Reproducibility archive for: Provenance auditing and independent annotation expose the limits of language model self-verification for gene sets

Archive accompanying the manuscript "Provenance auditing and independent annotation expose the limits of language model self-verification for gene sets". The archive contains the analysis workflow and figures: annotation-scoring and patient-level reanalysis code, figure code and rendered figures, derived tables, completed independent-annotation forms, frozen PubMed evidence packs (identifiers and metadata), and archived outputs of the historical language-model workflow. The directory layout mirrors the authors’ working directory so that scripts run from the archive root without path changes. Code is licensed under MIT; data, derived tables and documentation under CC BY 4.0. See README.md, LICENSE.md and MANIFEST.csv in the archive for contents, reproduction instructions and file provenance.