Content Pipeline Tool and Team Foundation

I run my own Team Foundation server and use it to collaborate with my team. It’s a great tool.

One issue we’ve run into is with maintaining asset hierarchy for our projects.
When empty folders are added to the project via the Content Pipeline Tool they are not saved and thus not detected by Visual Studio as a change to be included in the next Check-In. The .mgcb file is updated and that is the only item that gets checked in and none of the new folders are retained in the Content Pipeline Tool when opened again yet the folders still exist on disc and an error is generated when trying to recreate the folder structure.

Currently we’re using an empty .txt file as an anchor for the folder so it gets added properly.

Is there a way to retain the empty folders in the Content Pipeline Tool to allow them to be checked in?
Is this by design to not retain empty folders?

It is the same problem when adding an empty folder to a project, which is finally not copied along the binaries if it is empty. I think the only solution is the dummy file in each folder or creation of the folder at runtime