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How can I map a three-finger tab on the touchpad to a middle mouse click? In another question I've found

synclient TapButton3=2

and this works, but it seems a bit strange to run a shell script on each startup. Isn't there a configuration anywhere?

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This can be achieved in an Xorg config file. First create the directory /etc/X11/xorg.conf.d and copy 70-synaptics.conf over from /usr/share/X11/xorg.conf.d/

sudo mkdir /etc/X11/xorg.conf.d
sudo cp  /usr/share/X11/xorg.conf.d/70-synaptics.conf /etc/X11/xorg.conf.d/

Then change it to

Section "InputClass"
        Identifier "touchpad catchall"
        Driver "synaptics"
        MatchIsTouchpad "on"
        MatchDevicePath "/dev/input/event*"

        Option          "TapButton1"            "1"
        Option          "TapButton2"            "3"     # multitouch
        Option          "TapButton3"            "2"     # multitouch
EndSection

This blog post explains the new layout of the X11 config files:

The /usr/share/X11/xorg.conf.d is for the Distro's and you are not suppose to muck with stuff in there. Instead the user is suppose to put custom files in /etc/X11/xorg.conf.d. You may need to create that directory. The .conf files in /etc/X11/xorg.conf.d run after the ones in /usr/share/X11/xorg.conf.d so they control or override anything in /usr/share/X11/xorg.conf.d. Despite that I still usually number them a bit higher. So if I'm modifying the 50-wacom.conf in /usr/share/X11/xorg.conf.d I'll call the custom .conf file in /etc/X11/xorg.conf.d 52-wacom.conf. Maybe a bit of overkill.

For explanations on the available options, see the debian wiki

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