medsci-skills 5.20.0 → 5.21.0

package/README.md

@@ -288,6 +288,10 @@ The E2E pipeline (`orchestrate --e2e`) produces everything up to `qc/`. The `sub
 
 ## What's New
 
+**v5.21** — verification-layer batch, mostly promoted from real submission failures. A **marked (tracked-changes) manuscript** is now built by driving Word's Compare from the command line and proved by a **round trip** — accepting every revision must reproduce the revised paper exactly, rejecting every revision must reproduce the original — and the gate is **move-aware**, because Word encodes a relocated paragraph as `w:moveFrom`/`w:moveTo` and an insert-and-delete-only verifier calls a good file corrupt. Every detector's `qc/*.json` now **names the detector that wrote it**, so an artifact can be traced back to the check that produced it (a CI-enforced contract). Two `/verify-refs` precision defects: a Unicode hyphen in a surname fired `MISMATCH` — the verdict that means *fabricated author* — on a correct reference, and a Better BibTeX brace-protected surname was read as a corporate author, **silently skipping** the author check the tool exists to perform. New gates: publisher markup in a `.bib` title (`<scp>WHO</scp>` renders as garbage and no gate looked at the printed title), **complete/quasi separation** before a logistic model is fitted (a pathognomonic sign has an empty cell by construction; `glm` returns OR = 0.00, *p* = 0.99, and an AUC that gets reported), and a probe + gate for manuscripts claiming a system **improved itself** (which rung of the verification hierarchy said so?). `/find-cohort-gap` now accepts a **local codebook** — an institutional registry or EMR export, not only a named public cohort — enumerating variables verbatim with provenance rather than letting a model summarise them. Additive and backward-compatible; **55 skills / 46 guidelines / 61 integrity detectors / 23 domain-probe modules**. (See the [CHANGELOG](CHANGELOG.md) for v5.0–v5.20.)
+
+**v5.20.1** — audit-driven coherence fixes. A real `/orchestrate --e2e` state-transition bug (the pipeline halted at step 3 because it required a DOCX that is only rendered at step 7), all 55 skills made routable from the single entry point with a CI reachability gate, and a README plugin-count that had drifted from the marketplace SSOT (now gated). No skill/detector change.
+
 **v5.20** — reviewer-arithmetic gates. Five deterministic `self-review` detectors promoted from a peer-review cycle, each recomputing what a manuscript already prints: `check_table_percentages` (an `n (%)` cell vs its column denominator), `check_nested_group_comparison` (a P value comparing an analysed subset against the parent cohort that **contains** it — nested, invalid), `check_reported_p_from_counts` (rebuilds each 2×2 row and recomputes Fisher / Pearson χ² ± Yates in **pure stdlib**, calibrating the family on rows that reproduce), `check_dta_denominators` (sensitivity/specificity denominators vs the reference-standard category counts, behind a matching grand total), and `check_paired_difference_estimator` (an odd-n integer-scale median cannot be non-integer; a zero-width CI; an unnamed estimator). Plus `/peer-review` request-type discipline (disclosure vs computation) and impossibility-claim verification. Additive and backward-compatible; **55 skills / 46 guidelines / 57 integrity detectors / 22 domain-probe modules**. (See the [CHANGELOG](CHANGELOG.md) for v5.0–v5.19.)
 
 **v5.19** — reviewer-safety + reporting-checklist batch. A **PDF hidden-text / prompt-injection guard** for `/peer-review` — a PyMuPDF extractor plus a stdlib detector that catch a review-steering instruction hidden in a submitted PDF (white-on-white text, sub-visible fonts, off-page glyphs, invisible render mode, or a document-metadata field) before an LLM ingesting the text layer can be steered by it, and emit visible-only text to feed a model instead of the raw PDF; plus the **TARGET** (target-trial emulation; Cashin et al., *JAMA* 2025) and **REMARK** (prognostic tumour-marker; McShane et al.) reporting checklists. Additive and backward-compatible; **55 skills / 46 guidelines / 52 integrity detectors / 22 domain-probe modules**. (See the [CHANGELOG](CHANGELOG.md) for v5.0–v5.18.)
@@ -356,7 +360,7 @@ The E2E pipeline (`orchestrate --e2e`) produces everything up to `qc/`. The `sub
 
 **v4.1** ships distribution levers and a submission pre-flight gate — analysis-integrity detectors **24 → 25** (still 43 skills):
 
-- **Claude Code plugin marketplace** — `/plugin marketplace add Aperivue/medsci-skills`, then `/plugin` discovery of eight `medsci-*` category plugins generated from the catalog SSOT (`.claude-plugin/marketplace.json`).
+- **Claude Code plugin marketplace** — `/plugin marketplace add Aperivue/medsci-skills`, then `/plugin` discovery of nine `medsci-*` category plugins generated from the catalog SSOT (`.claude-plugin/marketplace.json`).
 - **MedSci-Audit detector registry** — the deterministic verification layer is now a named, enumerated, citable suite ([`MEDSCI_AUDIT.md`](MEDSCI_AUDIT.md) + generated `metadata/detectors_catalog.json`, six audit families).
 - **Hero-skill standalone mirrors** — `scripts/sync_hero_skill.py` mirrors a focused skill to its own star-funnel repo; first two live: [`Aperivue/verify-refs`](https://github.com/Aperivue/verify-refs) and [`Aperivue/check-reporting`](https://github.com/Aperivue/check-reporting).
 - **Placeholder/marker gate** — `check_placeholders.py` flags leftover `[@NEW:]` / `[version]` / `TODO` / template-URL markers before submission (the 25th detector).