Entry access rights can be used to manage documents and folders both separately or together, based on how you use scope. This is actually the same from 8.0 and later - there's no specific change in 9.0 for this - so you should be able to do what you want to do right now. If the idea is to allow users to rename docs but not folders, for example, you can set up two entry access right definitions on the folder - one scoped to the folder and sub folders that restricts rename, and one scoped to documents (both direct and within subfolders) that allows it. 

That's the general idea - using entry access scoping to define where you want your rights to apply. If you aren't able to attend the sessions that discuss this, please feel free to come talk to us I'm the information center.