Moved to flat (no subdirs) mode for doxygen

- The sub-directory mode of doxygen meant we could not predict the
  url for specific pages (e.g. Diagnostics.html) which makes linking
  to those pages from outside hard.

.doxygen

@@ -68,7 +68,7 @@ OUTPUT_DIRECTORY       =
 # performance problems for the file system.
 # The default value is: NO.
 
-CREATE_SUBDIRS         = YES
+CREATE_SUBDIRS         = NO
 
 # If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII
 # characters to appear in the names of generated files. If set to NO, non-ASCII