Refactor file writing - Remake Makefile.org into a template

It is time for Makefile.org to fold into the new regime and have a run
through util/dofile.pl.  This forces some information out of there and
into Configure, which isn't a bad thing, it makes Configure
increasingly the center of build information, which is as it should
be.

A few extra defaults were needed in the BASE template to get rid of
warnings about missing values.

Reviewed-by: Viktor Dukhovni <viktor@openssl.org>