Make doxygen pick up markdown.

'*.md' files put into the projects doc directory will be picked as part of
the documentation. '*.md' files in other locations of the source tree will
be ignored.

cmake/Doxyfile.in

@@ -837,7 +837,8 @@ FILE_PATTERNS          = *.c \
                          *.f \
                          *.for \
                          *.vhd \
-                         *.vhdl
+                         *.vhdl \
+			 */doc/*.md
 
 # The RECURSIVE tag can be used to specify whether or not subdirectories should
 # be searched for input files as well.