Can't get to this immediately, but want to make sure the idea is not forgotten.

A new refinement option should be added to allow merging repeated proteins to make it easier to take a document with protein repetition, and refine it into one where all peptides for a give protein are under a single instance of that protein.

Also, for proteins (with FASTA sequences, i.e. not peptide lists), it should be possible to drag the peptides to another protein with the same sequence to allow consolidation of peptides into a single protein instance by direct manipulation.