"Installation" version control together with "Project" version control

The multi-project feature with version control is super awesome but I haven't been able to figure out how to get it to work inside a Node-Red installation that is itself in a git repository.

I have a git repo with custom nodes, community nodes, theming, etc and when I clone the repo, the projects directory is empty because each project is its own repo with its own .git directory.

Is there a best practice to structure a node red install in version control that uses projects? I was thinking maybe submodules but wanted to see if anyone else has come up with something better.