Update the Doxygen config for the new version.

docs/Doxyfile

@@ -21,11 +21,11 @@ JAVADOC_AUTOBRIEF      = NO
 JAVADOC_BANNER         = NO
 QT_AUTOBRIEF           = NO
 MULTILINE_CPP_IS_BRIEF = NO
+PYTHON_DOCSTRING       = YES
 INHERIT_DOCS           = YES
 SEPARATE_MEMBER_PAGES  = NO
 TAB_SIZE               = 8
 ALIASES                =
-TCL_SUBST              =
 OPTIMIZE_OUTPUT_FOR_C  = NO
 OPTIMIZE_OUTPUT_JAVA   = NO
 OPTIMIZE_FOR_FORTRAN   = NO
@@ -46,6 +46,7 @@ INLINE_GROUPED_CLASSES = NO
 INLINE_SIMPLE_STRUCTS  = NO
 TYPEDEF_HIDES_STRUCT   = NO
 LOOKUP_CACHE_SIZE      = 0
+NUM_PROC_THREADS       = 0
 EXTRACT_ALL            = NO
 EXTRACT_PRIVATE        = NO
 EXTRACT_PRIV_VIRTUAL   = NO
@@ -54,6 +55,7 @@ EXTRACT_STATIC         = NO
 EXTRACT_LOCAL_CLASSES  = YES
 EXTRACT_LOCAL_METHODS  = NO
 EXTRACT_ANON_NSPACES   = NO
+RESOLVE_UNNAMED_PARAMS = YES
 HIDE_UNDOC_MEMBERS     = NO
 HIDE_UNDOC_CLASSES     = NO
 HIDE_FRIEND_COMPOUNDS  = NO
@@ -122,8 +124,11 @@ REFERENCES_LINK_SOURCE = YES
 SOURCE_TOOLTIPS        = YES
 USE_HTAGS              = NO
 VERBATIM_HEADERS       = YES
+CLANG_ASSISTED_PARSING = NO
+CLANG_ADD_INC_PATHS    = YES
+CLANG_OPTIONS          =
+CLANG_DATABASE_PATH    =
 ALPHABETICAL_INDEX     = YES
-COLS_IN_ALPHA_INDEX    = 5
 IGNORE_PREFIX          =
 GENERATE_HTML          = YES
 HTML_OUTPUT            = html
@@ -140,7 +145,7 @@ HTML_TIMESTAMP         = NO
 HTML_DYNAMIC_MENUS     = YES
 HTML_DYNAMIC_SECTIONS  = NO
 HTML_INDEX_NUM_ENTRIES = 100
-GENERATE_DOCSET        = YES
+GENERATE_DOCSET        = NO
 DOCSET_FEEDNAME        = "Doxygen generated documentation"
 DOCSET_BUNDLE_ID       = org.doxygen.Project
 DOCSET_PUBLISHER_ID    = org.doxygen.Publisher
@@ -167,8 +172,10 @@ GENERATE_TREEVIEW      = NO
 ENUM_VALUES_PER_LINE   = 4
 TREEVIEW_WIDTH         = 250
 EXT_LINKS_IN_WINDOW    = NO
+HTML_FORMULA_FORMAT    = png
 FORMULA_FONTSIZE       = 10
 FORMULA_TRANSPARENT    = YES
+FORMULA_MACROFILE      =
 USE_MATHJAX            = NO
 MATHJAX_FORMAT         = HTML-CSS
 MATHJAX_RELPATH        = http://cdn.mathjax.org/mathjax/latest
@@ -253,6 +260,8 @@ COLLABORATION_GRAPH    = YES
 GROUP_GRAPHS           = YES
 UML_LOOK               = NO
 UML_LIMIT_NUM_FIELDS   = 10
+DOT_UML_DETAILS        = NO
+DOT_WRAP_THRESHOLD     = 17
 TEMPLATE_RELATIONS     = NO
 INCLUDE_GRAPH          = YES
 INCLUDED_BY_GRAPH      = YES