ENG-432: Build bibliography database with live linking#80
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ENG-432: Build bibliography database with live linking#80madeleinesong wants to merge 5 commits intomainfrom
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JSON-backed BibliographyDB that tracks read/cited/relevant status per reference, supports citation network linking, and provides query functions for literature review and writing workflows. Includes 54 tests covering persistence, entry management, status tracking, live linking, queries, statistics, and export to CitationSource.
Adds BibEntry, BibliographyDB, BibliographyDBStats, ReadStatus, RelevanceLevel, VerificationStatus, load_bibliography_db, and save_bibliography_db to the paper package's public API.
Template now references the persistent bibliography-db.json file and documents how each agent (bibliographer, literature-reviewer, paper-writer, referee) interacts with the database through its query and update APIs. Bumps template_version to 2.
Adds bibliography database documentation to the agent's file protocol, citation workflow, and locate_bibliography steps. The agent now checks the database for duplicates before adding citations and persists all verification results to bibliography-db.json.
…on (ENG-432) Adds a bibliography_database section documenting how the literature reviewer should check the database before starting a review, update entries during the review, and record citation/related links between surveyed papers.
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Summary
BibliographyDB) that tracks read/cited/relevant status per reference, citation network links, and verification statesearch,filter_by_status,filter_by_tag,filter_by_phase,lookup_by_arxiv,lookup_by_doi) for literature review and writing workflows__init__.pyTest plan
tests/test_bibliography_db.pycovering persistence, entry management, status tracking, live linking, queries, statistics, and exporttest_paper_compiler_regressions.pyis unrelated (also fails on main)Closes ENG-432
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