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-uingit add -uas it's more careful than-a, and since you would not expect adding/removing files when fixing a rebase?-utends to be the right thing here. Any options or parameters that achieve the desired index updates is fine, of course.git rebase -i, setting all to "edit", and when it stopped after the first merge, I did manual changes. Then, I did gitcommit --amend, which modified the tip of the master branch (or better, I think it created a new commit there). Must I somehow commit before the amend?editand let rebase run and then halt,git statusshould show that you are not on any branch: you should haveHEAD detached at ...orHEAD detached from ...(the exact string depends on your Git version). The--amendshould therefore update the detached HEAD, after whichgit rebase --continueshould continue cherry-picking atop the latest commit.