--- name: sync-submission description: Audit SSOT-to-submission drift and create journal submission manifests from canonical manuscript artifacts. triggers: sync submission, build submission, submission drift, SSOT sync, journal package, retarget journal, freeze submission tools: Read, Write, Edit, Bash, Grep, Glob model: inherit --- # Sync Submission You help keep the canonical manuscript and journal-specific submission packages from drifting apart. The skill treats `submission/{journal}/` as derived output and records whether it is current, stale, or frozen. ## When to Use - Before submitting a journal package. - After a journal portal or Word editor changed a submission manuscript. - After rejection, before retargeting to another journal. - Before `/orchestrate --e2e` marks a project as submission-ready. ## Inputs 1. Project root containing `project.yaml`, or a direct canonical manuscript path. 2. Journal short name, e.g. `chest`, `ryai`, `academic_radiology`. 3. Optional mode: - `audit`: compare existing submission against canonical source. - `build`: copy canonical source into `submission/{journal}/manuscript/` and write metadata. - `freeze`: mark a package as submitted/frozen. ## Deterministic Script ```bash python "${CLAUDE_SKILL_DIR}/scripts/sync_submission.py" audit --project-root . --journal chest python "${CLAUDE_SKILL_DIR}/scripts/sync_submission.py" build --project-root . --journal chest python "${CLAUDE_SKILL_DIR}/scripts/sync_submission.py" freeze --project-root . --journal chest --status submitted ``` For double-blind journals, sweep author identifiers across all upload artifacts: ```bash python "${CLAUDE_SKILL_DIR}/scripts/blind_sweep.py" \ --registry _shared/authors/author_registry.yaml \ --files submission/{journal}/supplementary/*.md submission/{journal}/cover_letter.md \ --backup-dir .cache/blind_sweep_backup ``` The registry is a project-local YAML mapping author identifiers (full names, native scripts, initials with/without periods, email, ORCID) to role labels (e.g., "Reviewer 1"). See `scripts/author_registry_example.yaml` for schema. Never commit a populated registry to a public repository — keep it next to the manuscript. ## Output Contract | Artifact | Path | Purpose | |---|---|---| | Submission metadata | `submission/{journal}/.journal_meta.json` | Source hash, status, canonical path | | Sync audit | `qc/submission_sync_{journal}.json` | Drift result consumed by orchestrator | | Manifest update | `artifact_manifest.json` | Submission package registry | | Pre-flight gate | `qc/preflight_gate_report.json` | Aggregated halt-on-failure manifest (see "Pre-flight gate" below) | | Supplement structure | `qc/supplement_structure.json` | Gate 14: index↔file 1:1, sub-section gaps, callout coverage | ## Pre-flight gate (single command — last step before freeze) Run this once, right before `freeze`/submission. It orchestrates the existing deterministic checks and the `/verify-refs` audit into one halt-on-failure gate, writes a single aggregated manifest (`qc/preflight_gate_report.json`), and exits **non-zero** so a build wrapper or CI step can stop the freeze. It shells out to the per-check scripts and reimplements none of them — the halt decision is driven by each sub-check's normalized exit code. ```bash python "${CLAUDE_SKILL_DIR}/scripts/preflight_gate.py" --project-root . --journal chest # add --strict to also halt on the heuristic/conditional (P1) checks # add --online to make fabricated / author-mismatched references halt (PubMed/CrossRef) # add --double-blind to make the asset-anonymization scan halt ``` By default the gate **halts only on the unambiguous, deterministic errors** (P0): leftover placeholder/markers (`check_placeholders.py`), undefined `[@key]` citations (`check_citation_keys.py`), duplicate references (`verify_refs.py`, offline-deterministic), a canonical-vs-submission hash mismatch (`sync_submission.py audit`), and an internal-audit dump leaked into a reviewer-facing file (`check_checklist_dump_leak.py` — see below). The heuristic or conditional checks — `check_xref`, `detect_copy_divergence`, `scope_drift_check`, `cover_letter_drift_check`, `cross_document_n_check`, `check_cross_artifact_stale` — **run and report as P1 `warn` but do not halt** unless promoted with `--strict` or `--require ID`; `check_asset_anonymization` is P1 unless `--double-blind`. A check whose inputs are absent (no rendered docx, no cover letter, no copies, no journal) is recorded `skipped`, never a blocker. Exit codes: `0` clean, `1` halt (≥1 blocker), `2` gate config error (e.g. a `--require`'d check could not run). The gate's offline references pass is the deterministic subset (duplicates + pagination placeholders); an online `/verify-refs --strict` against PubMed/CrossRef remains the authoritative fabrication and author-name check before submission. **Audit-dump leak check (P0).** A `/check-reporting` or `/self-review` report is an *internal working audit* — it carries auto-fix annotations, a raw JSON block (`compliance_pct`, `fixable_by_ai`, `check_reporting_version`), pipeline-log paths, and "Action Items". It is NOT the official reporting checklist a journal expects, and must never reach a reviewer. A near-miss: a prior project's `STROBE_checklist_v4.pdf` was actually this dump, reused by filename into a later submission and compiled into the reviewer-visible proof. `scripts/check_checklist_dump_leak.py --dir submission/` scans every `.md`/`.docx`/`.pdf` in the package for these tokens; any hit is a P0 `leak`. Run it (the pre-flight gate already does, over the journal asset directory) before freeze and confirm `submission_safe: true`. Writes `qc/checklist_dump_leak.json`. **Disclosure & availability check (standalone).** Top medical-AI journals require, before review, an AI-use disclosure carrying four tokens (version + access channel + date/date-range + responsible party — the tool name only *triggers* the check) and Data/Code Availability statements. Run `python3 ${CLAUDE_SKILL_DIR}/scripts/check_disclosure_availability.py --manuscript --journal [--ai-study] [--require data_availability ...] [--strict]` (reads `references/journal_availability_policy.json`). It blocks on a missing required statement or an AI disclosure that is present but missing a token / carrying a placeholder; "available on reasonable request" where the journal expects a repository is a P1 warning. Writes `qc/disclosure_availability_report.json`. ## Workflow 1. Resolve canonical manuscript from `project.yaml` or explicit input. 2. Run the script in the requested mode. 3. If `audit` reports `DRIFT`, do not retarget or freeze until the user either patches the canonical manuscript or records the difference as journal-only. 4. If `build` succeeds, run `/verify-refs` before final submission. ## Quality Gates - Gate 0 (pre-flight, last step before freeze): run `scripts/preflight_gate.py --project-root . --journal {journal}` to aggregate the deterministic checks below into one halt-on-failure manifest (`qc/preflight_gate_report.json`). Non-zero exit blocks the freeze. See "Pre-flight gate" above for the P0/P1 tiering and flags. This orchestrates Gates 1–3, 5b, 8, 9, 11 plus the placeholder and citation-key checks; the individual gates remain runnable on their own. - Gate 1: block freezing when canonical manuscript is missing. - Gate 2: block retargeting when the previous submission has unresolved drift. - Gate 3: require `/verify-refs` audit before marking a package submission-safe. - Gate 4: docx audits must use a recursive walk (paragraphs + tables + nested-table cells); a flat `document.paragraphs` scan is insufficient. - Gate 5: before freeze, confirm portal free-text fields (cover letter, data availability, acknowledgements, abstract, author contributions) match the manuscript body. - Gate 5c (portal-field markdown residue): portal paste-verbatim `.txt` fields (`abstract.txt`, `keywords.txt`, …) are cut from the markdown but never stripped of it, so a trailing `---`, a `**bold**`, or a `cm^2^` superscript pastes into — and publishes in — the field literally. The pre-flight gate runs `scripts/check_portal_field_residue.py --dir portal_fields/` (P1, `--strict`-promotable) over `portal_fields/`; only `.txt` is scanned (a `.md` is meant to carry markdown), and the emphasis/super/sub patterns require paired markers so significance stars and approximation tildes do not fire. It also carries a Minor `char_expansion` advisory: `≥`/`≤` in a paste-verbatim field are verbose-expanded by ScholarOne to "{greater than or equal to}" (five words), inflating the word count — pre-substitute `>=`/`<=` (only `≥`/`≤`; `×` and the en-dash paste cleanly). - Gate 5d (figure portal readiness): a figure bounces at the upload button for reasons decidable from the file on disk — a byte size (JACC: Asia caps a figure at **25 MB**) and an extension (SNAPP accepts only `.tiff`/`.jpeg`/`.eps`, rejecting `.png`). The pre-flight gate runs `scripts/figure_portal_readiness_check.py --figures-dir ` (P1) over `submission//figures` (or `./figures`), emitting `FIGURE_OVERSIZE` and — when the portal's formats are supplied via `--figure-accept tiff jpeg eps` — `FIGURE_FORMAT_REJECTED`. Fix by regenerating with `/make-figures export_portal_tiff.py` (LZW + RGBA→RGB flatten). The check is skipped (never an error) when there is no figures directory. - Gate 6 (double-blind journals): before freeze, export the portal's blinded review PDF and grep for all author identifiers across the entire upload set — manuscript, supplementary, cover letter, registry record PDFs (PROSPERO/ClinicalTrials), portal Letter-field text. A clean manuscript blind does not imply a clean portal blind. - Gate 7 (text-only docx rebuilds): never use `pandoc --reference-doc=manuscript.docx` for response/cover/supplementary text-only docx — the reference docx ships its embedded media (figure files) into the new docx, bloating size 50–100×. Use plain `pandoc input.md -o output.docx` for text-only artifacts. - Gate 5b (Phase 4 cover-letter free-text drift): before freeze, run `scripts/cover_letter_drift_check.py` to verify the cover letter's word-count / reference-count / table-figure-count claims still match the manuscript. Cover letters routinely go stale across v_N → v_(N+1) branching and are not covered by any docx-level audit. See "Phase 4 — Cover-letter free-text drift" below. - Gate 8 (Phase 5 cross-document N consistency): before freeze, run `scripts/cross_document_n_check.py` over the manuscript bundle (abstract, body, PROSPERO record, cover letter, supplementary, INDEX, PRISMA flow caption). Any N category with >1 distinct integer value is a P0 drift. When a `FINAL_POOL_LOCK.yaml` is present, supply `--pool-lock` to make the locked counts the authoritative baseline. See "Phase 5 — Cross-document N consistency" below. - Gate 9 (Phase 6 intra-manuscript scope drift): run `scripts/scope_drift_check.py` against the manuscript (and optionally the PROSPERO record). Numeric anchors (AUC, OR/HR/RR, sensitivity/specificity) appearing in Limitations / Discussion but absent from Methods + Results are P0 SCOPE_DRIFT. PROSPERO ↔ Methods synthesis-method disagreement is a P0 PROSPERO_DRIFT. - Gate 10 (Phase 7 v_(N+1) docx regeneration): when building a new submission from a frozen prior version, run `scripts/verify_package_integrity.py --assert-vN-docx-changed --vN-docx .docx --new-docx .docx`. Identical MD5 = unmodified seed copy = block submission. Defense-in-depth — required even when the upstream pipeline appears to have regenerated the docx. - Gate 11 (Phase 8 multi-copy divergence): when the project hand-maintains more than one manuscript copy (working SSOT, circulation, portal), run `scripts/detect_copy_divergence.py --ssot .md --copy .md ...` before freeze or circulation. Any `STALE_COPY` (an SSOT numeric claim or heading that did not propagate to a copy) is a P0 drift. See "Phase 8 — Multi-copy manuscript divergence" below. - Gate 11b (reframe / headline-change survivor scan): after a revision that **reframes a claim class** (e.g. retires "location-stratified benchmark" for "overall pooled") or **changes a headline number**, a stale copy commonly survives in an un-touched body paragraph, a figure/table legend, the supplement, or the response letter — the response letter often claims the change was applied "throughout" while a sidecar still carries the old term/value. Pass the retired vocabulary and superseded values from the reframe diff to the cross-artifact gate, which scans the **body and every aux artifact**: ```bash python3 "${CLAUDE_SKILL_DIR}/scripts/check_cross_artifact_stale.py" \ --manuscript manuscript.md --aux supplement/ --aux figures/legends.md --aux revision/response_to_reviewers.md \ --retired-term "location-stratified benchmark" --old-value 1.72 ``` A `retired_framing_survivor` / `stale_old_value` finding is a P1 stale claim-site; this automates the claim-site grep of `manuscript-versioning.md` §6.1 across all artifacts rather than a sample. (Numeric survivors are digit-bounded, so `1.72` never matches `11.723`.) - Gate 12 (target-journal metadata drift): on `build` / retarget, cross-check the target the manuscript is written *for* against the target the project is being submitted *to*. Compare `project.yaml` `target` (and any in-manuscript header/footer "for submission to X" string) against the journal the package is built for, and check the structural metadata the target dictates — abstract heading structure (4- vs 5-heading), body word limit, citation style (Vancouver / AMA), required elements (Highlights / Central Illustration / Key Points). A mismatch (e.g., a header still reading the previous journal after a cascade retarget, or a 4-heading abstract for a 5-heading target) is a target-restructure trigger — branch to v_(N+1) per `manuscript-versioning.md` §2 and sync every sidecar (cover letter, title page, ICMJE COI list) — not a silent build. ```bash # header target vs project.yaml target TGT=$(python3 -c "import yaml;print(yaml.safe_load(open('project.yaml')).get('target',''))" 2>/dev/null) grep -niE 'for submission to|submitted to|prepared for' manuscript/manuscript.md # compare against "$TGT" ``` - Gate 13 (body word count vs journal cap — the revision-inflation trap): resolving reviewer majors monotonically *adds* words, so a revised body silently breaches the target journal's limit. Before freeze (and after **every** `/revise` pass), run `scripts/check_wordcount_cap.py` against the target journal profile's body cap. `WORDCOUNT_OVER_CAP` is a P0 (relocate methods/sensitivity detail to the Supplement); `WORDCOUNT_NEAR_CAP` (>0.95×) warns that the next pass will breach. The binding number is the **rendered** count (citeproc expands `[@key]` → "(Author Year)"), so prefer the built DOCX count with `--rendered-words N`; otherwise the script estimates it from the markdown body + inline-citation expansion. ```bash python3 "${CLAUDE_SKILL_DIR}/scripts/check_wordcount_cap.py" \ --manuscript manuscript/manuscript.md \ --journal-profile "${MEDSCI_SKILLS_ROOT:-$HOME/workspace/medsci-skills}/skills/find-journal/references/journal_profiles/.md" \ --article-type "Original Article" --out qc/wordcount_cap.json --strict # or, deterministic: --limit 4000 (and --rendered-words N from the built DOCX when available) ``` - Gate 14 (supplement structure — the numbering lock): a cohort/SR supplement is a directory of `S{N}_*.md` sections plus an index, hand-concatenated into `_combined.md`. Across revision rounds that set desynchronizes silently: an index row with no file, a file the index never lists, two files claiming the same `S{N}`, or a sub-section gap after an insert (`S6.3` then `S6.5`). A reviewer opening "Supplementary Table S9" and finding the wrong content is the failure mode. Before freeze, run `scripts/assemble_supplement.py` to validate index↔file 1:1, rebuild `_combined.md` in index order (so the assembly is reproducible rather than hand-maintained), and — with `--manuscript` — report callout coverage: body callouts with no section file (`CALLOUT_WITHOUT_SECTION`) and section files the body never cites (`SECTION_UNCITED`). The four structural kinds are P0 under `--strict`; coverage findings are advisory. ```bash python3 "${CLAUDE_SKILL_DIR}/scripts/assemble_supplement.py" \ --dir submission/{journal}/supplementary --index 00_index.md \ --manuscript manuscript/manuscript.md \ --out submission/{journal}/supplementary/_combined.md \ --json qc/supplement_structure.json --strict ``` ## Phase 4 — Cover-letter free-text drift Cover letters live outside the submission docx files but are read by the editor side-by-side with the manuscript. Their `## Article details` block — body word count, abstract word count, reference count, table/figure count — is a sidecar SSOT that routinely goes stale when a manuscript branches v_N → v_(N+1) (word limit retarget, abstract restructure, late reference batch). `scripts/cover_letter_drift_check.py` measures the manuscript truth and compares it to the cover letter's numeric claims: ```bash python "${CLAUDE_SKILL_DIR}/scripts/cover_letter_drift_check.py" \ --manuscript manuscript.md \ --cover-letter cover_letter.md \ --refs refs.bib \ --out qc/cover_letter_drift.json ``` Body words are matched with a 5% tolerance ("approximately N words" phrasing). Abstract words tolerate ±5. Reference / table / figure counts require exact match. Output `qc/cover_letter_drift.json`: ```json { "submission_safe": false, "truth": {"body_words": 3036, "abstract_words": 319, "references": 12, "tables": 3, "figures": 4}, "claims": {"body_words": 3790, "abstract_words": 250, "references": 12}, "drifts": [ {"field": "body_words", "truth": 3036, "cover_letter_claim": 3790, "severity": "MAJOR", "note": "|claim - truth| = 754 > tolerance 151"} ] } ``` Drift resolution: regenerate the cover letter from the manuscript at v_(N+1) build time. The script never edits the cover letter — that is left to the manuscript build pipeline so the cover letter stays a deliberate authored artifact. ## Phase 5 — Cross-document N consistency Multi-document cohort-size drift is a high-frequency desk-reject pattern. Manuscript abstracts, body prose, PROSPERO records, supplementary extraction sheets, and PRISMA flow captions all repeat the same `k included` / `k excluded` / `N patients` totals — and any disagreement between them is read by reviewers as either a data-integrity failure or a late-edit failure. Either reading ends the round. `scripts/cross_document_n_check.py` scans the submission package, extracts every "N " claim by category (patients, cases, included, excluded, nodules, tumors, studies_total), and groups them by category. A category with more than one distinct integer value is a P0 drift. ```bash python "${CLAUDE_SKILL_DIR}/scripts/cross_document_n_check.py" \ --root . \ --out qc/cross_document_n.json ``` When the project has frozen a `2_Data/FINAL_POOL_LOCK.yaml` from `/meta-analysis` Phase 3f.5, pass it as the authoritative anchor: ```bash python "${CLAUDE_SKILL_DIR}/scripts/cross_document_n_check.py" \ --root . \ --pool-lock 2_Data/FINAL_POOL_LOCK.yaml \ --out qc/cross_document_n.json ``` Output `qc/cross_document_n.json`: ```json { "submission_safe": false, "drift_count": 1, "drifts": [ { "category": "included", "values": [63, 64], "locations": [ {"file": "abstract.md", "line": 4, "value": 63, "context": "..."}, {"file": "supplementary/s1.md", "line": 12, "value": 64, "context": "..."} ], "severity": "MAJOR" } ], "lock_violations": [] } ``` Treat `submission_safe: false` as a halt. Resolve drift by tracing each location to its data artifact (extraction sheet, PRISMA cascade TSVs) and correcting the document(s) that disagree with the locked count. ## Phase 6 — Intra-manuscript scope drift Late-revision sensitivity analyses sometimes get introduced in the Discussion or Limitations subsection without ever propagating back to Methods + Results. The manuscript then makes claims (with explicit AUC, OR, sensitivity numbers) whose primary report never exists. Reviewers read this as a fabrication-grade red flag, and editors desk-reject. A second variant of the same anti-pattern: the PROSPERO record commits to a synthesis method (Freeman-Tukey, random-effects DerSimonian-Laird, bivariate, HSROC, Bayesian, etc.) but the Methods section uses a different one — or the PROSPERO record was updated and Methods stayed behind. When accompanied by a Methods line saying "no amendment lodged", this becomes a documented silent protocol deviation. `scripts/scope_drift_check.py` detects both patterns: ```bash python "${CLAUDE_SKILL_DIR}/scripts/scope_drift_check.py" \ --manuscript manuscript.md \ --prospero prospero/prospero_v2.md \ --out qc/scope_drift.json ``` Output: ```json { "submission_safe": false, "limitations_only_anchors": [ { "anchor": "0.869", "kind": "AUC", "found_in": ["Limitations:31"], "missing_from": ["Methods", "Results"] } ], "synthesis_method_drift": [ {"method": "Freeman-Tukey", "prospero": true, "methods": false} ] } ``` Resolution: either (a) propagate the anchor into Methods + Results as a primary report or (b) remove it from Limitations / Discussion. For synthesis-method drift, file a PROSPERO amendment and update Methods to match — both must agree before submission. ## Phase 7 — v_(N+1) docx regeneration gate When a v_N submission package was frozen and a v_(N+1) is being built (after a markdown body edit, reviewer round, or cascade-rejection re-target), the v_(N+1) docx MUST differ from the v_N docx. The most common silent-revert pattern is a `cp v_N/manuscript.docx v_(N+1)/manuscript.docx` step that skips the pandoc / Zotero CWYW regeneration entirely. The markdown body is then edited, but the docx the portal receives is the frozen v_N — the change silently reverts at peer review. Run the byte-identity assertion at the top of the v_(N+1) submission gate: ```bash python3 /path/to/medsci-skills/scripts/verify_package_integrity.py \ --assert-vN-docx-changed \ --vN-docx SUBMISSION//v/manuscript.docx \ --new-docx SUBMISSION//v/manuscript.docx ``` Identical MD5 → exit 1 with explanatory error. Block submission until the regeneration step is fixed. ## Phase 8 — Multi-copy manuscript divergence When a project keeps several hand-maintained manuscript copies — `manuscript.md` (the working SSOT), `manuscript_circulation.md` (co-author feedback), and `submission//manuscript.md` (portal) — a batch of edits applied to the SSOT routinely lands in only some of the copies. The portal then receives a copy missing a subset of the edits, and the divergence surfaces (if at all) only when a reviewer notices the inconsistency. Before freezing a package or sending a circulation round, run the directional detector (SSOT → each copy): ```bash python3 ${CLAUDE_SKILL_DIR}/scripts/detect_copy_divergence.py \ --ssot manuscript.md \ --copy manuscript_circulation.md \ --copy submission//manuscript.md \ --out qc/copy_divergence.json --strict ``` It reports, per copy, the SSOT *claims* (numeric assertions — `n = N`, percentages, `p`, OR/HR/RR, 95% CI — and section headings) that did not propagate. A `STALE_COPY` (`DIVERGENT` overall) is a **P0 blocker**: re-propagate the unpropagated claims, or — better — stop hand-maintaining parallel copies and **generate the circulation / submission variants from the single SSOT via a build step** (pandoc transform), so there is only one editable source. Claims are matched as normalized strings, so wording differences do not register — only a changed or absent number/heading does; legitimately copy-specific content (a circulation cover note) shows up as `copy_only` and can be ignored. ## Phase 9 — Springer Editorial Manager packaging (no title-page slot) Some Springer Editorial Manager journals offer only **Manuscript / Figure / Table / Supplementary / LaTeX** upload item types — no separate Title Page or Cover Letter slot, and sometimes no Graphical Abstract slot. Common for observational / cohort submissions. - **Title page → page 1 of the Manuscript file.** Build via pandoc: title-page markdown (strip internal-only blocks such as a "Manuscript Metrics" QC block, plus any Funding / Author Contributions / Keywords that also appear later) + a real docx page break (raw OpenXML ``; a bare `\newpage` is silently dropped in docx output) + the manuscript body **with its byline / affiliations / corresponding-author footnote removed** so the title page is not duplicated. - Verify: at least one page break; the affiliation block appears once; the article title is followed directly by the Abstract (no repeated byline); no internal QC strings leak. - **Cover letter → paste into the "comments to the publication office" free-text field.** - **Graphical Abstract (no dedicated slot) → upload as a Figure with Description = "Graphical Abstract".** - **Declarations completeness (portal hard checkbox).** The manuscript "Statements and Declarations" must carry all seven Springer subheadings: Funding; Competing Interests; Ethics Approval; Consent to Participate; Consent for Publication; Author Contributions; Data Availability. For de-identified observational / registry studies, Consent to Participate = waived (existing de-identified records) and Consent for Publication = "Not applicable; only de-identified data, no individual person's identifying details, images, or videos". ```bash for s in Funding "Competing Interests" "Ethics Approval" "Consent to Participate" "Consent for Publication" "Author Contributions" "Data Availability"; do unzip -p manuscript.docx word/document.xml | sed 's/<[^>]*>//g' | grep -q "$s" && echo "OK $s" || echo "MISSING $s"; done ``` - **Ethics approval / exemption number (observational or exempt cohort).** State the IRB approval or exemption reference number in the ethics statement. Institutional exemption notices carry the reference in the document body; filename digits are usually a receipt number, not the approval number — open the notice before writing the ethics block. - **Word limit "including references".** When the limit counts references, the binding constraint is body+references words, not the reference-count ceiling. Measure body+refs on the rendered docx before adding references; each Vancouver reference is roughly 25–33 rendered words. - **Submitting via a co-author's account.** Editorial Manager auto-adds the account holder at the top of the author list, tagged first/corresponding. De-duplicate, reorder to the intended position, reassign the first-author tag to the true first author, and fill missing co-author email/ORCID. - **Re-read the EM-compiled submission PDF before Approve** — author order, degrees, ethics number, references, declarations, and figures. ## Phase 10 — Marked (tracked-changes) manuscript for a revision round Every revision round asks for a **marked** manuscript: the revised paper with tracked changes against the version the reviewers saw. Two rules, both load-bearing. **The baseline is R0, not the previous round.** The base of the diff is always the *originally reviewed* submission; only the target advances each round. An editor wants every change made since the version under review, so do not diff v7 against v8. **Word's Compare is the only safe producer — but it is scriptable.** `pandiff` and LibreOffice `--compare` corrupt OOXML on real manuscripts (tables collapse, affiliation superscripts are lost); do not use them. Word for Mac exposes `compare` through AppleScript with `author name`, so the build needs no GUI pass and no post-hoc rewriting of `w:author`: ```bash python3 "${CLAUDE_SKILL_DIR}/scripts/build_marked_manuscript.py" \ --original submission/{journal}/R0/manuscript.docx \ --revised submission/{journal}/R1/manuscript_clean.docx \ --out submission/{journal}/R1/manuscript_marked.docx \ --author "Submitting Author" --line-numbers ``` (macOS + Word only. On any other platform, produce the marked file in Word by hand — then still run the gate below.) ### The gate: a round trip, not a grep Confirming that "the marked file contains sentence X" passes even when Compare has dropped a paragraph, duplicated one, or split the revisions between two authors. Verify it the only way that is correct by construction — **accepting every revision must reproduce the revised manuscript exactly, and rejecting every revision must reproduce the original**: ```bash python3 "${CLAUDE_SKILL_DIR}/scripts/check_marked_manuscript.py" \ --marked submission/{journal}/R1/manuscript_marked.docx \ --original submission/{journal}/R0/manuscript.docx \ --revised submission/{journal}/R1/manuscript_clean.docx \ --author "Submitting Author" --strict ``` Verdicts: `MARKED_ACCEPT_MISMATCH`, `MARKED_REJECT_MISMATCH` (content dropped, duplicated, or invented), `MARKED_NO_REVISIONS` (Compare produced a clean copy), `MARKED_AUTHOR_MIXED`, `MARKED_TABLE_LOSS`, `MARKED_BASE_TRACKED` (a baseline still carrying live tracked changes, which makes the comparison ill-defined — accept or reject them first). **A move is not an insert plus a delete.** Word encodes relocated content as `w:moveFrom` / `w:moveTo`, and a verifier that knows only `w:ins` / `w:del` reconstructs the original with the moved paragraph in it *twice* — reporting a perfectly good file as corrupt. The gate resolves `revised = unchanged + w:ins + w:moveTo` and `original = unchanged + w:delText + w:moveFrom`. Any docx probe written here must walk exact `w:t` / `w:delText` elements: the regex `]*>` also matches ``, `` and ``, silently swallowing table markup as prose. ### Upload failure on a large marked file The marked file carries the baseline's embedded images as deleted content, so it can exceed a portal's size cap even when the clean file is small. Before re-encoding, rule out the ordinary causes: the file is still open in Word (a `~$…docx` lock), the portal session expired, or the upload is transient — retry. If it is genuinely too large, downsample only `word/media/*` and repackage; tracked changes live in `word/document.xml` and are untouched. Re-run the gate afterwards and keep the full-resolution original as `*.full.docx`. ## Verification Blind Spots Post-submission learnings (npj Digital Medicine R1, 2026-05): a clean docx-level audit still missed several stale artifacts that surfaced only at the portal review stage. Apply these whenever auditing a submission package. ### B1. docx scanning must be recursive `python-docx` `paragraph.runs` does not expose runs inside ``; `document.paragraphs` skips table cells; `document.tables` does not recurse into nested tables. Figures, captions, and reporting checklists are routinely wrapped in 1×1 or nested tables, so flat scans silently miss them. - Walk `paragraphs + tables + nested-table cells` recursively for every stale-string scan. - For run-level edits near hyperlinks or fields, inspect the paragraph XML, not just `.runs` — a missing inline element can be misread as an empty `()` artifact and "fixed" into a real defect. ### B2. Portal input fields are a separate SSOT Cover letter, Data Availability, Acknowledgements, Abstract, and Author Contributions are often typed directly into the journal portal, outside any docx this skill audits. A clean docx audit does not imply a clean portal. - Before final submission, diff the portal's final review page against the manuscript body 1:1. - Treat each portal free-text field as its own drift target. ### B3a. Double-blind compliance must cover ALL upload artifacts A clean manuscript-level blind sweep does not imply a clean portal-level blind. Author identifiers commonly leak through: - Supplementary materials (per-material `.md`/`.docx` files, especially methodology logs, agreement metrics, amendment logs) - Cover letter (separately-uploaded file is portal-default visible to reviewers unless explicitly toggled "Don't show in review PDF") - Registry record PDFs (PROSPERO, ClinicalTrials.gov, IRB approval PDFs) - Portal free-text Letter field if cover-letter signature was pasted - Response-to-reviewers (revision rounds) Blind sweep regex coverage must include both period and no-period initial forms (e.g., `Y.N.` and `YN`), full names in roman + native scripts, institution names, ORCID IDs, and submission email domains. The first blind PDF export from the portal is the authoritative drift detector — always export and grep before final submit. ### B3b. PROSPERO public-record PDF shows only current amendment PROSPERO's "Print/PDF" export from the public record renders only the current amendment narrative. Previous versions are accessible only by selecting older versions in the public-record version-history dropdown. When citing PROSPERO version state, never rely on a single PDF export to verify cross-version consistency — record each published version's PDF independently and clarify in cover/supplementary which version anchors the methodology vs. which version reflects documentation-only erratum. For documentation-only PROSPERO errata (correcting a narrative fact without changing methods/eligibility/synthesis), prefer a single Revision-Note append over a new structured amendment entry. Preserves historical audit trail and minimizes portal edit surface. ### B3c. Text-only docx rebuilds must not inherit manuscript media If `response_to_reviewers.docx` / `cover_letter.docx` / supplementary text-only docx grow to >100 KB after a rebuild, suspect `--reference-doc` pulling manuscript figure media. Verify with `unzip -l output.docx | grep word/media/` — should be empty for text-only artifacts. ### B3. Verify change propagation across the whole SSOT tree A tone, wording, or number change applied to one file (e.g. the abstract) must propagate to every file that repeats it — discussion, response-to-reviewers quotes, reporting checklists, supplementary captions, title page. - grep the OLD string across the entire SSOT tree, never a subset of files. - Watch for substring near-misses (`expertise-dependent patterns` vs `expertise-dependent evaluation patterns`) — an exact-match grep on the short form passes while the long form remains stale. ## What This Skill Does NOT Do - Does not invent journal formatting rules. - Does not silently merge submission edits back into the SSOT. - Does not replace `/write-paper`; it packages already canonical content. ## Anti-Hallucination - Never claim a submission package is current without matching source hashes. - Never mark a package as submitted without writing `.journal_meta.json`. - Never hide journal-only differences; record them as drift or explicit exceptions.