Refactor Code Protocol

Refactor Code Protocol

Safe refactoring with automatic output verification.

Steps

1. Establish a Baseline

Run /verify-outputs [target] baseline to record output checksums before any changes.

2. Read the Applicable Conventions

Read the relevant language conventions in code/AGENTS.md:

  • R: R section
  • Julia: Julia section
  • MATLAB: MATLAB section

Also read the Refactoring Protocol section of AGENTS.md.

3. Apply Only Approved Transformations

  • Comment style
  • Whitespace and indentation
  • Variable grouping and section organization
  • Missing documentation
  • Language-specific style conventions

Do not change logic, tolerances, function signatures, or dead-code behavior.

4. Verify Outputs

Run /verify-outputs [target] to compare against the baseline checksums.

5. Present Results

  • If outputs match, present the diff and report that the refactoring preserved outputs.
  • If outputs mismatch, revert all changes and report what broke.

6. Review

Run the appropriate review skill after the refactor.

Important

  • The only acceptable outcome is identical output.
  • Dead code may be flagged but not removed.
  • Revert everything on any output mismatch.