ -12740,12 +11942,6 @@
"source_group": "docs",
"text": "На этой основе вводится единый генератор `scripts/schema/generate_schema_artifacts.py`,"
},
- {
- "path": "docs/site/02-architecture/decisions/ADR-037-canonical-schema-generation/index.html",
- "line": 23521,
- "source_group": "docs",
- "text": "На этой основе вводится единый генератор scripts/schema/generate_schema_artifacts.py,"
- },
{
"path": "scripts/schema/README.md",
"line": 28,
@@ -12819,7 +12015,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 15,
+ "reference_count": 11,
"references": [
{
"path": "docs/00-project/TOOLS.md",
@@ -12846,28 +12042,28 @@
"text": "python scripts/schema/validate_pipeline_configs.py"
},
{
- "path": "docs/site/00-project/TOOLS/index.html",
- "line": 23617,
- "source_group": "docs",
- "text": "
validate_pipeline_configs.pyconfig_gap_analysis.py, validate_pipeline_configs.pycreate_pipeline.pyaudit_structure.py, create_pipeline.pyИнструмент src/tools/differentiate_linkstyle.py классифицирует связи по 6 семантическим типам:
"
+ "path": "src/tools/README.md",
+ "line": 252,
+ "source_group": "scripts",
+ "text": "### differentiate_linkstyle.py"
},
{
- "path": "docs/site/02-architecture/diagrams/governance/DIAGRAM-WORKFLOW-GUIDE/index.html",
- "line": 24550,
- "source_group": "docs",
- "text": "python src/tools/differentiate_linkstyle.pypython src/tools/differentiate_linkstyle.py # "
+ "path": "src/tools/README.md",
+ "line": 261,
+ "source_group": "scripts",
+ "text": "python src/tools/differentiate_linkstyle.py --dry-run"
}
]
},
@@ -13200,7 +12384,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 17,
+ "reference_count": 16,
"references": [
{
"path": "docs/00-project/TOOLS.md",
@@ -13208,12 +12392,6 @@
"source_group": "docs",
"text": "| `file_merger.py` | src/tools/ | Нет | — | — | Объединение файлов с метаданными "
},
- {
- "path": "docs/site/00-project/TOOLS/index.html",
- "line": 23529,
- "source_group": "docs",
- "text": "file_merger.pysrc/tools/generate_json_field_typing_inventory.py."
- },
{
"path": "tests/architecture/test_non_chembl_json_field_typing_policy.py",
"line": 115,
@@ -13350,7 +12528,7 @@
"type": "py",
"status": "supporting",
"agent_usage": [],
- "reference_count": 17,
+ "reference_count": 8,
"references": [
{
"path": "docs/05-operations/deployment/neo4j-audit-instance-guide.md",
@@ -13407,7 +12585,7 @@
"type": "py",
"status": "active",
"agent_usage": [],
- "reference_count": 6,
+ "reference_count": 5,
"references": [
{
"path": ".github/workflows/schema-governance.yml",
@@ -13433,12 +12611,6 @@
"source_group": "docs",
"text": "| `verify_schema_parity.py` | src/tools/ | Да | — | — | Верификация Silver↔Gold schema parity "
},
- {
- "path": "docs/site/00-project/TOOLS/index.html",
- "line": 23521,
- "source_group": "docs",
- "text": "verify_schema_parity.py