AGENTS.md

1# Zotero + PubMed MCP Codex Harness
2 
3These are the workspace instructions for Codex when using Zotero Keeper and
4PubMed Search MCP through the VS Code extension.
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6## Goal
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8Help the user search biomedical literature, inspect papers, and import selected
9articles into Zotero without losing provenance or overwriting user choices.
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11## Working Style
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13- Use Traditional Chinese unless the user asks otherwise.
14- Explain search/import steps briefly.
15- Ask before importing anything into Zotero.
16- Keep PubMed search/discovery/export work in PubMed Search MCP.
17- Keep persistence, collection selection, and Zotero inspection in Zotero Keeper.
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19## Core Workflow
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211. Start broad literature discovery with `unified_search`.
222. Use `parse_pico` and `generate_search_queries` for clinical or comparison questions.
233. Reuse session state with `get_session_pmids`, `get_cached_article`, and `get_session_summary`.
244. Use related/citing/reference/fulltext tools for follow-up instead of rerunning the same search.
255. Before saving to Zotero, call `list_collections` unless the destination is already confirmed.
266. Check duplicates with `check_articles_owned`.
277. Use `import_articles` as the default PubMed-to-Zotero handoff.
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29## Repository Work
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31- Treat `.codex/skills`, `.claude/skills`, `.cline/skills`, and `.clinerules` as bundled assistant harness assets.
32- Run `npm run sync-assets` before packaging the VSIX.
33- Keep `vscode-extension/resources/repo-assets/**` synchronized with its source files.
34- Preserve custom user `AGENTS.md`, Copilot instructions, and Cline settings during extension install/update flows.
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36## Guardrails
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38- Do not import into the Zotero root collection without explicit confirmation.
39- Do not assume the target collection.
40- Do not repeat searches when session state already contains the relevant PMIDs.
41- Distinguish peer-reviewed articles, preprints, and metadata-only records.
42- Keep NCBI email/API-key and institutional access settings intact.
43 
44## Related Files
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46- `.codex/skills/zotero-keeper-harness/SKILL.md`
47- `.codex/skills/pubmed-search-mcp-harness/SKILL.md`
48- `.github/zotero-research-workflow.md`
49- `.github/agents/research.agent.md`
50- `.claude/skills/pubmed-*`
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