A reference-management workflow for medical manuscripts. It validates citation keys, formats references for a journal, checks links between manuscript text and Word documents, converts citation markers, and can add live Zotero fields.

Use it to validate references, render journal-style citations, convert citation markers, check manuscript-to-DOCX cross-references, and insert Zotero field codes.

It catches broken or mismatched citations and keeps reference formatting consistent when a manuscript changes journals. It also supports Word documents that collaborators can update through Zotero.

manage-refs — Skill for Claude Code by Aperivue

Install

Getting it into your agent

One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.

Any agent

npx skills add Aperivue/medsci-skills --skill manage-refs

Clone the repo

git clone --depth 1 https://github.com/Aperivue/medsci-skills

Made for: Claude Code.

Or install medsci-literature, the plugin that ships this one along with the rest of its 6 skills.

Wrote this? Show the measurements

A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.

README.md

[![agentmods](https://agentmods.dev/badge/skills/aperivue/medsci-skills/manage-refs/github.svg)](https://agentmods.dev/skills/aperivue/medsci-skills/manage-refs)

Your own site

<a href="https://agentmods.dev/skills/aperivue/medsci-skills/manage-refs"><img src="https://agentmods.dev/badge/skills/aperivue/medsci-skills/manage-refs/github.svg" alt="Measured on agentmods" height="20"></a>

Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.

Your own site · 80×15

<a href="https://agentmods.dev/skills/aperivue/medsci-skills/manage-refs"><img src="https://agentmods.dev/badge/skills/aperivue/medsci-skills/manage-refs.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 144 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 5,450 The whole file, excluding the scripts and references it only reads on demand.

Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits

NVIDIA SkillSpector warn 7 Sept 2026

SkillSpector: 1 finding, up to medium

These are SkillSpector’s own severities. On a checked sample its high-severity flags on skills were ~96% false positives — a documented command, a public API, a “never do X” rule — so we show them as a caution to read, not a verdict. Why →

medium Agent Snooping · line 23
Skill enumerates or reads other installed skills. Access to other skills' SKILL.md files or the skills directory reveals prompt instructions, capabilities, and secrets that should be invisible to peer skills.

Fix: Remove all code or instructions that list or read other skills' files or directories. Skills should operate independently; cross-skill access is a privilege escalation.

How audits are shown

Origin original No closer match found in the catalogue.

Token cost

What it costs to keep this loaded

Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.

Model	Per session	Once invoked
Fable 5.1	$0.00144	$0.05450
Opus 5	$0.00072	$0.02725
Sonnet 5	$0.00029	$0.01090
Haiku 4.5	$0.00014	$0.00545

Measured 11d ago against content hash 16a7ddf44125, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-10, from the pricing page.

Security

Grade A, and why

manage-refs scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 11d ago.

The scan reads SKILL.md. This mod also ships 21 executable files (scripts/_vendor_citation_writer.py, scripts/check_bib_title_markup.py, scripts/check_citation_keys_challenge/verify.sh, …), listed below but not scanned — reading those needs a real analyzer, not pattern matching.

A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.

Nothing flagged

None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.

skills/manage-refs/SKILL.md · 338 lines

How it starts

The opening of the file, as written. The whole thing — 338 lines — stays where its author put it; the contents beside it link to each section on GitHub.

Manage-Refs Skill

Canonical source (issue #16). This SKILL.md is the single canonical reference for the reference-workflow (validate keys → render CSL → convert markers → QC cross-references → inject Zotero CWYW). Audit-only bib verification is owned by skills/verify-refs/SKILL.md. Any user-scope rule or external note about reference handling should point here (workflow) or to verify-refs (audit) rather than restating the "how", to prevent drift.

You are routing reference-handling work for a medical manuscript. The user is somewhere in the lifecycle — drafting, building a circulation DOCX, swapping CSL after a journal rejection, fixing a cross-reference defect surfaced by QC, or wiring up live Zotero field codes for a co-author Word workflow. Pick the right tool from the decision table; do not invent a parallel pipeline.

Why This Skill Exists

Reference handling spans every late-stage skill: /write-paper builds the first DOCX, /revise rebuilds it after each reviewer round, /peer-review emits a critique that quotes references back, /sync-submission packages the final tarball, /find-journal informs CSL swaps on rejection cascade, and /verify-refs audits the bibliography. Until 2026-05-01 these scripts lived under skills/write-paper/scripts/, which made /revise and /sync-submission silently depend on a sibling skill — a layering inversion that broke when /write-paper was loaded into a non-research project. Moving the lifecycle tools here turns reference handling into a first-class concern with one decision tree, one set of CSL files, and one provenance file (NOTICE.md) for the vendored Zotero CWYW writer.

Validated 2026-05-01 against a 21-reference meta-analysis manuscript (a meta-analysis project's submission) for both pandoc-citeproc and Zotero-CWYW paths.

Anti-Hallucination Guarantees

Citekey discipline (Phase 0): every in-text citation must be [@bibkey] resolvable in refs.bib. scripts/check_citation_keys.py is a hard gate — UNDEFINED keys exit non-zero and block the build.

Read the full file on GitHub · 338 lines

Files

What ships with it

53 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.

Changes

What this file has done since we first saw it

Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.

11d ago First seen · 338 lines · 144 tokens per session scan A 16a7ddf44125

Subscribe to this mod's changes

manage-refs is a skill published in the GitHub repository Aperivue/medsci-skills (292 stars, last pushed 3d ago), licensed MIT. It adds 144 tokens to every session and 5,450 once invoked, about $0.0007 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.

Claude Code Documents Research biostatistics claude-skills clinical-research diagnostic-accuracy literature-review

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manage-refs