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MergeMessageFormatter.addConflictsMessage() should prefix all lines with # like native git does. JGit also adds an empty line before "Conflicts" that isn't present in a MERGE_MSG file written by canonical git for a merge/rebase/cherry-pick conflict.
Actually, it should prefix them with core.commentChar.
New Gerrit change created: https://git.eclipse.org/r/c/jgit/jgit/+/189726
Gerrit change https://git.eclipse.org/r/c/jgit/jgit/+/189726 was merged to [master]. Commit: http://git.eclipse.org/c/jgit/jgit.git/commit/?id=1fd15e40cc7bf67c30849abc3030de8568246a4e