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

```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) |

## 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 <file> --journal <stem> [--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 warnin