Add include directories as source dirs

src/doxygen.cfg

 #---------------------------------------------------------------------------
 # configuration options related to the input files
 #---------------------------------------------------------------------------
-INPUT                  = @SRCDIRS@
+INPUT                  = @SRCDIRS@ \
+                         include \
+                         arch/@ARCH@/include
 FILE_PATTERNS          = 
 RECURSIVE              = NO
 EXCLUDE                =