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When two logical model are combined to calculate the complete traversals, part of the right side (theirs) is override with part of the base traversal. As this is trigger by the order the logical model gets available, it may manifest randomly. This may cause: 1) 'Mixed stages not allowed' issue 2) An internal error occurred during: "Merging with refs/heads/xxxxxx" due to a java.lang.RuntimeException: The resource 'platform:/resource/XXXX/xxxx.uml' already exists at that location. 3) Changes from the branch to merge (right side) are not considered and not detected at all.
It may also manifest with files that has been removed on left side appear again.... as it may be added now from the base side to the right side.
New Gerrit change created: https://git.eclipse.org/r/106201
This looks like a copy paste error, thanks for the report!
Gerrit change https://git.eclipse.org/r/106201 was merged to [master]. Commit: http://git.eclipse.org/c/emfcompare/org.eclipse.emf.compare.git/commit/?id=1d50199069c486f45e47b70f4e4e907b1ccfb42c