conduct contig and genome gathers together to avoid rebuilding LCA

[bluegenes]

In thumper, I'm doing genome and contig gathers --> LCA at the same time, to avoid building LCA twice. Figured I'd port my changes back over here, in case they're of any use to you.

I guess this does remove some flexibility, as you not longer have access to the LCA in compare_taxonomy 🤷‍♀️