you can set file roots on the project or folder level. in project settings, there's a tab to set file roots at the project level. On the folder management page, there is not. There is an action to do just this, FileContentController.ShowAdminAction, but it doesnt seem that we really expose this anywhere. Is you add a files webpart, hit customize, then 'configure file roots' and you get there. Kinda hidden though.

Is there a more direct entry point? What would you think about making this 'manage file roots' page a tab under folder management?