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

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 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.

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.