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There are two ways to "solve" this problem. 1. Upgrade the version numbering in the deltas reconciler (refer to bug 317954). The deltas.xml will then be ignored and the user will start with a "blank" model. 2. Upgrade the user's model after the deltas have been applied by introducing an MArea into their perspectives where applicable (depending on whether they have an 'org.eclipse.ui.editorss' MPartSashContainer or not?).
Created attachment 181495 [details] E4Application patch v1 Eric, please take a look.
Eric gave me his +1 on IRC.
Verified on Windows XP with I20101025-1602 by loading a deltas model from I20100922-0843.