I have got a virtual private server with nginx Virtual Hosts setup (Server Blocks).
I\'ve installed Git and got my ssh keys authenticated with GitHub.
I have
I was facing the same issue but it was not a permission issue.
When you are doing git clone it will create try to create replica of the respository structure.
When its trying to create the folder/directory with same name and path in your local os process is not allowing to do so and hence the error. There was "background" java process running in Task-manager which was accessing the resource of the directory(folder) and hence it was showing as permission denied for git operations. I have killed those process and that solved my problem. Cheers!!