CCS Command Line Project Create - Virtual Folders

I am trying to create a CCS project with virtual folders from the command line. I have no issue linking in all the files I need but they create folders in my projects directory (which I do not want). This is what I currently see in CCS:

Here is an example of a project I made manually with virtual folders:

I noticed in the .project file for the correctly generated one they have some linked resources with <type>2</type> that represent the virtual folders. I am basically wanting to figure out how to create those when doing a command line project create.

Thanks for the help,

Zack L.