diff --git a/doc/doxygen.conf b/doc/doxygen.conf
index 9007f6097..0fd6387d5 100644
--- a/doc/doxygen.conf
+++ b/doc/doxygen.conf
@@ -70,7 +70,7 @@ OUTPUT_DIRECTORY       = doc
 # performance problems for the file system.
 # The default value is: NO.
 
-CREATE_SUBDIRS         = NO
+CREATE_SUBDIRS         = YES
 
 # 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
@@ -2671,7 +2671,7 @@ DOT_TRANSPARENT        = NO
 # The default value is: NO.
 # This tag requires that the tag HAVE_DOT is set to YES.
 
-DOT_MULTI_TARGETS      = NO
+DOT_MULTI_TARGETS      = YES
 
 # If the GENERATE_LEGEND tag is set to YES doxygen will generate a legend page
 # explaining the meaning of the various boxes and arrows in the dot generated