/claim #16

Contributes to #16.

Summary

• Adds a self-contained research-protocol-trace module for the AI-Powered Research Assistant Suite bounty.
• Focuses on registered protocol / preregistration consistency rather than another broad assistant suite.
• Maps manuscript claims to registered outcomes, planned analyses, evidence artifacts, and reproducibility runs.
• Flags selective-reporting risks such as unreported primary outcomes, post-hoc analyses, threshold-adjacent p-values, missing citation context, and underpowered exploratory claims.
• Includes a sample study package, requirement map, tests, CLI demo, SVG demo frame, and short MP4 demo artifact.

Why this slice is distinct

Existing #16 submissions cover broad readiness engines, quality gates, research copilots, and general peer-review/reproducibility workflows. This PR specifically targets the protocol trace boundary: whether a manuscript’s claims can be audited against a registered protocol, evidence artifacts, execution records, and unreported registered outcomes before submission.

Demo

• research-protocol-trace/docs/demo.mp4
• research-protocol-trace/docs/demo.svg
• cd research-protocol-trace && npm run demo

Demo output:

Protocol trace score: 62 (hold)
Registered protocol: OSF-SCNC-7421
Claims traced: 3
Selective reporting status: review-needed
Unreported registered outcomes: 1
Top reviewer action: Claim references an unregistered or post-hoc analysis.
Top research gap: Resolve protocol gap for Cell viability after perturbation
Digest: 5a7b36c2505bc13f7aad4677d2b2f199d45ebdd8cec47d2875f2eba41f1ca30e

Verification

cd research-protocol-trace
npm run check
npm test
npm run demo
ffprobe -v error -select_streams v:0 -show_entries stream=codec_name,width,height,duration -of default=noprint_wrappers=1 docs/demo.mp4
cd ..
git diff --check
git diff --cached --check
rg -n 'api[_-]?key|private[_-]?key|password|secret|token|wallet|ssn' research-protocol-trace || true

Local results:

research-protocol-trace tests passed
codec_name=h264
width=1280
height=720
duration=4.000000

AI-assisted with OpenAI Codex; I reviewed the implementation and local validation before submitting.