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If user deletes package from project (using Delete on that package) package is still displayed in Explorer (but not it's content) although it's not on the disk anymore.
Sounds like some look is not refreshed properly.
Subcomponent changed to looks
Created attachment 8091 [details] stack trace with ISE
Seems to be still the problem, the ISE is thrown and package's node doesn't disappear.
*** This issue has been marked as a duplicate of 27612 ***
Verified.