doxygen says these options are obsolete

Doxyfile.in

@@ -446,12 +446,6 @@ MAX_INITIALIZER_LINES  = 30
 
 SHOW_USED_FILES        = YES
 
-# If the sources in your project are distributed over multiple directories 
-# then setting the SHOW_DIRECTORIES tag to YES will show the directory hierarchy 
-# in the documentation. The default is NO.
-
-SHOW_DIRECTORIES       = NO
-
 # Set the SHOW_FILES tag to NO to disable the generation of the Files page.
 # This will remove the Files entry from the Quick Index and from the 
 # Folder Tree View (if specified). The default is YES.
@@ -760,12 +754,6 @@ HTML_FOOTER            =
 
 HTML_STYLESHEET        = 
 
-# If the HTML_ALIGN_MEMBERS tag is set to YES, the members of classes, 
-# files or namespaces will be aligned in HTML using tables. If set to 
-# NO a bullet list will be used.
-
-HTML_ALIGN_MEMBERS     = YES
-
 # If the GENERATE_HTMLHELP tag is set to YES, additional index files 
 # will be generated that can be used as input for tools like the 
 # Microsoft HTML help workshop to generate a compiled HTML help file (.chm) 
@@ -1047,18 +1035,6 @@ GENERATE_XML           = NO
 
 XML_OUTPUT             = xml
 
-# The XML_SCHEMA tag can be used to specify an XML schema, 
-# which can be used by a validating XML parser to check the 
-# syntax of the XML files.
-
-XML_SCHEMA             = 
-
-# The XML_DTD tag can be used to specify an XML DTD, 
-# which can be used by a validating XML parser to check the 
-# syntax of the XML files.
-
-XML_DTD                = 
-
 # If the XML_PROGRAMLISTING tag is set to YES Doxygen will 
 # dump the program listings (including syntax highlighting 
 # and cross-referencing information) to the XML output. Note that 
@@ -1264,7 +1240,7 @@ HAVE_DOT               = NO
 # DOTFONTPATH environment variable or by setting DOT_FONTPATH to the directory 
 # containing the font.
 
-DOT_FONTNAME           = FreeSans
+DOT_FONTNAME           =
 
 # By default doxygen will tell dot to use the output directory to look for the 
 # FreeSans.ttf font (which doxygen will put there itself). If you specify a