Introduced Utils::IO namespace along with serializer code for GFF3 and human-readable formats. Pre-release, not intended for public use.
Also added Utils::BiotypeMapper that performs ontology mappings.

This enables to have multiple sources of GO terms. The GO terms extracted
from the GFF file will be processed as 'DIRECT' xrefs linked to genes

	formatting

	safe use of @aliases (don't expect registry to make copy of the list)

	quote argument names and values

Add gene_score_threshold (0.125).

(zero by default in the code, but set to 0.125 in the default.conf
configuration file).

found in get_adaptor().  Suggested by jm18 on dev.

Also reformat get_alias() and get_DBAdaptor().

table to the SQL file.

Bio::EnsEMBL::IdMapping::InternalIdMapper::EnsemblTranscriptGeneric::biotype
to plugins to run.