Could not create work tree dir 'example.com'.: Permission denied
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!!