RE: Nonexistent changes appear rebasing but only with rebase.backend=apply
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> This might not be caused by rebase command itself, but rather by some
> previous operations which might have accidentally "broken" something
> and that the rebase simply makes them appear.
> You need to know that commit 4 is the result of several squash and
> reordering of multiple commits; is it possible that some of those
> operations have created some "leftovers" ?
Smells like the reflog.
Have you tried --no-fork-point?
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Felipe Contreras