What is zotero-keeper-harness?

A development workflow guide for maintaining a Zotero and PubMed assistant in the Pharmacy MCP repository. Zotero manages personal research libraries, while PubMed is a database for biomedical literature.

It helps contributors follow repository rules, run tests, linting, type checks, security scans, builds, release-artifact audits, and skills audits.

It keeps local-library features separate from literature-search features and gives contributors a consistent way to check changes before release.

zotero-keeper-harness — Skill for Claude Code and Codex by u9401066

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 u9401066/pharmacy-mcp --skill zotero-keeper-harness

Clone the repo

git clone --depth 1 https://github.com/u9401066/pharmacy-mcp

Made for: Claude Code, Codex.

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/u9401066/pharmacy-mcp/zotero-keeper-harness/github.svg)](https://agentmods.dev/skills/u9401066/pharmacy-mcp/zotero-keeper-harness)

Your own site

<a href="https://agentmods.dev/skills/u9401066/pharmacy-mcp/zotero-keeper-harness"><img src="https://agentmods.dev/badge/skills/u9401066/pharmacy-mcp/zotero-keeper-harness/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/u9401066/pharmacy-mcp/zotero-keeper-harness"><img src="https://agentmods.dev/badge/skills/u9401066/pharmacy-mcp/zotero-keeper-harness.svg" alt="Reviewed on agentmods" width="80" height="20"></a>

Per session 47 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.

When invoked 432 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.

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	$0.00047	$0.00432
Opus 5	$0.00023	$0.00216
Sonnet 5	$0.00009	$0.00086
Haiku 4.5	$0.00005	$0.00043

Measured 12d ago against content hash 4e4426c8cdcf, method: parsed. Prices are Anthropic first-party input rates as of 2026-09-12, from the pricing page.

Security

Grade A, and why

zotero-keeper-harness 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 12d ago.

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.

.cline/skills/zotero-keeper-harness/SKILL.md · 40 lines

What it actually says

Zotero Keeper: Cline Harness Skill

Use this skill when working in this repository with Cline and you need the reliable loop: understand the Zotero/PubMed boundary, make a scoped change, and verify Pharmacy MCP. Extension-specific Zotero Keeper commands are legacy reference material unless an external extension repository is explicitly opened.

What To Use First

Rules: .clinerules/
Workflows: .clinerules/workflows/
- Run /zotero-full-check.md for local gates.
- Treat extension release workflows as legacy unless the referenced paths exist.
- Run /zotero-skills-audit.md after changing skills or rules.
Existing skills: .claude/skills/
- If a .claude/skills instruction conflicts with current repo behavior, prefer .clinerules/.

Pharmacy MCP Canonical Commands

Tests: uv run pytest --cov=src --cov-report=term-missing
Lint: uv run ruff check src tests scripts
Type check: uv run mypy src
Security scan: uv run bandit -q -r src
Build: uv build
Artifact audit: uv run python scripts/audit_release_artifacts.py dist

Product Guardrails

Keep Zotero local-library behavior separate from PubMed literature-search behavior.
Use import_articles as the preferred bridge from PubMed results/RIS into Zotero.
Do not bypass the NCBI email policy; use explicit settings or the git email fallback.
Do not run npm, VSIX, mcp-server/, vscode-extension/, or external/pubmed-search-mcp/ commands from this repository unless those paths exist in the active workspace.

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.

12d ago First seen · 40 lines · 47 tokens per session scan A 4e4426c8cdcf

Subscribe to this mod's changes

zotero-keeper-harness is a skill published in the GitHub repository u9401066/pharmacy-mcp (3 stars, last pushed 1mo ago), licensed Apache-2.0. It adds 47 tokens to every session and 432 once invoked, about $0.0002 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 2026-08-31.

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