MCP Zotero (DEPRECATED)

This skill is deprecated. The Zotero MCP integration has been replaced by a local BibTeX pipeline that avoids database locking and sync conflicts.

Migration Guide

What Changed

Before: Zotero MCP server (mcp-zotero) interfaced with Zotero's local SQLite database
After: references.bib is the canonical metadata store; PDFs/EPUBs live in library/pdfs/, converted markdown in library/markdown/

How to Migrate

Export your Zotero library as BibTeX (File → Export Library → BibTeX)
Run the migration script:
```
python plugins/sociology-skillset/scripts/migrate-zotero.py \
  --bib exported.bib \
  --files ~/Zotero/storage \
  --output-dir .
```
This copies your PDFs/EPUBs to library/pdfs/, converts them to markdown, and creates references.bib with pdf_path and md_path fields.

For new papers, use the ingest script instead of Zotero:

python plugins/sociology-skillset/scripts/ingest.py --file paper.pdf
python plugins/sociology-skillset/scripts/ingest.py --file book.epub --doi 10.xxxx/xxxxx

What Replaces What

Before (Zotero MCP)	After (Local Library)
`search_items(query=...)`	Search `references.bib` by author/title/year
`get_item(item_key=...)`	Look up entry in `references.bib` by citation key
`download_attachments(...)`	Read from `library/pdfs/` directly
Zotero RAG semantic search	`uv run plugins/sociology-skillset/scripts/rag.py search "query"`
`add_item(...)`	`python ingest.py --file paper.pdf`

Skills That Use the New Pipeline

All downstream skills (lit-synthesis, reading-agent, bibliography-builder, peer-reviewer, argument-builder) now read from references.bib and library/ instead of calling Zotero MCP tools.

Legacy Files

The guides/ and references/ subdirectories in this skill are preserved for reference but are no longer maintained.