build: Split Makefile.in.

This trims down Makefile.in to contain only the initializations of
Make variables with their autoconf counterpart. The new Makefile.real
contains the second part, including all recipes.

With this commit, Makefile.in needs to be changed only when
configure.ac introduces new variables. In this case a full
autoconf, configure, make cycle is necessary anyway. However, if
only Makefile.real changes, a simple make run should be enough to
update everything.