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I'd like to raise window if it's covered by another window, otherwise lower it, with some shortcut mouse (click + extra keys).

Knowing that a window (that you are interested in) is in a region close of where your mouse is you can, you can scan the windows which are under your mouse.

This was possible before in some older GNOME desktop. And this is also possible on the CDE of Solaris.

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Shift+Alt+middle-click on the title bar moves a window to the background (at least on my system; if this is not default behaviour please correct me and I'll try to find out how I did it). That's probably not exactly what you want though?

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