What's the best way to apply a cruft (or cookiecutter) template to an existing Git/GitHub project, which doesn't use any cookiecutter template so far?
In most cases, this would be a bad idea. Cookiecutter will override the contents of your folder. Any existing files, matching to template files, will be overridden with the template ones. So if you already have real logic inside those files, it gets lost.
If you want to adopt some good practices from the template, better do it manually and not by applying it on the existing project.