template-methods-orchestration · diff

v1.0.0 to v1.0.0

3 added, 1 removed. Audit A to A.

---

name: template-methods-orchestration

description: |

Repo-wide methods orchestration workflow for the Research Project Template. USE WHEN

the user asks to add, audit, improve, or validate methods, methodology, method

contracts, stage-to-method wiring, artifact/evidence provenance, or orchestration

across template projects.

metadata:

version: "1.0.0"

last_updated: "2026-05-25"

status: active

data_access_level: verified_only

task_type: open-ended

modes:

- audit

- plan

- repair

related_skills:

- template-pipeline-debugging

- template-reproducibility-audit

- template-manuscript-claim-verification

- template-validation-quality

---

# 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 the target project(s).

+ 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.

3. **Repair source layers** - update `src/`, thin scripts, manuscript source, or

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

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

then rerun methods plan with `--check`.

5. **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](../pipeline-debugging/SKILL.md)

- Evidence/claim mismatch -> [manuscript-claim-verification](../manuscript-claim-verification/SKILL.md)

- Rebuild drift -> [reproducibility-audit](../reproducibility-audit/SKILL.md)

- Validation CLI failures -> [validation-quality](../validation-quality/SKILL.md)