A bevy of subtle fixes. Primarily #597750 because we no longer 'do' site id....

A bevy of subtle fixes. Primarily #597750 because we no longer 'do' site id. Also fixed restore which left you with a broken site, and handled the fact that
the drush_config_file function would only give us the right value when we were bootstrapped to that level.

this meant we couldnt regenerate the site drushrc.php until we'd bootstrapped to drupal_configuration, which meant during restore it would always use the old values.

Also when the restore task finished, the save_site_config malarky would end up writing the old values over the correct ones.