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If you install the attached test project, build it and then switch off build automatically you will notice that when you restart the workbench you will not get the "Advises" and "Advised By" menus when you right click on the gutter markers, which is one of the ways to test that persistence has worked. I also had ClassCastExceptions in the error log. I believe there will also be related cases that fail because you can have any depth of nested inner classes and aspects. This is because the model does not persist information about inner classes or aspects more than one level deep.
Created attachment 20827 [details] Test project
Fixed in RC1