I would not go around these files with git at all. I would put them in yours .gitignore, so git ignores them and puts the template files (e.g. foo.templatefor a file with a name, fooor maybe template/foo) in git. Then, when you clone the repos, you can copy and modify them, and git will not do anything with the copies, still managing the templates. If you have several of these files, you can provide a script or make a rule or something similar to populate all your configuration files from your templates to simplify setup.
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