I have the source of an org which was retrieved using a pre-30 release version. Before release 30, a retrieve would include permissions for required fields, and a deploy would successfully push those permissions to the org. But as of release 30, permissions for required fields are no longer retrievable or deployable. Why?

Updating to version 30 of the Force.com IDE causes the deployment to fail since the source includes permission sets which have permissions for required fields. I'm having a hard time understanding why this change was put in place. How is our development team supposed to handle adding permissions for required fields and committing those changes in source to a repository to share?