Drush won't run if multisite folder changed on initial deploy

[Unitoch]

When creating a new deploy with a multisite installation, the multisite variable will create a new name for the sites/mysitename/ folder. This causes an error with the code registry, which means Drush can't bootstrap, and thus can't clear the cache, and the whole deploy process rolls back

PHP Fatal error: require_once(): Failed opening required '/home/aaimmta/domains/mnmusicteachers.com/code/staging/current/sites/mnmusicteachers.com/modules/contrib/entity/includes/entity.inc' (include_path='.:/usr/local/php5/lib/php') in /home/aaimmta/domains/mnmusicteachers.com/code/staging/releases/20111017151748/includes/bootstrap.inc on line 2913

You can get around this by doing a regexp replacement on the database, but it'd be nicer and safer if we could find some sort of variable or method that protects our DB a bit more than simply replacing all instances in the DB. Ideally we'd rebuild the registry, though most ways I can find to rebuild the registry require Drupal to bootstrap. So we have a problem where Drupal can't bootstrap because the registry is wrong, and we can't fix the registry because Drupal can't bootstrap.

There may be some workarounds to this. http://drupal.org/project/registry_rebuild is a module for rebuilding the registry for these types of situations, so maybe we can automatically download this and/or write a script based on it. There's also a method to rebuild the registry in Drupal's API: http://api.drupal.org/api/drupal/includes--bootstrap.inc/function/registry_rebuild/7. We might be able to use something from there to create a workaround.