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I am a frequent user of the keyboard shortcut Alt+Tab to switch focus between windows. I use a Chrome extension called Pure Pomodoro. This extension provides a simple timer window that automatically always stays on top of all other windows.
Because of its nature of being a window that only provides a timer, I don't want this window to be included in the Alt+Tab switching windows behaviour.
Thus is it possible to exclude specific windows from being considered in Alt+Tab?
I don't think this is possible, and I also don't think it will be a feature that will be implemented in the future. As you may be aware, elementary OS will always try to have the least amount of settings possible to keep the interface simple and clean, so supporting something that only a few will understand and actually use vs confusing or cluttering the interface for the rest isn't going to happen.
Regarding your case, have you tried Tomato?, it's an app to do what you want and was designed specifically for elemenary OS, currently it has the same problem of appearing when using Alt+Tab, but maybe the developer could add a setting for this to happen (he actually has a blueprint about adding a new preferences dialog for it, you can suggest the idea to him there). I think the chance of getting this setting on the application is much higher than the ones of elementary OS supporting the feature you want.
