Does this really work? The whole premise of DRUSH_BOOTSTRAP_DRUPAL_CONFIGURATION is that Drush has included settings.php but no other part of Drupal. Therefore, I'm surprised that an autoloader would be available to handle Database class instantiation. Has anyone tested site-install with this PR? Another good thing to test is to configure settings.php and point it at a random DB (not Drupal). sql-query should still work. I don't think it will with this patch. Aegir relies on this AFAIK. sql-sync as well.