Fix the warnings and scary errors on site migrate (subdir).

Undefined offset: 1 Subdir.php:46
Undefined offset: 1 Subdir.php:46
Undefined variable: parent_site SubdirVhost.php:61
unlink(/var/aegir/config/server_master/nginx/vhost.d/): Is a directory FileSystem.php:122
Undefined variable: parent_site SubdirVhost.php:61