`this.dex.deepClone` still exists as an alias to `Utils.deepClone` for
use in `data/`. I'll need to spend more time figuring out the correct
solution there.
This replaces the old approach with a new "clear everything except a
whitelist" approach, which should overall involve much less code and
lead to fewer bugs of the "the path changed for a module and I forgot
to update the uncache paths" variety.
I considered a lot of other approaches, but they seem to have more
flaws without any advantages in exchange for them. (We moved away
from `uncacheTree` because it only tracks the first require: there's
no way to get a full list of dependents for a module, only its first
dependent.)