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In the Package Explorer you are able to specify a custom filter, e.g. filter all packages that contain internal via a filter *.internal.* There is no option in the Project Explorer to do something similar. Not sure if Bug 473548 has the same meaning, as that bug has no description. From the descriptions Bug 171289 sounds matching. But I'm not 100% sure. IMHO this will become more important with Neon, because the Project Explorer replaces the Package Explorer as default.
(In reply to Dirk Fauth from comment #0) > IMHO this will become more important with Neon, because the Project Explorer > replaces the Package Explorer as default. Only in the PDE perspetive, the JDT people will still use Package Explorer. Contributions are welcome.