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CONTRIBUTING.md

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Contributing

This repository is a template designed for academic researchers to fork and customize. Contributions back to the template should help all users, not just one fork.

What we welcome

  • Bug fixes in shared infrastructure (skills, agents, rules, hooks, scripts).
  • New skills/agents/rules that generalize across academic domains (economics, biology, physics, CS, etc.).
  • Documentation improvements — guide, README, examples, troubleshooting.
  • Pedagogical improvements — clearer onboarding, better Day 1 experience.
  • 2026+ Claude Code feature integration — when new hooks, frontmatter fields, or capabilities ship.

What belongs in your fork (not here)

  • Project-specific lectures, papers, or data.
  • Custom domain-reviewer content (econometrics-only, biology-only, etc.) — keep yours in your fork; PR back the template not the instance.
  • Personal preferences (your favorite color in theme-template.scss).
  • Local paths, API keys, machine-specific settings.

Before you open a PR

  1. Open an issue first for new features or non-trivial changes. We may already be working on it or have a different design in mind.
  2. Read CLAUDE.md and the guide so your contribution fits the existing patterns.
  3. Run the validate script to confirm you don't break the onboarding path: 
    ./scripts/validate-setup.sh
  4. Run quality gates on any .qmd, .tex, or .R you modify: 
    python3 scripts/quality_score.py path/to/file
  5. Test against ≥2 domains when adding skills/agents — show that your contribution generalizes.
  6. Update both README and the guide when adding features. Skill counts must agree across CLAUDE.md, README.md, docs/index.html, and guide/workflow-guide.qmd.

PR style

  • Branch naming: feat/short-name, fix/short-name, chore/short-name, docs/short-name.
  • Commit messages: imperative mood ("add", "fix", "refactor"), explain why in the body.
  • Co-author Claude if Claude Code helped: Co-Authored-By: Claude Opus 4.6 <[email protected]>.
  • Use the PR template (auto-loaded when you open a PR).
  • Squash before merging if your branch has many WIP commits.

Running /deep-audit before submitting

We use /deep-audit to catch consistency drift across the repo (skill counts, hook configs, doc references). Run it before opening your PR:

/deep-audit

If it surfaces issues, fix them in the same PR.

Code of conduct

Be kind. Academic work is hard enough without rude reviews. If you disagree with a decision, explain why with examples — don't just say "this is wrong."

Questions?

Open an issue with the question label.