reference-check

name: reference-check description: Cross-check manuscript references against Zotero library

Cross-check manuscript references against a Zotero library and report match status.

ONLY use zotero_search_items and zotero_semantic_search for lookups
NEVER call zotero_get_item_fulltext, zotero_get_item_children, or fetch — these return full paper text and will overload context
Use zotero_get_item_metadata (with include_abstract=false) only if additional metadata fields are needed for disambiguation
Match decisions must be based on metadata only (title, author, year, venue, DOI)

Read manuscript_file content (markdown, text, or pasted prose)
Extract all unique references from both reference list sections and inline (Author, Year) citations
Normalize each reference to {author, year, title} tuple; assign ref IDs (R1, R2 ...)
For each reference, search Zotero via zotero_search_items using "author year" query (metadata-only lookup)
If zotero_search_items returns no match, fall back to zotero_semantic_search using the title (metadata-only lookup)
Classify each reference as matched (confident Zotero hit), possible_match (low-confidence candidate found), or not_found
For possible_match and not_found, record the closest Zotero candidate title and key if any
Produce reference_check_report as a markdown table with columns: ref_id, author_year, title, status, zotero_key, closest_match
Append a summary section with counts: total references, matched, possible_match, not_found

If manuscript_file is unreadable, request a valid file path and pause
If no references are extracted, warn that no citations were found and stop
If Zotero MCP is unavailable, report connection error and suggest checking Zotero desktop is running
If zotero_semantic_search fails, skip fallback and mark reference as not_found