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Use a new template doc/build_man_files.sh.in to include @top_srcdir@/doc @top_srcdir@/man as appropropriate. Update doc/Doxyfile.in in a similar way (and coap/ to coap2/) Makefile.am autogen.sh configure.ac taught about doc/build_man_files.sh.in Update doc/Makefile.am to include $(top_srcdir) and $(top_builddir)