security/gnupg: Stop running autoreconf and directly patch doc/Makefile.in

It turned out running autoreconf causes unexpected side effect that
gpg displays message as following.

gpg: NOTE: THIS IS A DEVELOPMENT VERSION!
gpg: It is only intended for test purposes and should NOT be
gpg: used in a production environment or with production keys!

So stop running autoreconf to regenerate doc/Makefile.in from patched
doc/Makefile.am, and directly patch doc/Makefile.in instead.

This partially reverts commit dd1496c651a27f6327bf030f8671e7291012cc69.

Reported by: gahr
Approved by: portmgr (implicit, just fix it)
Fixes: dd1496c651a2 security/gnupg: Update to 2.4.6