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Steps to reproduce: If a reference is populated with values [a0, a1, a2, a3, a4] in the ancestor. I modify it locally by moving a2 to the head of the list [a2, a0, a1, a3, a4]. It has been remotly modified by moving a2 to the queue of the list [a0, a1, a3, a4, a2]. checkReferenceUpdates(DiffGroup, Match3Elements, EReference) never falls in a case where it can create a conflictual ReferenceOrderChange.
Conflict detection on EMF Compare 1.* "reference order" difference was impossible (rather, extremely complex) because of the way they were detected. EMF Compare 2 properly detects these conflicts.