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At the moment rebase (and pull with rebase) always performs a flattening rebase, losing merge commits. It should be possible to rebase merge commits, keeping their merging nature intact. C Git supports this when the --preserve-merges command line option to git rebase is specified. C Git preserves merges by simply redoing them, which loses conflict resolutions and other changes that went into the original merge (e.g. compile fixes to adapt to the new branch base). Preferably, JGit should try to rebase merge commits as-is, keeping the changes that went into a merge after automatic merging intact.
Proposed implementation: https://git.eclipse.org/r/#/c/29770/
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