Manage-Refs Skill

Pick the tool from the Decision Tree; do not invent a parallel pipeline. References are never hand-typed: the list is always rendered by pandoc citeproc + journal CSL or by the Zotero Word plugin (CWYW). This skill writes (renders, injects, converts); bibliographic correctness against PubMed/CrossRef stays in /verify-refs — one read-only audit, one writer.

Decision Tree

Workflows

A. Pandoc citeproc (default for solo authors and final submissions)

User provides manuscript.md with [@bibkey] citations + refs.bib.

1. Gate: python3 "${CLAUDE_SKILL_DIR}/scripts/check_citation_keys.py" manuscript.md refs.bib

— exits non-zero on UNDEFINED keys. Fix and re-run. A [@NEW:topic_slug] drafting placeholder from /write-paper is reported as UNDEFINED too: resolve each by adding the citation to Zotero (/lit-sync then refreshes refs.bib) and replacing the placeholder with the real [@bibkey]. Never let a [@NEW:...] reach a rendered DOCX.

1. Render:

   "${CLAUDE_SKILL_DIR}/scripts/render_pandoc.sh" \
     -j european-radiology \
     -i manuscript.md \
     -b refs.bib \
     -o manuscript_final.docx

For the current inventory and what each style renders, read citation_styles/README.md — that table is the registry. render_pandoc.sh also lists what is on disk when -j names a style it cannot find, so ask the script rather than trusting a list written here. Two standing fallbacks: use radiology for RYAI and vancouver for JVIR (neither has a dedicated CSL). A cited key that is not in the .bib makes the render exit 5 and name the key: pandoc prints it as (key?) in the output and does not fail on its own.

1. QC:

   python3 "${CLAUDE_SKILL_DIR}/scripts/check_xref.py" \
     --md manuscript.md --docx manuscript_final.docx \
     --out qc/xref_audit.json --strict

Treat submission_safe: false as a halt. Route fixes by symptom — see the table in references/check_xref_symptoms.md.

1. Audit hand-off: invoke /verify-refs for the PubMed/CrossRef audit

before sign-off.

B. Zotero CWYW (co-author Word workflow)

User has a markdown SSOT and wants reviewers to edit citations directly in Word. Each reference must already exist as a Zotero item; the user supplies a [N] → ZoteroKey mapping.

1. Convert markers:

   python3 "${CLAUDE_SKILL_DIR}/scripts/md_marker_convert.py" \
     --input manuscript.md --output manuscript_keys.md \
     --map ref_map.json --to-keys

The conversion never guesses a Zotero key for a number: unmapped markers stay as [N], are reported on stderr, and make the script exit 1 (the partial output is still written; pass --allow-partial to accept it). Ranges such as [1-3] are expanded. Any bracketed number counts as a marker, so a year in brackets ([2019-2021]) is reported UNMAPPED too. Optionally stage with --active-ns 1,2,3,4,19 for a sample build first (a 5-reference sample limits the Word Refresh blast radius while debugging).

1. Render to .docx with pandoc (workflow A) so the body has plain text

[@key] markers, OR pre-build a .docx some other way that still contains plain [@key] text.

1. Inject CWYW:

   python3 "${CLAUDE_SKILL_DIR}/scripts/inject_zotero_cwyw.py" \
     --input manuscript_keys.docx --output manuscript_cwyw.docx \
     --user-id <zotero-user-id> --keys-from keys.txt

The script fetches item metadata live from the local Zotero connector (port 23119), so Zotero must be running locally; there is no web-API fallback. Any HTTP failure aborts with a non-zero exit, so a partial bibliography never reaches the user. Never invent Zotero metadata.

1. First-build instruction (REQUIRED): the script writes an empty ADDIN ZOTERO_BIBL

stub, which Word's Zotero Refresh treats as user-customized and refuses to populate. Open the output in Word → Zotero tab → Add/Edit Bibliography once. After that, Refresh keeps citations and bibliography in sync as authors edit.

1. Surgical patches are unsafe: for ref additions in later rounds, edit

the markdown SSOT and rebuild the whole .docx instead of regex-patching the post-CWYW file. Zotero's rendered [N] superscripts can collide with plain [N] markers and corrupt the field codes.

C. Cascade rejection re-render (find-journal hand-off)

User got rejected from journal A and /find-journal recommended journal B.

1. Confirm the new CSL exists in citation_styles/ (or fetch from

https://citationstyles.org/styles and drop in).

1. Re-run render_pandoc.sh -j <new-csl> against the same manuscript.md +

refs.bib.

1. Re-run check_xref.py --strict.
2. Re-run /verify-refs if any new references were added during the

inter-journal revision.

D. Cross-reference QC only

User shipped a manuscript and a reviewer flagged a Table/Figure mismatch.

1. Run check_xref.py --strict on the current manuscript.md + .docx.
2. Inspect qc/xref_audit.json. Body caption is the SSOT — fix manuscript.md

and rebuild, never patch the .docx by hand.

1. See references/check_xref_symptoms.md for the

MISSING_BODY / MISSING_DOCX / MISMATCH triage table.

1. For journals that accept figures and tables as separate attachment files

(European Radiology, Radiology, AJR, JVIR, KJR, and most medical journals), pass --allow-separate-attachments. It downgrades two rows, reported apart because their evidence differs:

• MISSING_DOCX — a --docx was supplied and proved the float is not in

the rendered main document. That is what a separate attachment looks like.

• MISSING_BODY with no `--docx` supplied — nothing was checked. Excused on your word,

printed as EXCUSED WITHOUT EVIDENCE, and counted in summary.downgraded_unchecked.

MISMATCH stays P0. So does MISSING_BODY when the float is in the rendered DOCX — that is SSOT drift, which no attachment policy excuses.

Run once with `--docx` before submitting. The flag is a declaration, not a verification; supplying the DOCX is what converts an excuse into evidence.

D'. v_(N+1) docx regeneration check (build-time companion)

When building v_(N+1) from a frozen v_N, the v_(N+1) docx MUST differ from v_N docx by content — a byte-identical copy is a silent seed-copy that will revert markdown edits at peer review. check_xref.py carries two flags for the build-time companion to the submission-time gate in /sync-submission's scripts/verify_package_integrity.py --assert-vN-docx-changed:

python3 "${CLAUDE_SKILL_DIR}/scripts/check_xref.py" \
    --md manuscript_v2.md \
    --docx manuscript_v2.docx \
    --vN-docx-md5 manuscript_v1.docx \
    --vN-md manuscript_v1.md \
    --strict

• --vN-docx-md5 alone: MD5 identity check. Identical bytes = FAIL.
• --vN-docx-md5 + --vN-md: additionally extracts the markdown-only diff

between v_N and v_(N+1) and verifies each ≥40-char diff line appears verbatim (whitespace-normalized, case-insensitive) in the new docx body XML. Missing diff lines = body did not pick up the markdown edits.

Output records the result under vN_docx_check in qc/xref_audit.json. Either failure mode causes a non-zero exit even without --strict.

E. Master pre-submission gate (recommended end-to-end chain)

The single entry point that combines workflows A and D plus /verify-refs into one aborting chain. Use this immediately before submission or before circulating a v_N package to senior co-authors.

bash "${CLAUDE_SKILL_DIR}/scripts/pre_submission_gate.sh" \
    --md manuscript/manuscript.md \
    --bib manuscript/_src/refs.bib \
    --docx submission/<journal>/manuscript.docx \
    --allow-separate-attachments    # omit if the journal accepts inline figures/tables

Stage order (first failure aborts):

1. check_citation_keys.py manuscript.md refs.bib — UNDEFINED / UNUSED keys
2. check_bib_title_markup.py --strict — publisher markup / tag-strip fusion in .bib titles
3. verify_refs.py refs.bib --strict — PubMed / CrossRef per-entry verification
4. render_pandoc.sh -S -j <csl> -i ... -b ... -o ... — invoked only when --docx is omitted

(--journal <csl>, default vancouver)

1. check_xref.py --md ... --docx ... --strict [--allow-separate-attachments]

On success the chain writes qc/pre_submission_gate.json (plus the per-stage artifacts qc/bib_title_markup.json, qc/reference_audit.json and qc/xref_audit.json) with submission_safe: true. On any failure the JSON records the failing stage and exit code, and the script exits non-zero — do not submit until the failing stage passes.

The gate does not reimplement any check; it calls the existing scripts as subprocesses. A new check belongs in the underlying script, which the gate then picks up.

F. BibTeX author-format corruption (rendered-name check)

Entries written as author = {Surname AB and Surname2 CD} (family + initials, no comma) make BibTeX treat the last token as the family name, rendering "AB S, CD S2". Always store author = {Family, Full Given}. Concatenated initials even with a comma (Family, AB) still collapse to a single initial under CSL initialize-with, so use the full forename from PubMed efetch.

/verify-refs compares bib content against PubMed but does not see the rendered output; grep the rendered docx and the bib separately:

unzip -p out.docx word/document.xml | sed 's/<[^>]*>//g' | grep -oE "[A-Z]{2} [A-Z], [A-Z]{2} [A-Z]"   # corruption signature in output
grep -nE 'author\s*=\s*\{[A-Z][a-z]+ [A-Z]{1,3}( |\})' refs.bib                                          # no-comma source entries

Quality Gates

This skill defines three submission gates and one user approval gate:

• Gate 1 (citekey integrity): check_citation_keys.py exits non-zero on

UNDEFINED keys. The pipeline halts; the user reviews and fixes.

• Gate 2 (cross-reference integrity): check_xref.py --strict exits 1 on

any MISSING_DOCX / MISSING_BODY / MISMATCH row (a float the markdown defines but the DOCX lacks is MISSING_DOCX even when no in-text citation of it was recognised; a legend inside an HTML comment or fenced code is not rendered, so it stays UNCITED). With --docx and no python-docx it exits 2: the DOCX audit did not run. The user reviews qc/xref_audit.json and resolves before proceeding. Under --allow-separate-attachments, check summary.downgraded_unchecked as well as submission_safe: a non-zero count means rows passed without being checked.

• Gate 3 (audit hand-off): before sign-off, the user must run

/verify-refs and confirm submission_safe: true in qc/reference_audit.json. This skill never marks the bibliography audited on its own.

• User approval gate (CWYW first build): the user must perform Word →

Zotero → Add/Edit Bibliography manually after the first inject_zotero_cwyw.py build. The skill cannot automate this and warns on stderr that it is required.

Provenance

scripts/_vendor_citation_writer.py is vendored from alisoroushmd/zotero-mcp @ ed5dfb71, MIT licensed. See NOTICE.md and LICENSE.zotero-mcp.

Known Limitations

• Webpage / non-journal item types: handled by the patched

zotero_to_csl_json that fetches Zotero's native CSL-JSON; do not bypass this patch.

• "Table 1 and 2" (singular kind word, number list): check_xref.py reads only

Table 1 from it; parsing a bare number after "and" in prose would read "Table 1 and 2 patients" as a citation. A float defined in the markdown but absent from the DOCX is still blocked as MISSING_DOCX; one that is neither defined nor rendered is not seen. Write "Tables 1 and 2" or "Table 1 and Table 2".