train: update extended schema, aliases, signals from gold tests

train: update extended schema, aliases, signals from gold tests

train: update extended schema, aliases, signals from gold tests

train: update extended schema, aliases, signals from gold tests

Rename data/rag/index/doc_meta_species to data/rag/index/doc_meta_species.json

Create doc_meta_species

Create doc_meta_genus.json

Create embeddings_species.npy

Create index/embedding_genus.npy