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In Gnome Shell, there are actually two ways of switching between windows. The one this extension supports is set to alt+tab by default on Ubuntu. Vanilla Gnome Shell, however, uses a different one, which is set to both keyboard shortcuts Alt+Tab and Super+Tab (on Ubuntu it's probably Super+Tab only): This one doesn't toggle windows, but applications - always only the first window per application. This is super useful in combination with Super+` (or Alt+` - they both work), which toggles the windows of currently active app. I prefer the combination of these two over the Ubuntu default setting because you are circling less windows in total.
Anyway, this extension only supports the "toggle windows" functionality, but not the "toggle apps" functionality. On my vanilla gnome shell system, when I press alt+tab (or super+tab), it toggles apps instead of windows (this is the default gnome shell setup, different from ubuntu) and all minimized apps are still there.