Methods orchestration

Natural invoke

• "Improve all methods orchestration repo-wide"
• "Make sure methods match the pipeline and artifacts"
• "Audit methodology sections against stage contracts"
• "Add method contract validation for this project"

Workflow

1. Build the plan - run infrastructure.methods for one project or --all-public.
2. Check surfaces - manuscript methods files, pipeline.yaml stage

contracts, artifact manifest, evidence registry, and validation commands.

1. Repair source layers - update src/, thin scripts, manuscript source, or

stage contracts. Do not edit generated output/ as a fix.

1. Regenerate and validate - run core pipeline or focused stage commands,

then rerun methods plan with --check.

1. Document routing - update AGENTS/README when method ownership or commands

changed.

Verification commands

bash
uv run python -m infrastructure.methods plan --project <project> --format markdown
uv run python -m infrastructure.methods plan --project <project> --format json --check
uv run python -m infrastructure.methods plan --all-public --artifact-mode source --format json
uv run python -m infrastructure.methods plan --all-public --artifact-mode rendered --format json
uv run python scripts/runner/execute_pipeline.py --project <project> --core-only
uv run python -m infrastructure.validation.cli prerender projects/<project>/manuscript --repo-root .
uv run pytest tests/infra_tests/methods -q

Handoffs

• Broken stage behavior -> pipeline-debugging
• Evidence/claim mismatch -> manuscript-claim-verification
• Rebuild drift -> reproducibility-audit
• Validation CLI failures -> validation-quality