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Doesn't this come from git itself? If you try `git add -p <file>`, it'll chunk just as "bad".

Yes, git generally stages just hunks with the patch add mechanism, but it is possible to stage single lines, but it is a bit tedious, see: https://kennyballou.com/blog/2015/10/art-manually-edit-hunks...

You can edit the hunk manually. I believe it's also possible to construct a hunk to apply entirely from scratch as long as you get the header right.