doc/Doxyfile.in: adjust paths to top_builddir
doc/Doxyfile.in: adjust paths to top_builddir

If we work out of tree some files are build in top_builddir and not in
top_souredir.
Also fix up the used libcoap API versin by using a global variable here.

authmillenon/libcoap,authmillenon/libcoap,authmillenon/libcoap