If a version-controlled file is ignored by git, and a conflict arises on the file, and I use mergetool to resolve the conflict, then mergetool fails with a message like: The following paths are ignored by one of your .gitignore files: a Use -f if you really want to add them. The problem disappears if I edit the git-mergetool script to always pass -f to "git add", but I'm not sure if that's the right fix; I have a vague feeling that "git-update-index --add" could be more correct. I have attached a script that reproduces the problem.