Drush doesn't modify the conf array early enough in bootstrap

When using the $override array in an rc file to override the 'site_frontpage' variable, the override doesn't happen early enough in the bootstrap process to effect what path is actually put into $_GET. This is because $_GET is set during DRUPAL_BOOTSTRAP_PATH, but drush doesn't override the $conf array until after the full bootstrap process is finished. The attached patch has a fix that splits the bootstrap process after DRUPAL_BOOTSTRAP_CONFIGURATION, overrides the $conf array, and then finishes the bootstrap.