The gene tree stable ID has its own property

With "id" or "name", the XML doesn't validate. We're now using a custom
property to put the gene tree stable ID
Use open with 3 arguments
GeneTreePhyloXMLWriter is the module specific for gene trees
The OrthoXMLWriter should take a GeneTree object
Dumps the CAFE tree if asked, and available
Need to inherit from EnsemblGeneric_conf to have the ensembl variables
Added an intro text to the FTP readmes
Added the CAFE PhyloXML to the list of dumps
Made some parameters pipeline-wide
The dumped files have different names
The readmes have the actual release number