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I'm not sure if this bug is in Platform or JDT. In the Debug Perspective I opened Display, entered a statement and chose Inspect from the context menu. A lightweight window opened. After that I closed Display and the lightweight window stayed. It would't go away until I restarted Eclipse. "Ctrl + Shift + I" binding didn't work anymore after closing Display. I tried this with the Editor view in the Debug Perspective and the result was same. Seems like closing the parent window doesn't close the lightweight windows opened by it. Maybe somebody finds that useful, but you have to put at least some kind of closing option to the lightweight window. This might apply for all LightWeight windows.
I was able to close the pop-up by placing the cursor in the pop-up an pressing ESC. However, the pop-up should close when its parent view/editor is closed. (I notice that the outline pop-up in the editor closes when its editor is closed).
Same is true for DisplayPopups. InformationPresenter is responsible for closing the shell. Moving to TEXT for comment. Code which creates the Inspect Popup is in PopupInspectAction.showPopup(...)
This has been fixed a while ago.