One has to keep in mind that the ./configure script only
works in a Unix environment. This limits the use of
doxymacs to emacs on Unix. But one of the major
benefits of emacs is that it exists on almost any
platform and that emacs lisp code is system
independent. We should not discard this nice feature
of lisp and add dependencies to specific configuration
tools which are not system independent.
Now, those poor creatures who must use WinNT and want
the newest version of doxymacs must either install
change the doxymacs.el file per hand to eliminate the
autoconf variables from it. Not very good...
Of cause I know of the advantages of the autoconf tools for
C programs and the C parser only runs in a Unix environment
anyway so that I would suggest that only the C part of the
doxymacs package is configured with autoconf. The lisp
stays system independent and customizing the few default
variables by hand is still no big deal.