Rename project-owned entrypoints, resource directories, classes and helpers to BioMod/biomod, and update imports, notebooks, documentation and command examples. Preserve old CLI flags as aliases and keep serialized state/configuration keys, raw gene-set IDs, result schemas and third-party interfaces compatible. Move the existing checkpoint/configuration pair to weight/BioMod.pth and weight/BioMod.pkl using their unchanged objects. Remove only the eight approved duplicate files from the source module-data directory and nested attention package; retain the shared copies. Raw datasets, legacy reference data copies and all weight contents remain unchanged. Validation: 90 Python 3 files, 65 notebook cells, 12 utility tests, 7 synthetic backbone comparisons and 10 classifier comparisons passed. No real model weights or datasets were deserialized, and no real-data training was run.
