sync-submission

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

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:

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)

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.

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), and a canonical-vs-submission hash mismatch (sync_submission.py audit). 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.

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 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 <prev>.docx --new-docx <next>.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 <ssot>.md --copy <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 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.

  # 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"
  

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:

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:

{
  "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.

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:

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:

{
  "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:

python "${CLAUDE_SKILL_DIR}/scripts/scope_drift_check.py" \
    --manuscript manuscript.md \
    --prospero prospero/prospero_v2.md \
    --out qc/scope_drift.json

Output:

{
  "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:

python3 /path/to/medsci-skills/scripts/verify_package_integrity.py \
    --assert-vN-docx-changed \
    --vN-docx SUBMISSION/<journal>/v<N>/manuscript.docx \
    --new-docx SUBMISSION/<journal>/v<N+1>/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/<journal>/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):

python3 ${CLAUDE_SKILL_DIR}/scripts/detect_copy_divergence.py \
  --ssot manuscript.md \
  --copy manuscript_circulation.md \
  --copy submission/<journal>/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 <w:br w:type="page"/>; 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".

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.

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 <w:hyperlink>; 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.