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the method "public void delete(AbstractStackFrame frame, Object modelElement)" in org.eclipse.m2m.atl.engine.emfvm.adapter.EMFModelAdapter does not remove cross-references that may point to the removed element. Consequently a "object [...] is not contained in a resource" error will be shown on the console when serializing to XMI. Although, the XMI file will be correct because EMF simply does not serialize the dangling edge, this is problematic in the case when the in-memory model is reused without serialization-deserialization.