Merge message and message_up, remove ambiguity in message between GO and
annotation count.  Add notes for upcoming refactor.

and do not output '"' for repeated values in sheet, this allows for
sorting/filtering afterwards.

mainly use data frames now.

- Remove get_rate_model_to_files.
- Replace get_AIC, get_gains_losses with parse_badirate_result.
- Partially refactor get_badirate_output_frame using dicts as
  main data structure.

Turns out v1.5 was v1.70b all along, so now we use that one again which
does support -bmodel GR and has the output expected by Lennart's code.

and include species even when they have no parent node.

and:

- Mention count_groups.tsv in doc.
- Use snake case TSV headers instead.

- Split run_badirate and add to main.nf
- Various refactors