diff --git a/docs/doxygen.conf.in b/docs/doxygen.conf.in
index 7a74246..da86688 100644
--- a/docs/doxygen.conf.in
+++ b/docs/doxygen.conf.in
@@ -68,7 +68,7 @@
 # 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
@@ -2117,7 +2117,7 @@
 # set to NO
 # The default value is: YES.
 
-HAVE_DOT               = YES
+HAVE_DOT               = @HAVE_DOT@
 
 # The DOT_NUM_THREADS specifies the number of dot invocations doxygen is allowed
 # to run in parallel. When set to 0 doxygen will base this on the number of