This is why i recommend not committing actual dotfiles but committing templates instead.

Yadm, a thin wrapper around git allows for alternate files, encryption and templating. See my post https://news.ycombinator.com/item?id=19594859

https://github.com/thingfox/dotfiles

https://yadm.io/docs/encryption

https://yadm.io/docs/bootstrap

https://yadm.io/docs/alternates