Drush fails if there is a settings.php file somewhere above the Drupal Root.

From https://drupal.org/node/538702.  This stalled because we could not reproduce the condition that caused this error.  Recently, Moshe encountered this problem on his system; a misplaced settings.php above his document root caused uri to be miss-set, and as a result, the system would not bootstrap.  On my system, a misplaced settings.php would cause uri to be miss-set, but strangely enough, the correct sites folder would be selected, and bootstrapping would succeed (except with an incorrect uri).

This patch solves the problem of miss-setting the uri.  In theory, this should also prevent the problems caused that prevented the siits from bootstrapping.