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On Cinnamon, you can set a hotkey to force the active window into full screen mode; many programs have a full screen toggle built in. What I'm wondering is, what's the command that's being sent? How would you issue such a command in a terminal emulator to resize an application window so that it includes the space occupied by taskbars/panels?

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    It's setting the _NET_WM_STATE_FULLSCREEN atom on the window. Nov 5, 2017 at 20:22
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    Have a look at wmctrl.
    – dirkt
    Nov 6, 2017 at 8:19

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Based on @dirkt's comment I went and had a look at wmctrl, which is a command line tool that lets you set these yourself. If you'd like to do things like toggle fullscreen for whatever programs you like from a shell script or any other custom place, this is ideal for that.

Here's an example that toggles fullscreen for the currently active window:

wmctrl -r ':ACTIVE:' -b toggle,fullscreen

For more details on what you can do with this see the man page and for some example see this tutorial.

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