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Is it possible to restrict users with Publisher roles to access and publish to specific folders only?
No, up to ArcGIS for Server 10.3.1, it is not possible to restrict users with Publisher roles to access and publish to specific folders only. To restrict a user’s access to a specific folder, assign the User role, instead of the Publisher role. The Publisher role automatically gets implicit access permissions to all services/folders, and cannot be overridden by the security settings in a folder.
For more information, refer to the following documentation, ArcGIS for Server: Managing roles in Manager and ArcGIS for Server: Editing permissions in Manager.