Did Source Control delete my ThirdParty folder?

I have a new UE project which has (or at least, HAD) in it’s root a “ThirdParty” folder which contained some custom C++ libraries and headers I was using in the project.

I decided to activate Source Control with Git in the Editor and it seemed to create the repository and commit the project fine.

However, my ThirdParty folder has totally disappeared? No record of it in git logs? It’s not in the Recycling… it’s just disappeared?

Did the Editor clean out anything that wasn’t UE project specific? Slightly annoying, but not the end of the world. I’m keen to find out what happened though?