doc: Upgrade Doxygen config

This will get rid of the following warnings:

    warning: Tag 'OUTPUT_TEXT_DIRECTION' at line 102 of file '/build/libmypaint/doc/Doxyfile' has become obsolete.
             To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
    warning: Tag 'TCL_SUBST' at line 260 of file '/build/libmypaint/doc/Doxyfile' has become obsolete.
             To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
    warning: Tag 'CLANG_ASSISTED_PARSING' at line 1068 of file '/build/libmypaint/doc/Doxyfile' belongs to an option that was not enabled at compile time.
             To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u", or recompile doxygen with this feature enabled.
    warning: Tag 'CLANG_OPTIONS' at line 1076 of file '/build/libmypaint/doc/Doxyfile' belongs to an option that was not enabled at compile time.
             To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u", or recompile doxygen with this feature enabled.
    warning: Tag 'CLANG_DATABASE_PATH' at line 1086 of file '/build/libmypaint/doc/Doxyfile' belongs to an option that was not enabled at compile time.
             To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u", or recompile doxygen with this feature enabled.
    warning: Tag 'COLS_IN_ALPHA_INDEX' at line 1104 of file '/build/libmypaint/doc/Doxyfile' has become obsolete.
             To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
    warning: Tag 'HTML_TIMESTAMP' at line 1240 of file '/build/libmypaint/doc/Doxyfile' has become obsolete.
             To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
    warning: Tag 'FORMULA_TRANSPARENT' at line 1532 of file '/build/libmypaint/doc/Doxyfile' has become obsolete.
             To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
    warning: Tag 'LATEX_SOURCE_CODE' at line 1834 of file '/build/libmypaint/doc/Doxyfile' has become obsolete.
             To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
    warning: Tag 'LATEX_TIMESTAMP' at line 1850 of file '/build/libmypaint/doc/Doxyfile' has become obsolete.
             To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
    warning: Tag 'RTF_SOURCE_CODE' at line 1924 of file '/build/libmypaint/doc/Doxyfile' has become obsolete.
             To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
    warning: Tag 'DOCBOOK_PROGRAMLISTING' at line 2029 of file '/build/libmypaint/doc/Doxyfile' has become obsolete.
             To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
    warning: Tag 'CLASS_DIAGRAMS' at line 2216 of file '/build/libmypaint/doc/Doxyfile' has become obsolete.
             To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
    warning: Tag 'DOT_FONTNAME' at line 2258 of file '/build/libmypaint/doc/Doxyfile' has become obsolete.
             To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
    warning: Tag 'DOT_FONTSIZE' at line 2265 of file '/build/libmypaint/doc/Doxyfile' has become obsolete.
             To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
    warning: Tag 'DOT_TRANSPARENT' at line 2491 of file '/build/libmypaint/doc/Doxyfile' has become obsolete.
             To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"

We used the default values for those keys so the removal does not affect us.