I would know if there is a way to include a file in a repo, but that it is automatically ignored after the user cloned the repo..
It would be great for configuration
One way is to run git update-index --assume-unchanged filename.txt
git update-index --assume-unchanged filename.txt
Another way is to commit template versions of the files, do your clone, copy the templates and have the copied files in your .gitignore.
Unfortunately both approaches require you to do something after cloning.