Doxygen: update Doxyfile.in to version 1.8.13

Fix warnings:
warning: Tag `SYMBOL_CACHE_SIZE' at line 299 of file `./Doxyfile' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag `SHOW_DIRECTORIES' at line 487 of file `./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_ALIGN_MEMBERS' at line 823 of file `./Doxyfile' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag `USE_INLINE_TREES' at line 976 of file `./Doxyfile' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag `XML_SCHEMA' at line 1169 of file `./Doxyfile' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"
warning: Tag `XML_DTD' at line 1175 of file `./Doxyfile' has become obsolete.
         To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"