Remove deprecated doxygen flags

Running 'doxygen -u Doxyfile.in' in the source root produces the
following results:

• SYMBOL_CACHE_SIZE at line 301 has become obsolete. This tag has been removed.
• SHOW_DIRECTORIES at line 507 has become obsolete. This tag has been removed.
• HTML_ALIGN_MEMBERS at line 881 has become obsolete. This tag has been removed.
• USE_INLINE_TREES at line 1067 has become obsolete. This tag has been removed.
• XML_SCHEMA at line 1311 has become obsolete. This tag has been removed.
• XML_DTD at line 1317 has become obsolete. This tag has been removed.

Signed-off-by: Richard B Winters <rik@mmogp.com>
Reviewed-by: Jan Friesse <jfriesse@redhat.com>