Reorganize some helper code
Reorganize some helper code

The logic for determining where chromosomes, gene annotations, and gff
files is best centralized. This makes it easier for me at least to think
about.

RNAcentral/rnacentral-import-pipeline,RNAcentral/rnacentral-import-pipeline,RNAcentral/rnacentral-import-pipeline,RNAcentral/rnacentral-import-pipeline