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If XRANDR is availible, we track the first (or primary) output per crtc (== xinerama monitor) so when the monitors change we can try to find the same output and move windows there. If we can't find the original monitor in the new set (or XRANDR is not supported) we move the window to the primary monitor. https://bugzilla.gnome.org/show_bug.cgi?id=645408
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