This is not a bug and should be closed as invalid.

There are two xorg.conf.d locations.

The xorg.conf.d located at /usr/share/X11/xorg.conf.d is for the Distro.
Users should not be adding custom .conf files in this location as they
may be overwritten by the Distro.

The location for user custom .conf files is /etc/X11/xorg.conf.d and
that is where xinput_calibrator should be suggesting its calibration
.conf be placed.

This is per Peter Hutterer a X.org developer.

It looks like Ubuntu usually doesn't have an /etc/X11/xorg.conf.d
directory by default so simply make one.  The /etc/X11/xorg.conf.d runs
after the /usr/share/X11/xorg.conf.d and what runs last controls.  So
the 99 xinput_calibrator suggests for the calibration .conf file number
is maybe a bit excessively high.  52 or so would be fine.

Actually if there is a bug here it is that the /etc/X11/xorg.conf.d
directory is not present by default.  A README  in it and
/usr/share/X11/xorg.conf.d should explain where to place custom .conf
files.

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https://bugs.launchpad.net/bugs/776946

Title:
  xinput_calibrator shows incorrect path for xorg.conf.d

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