The autoconf build replaced the static Doxyfile with a Doxyfile.in
template. In the autoconf build, the config.status script applies
substitutions to generate the actual Doxyfile. This made the generic
doc/Makefile non-functional.

Apply similar substitutions directly with the makefile so we can
still build documentation outside the context of the autoconf build.

Also add a 'distclean' target to remove the generated Doxyfile.