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I have commit-x (a small one-liner) in a public repo-x, and when I merge in changes from a branch-y in repo-y, I realize that the upstream changes necessitate duplication of logic in commit-x.
Can I make the necessary change while manually merging conflicts? Or should I make a new commit after the merge that fixes it?
That is a social question, so “if you think so, yes, you can do that” is the honest answer.
Is it a good idea? I don’t think so. The more changes you make in the merge, the harder it is to tell why that one little thing was done. Making another commit afterwards makes it clear what, when, and why it was done.