Allow to put `.template/` folder not in repo-folder struture.

My colleagues are complaining that my `.template/`-folder is included in the repo and that as such it is included in git.
I don't want to `.gitignore` this, because from time to time I'm doing a `git clean -dxf` and that would remove the folder.

So is there a possibility to change extension that I will also look in eg. `%USERPROFILE%/addnewfile` ?