new module. The clipping code is centralised, so that it can be used anywhere without duplication. It can clip, mask or softmask the polyA and the polyT if any.

list_geneIds made consistent with list_gene_stable_ids and both rather return an arrayref, to be fashionable

 - These method calls in Gene.pm are delegated to Transcript.pm
 - The calls are species specific, removing the need to query the priority
   column the external_db table.