build: Make changes to scotch build permanent.

Every time you configured with internal scotch, you'd get modifications
to its Makefiles which git would show as modified. This is troublesome
whenever you want to commit or change branches, because you'd have to
remember not to keep those changes.

The changes to the scotch Makefiles are independent of any options you
might pass to configure (except that they aren't done if you aren't
using internal scotch). We can just make them permanently in git,
especially because the changes have been made upstream in scotch as
well.