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For example, I have two monitors, each with gnome-terminal maximized. When I select one of the instances of gnome-terminal I don't want the one on the other monitor to get focus as well (because I often have something I want to look at at the same time on the other monitor).

Note that it's only when I select the window using Alt-TAB. If I click on a window with the mouse or select the sub-window with Alt-` it does what I expect (i.e. doesn't focus the other windows).

I don't really want to switch away from the default alt-tab switcher. Is there a way to do this with the default alt-tab switcher?

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Apparently there's no way to do it. One workaround, however, is to use the "window switcher" instead. Set:

gsettings set org.gnome.desktop.wm.keybindings switch-applications '["<Super>Tab"]'
gsettings set org.gnome.desktop.wm.keybindings switch-windows '["<Alt>Tab"]'

With that, Super-TAB will execute the default application switcher where application windows are grouped together, and Alt-TAB will execute a more classical switcher where every window of all applications is shown separately.

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