doc: update Doxygen configuration

doc: update Doxygen configuration

Use "doxygen -s -u doc/Doxyfile.in"; the update fixes some warnings
when building the documentation with Doxygen 1.8:

warning: Tag `SHOW_DIRECTORIES' at line 79 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 149 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 176 of file Doxyfile has become obsolete.
To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u"