[rednafi]

Do you run your changes in the original location?

The canonical workflow is this: you run chezmoi cd and make changes there first. Only then do you run chezmoi apply to propagate the changes to the original location.

The source of truth is always what lies in the chezmoi directory, not the other way around.

So if you’re experimenting with the dotfiles in their original location, running chezmoi apply will override them with the snapshot in the chezmoi directory. The vimdiff doesn’t do much here.

If you want to retain your changes there, you’ll have to manually copy them over to the chezmoi directory. This is a bit awkward, but having a consistent source of truth makes the behavior easier to reason about. I rarely look at the diff.