Clean out remaining old goa references (e.g. rna, complex) now that we've switched to goa "plus" files

[kltm]

This is a follow-on from #2214

Basically, in the main pipeline and in the NEO build, there are still from traces of the old metadata. While I don't think it's actually causing any data changes for the moment, I think it would be good to remove any remaining traces, as it is making debugging (possibly related) issues difficult.

[kltm]

@pgaudet I'm trying to clean things out of the metadata that are confusing, as part of a debug process that started with following up on geneontology/noctua#902

In metadata/datasets/goa.yaml, we cleaned out the GAF-related stuff, so that there is only a single file. That fixes things for our downloads and AmiGO.
However, the way that neo builds (for noctua entities) is a little more...abstract. To that end, I think it might be good to:

First, remove all of the GPAD files from goa.yaml, as I don't think we use them and don't see a purpose in having them except creating noise for ourselves.

Second, clarify the contents of the GPI files and see if we want to keep them separate (e.g. goa_dog_complex.gpi.gz /goa_dog_isoform.gpi.gz) or if those can also be unioned into a single file. This will have some consequence in how the NEO build proceeds.