I agree that that's not well supported, because it kind of goes against the grain of git thinking about project versions rather than file or directory versions.

I agree that that's not well supported, because it kind of goes against the grain of git thinking about project versions rather than file or directory versions. What you should probably do in this case is use git merge nevertheless, but reset all changes outside of the directory of interest before committing the merge. This way, you get the history of the merge in the DAG, which will make git's merge resolution work. Unfortunately, I'm not aware of a built-in way of doing this.