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If there are extra content objects in .gmfgen (e.g. custom model for PropertySections in gmfgraph editor), they should be preserved during gmfmap->gmfgen transformation
We do our best to update external references now (using Reconciler rules), still, some of them may not get updated and lead to exceptions during resource serialization. An option org.eclipse.gmf.bridge.ui/transform/ignore-dangling-on-save=false was introduced to ignore such references (reference will be lost and one will need to set its value manually afterwards)
Related bug #181187
[target cleanup] 2.0 M7 was the original target milestone for this bug
[GMF Restructure] Bug 319140 : product GMF and component Reconciler was the original product and component for this bug