Make use of all available references throughout the pipeline

We had a primary reference that was the only one being used as a blast reference for ab initio annotations. Multiple references were only really being used by RATT. We now use the unique ref cds fasta file from onegene as the blast reference. Expected fixes are also made for the eggNOG stage of the pipeline, but that was already in disrepair and not really well-supported. Annomerge's ref_annotations dictionary now looks up gene annotations by reference genome.