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If Navigator view contains class members like methods and fields, then after closing source file in Source view this view isn't cleared/closed as well.
I am not sure, what do you mean by : " ... isn't cleared/closed as well." Does it mean , the content of the Nevaigator window stays opened and visible?
*** Issue 63691 has been marked as a duplicate of this issue. ***
It works for me in NB dev (200608091800)