Can't clone to existing directory, can't create project in existing directory

When I want a project to use source control, I create the project in GitHub and add in the .gitignore and readme and whatever else. I then clone that to my Unreal Projects folder. Then, I launch Unreal Engine and create the new project with the same name as the cloned folder. In 4.9, this worked. I would be able to immediately push all the new files that the engine created and have the template project up on GitHub.

Now, on 4.11, I’m unable to do this. Unreal Engine will not allow me to create a project with the same name as an existing folder, and Git won’t allow me to clone to an existing folder that isn’t empty. Is there a way around this? I don’t particularly want to have a top-level folder containing the .git, and a folder containing the entire Unreal project.

I did manage a work-around. Created the project in Unreal, moved the files out of the directory, cloned the git project, then moved the files back in. I’m just wondering if this is the intended behaviour now?