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When you click in the code editor for a given class, that class is NOT selected in the Hierarchy pane. This behavior is *different* then the Types pane which does select the right class. My custom perspective has a Packages pane, Hierarchy pane and a code editor pane. My packages pane is really a pane with a Packages Tab and a Projects Tab. I really would like to work in this perspective but I am running into a lot of hickups. Thank you.
There is a preference to control that behaviour: Java->Link Type Hierarchy View.... Please note that this only works if the type is present in the hierarchy. The reason is that building a type hierarchy is expensive. There are no plans to improve this for 2.x or 3.x.