Doxygen configuration cleanup
The Doxygen configuration appears to have been little maintained for the past 12 years. A couple things worth looking into:
1) What is the apps.tag tarnslation and incorporation into the Programmer and developer documentation doing? - Document it.
2) FILE_PATTERNS and INPUT and other Paths don't seem to be particularly consistent - done in both .conf and Makefile.
3) Can the USE_MDFILE_AS_MAINPAGE be used in place of the isisAppsDoxyDefs.doxydef