Add `hybran standardize` command and make reference deduplication default

Rather than making a final decision before annotation, you can have both options later. Making reference deduplication / paralog collapse happen by default allows the pipeline to run more smoothly, while having hybran standardize to run afterwards removes all generic gene names and reintroduces different paralogs' names, as well as ab initio annotations that were hidden. The result is something that makes more sense to upload to a public database.

Mitigates #52