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The selection and the expansion state of a Common Navigator (eg. Project Explorer) is not persisted. This should be handled by the Common Navigator framework itself (maybe as an option). This must be framework feature because content providers cannot restore the global selection and expansion state on their own without knowledge about other content extensions. They would eventually get in conflict with one another.
In general, this practice is no longer practiced (e.g. Package Explorer) because of the extra performance impact of restoring the state. In the case of the Common Navigator Framework, the problem is potentially very bad because of the amount of content that can be displayed -- and the number of plugins that could be required to load to restore the state. I'm deferring this to 3.3 for now, but it's likely that a fix will only be provided if there is enough community support for it.
*** Bug 250352 has been marked as a duplicate of this bug. ***
*** Bug 295942 has been marked as a duplicate of this bug. ***
Performance issues? Why not making it optional then and let users decide if they are willing to pay the price?