template-methods-orchestration
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.
Best use case
template-methods-orchestration is best used when you need a repeatable AI agent workflow instead of a one-off prompt.
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.
Teams using template-methods-orchestration should expect a more consistent output, faster repeated execution, less prompt rewriting.
When to use this skill
- You want a reusable workflow that can be run more than once with consistent structure.
When not to use this skill
- You only need a quick one-off answer and do not need a reusable workflow.
- You cannot install or maintain the underlying files, dependencies, or repository context.
Installation
Claude Code / Cursor / Codex
Manual Installation
- Download SKILL.md from GitHub
- Place it in
.claude/skills/methods-orchestration/SKILL.mdinside your project - Restart your AI agent — it will auto-discover the skill
How template-methods-orchestration Compares
| Feature / Agent | template-methods-orchestration | Standard Approach |
|---|---|---|
| Platform Support | Not specified | Limited / Varies |
| Context Awareness | High | Baseline |
| Installation Complexity | Unknown | N/A |
Frequently Asked Questions
What does this skill do?
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.
Where can I find the source code?
You can find the source code on GitHub using the link provided at the top of the page.
SKILL.md Source
# 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). 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 scripts/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)
Related Skills
infrastructure-orchestration
Python CLI and menu orchestration for pipeline runs — project slug validation, interactive picker, PipelineRunner wrapping PipelineExecutor, per-stage logs, secure pipeline wrapper. Use when extending run.sh behavior, fixing menu/CLI routing, or testing discovery helpers.
infrastructure-methods
Methods orchestration contract builder for template projects. Use when mapping pipeline stages, manuscript methods, artifact manifests, evidence registries, and validation commands into one reproducible methods plan.
template-validation-quality
Run validation CLI, prerender, markdown/PDF/integrity gates, and QA workflows for the Research Project Template. USE WHEN validate manuscript, check PDF for ?? refs, prerender gate, link checker, output integrity, or pre-commit validation — even without validation_quality prompt.
template-test-creation
Create pytest suites under the no-mocks policy — real data, temp files, subprocess, pytest-httpserver. USE WHEN adding tests, raising coverage, testing new src/ module, or user forbids mocks.
template-reproducibility-audit
Deterministic reproducibility audit — fixed seeds, regenerate-from-clean, double-run diff before Zenodo/arXiv/release. USE WHEN outputs drift between runs, "worked on my machine", need regenerate-from-clean proof, or pre-release reproducibility check — even without naming docs/prompts.
template-refactoring
Clean-break refactors with migration for the Research Project Template — move logic to src/, split modules, rename APIs with test updates. USE WHEN restructuring code, extracting modules, removing duplication, or migration without behavior change.
template-pipeline-debugging
Systematic pipeline DAG failure triage for the Research Project Template. USE WHEN ./run.sh or execute_pipeline.py fails, a stage stalls (setup, tests, analysis, render, validate, LLM, copy), pytest/coverage gate fails mid-pipeline, PDF render or validate breaks, Project Analysis finishes too fast with no figures, or user says pipeline debug, stage failed, resume checkpoint, core-only triage — even without naming this skill or docs/prompts.
template-manuscript-cross-references
Audit or author registry-driven manuscript cross-refs — labels.yaml, [[FIG:]], [[THMREF:]], [[VAR:]] tokens. USE WHEN fixing figure/equation/theorem numbering, orphan registry keys, hard-coded "Theorem 7.3" in prose, or [[MISSING:]] injection failures — even for Pandoc projects that also use a YAML registry.
template-manuscript-creation
Scaffold a research manuscript and project layout from a research brief — sections, config.yaml, src/, scripts/, tests. USE WHEN starting a new paper, new projects/ tree, manuscript from topic description, or aligning with template_code_project exemplar — even without copy-paste prompts.
template-manuscript-claim-verification
Triple-pass verification of every manuscript claim against code, data, refs, and renderer; repair prose while staying renderable. USE WHEN pre-submission, pre-Zenodo, pre-arXiv, abstract numbers disagree with CSV, citations do not support sentences, or user asks to triple-check / verify every claim — even without docs/prompts. Not for casual PDF summary.
template-feature-addition
End-to-end feature work across src/, scripts/, tests/, manuscript, and docs for the Research Project Template. USE WHEN adding a pipeline-visible feature, new analysis stage, manuscript-facing output, or cross-layer integration — even without feature_addition prompt.
template-documentation-creation
Author or refresh AGENTS.md and README.md for template directories — accurate commands, Mermaid where helpful, link _generated/active_projects.md. USE WHEN folder needs AGENTS, README audit, doc contract fix, or signposting after code change — even without documentation_creation prompt.