For those who use old query.php API interface:
Per http://bugzilla.wikimedia.org/show_bug.cgi?id=12881 , query.php has been fully ported to the api.php, and thus no longer needed. Unless there are significant reasons to keep it around, it will be removed both from the extensions and from the mediawiki sites fairly soon.
If you are still using it, see http://www.mediawiki.org/wiki/API description on how to use the new api.php.
Thanks for all the support!
--Yuri