yeah that's how it's meant to be. that way on your live server if you've got ssh access you can clone your repo on beanstalk recursively as the links will still be kept in the .gitmodules file and under .git/config.
It's actually a lot tidier because the core should never be part of your app and by not even having the core in your repo it further reinforces it. Also, if you update the core, you won't have to commit those changes in your local repo when you pull from fuel's repo
so by having submodules, when I used it with beanstalkapp.com , the submodules (like core) weren't automatically FTP'd to my servers. is this something that's supposed to happen? are files not stored in the repository but only referenced to?
thanks,
Donate
that cleared it up for me