zotero-keeper-harness

name	zotero-keeper-harness
description	Codex harness for Zotero/PubMed assistant workflows bundled with Pharmacy MCP. Triggers: zotero keeper, zotero mcp, full check, release checklist, workflow, Codex.

Zotero Keeper: Codex Harness Skill

Use this skill when working with Codex on the installed Zotero + PubMed MCP workspace harness. In this repository, treat extension-specific Zotero Keeper commands as legacy reference material unless an external extension repository is explicitly opened.

What To Read First

• AGENTS.md for Codex workspace instructions.
• .github/zotero-research-workflow.md for the end-user research flow.
• .clinerules/ for repo and release guardrails that also apply to Codex.
• .claude/skills/pubmed-* for user-facing research skills.

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 NCBI email policy; use explicit settings or 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.