Fix the doc makefile.
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.
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