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The fields that contain CQs, contributors, contributions, etc. should be marked as unordered in the ecore. We really don't care about order, but since EMF Compare takes this into consideration, marking these fields as such will significantly reduce the clutter in the compare dialog.
Ecore has been updated and Java code has been regenerated. Testing reveals that this works! Marking as FIXED.
Created attachment 178972 [details] mylyn/context/zip
Actually marking as FIXED <sigh/>