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Being able to open multiple views of the same book is a feature. For instance, suppose you make some changes to the conversion settings and reconvert, you can open the old and new files side by side to see the effect. Or you can view different parts of the same book side by side, which is very useful for reference works.
As for listing windows, that I have no idea how to do, since each viewer window is a completely separate process. Every viewer window should show up as an icon in the dock.
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