Prism changed structure quite a bit. Most of the previously-public
structs are now opaque. This requires quite a bit of changes
internally.

It also triggered some unrelated changes, which were necessary
because Prism's main header used to pull in standard headers. So
box.c and jit.c are now no longer transitively getting all the
headers they needed.

Just clean the directory if it exists and is empty.

It is needed before updating the timestamp for prism/srcs.mk.

This reverts commit 5a2cedd051634d6d1c8fbf48b0327f8cd8eec495.

The CI is telling us to revert the diff:
https://github.com/ruby/ruby/actions/runs/17679836157/job/50251138515

Update included file list automatically.