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I created a file /usr/share/X11/xorg.conf.d/90-keyboard.conf containing

Section "InputClass"
        Identifier      "Defaults"
        MatchIsKeyboard "true"
        Option          "XkbOptions"    "ctrl:nocaps,compose:menu,terminate:ctrl_alt_bksp"

It looks like it's getting picked up; in /var/log/Xorg.0.log it says

[  3772.382] (II) XINPUT: Adding extended input device "AT Translated Set 2 keyboard" (type: KEYBOARD, id 10)
[  3772.382] (**) Option "xkb_rules" "evdev"
[  3772.382] (**) Option "xkb_model" "pc104"
[  3772.382] (**) Option "xkb_options" "ctrl:nocaps,compose:menu,terminate:ctrl_alt_bksp"

But it has no apparent effect; caps lock is still caps lock. Am I missing something obvious?

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