conditional use of unrelated features before doxygen had Markdown support
Moved the Doxygen check to an external m4 file to facilitate sharing with other projects

Lacking AM_COND_IF in automake-1.10, I'm holding back on standardizing the Makefile.am content for doc generation
automake-1.10 (2006) is the standard in latest XCode so it's the most available in a major platform.  Lowest-common-denominator, unfortunately.
avoid false-positive in diff checking