Move methods around to more appropriate modules rather than refactor.py. In fact refactor.py is ambiguous and we can probably move everything else out of there to help makes things a bit more clear.
Bunch of refactoring and cleanup.

* Get rid of refactor.py module, moving its methods in more appropriate
      locations.
* Get rid of io.py since its one method get_genome_record() really
      belongs in biopython_util.py.
When distributing codon replacement, make sure the partial data dir exists.