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we are encountering several problems where bundles from the target or workspace are just not resolving and import/require wirings are just not setup properly. This has been an ongoing low-grade issue but as we get more and more bundles using import-package the situation is getting pretty bad. We used up half a day yesterday trying to figure out how to get these resolved. In the absence of a state inspector that would help users see what the problems are or a fix to whatever problems there might be, would it make sense to have a "Flush the PDE State" button somewhere? This can be a temporary thing but right now the situation is inhibiting forward progress on several fronts.
Maybe another possibility is for PDE builder to hook into the Project -> Clean event?
Have you tried the Reload button on the Target Platform Preference page? When you reload your target platform (and click ok), the PDEState is discarded and a new one is created. Also, the workspace bundles are re-added to the new state. Rebuilding the state upon a project clean is a bad idea. The operation is not a very speedy one (especially on larget target platforms). It is a good idea, I just don't think this is practical due to performance reasons.
Since the reload button seems to be a work around for flushing the state, I'm marking as Won't Fix. If this work around does not fix your problems in the future, please reopen this bug.