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feat(submission-package): collect and cross-check ICMJE COI disclosures - #153

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feat/coi-submission-step
Oct 21, 2026
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sajor2000 merged 1 commit into
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feat/coi-submission-step

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@sajor2000 sajor2000 commented Oct 21, 2026 •

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Implements Option B from #143: the submission lane now collects and cross-checks ICMJE COI disclosures as a workflow step inside method-submission-package, rather than adding a standalone skill (the audit closure record's lean).

  • SKILL.md step 4c — collect per-author ICMJE disclosure data (financial activities, funding, affiliation; ICMJE Recommendations II.D), write form-ready data only under manuscript/coi/ (each author signs their own form), and cross-check the manuscript's COI statement against the collected data and every funder named in the manuscript, cover letter, or registry entry. Missing statement, a funder present in one source but absent from another, or a "no conflicts" claim contradicted by the data blocks the package.
  • references/journal-package-checklist.md — matching checklist item.
  • evals/methodsmith/skill-creator/method-submission-package/ — COI expectations folded into evals 1 and 3 (shape fixed at 3 evals / 20 triggers per the contract test); one trigger query swapped for the COI form-data ask.
  • evals/methodsmith/cases/method-submission-package-coi-cross-check/ — new repository-owned behavioral case: funder named in Funding, absent from a "no conflicts" statement -> readiness blocked, never ready-for-signoff. Synthetic fixtures only.

Closes #143

Validation

  • bun run eval:validate — pass (new case validates)
  • bun test — full suite green (eval-shape and contract tests included)
  • bun run release:validate — in sync (55 agents, 68 skills); no release-owned files touched
  • Added ICMJE COI collection and cross-checking to method-submission-package.
  • Added per-author disclosure data under manuscript/coi/.
  • Blocked readiness for missing or inconsistent COI data.
  • Added journal-package checklist and evaluation coverage.
Contributing author Lines added Lines removed
JC Rojas 102 2

MedSci audit gap #5 remainder (submission lane; closes the open decision in
#143 by implementing Option B): the submission lane now handles ICMJE COI
instead of demanding a standalone skill.

- SKILL.md step 4c: collect each author's ICMJE disclosure data (financial
  activities, funding, affiliation; ICMJE Recommendations II.D), write
  form-ready data only under manuscript/coi/ — never sign for an author —
  and cross-check the manuscript's COI statement against the collected data
  and every funder named in manuscript, cover letter, or registry. Missing
  statement, funder in one source but not another, or a "no conflicts"
  claim contradicted by the data blocks the package.
- journal-package-checklist.md: matching checklist item.
- evals: COI expectations folded into evals 1 and 3 (fixed shape: 3 evals,
  20 triggers), one trigger query swapped for the COI form-data ask, and a
  new repository-owned behavioral case method-submission-package-coi-cross-
  check (funder named in Funding, absent from a no-conflicts statement ->
  readiness blocked; no signoff) with synthetic fixtures only.

Closes #143

Co-authored-by: factory-droid[bot] <138933559+factory-droid[bot]@users.noreply.github.com>
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coderabbitai Bot commented Oct 21, 2026

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Reviewing files that changed from the base of the PR and between 2f55e3b and c6366dd.

📒 Files selected for processing: 8
  • evals/methodsmith/cases/method-submission-package-coi-cross-check/case.yaml
  • evals/methodsmith/cases/method-submission-package-coi-cross-check/fixtures/manuscript.qmd
  • evals/methodsmith/cases/method-submission-package-coi-cross-check/fixtures/sap.md
  • evals/methodsmith/cases/method-submission-package-coi-cross-check/prompt.md
  • evals/methodsmith/skill-creator/method-submission-package/evals.json
  • evals/methodsmith/skill-creator/method-submission-package/trigger-evals.json
  • plugins/methodsmith/skills/method-submission-package/SKILL.md
  • plugins/methodsmith/skills/method-submission-package/references/journal-package-checklist.md
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@sajor2000
sajor2000 merged commit 7a61c2c into main Oct 21, 2026
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@sajor2000
sajor2000 deleted the feat/coi-submission-step branch October 21, 2026 03:33
@github-actions github-actions Bot mentioned this pull request Oct 21, 2026
sajor2000 added a commit that referenced this pull request Oct 21, 2026
Gaps #3, #5, #7, #10 closed (PRs #150, #151, #153, #154); #1, #6, #8
tracked as issues #141, #144, #146 with scoping; #9 wontfix as #147.

Co-authored-by: factory-droid[bot] <138933559+factory-droid[bot]@users.noreply.github.com>
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ICMJE COI: standalone skill vs step in method-submission-package (MedSci audit gap #5)

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