Deprecate / remove config option prokka_fn_snames

[ewels]

prokka_fn_snames predates the more generic use_filename_as_sample_name and can be replicated with the following:

use_filename_as_sample_name:
  - prokka

We should update the prokka docs and remove this option. If possible triggering an error if it's used, so that it doesn't silently stop working for end users.