That feature has been deprecated in 6.0.0 and the 'File access' tab in the project security dialog will no longer be shown if you do not still have these rules in your project.
Unfortunately, we forgot to remove the note referring to that tab in the properties dialog of System.FileDocument and System.Image. That has been fixed and is scheduled for 6.2.0.
Apparently the release notes did not mention this either. I added this information to the release notes for 6.0.0.
Apologies for the inconvenience.
Although not explicit described in the release notes I assume that the use of native filedocuments is no longer supported from 6.0. You should always inherit your own entity.
Do you have a case in which that is not sufficient?