medsci-skills 4.7.0 → 4.9.0

package/README.md

@@ -11,6 +11,7 @@
 [![CI](https://img.shields.io/github/actions/workflow/status/Aperivue/medsci-skills/validate.yml?branch=main&style=flat-square&label=CI)](https://github.com/Aperivue/medsci-skills/actions/workflows/validate.yml)
 ![Skills](https://img.shields.io/badge/Skills-45-brightgreen?style=flat-square)
 [![npm](https://img.shields.io/npm/v/medsci-skills?style=flat-square&label=npm&color=cb3837)](https://www.npmjs.com/package/medsci-skills)
+[![Watch the 2-min intro](https://img.shields.io/badge/▶_Watch-2--min_intro-FF0000?style=flat-square&logo=youtube&logoColor=white)](https://youtu.be/MclQ_RIofpE)
 [![good first issues](https://img.shields.io/github/issues/Aperivue/medsci-skills/good%20first%20issue?style=flat-square&label=good%20first%20issues&color=7057ff)](https://github.com/Aperivue/medsci-skills/contribute)
 
 [![Agent Skills](https://img.shields.io/badge/Agent_Skills-standard-blue?style=flat-square)](https://agentskills.io)
@@ -267,6 +268,17 @@ The E2E pipeline (`orchestrate --e2e`) produces everything up to `qc/`. The `sub
 
 ## What's New
 
+**v4.9** — analysis-integrity hardening promoted from real review cycles, plus journal-mechanics additions. Additive and backward-compatible; still 45 skills / 36 guidelines, analysis-integrity detectors **32 → 36**:
+
+- **Four new gates** — a **duplicate-bibliography** check (`check_reference_duplication.py`) for the hybrid `[@key]` + hand-typed `## References` build that renders the list twice; a **cross-script binning / composite-indicator** consistency check (`check_binning_consistency.py`, `BINNING_DRIFT` / `DERIVED_DEF_DRIFT`) for a derived categorical or composite indicator defined inconsistently across analysis scripts; a **float citation-order** check (`check_citation_order.py`) for numbered Tables/Figures not first cited in ascending order per series; and an **audit-dump leak** gate (`/sync-submission`) that blocks a `/check-reporting` output mistakenly attached as a submission file.
+- **KJR technical-check conventions + percentage-decimal style**, reader-allocation-under-burden and generative-image-as-study-object reporting (`/design-ai-benchmarking`, `/check-reporting`), and a **Liver International** CSL with that journal's submission mechanics (`/manage-refs`).
+
+**v4.8** is the **review-harvest batch** — deterministic detector hardening promoted from real-manuscript review cycles. Additive and backward-compatible; still 45 skills / 36 guidelines, analysis-integrity detectors **30 → 32**:
+
+- **Two new gates** — `check_supplement_hygiene.py` lints the rendered supplement / tables / caption files (not just the manuscript) for §-labels, placeholders, build markers, response-letter framing, and unresolved body↔supplement cross-references; `check_null_calibration.py` flags a headline negative/equivalence claim made without a minimum-detectable-effect / power / equivalence statement.
+- **Four detector false-positive fixes** — gates no longer fire on a recommended colorblind-safe palette, author-footnote `§` daggers, a correctly-hedged disclaimer, or a tier-label digit; each with a regression fixture and three newly CI-wired test suites.
+- **Nine reviewer-side domain probes** (SR/MA, observational, diagnostic, AI-overclaiming, survival) plus a `/design-study` design-stage ceiling gate for perceptual/reader-AI studies and a reusable confidence-weighted-rating→AUC monotonicity template.
+
 **v4.7** is the **self-update foundation** — physician-researchers stay current without GitHub, git, or a terminal. Additive and backward-compatible; still 45 skills / 36 guidelines / 30 detectors:
 
 - **Transactional, crash-recoverable installer.** Each install runs through a durable journal state machine recovered on the next run (roll back / forward-clean / fail-closed), with per-target SHA-256 inventories — your modified or third-party skills are backed up and never clobbered or auto-deleted.
@@ -349,7 +361,7 @@ Earlier in this series: analysis-integrity guards (confounding completeness, cla
 | **Battle-tested** | Used on real manuscript submissions by a practicing physician-researcher | Unknown provenance and validation |
 | **Depth per skill** | 150-600 lines of documentation + bundled reference files (curated journal profile library, checklists, formula sheets, code templates) | Typically thin SKILL.md templates |
 
-**MedSci-Audit** — the verification edge in the first rows above is a named suite of **28 deterministic detectors** (citation & reference integrity, cohort & pool arithmetic, scope/estimand contracts, reporting compliance, and more) that catch fabricated or drifted content before a manuscript reaches a reviewer. See **[`MEDSCI_AUDIT.md`](MEDSCI_AUDIT.md)** for the suite, its six families, and its evaluation evidence.
+**MedSci-Audit** — the verification edge in the first rows above is a named suite of **36 deterministic detectors** (citation & reference integrity, cohort & pool arithmetic, scope/estimand contracts, reporting compliance, and more) that catch fabricated or drifted content before a manuscript reaches a reviewer. See **[`MEDSCI_AUDIT.md`](MEDSCI_AUDIT.md)** for the suite, its six families, and its evaluation evidence.
 
 ---
 
@@ -594,6 +606,17 @@ Projects declare their source-of-truth layout in `SSOT.yaml`, and a `qc/migratio
 ### Skills Work Together
 Skills call each other. `check-reporting` invokes `make-figures` for PRISMA diagrams. `write-paper` calls `search-lit` for citation verification. `self-review` delegates reporting compliance to `check-reporting`. `calc-sample-size` output feeds directly into `write-protocol`'s IRB justification section.
 
+### Skill boundaries — which to use, and in what order
+The skill set is deliberately *specialized, not consolidated* — each skill owns a distinct artifact or lifecycle step, so the routing stays precise. The boundaries that are easy to confuse:
+
+- **Reference pipeline** — `search-lit` (discover candidates) → `lit-sync` (sole writer of `refs.bib`, syncs Zotero/Obsidian) → `manage-refs` (render CSL / inject CWYW / cross-ref QC, sole writer of the rendered DOCX) → `verify-refs` (read-only audit; never edits `refs.bib`). They are one pipeline, not four overlapping tools.
+- **Language passes run in order** — `humanize` (remove AI-writing tells) → `polish-language` (deterministic ESL/house-style consistency: abbreviations, spelling, en-dashes, p-value case) → `academic-aio` (AI-search/GEO visibility). Three sequential passes with non-overlapping jobs.
+- **Manuscript type picks the skill** — `write-paper` (original/IMRAD articles, case reports, MAs) vs `review-paper` (narrative / scoping / systematic literature reviews) vs `revise` (reviewer-response + tracked changes). Different structures and reporting guidelines.
+- **Author vs external reviewer** — `self-review` is your own pre-submission check (anticipated comments); `peer-review` drafts a journal-facing review as an external reviewer. Same domain probes, different user and output.
+- **Project entry** — `intake-project` classifies and scaffolds a *new or messy folder*; `orchestrate` routes a *goal or task* ("help me write a paper"). Start with `intake-project` when you have files but no structure, `orchestrate` when you have a task but no plan.
+- **Study design** — `design-study` covers general validity (analysis unit, leakage, comparator, validation) **and** carries a design-stage ceiling gate for perceptual / observer / reader / visual-Turing-test / image-provenance studies; `design-ai-benchmarking` specializes in AI-vs-human-expert evaluation (rubrics, calibration probes, LLM-as-judge).
+- **Content vs template** — `write-protocol` drafts IRB/ethics scientific content; `fill-protocol` renders that content into an institutional Word template without breaking its formatting.
+
 ### Validation status — available vs CI-gated vs evaluated
 Be precise about what "validated" means here — the three tiers are different facts:
 - **Available** — every bundled skill and deterministic detector. The current totals are the single source of truth in [`metadata/catalog_counts.json`](metadata/catalog_counts.json) and [`MEDSCI_AUDIT.md`](MEDSCI_AUDIT.md).

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+      "sha256": "e3bf7dd2e0871ce6905abc1d33a26c7afac76a93d184bfe2d431af97d0622f74"
+    },
+    {
+      "path": "skills/self-review/scripts/check_citation_order.py",
+      "size": 8705,
+      "sha256": "38525b4dd3ca8c9d99f090e4d42b65f10baf442f56fc4eac5174fb6ba13d90bb"
     },
     {
       "path": "skills/self-review/scripts/check_claim_artifact.py",
@@ -2963,19 +3008,24 @@
     },
     {
       "path": "skills/self-review/scripts/check_classical_style.py",
-      "size": 10067,
-      "sha256": "5cf7f9a331a4ebcb6f8523fcb5fd1b872079e3bb6e00bf9821a03d504174fdaa"
+      "size": 12210,
+      "sha256": "c973ee8b776f28515439fb185e1254e08e62c2e1410e260f18a824241a331af0"
     },
     {
       "path": "skills/self-review/scripts/check_cohort_arithmetic.py",
-      "size": 23363,
-      "sha256": "4ef7bded82091bc6cac8bf35cfa19bc1651acb7e0df2aa8b742bd7a04c8b3991"
+      "size": 23868,
+      "sha256": "55933d25d824bf073c0a8b7abc42d2f160c459a288ab932c50d63cf8c03afd37"
     },
     {
       "path": "skills/self-review/scripts/check_confounding_completeness.py",
       "size": 21506,
       "sha256": "7d3e67074d58a28ffee52ce64b486231f103a3ddcaf6b3b6ee83ba5f89c63bc2"
     },
+    {
+      "path": "skills/self-review/scripts/check_null_calibration.py",
+      "size": 7594,
+      "sha256": "9ddff01722c34efb6ffd757ae762c6ee12f5993bf13b11313c2e20b60b26cab3"
+    },
     {
       "path": "skills/self-review/scripts/check_panel_diversity.py",
       "size": 15324,
@@ -2998,8 +3048,13 @@
     },
     {
       "path": "skills/self-review/scripts/check_scope_coherence.py",
-      "size": 9538,
-      "sha256": "45915b2736f0356e1b2e827939090e5034a01ba5c310b952dd13ad6f2df45a61"
+      "size": 10818,
+      "sha256": "820dfc264c2a4f62c79c0c7123a3e1a8b59a100b89654617a08ff55deeb25a75"
+    },
+    {
+      "path": "skills/self-review/scripts/check_supplement_hygiene.py",
+      "size": 11088,
+      "sha256": "f89027472cdf0258357c3b0f0b0f3fec09b5ea65cc1373292797b818d1acf444"
     },
     {
       "path": "skills/self-review/skill.yml",
@@ -3023,14 +3078,19 @@
     },
     {
       "path": "skills/sync-submission/SKILL.md",
-      "size": 26836,
-      "sha256": "7aa91cc5355c3257877e0e9fdb12b60a7315f3865faa225ece32a4cc6a9c2d76"
+      "size": 27787,
+      "sha256": "4da14c76c6c9326d31ee93e9515854291cba2c48692eb85cf5d9f6f4301ce465"
     },
     {
       "path": "skills/sync-submission/references/journal_availability_policy.json",
       "size": 1257,
       "sha256": "6d278675d7c734aa3589165817f5413cc46c44402ea15039e51052ab2f52c0a8"
     },
+    {
+      "path": "skills/sync-submission/scripts/_yaml_frontmatter.py",
+      "size": 1669,
+      "sha256": "028fa8c4f7a4440c72d693a2ba6d4799410de0c565c61bd30d68eb0e7c208c78"
+    },
     {
       "path": "skills/sync-submission/scripts/assemble_supplement.py",
       "size": 8979,
@@ -3051,6 +3111,11 @@
       "size": 13869,
       "sha256": "caba039c6cfbfa09aec681a9840c7e0b5650cccdf9e00ddfd869557b0fec57c8"
     },
+    {
+      "path": "skills/sync-submission/scripts/check_checklist_dump_leak.py",
+      "size": 8745,
+      "sha256": "320765b9e975601fc2d73ce15a65b1419668982630c3b7546d0909158e5a5374"
+    },
     {
       "path": "skills/sync-submission/scripts/check_cross_artifact_stale.py",
       "size": 8286,
@@ -3063,13 +3128,13 @@
     },
     {
       "path": "skills/sync-submission/scripts/check_wordcount_cap.py",
-      "size": 10053,
-      "sha256": "7d47c194bdde03accbb6fab6347621cb3efdec17131651d7e58b4a69b4f0f0c6"
+      "size": 9788,
+      "sha256": "16fecbceae672e4192a138a0509321ea367f61079ca4ef4d630667b1e64eda58"
     },
     {
       "path": "skills/sync-submission/scripts/cover_letter_drift_check.py",
-      "size": 16554,
-      "sha256": "3188551ea2557ec7445f668a4d4b64396e94c5d691114b3d5bf52a16ef27cd7b"
+      "size": 16001,
+      "sha256": "347c5b702fbe9375899795791a34e8a60e246253bafb53b15ebb59d51dd45e7d"
     },
     {
       "path": "skills/sync-submission/scripts/cross_document_n_check.py",
@@ -3083,8 +3148,8 @@
     },
     {
       "path": "skills/sync-submission/scripts/preflight_gate.py",
-      "size": 20061,
-      "sha256": "e3e7a300f258cab373410504c1f48d27a1b75c49a12d7fa5cc0f8ba62ab86c4b"
+      "size": 20954,
+      "sha256": "f4be9edf587ec5ea2b7fb782e4912173b78a4fe2035720e6d0681b3d8f36340f"
     },
     {
       "path": "skills/sync-submission/scripts/scope_drift_check.py",
@@ -3403,8 +3468,8 @@
     },
     {
       "path": "skills/write-paper/references/journal_profiles/KJR.md",
-      "size": 10367,
-      "sha256": "e74e6454054dc3665c6012b973020222f9d02e469d195a60b2570e850fc23e2c"
+      "size": 12737,
+      "sha256": "ea71f1be90ff7088ba8931c97515f221486ca7ac9c7079fefba25417e7a0e932"
     },
     {
       "path": "skills/write-paper/references/journal_profiles/Korean_Circulation_Journal.md",
@@ -3423,8 +3488,8 @@
     },
     {
       "path": "skills/write-paper/references/journal_profiles/Liver_International.md",
-      "size": 9474,
-      "sha256": "50b7cc65792c17b406ffa4cb32cfb54963d0972b71e48730d4e92a7172dcbe12"
+      "size": 12174,
+      "sha256": "4a12d53605045b20aabc827e4b803edd73f603b6112ced34ec8acfef965950aa"
     },
     {
       "path": "skills/write-paper/references/journal_profiles/Medical_Image_Analysis.md",

package/metadata/distribution_manifest.json

@@ -1,6 +1,6 @@
 {
   "schema_version": 1,
-  "version": "4.7.0",
+  "version": "4.9.0",
   "owned_skills": [
     "academic-aio",
     "add-journal",

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "medsci-skills",
-  "version": "4.7.0",
+  "version": "4.9.0",
   "description": "MedSci Skills — a medical/scientific research skill suite for AI coding agents (Claude Code, Codex, Cursor, Copilot). The npm package is a terminal-friendly installer shortcut; the canonical distribution remains the GitHub repository and the Claude Code plugin marketplace.",
   "license": "SEE LICENSE IN LICENSE",
   "homepage": "https://github.com/Aperivue/medsci-skills#readme",

package/skills/MAINTENANCE.md

@@ -0,0 +1,68 @@
+# Skill Script Maintenance — taxonomy & wiring rules
+
+Every `.py`/`.sh` under `skills/*/scripts/` and `skills/*/tests/` falls into one of
+four categories. Misclassifying one is how a detector goes "dormant" (counted in the
+catalog but never invoked) or how a regression test gives false coverage (exists but
+never runs in CI). This file is the source of truth for which is which and what each
+category must satisfy.
+
+## 1. Counted analysis-integrity detector
+
+A script whose **filename** matches the catalog glob — `check_*.py`, `detect_*.py`,
+`derive_*.py`, or `verify_refs.py` — under `skills/*/scripts/`. The glob is the SSOT:
+`scripts/gen_detectors_catalog_json.py` and `scripts/validate_catalog_consistency.py`
+both count these and they must agree with `metadata/catalog_counts.json`
+(`integrity_detectors`).
+
+A counted detector MUST:
+- be registered in `scripts/gen_detectors_catalog_json.py` `FAMILY_BY_ID` (an unmapped id
+  fails generation), and bump `metadata/catalog_counts.json` + `MEDSCI_AUDIT.md` when added;
+- be **invoked** from its skill's `SKILL.md` (a named workflow step) — otherwise it is
+  dormant (counted but never run on a real manuscript);
+- have a **CI-wired** regression test (a `tests/test_*.sh` step in
+  `.github/workflows/validate.yml`) with PII-free synthetic fixtures.
+
+> Naming trap: a reusable helper must NOT be named `check_*`/`detect_*` or it inflates the
+> detector count. Prefix helpers with `_` (see category 2).
+
+## 2. Helper / library module
+
+Shared logic imported by other scripts in the **same** skill (skills are self-contained —
+no cross-skill imports). Name it with a leading underscore (`_yaml_frontmatter.py`) or a
+plain verb (`fill_journal_abbrev.py`) so the detector glob never counts it. Helpers do not
+need their own SKILL.md step, but if a user runs them directly they should be listed in the
+skill's tool table (e.g. `manage-refs` documents `fill_journal_abbrev.py`).
+
+## 3. Run-once authoring tool
+
+A generator a maintainer runs by hand to (re)build a committed asset — NOT invoked at skill
+invocation. These are intentionally not wired into any SKILL.md step. Keep them; document
+their purpose in their own docstring. Current run-once tools:
+
+- `skills/make-figures/scripts/build_jacc_template.py` — rebuilds the committed JACC Central
+  Illustration PPTX template (`references/visual_abstract_templates/jacc_central_illustration.pptx`).
+- `skills/make-figures/scripts/extract_exemplar_from_pdf.py` — extracts a figure region from a
+  PDF page to grow the make-figures Critic-Loop exemplar reference set.
+
+## 4. Test fixture / regression test
+
+Lives under `skills/<skill>/tests/`. A `test_*.sh`/`test_*.py` is only real coverage if it
+is wired into `.github/workflows/validate.yml` as a `run:` step. **Adding a test file is not
+enough** — if it is not listed in `validate.yml` it never runs and gives false confidence.
+When you add a detector and its test in the same PR, add the `validate.yml` step in that PR.
+
+## When you touch a skill script — checklist
+
+1. New `check_*`/`detect_*` detector → register in `gen_detectors_catalog_json.py`
+   (`FAMILY_BY_ID`) + bump `catalog_counts.json` + `MEDSCI_AUDIT.md` + wire into the skill's
+   `SKILL.md` + add a CI-wired test. Then run all three generators in `--check` mode.
+2. New helper → underscore/plain name (never `check_*`), import only within the same skill.
+3. New asset/fixture file → re-run `python3 scripts/gen_distribution_manifest.py` (it tracks
+   payload files and hashes; tests are excluded from the distributed payload but the manifest
+   `--check` still gates on edited payload scripts).
+4. New/edited test → add its `run:` step to `.github/workflows/validate.yml`.
+
+Run the full local CI-mirror before pushing (see the repo `CONTRIBUTING.md` / `validate.yml`
+gates): `validate_skills.sh`, the three `gen_*.py --check`, `validate_catalog_consistency.py`,
+`check_version_consistency.py`, `gen_skill_docs.py --check`, `check_locale_inventory.py`,
+`validate_routing_assets.py --strict`, and the installer tests.

package/skills/analyze-stats/SKILL.md

@@ -55,6 +55,8 @@ from `analysis_guides/` to ensure correct methodology and reporting.
 
 ### Phase 2: Analysis Plan
 
+**Precondition (observational studies).** Before proposing an analysis plan for an observational design (cohort, case-control, cross-sectional, registry, or survey), confirm that a literature-grounded variable operationalization exists — a `variable_operationalization.md` from `/define-variables`, or an equivalent codebook-backed definition table. If none exists, **warn** the user and recommend running `/define-variables` first, so exposure / outcome / covariate definitions and cutoffs are citation-backed rather than invented ad hoc from the data dictionary (ad-hoc phenotype/cutoff definitions are a common reviewer-rejection trigger for observational work — see the dictionary-first discipline). This is a WARN, not a hard block: proceed on explicit user confirmation, recording that the operationalization artifact was not available. For stricter projects, treat the missing artifact as a hard stop until `/define-variables` has run. (This mirrors the same precondition already enforced in `/write-protocol` before drafting Methods.)
+
 Based on the data structure and research question, propose an analysis plan:
 
 1. **Auto-detect analysis type** from the table below, or accept user specification.

package/skills/analyze-stats/scripts/check_generated_code.py

@@ -145,9 +145,15 @@ def check_text_common(src: str, lang: str) -> list[dict]:
     for m in NUM_LITERAL_BODY.finditer(src):
         body = m.group(1)
         # ignore obvious non-data: ranges, single repeated, function-call args with kwargs
-        nums = NUM_TOKEN.findall(body)
         if "=" in body:  # kwargs like figsize=(8,6) or linspace(0,1,...) — not table data
             continue
+        # A list/tuple of string literals (e.g. a hex-color palette
+        # ['#000000','#E69F00',...] — exactly the colorblind-safe WONG palette that
+        # make-figures recommends) is NOT hand-typed tabular data. Strip quoted
+        # substrings before counting numeric tokens, so digits living inside string
+        # literals (the "00" in '#E69F00', RGBA codes, category labels) don't make a
+        # string list look table-shaped. Genuine numeric data is unquoted.
+        nums = NUM_TOKEN.findall(STR_LITERAL.sub("", body))
         if len(nums) >= DATA_LITERAL_STANDALONE or (len(nums) >= DATA_LITERAL_MIN and has_read):
             ln = src[:m.start()].count("\n") + 1
             claims.append({