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When an element is nillable and has a type that is or is derived from ID, IDREF or IDREFS, section 3.15.5 of the spec is not clear about what happens to the ID/IDREF Table: whether such element is ignored, or its actual value should be take into account (which doesn't seem to be possible).
Proposal: when xsi:nil is true on an element, then it's not added to the ID/IDREF Table. Resolution: adopted at 2006-11-17 telecon.