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Unfortunately adding just the 3-way merge class quiets the error but does not appear to correctly merge.  Here's a commit that tries to handle the section explicitly.  It doesn't work for my (complicated) rebase -- it fails with a key error looking up some hex string identifier.  I don't have clean test data for this, so I can't say if your change works for simpler cases, or if my additional changes address the issue, or if there's more to be done 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