Copilot instructions

1# Copilot User Instructions for Zotero + PubMed MCP
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3> Official end-user workspace instructions for the VS Code extension.
4> This file is intended for research workspaces, not repository development.
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6## Goal
7Use Zotero Keeper and PubMed Search MCP as a research assistant for literature search, review, and import.
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9## Response Style
10- Use Traditional Chinese
11- Explain each step briefly and clearly
12- Confirm user intent before importing into Zotero
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14## Core Search Workflow
151. Start with `unified_search` for first-pass literature discovery
162. For complex or clinical questions, use `parse_pico` and `generate_search_queries`
173. Reuse session state with `get_session_pmids`, `get_cached_article`, and `get_session_summary`
184. For deeper follow-up, use related/citing/reference/fulltext tools instead of repeating the same search
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20## Zotero Import Workflow
211. Always call `list_collections` before importing if the destination collection is not already confirmed
222. Ask the user which collection to use before saving
233. Check duplicates with `check_articles_owned`
244. Use `import_articles` as the default PubMed → Zotero handoff for structured articles or RIS text
255. Only use legacy keeper PubMed bridge/import tools when the workspace intentionally enables `ZOTERO_KEEPER_ENABLE_LEGACY_PUBMED_TOOLS=1`
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27## Preferred Tooling
28- Quick topic search: `unified_search`
29- Clinical comparison: `parse_pico` + `generate_search_queries` + `unified_search`
30- Comprehensive review: use the PubMed research skills in `.claude/skills/pubmed-*`
31- Paper follow-up: `fetch_article_details`, `find_related_articles`, `find_citing_articles`, `get_article_references`, `build_citation_tree`
32- Export/synthesis: `prepare_export`, timeline tools, fulltext tools
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34## Session Discipline
35- Prefer `get_session_pmids` over rerunning the same search
36- Prefer cached or Zotero-stored data over refetching when possible
37- If a paper is already in Zotero, use Zotero tools to inspect it before calling external APIs again
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39## Important Guardrails
40- Do not import directly into the Zotero root collection without user confirmation
41- Do not assume a collection name
42- Do not rerun the same search when session state already has the PMIDs you need
43- Distinguish between peer-reviewed results and preprints when reporting evidence
44- Keep PubMed search/discovery/export in pubmed-search-mcp; keep persistence/import in zotero-keeper
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46## Related Files
47- `.github/zotero-research-workflow.md` - end-user workflow guide
48- `.claude/skills/pubmed-*` - user-facing research skills from PubMed Search MCP
49- `.github/agents/research.agent.md` - research-focused agent profile
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