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I ended up doing more improvements to the theme_upgrade2 branch that I don't want to save anything from the master branch. It looks like the strategy to replace the master branch would be this: https://stackoverflow.com/questions/2763006/make-the-current-git-branch-a-master-branch
git checkout better_branch
git merge --strategy=ours master # keep the content of this branch, but record a merge
git checkout master
git merge better_branch # fast-forward master up to the merge