New API method to set a GenomeDB as non-default
New API methods to manipulate collection species sets
More GenomeDB-manipulation options in update_genome

As more API methods have been introduced into SpeciesSet and GenomeDB
adpators, we can have simple options in update_genome.pl to add or remove a
species in a collection, and to set a species as non-default.
This leads to the removal of the short-lived undefault_genome.pl
Update the documentation for the new options
Use Pod::Usage for the doc