Programming Refactor Review
Status as of 2026-09-13: trimmed to the ordering discipline and the evidence rules. The checklists of what counts as dead code, a simplification, or an optimization were removed — that is standard practice, and listing it crowded out the part that is actually a constraint.
Review order
Question the requirement, delete, simplify, then optimize, then automate — in that order. This is a strict ordering, not motivational advice: optimizing code that should have been deleted is the failure this skill exists to prevent. Skip ahead only when the user asked for a narrow task.
For performance work, check in this order: remove unnecessary work, reduce passes, change the algorithm, change the representation, reduce copying, parallelize, then optimize individual operations. Measure the effect of each candidate change.
Evidence rules
- A deletion recommendation carries its own safety check. Name the specific thing that would catch you being wrong — the call-site search, the test, the fixture comparison, the log. "Probably unused" without a check is not a finding.
- Performance claims are measured or hedged, never asserted. Say "profile to confirm" and mean it. A benchmark plan needs realistic input sizes, a correctness comparison against baseline, and a stated success threshold.
- Automate only what is stable. A repeated workflow with detectable failure and well-defined output qualifies. A workaround, or a design still under question, does not.
Output
Lead with the deletion or simplification with the largest supported effect. One-line verdict: delete, simplify, optimize, or automate. Keep correctness issues, maintainability issues, performance risk, and automation opportunities visibly separate — they carry different urgency and the reader triages on that. Offer a concrete patch where there's enough context to write one.
Bioinformatics pipelines in this project have recurring specific smells worth checking: dense arrays where sparse would do, repeated BAM/FASTA parsing, redundant coordinate conversions, avoidable decompression, accidental O(n²).