This is a cherry-pick of a24324e3 from 21.2.
I had to comment out some config files that don't seem to work in R22, that should be fixed separately. For now I'd rather have consistent code between 21.2 and master. From what I can tell this doesn't actually break anything, but the tests that are failing are essentially new.
I also added a second commit that allows to call configure on the pileup sequence (again) like for any other CP algorithm sequence. It is a no-op right now, but since it does more than just manage the temporary copies, I figured it is better to keep it around. This will have to be (manually) swept back into 21.2 once this is merged.
cc @jburr