Run git config cleanup before creating the template dir
What does this MR do?
Ensures that the git template is not removed when clean_git_config is enabled.
Why was this MR needed?
To have configs from the git template to be picked up.
What's the best way to test this MR?
Generally, ensure that setting we configure via git template are used, examples are:
- see, that there is no warning re. default branch
- see, that custom CA certs are used