Problem with `xkbOptions` - it doesn't seem to take effect

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Not sure if it is true for GNOME Flashback, but regular GNOME uses gnome-settings-daemon to manage keyboard configuration. And its keyboard manager uses GSettings to store the keyboard configuration, only using the xkb config for initial set up:

You can clean up the settings using

gsettings reset org.gnome.desktop.input-sources xkb-options
gsettings reset org.gnome.desktop.input-sources sources

and the system defaults should be picked up after re-login.

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