Clone the repository, create your branch "with_comment". Every time you want to sync with the upstream repo, you pull in the master branch where you have done n

Clone the repository, create your branch "with_comment". Every time you want to sync with the upstream repo, you pull in the master branch where you have done no modification, and merge to you comment branch whenever your need/want. I don't think there is any way to have the conflict automatically resolved if you cannot commit (and have other people actually resolving the conflicts)