Repair Pod::PlainText patch

Not actually sure why we need this.  Seems a bit suspicious that we
have had it for this long but nobody else has needed it.
Don't remove empty files when regenerating patches

When we regen the patches, we need to keep the empty file so that
the new patch has the removal diff.
Correct the patch that disappeared due to patch -E

Oops, good thing I was checking those.