cleanupnodes: drop special casing around prune markers (API)
The `cleanupnodes` has logic to skip the creation of "prune" markers if the
changeset is already obsolete. This feels strange and gets in the way of code
changes to tracks folds. Now that callers no longer request such prune, we can
drop this logic.
In many cases, pruning through cleanupnodes should be replaced by internal
phase usage.