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chore: 馃 sync copilot instructions - 2026-09-18 #231

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kelly-sovacool merged 1 commit into from
Sep 18, 2026
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chore: 馃 sync copilot instructions - 2026-09-18 #231

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6 changes: 4 additions & 2 deletions .github/copilot-instructions.md
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# CoPilot Instructions for CCBR Repositories

If the repo contains an `AGENTS.md` file, refer to that file instead of this one. `AGENTS.md` takes precedence over `.github/copilot-instructions.md`.

## Reviewer guidance (what to look for in PRs)

- Reviewers must validate enforcement rules: no secrets, container specified, and reproducibility pins.
- If code is AI-generated, reviewers must ensure the author documents what was changed and why, and that the PR is labeled `generated-by-AI`.
- If code is AI-generated, reviewers must ensure the author documents what was changed and why, and that the PR is labeled `AI-assisted`.
- Reviewers should verify license headers and ownership metadata (for example, `CODEOWNERS`) are present.
- Reviews must read the code and verify that it adheres to the project's coding standards, guidelines, and best practices in software engineering.

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2. **Pre-merge check (GitHub Action)**: verify `.github/copilot-instructions.md` is present in the repository and that new pipeline files include a `# CRAFT:` header.
3. **Lint jobs**: `ruff` for Python, `shellcheck` for shell, `lintr` for R, `nf-core lint` for Nextflow, or Snakemake lint checks where applicable.
4. **Secrets scan**: run `TruffleHog` or `Gitleaks` on PRs to detect accidental credentials.
5. **AI usage label**: if AI usage is declared, an Action should add `generated-by-AI` label (create this label if it does not exist); the PR body should end with the italicized Markdown line: _Generated using AI_, and any associated commit messages should end with the plain footer line: `Generated using AI`.
5. **AI usage label**: if AI usage is declared, an Action should add `AI-assisted` label (create this label if it does not exist); the PR body should end with the italicized Markdown line: _AI-assisted_, and any associated commit messages should end with the plain footer line: `_AI-assisted_: <model>` (fill in <model> with the actual model, e.g. Claude Sonnet 5, if known.

_Sample GH Action check (concept): if AI usage is declared, require an AI-assistance disclosure field in the PR body._

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