research-repo-doctor: Instructions file for GitHub Copilot

GitHub Copilot Instructions

Research Repo Doctor (rrdoctor) is deterministic, local-first research reproducibility infrastructure. Keep the core scanner offline and key-free.

Use rrdoctor itself as the objective definition of done for agent changes:

python -m rrdoctor scan . --format json --output baseline.json
python -m rrdoctor plan . --output plan.md
# Work through plan.md without weakening checks.
python -m rrdoctor scan . --baseline baseline.json --fail-on-new error

For implementation work, keep changes aligned with the existing architecture:

• Rules live under src/rrdoctor/rules/ and must be deterministic.
• Every rule needs an RRD id, severity, message, evidence, remediation text, tests, and a docs/checks.md entry.
• Auto-fixes must be idempotent, non-destructive, and must never overwrite existing files.
• Do not add network calls, hosted-service requirements, or API keys to the core scan path.
• Mask secret-like values in all reported evidence.
• Prefer small, conservative heuristics over broad claims that create noisy first-run findings.

Before proposing a PR, run:

ruff format --check .
ruff check .
pytest
python -m mypy
python -m rrdoctor scan . --profile standard --fail-on none --quiet

If a change touches trusted dynamic verification, also test the relevant rrdoctor verify --run --fail-on error behavior on a controlled fixture. Never run untrusted external repository code as part of normal scan behavior.