Tested in a Xenial machine, upgrading packages to:

x11-common:
  Installato: 1:7.7+13ubuntu3.1
  Candidato:  1:7.7+13ubuntu3.1
  Tabella versione:
 *** 1:7.7+13ubuntu3.1 500
        500 http://ppa.launchpad.net/ci-train-ppa-service/3303/ubuntu 
xenial/main amd64 Packages
        500 http://ppa.launchpad.net/ci-train-ppa-service/3303/ubuntu 
xenial/main i386 Packages
        100 /var/lib/dpkg/status
     1:7.7+13ubuntu3 500
        500 http://it.archive.ubuntu.com/ubuntu xenial/main amd64 Packages
        500 http://it.archive.ubuntu.com/ubuntu xenial/main i386 Packages
nux-tools:
  Installato: 4.0.8+16.04.20180622.2-0ubuntu1
  Candidato:  4.0.8+16.04.20180622.2-0ubuntu1
  Tabella versione:
 *** 4.0.8+16.04.20180622.2-0ubuntu1 500
        500 http://ppa.launchpad.net/ci-train-ppa-service/3303/ubuntu 
xenial/main amd64 Packages
        100 /var/lib/dpkg/status
     4.0.8+16.04.20170816-0ubuntu1 500
        500 http://it.archive.ubuntu.com/ubuntu xenial-updates/main amd64 
Packages
     4.0.8+16.04.20160209-0ubuntu2 500
        500 http://it.archive.ubuntu.com/ubuntu xenial/main amd64 Packages

Running unity works propery, after upgrade, nux-tools is kept and file
not run... After autoremove, it gets removed and gnome-shell runs
properly.

** Tags removed: verification-needed-bionic verification-needed-xenial
** Tags added: verification-done-bionic verification-done-xenial

** Tags removed: verification-needed
** Tags added: verification-done

** Changed in: nux (Ubuntu Artful)
       Status: Fix Committed => Won't Fix

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Matching subscriptions: Ubuntu 16.04 Bugs
https://bugs.launchpad.net/bugs/1768610

Title:
  leftover conffile forces GNOME is software rendering

Status in nux package in Ubuntu:
  Fix Released
Status in xorg package in Ubuntu:
  Fix Released
Status in nux source package in Xenial:
  Fix Committed
Status in xorg source package in Xenial:
  Fix Committed
Status in nux source package in Artful:
  Won't Fix
Status in xorg source package in Artful:
  Won't Fix
Status in nux source package in Bionic:
  Fix Committed
Status in xorg source package in Bionic:
  Fix Committed

Bug description:
  [ Impact ]

  GNOME shell and other 3D programs run using software rendering after
  unity removal.

  This SRU covers only the upgrade case or if nux-tools removal happens
  after this update, for people who already upgraded and in broken state
  another SRU will follow.

  [ Test case - FOR WHO UPGRADES TO BIONIC/ARTFUL ]

  · Install xenial
  · Upgrade (nux-tools) and ensure that unity is still properly running after
    a logout/login cycle.
  · Upgrade to bionic or artful
    (assuming you're using a GNOME session)
  · sudo apt remove nux-tools
  · log into your session
  . From terminal:
    - printenv LIBGL_ALWAYS_SOFTWARE
    Should print nothing (and return an error)

  Same should happen if you don't remove nux-tools but you change
  `/usr/lib/nux/unity_support_test` not to run properly (replace with a script 
exiting 1), but you're running a GNOME session.

  · If running Unity session instead, ensure that
    printenv LIBGL_ALWAYS_SOFTWARE equals 1 in case that you're running
    in an environment with no 3d support (VMs are easy tests)

  [ Test case - FOR WHO HAS ALREADY UPGRADED TO BIONIC/ARTFUL AND
  REMOVED UNITY ]

   · remove nux-tools from artful/bionic-release (pre-sru), upgrade,
     reinstall nux-tools (no prompt)
   · remove nux-tools from bionic-proposed/updates (sru), upgrade, reinstall
     nux-tools (nothing should be prompted)
   · modify config file, remove nux-tools, upgrade, reinstall nux-tools (should 
prompt)
   · install nux-tools, upgrade, no prompt

  You end up with either no /etc/X11/Xsession.d/50_check_unity_support,
  its new contents or you are asked what to do if you've changed it
  before. Never the old content.

  [ Regression Potential ]

  Unity desktops with no 3d support could not start anymore.

  ===========================

  After an upgrade from 17.10 to 18.04, I noticed that all gnome windows
  animations were gone.  After some digging, it seems that gnome-session
  incorrectly assumes that my graphics has no acceleration, when in fact
  it does: it's a i5-2520M CPU @ 2.50GHz with Intel integrated graphics
  (i915 driver).

  I've tried this with and without the xserver-xorg-video-intel package
  (a.k.a. Intel driver) with the same behavior.

  The output of gnome-session-check-accelerated is: llvmpipe (LLVM 6.0,
  256 bits)  however the system should have DRM 2.0 capability.

  GL checks (e.g. glxinfo, glxgears produce the expected output from a
  working DRM system).

  mesa-utils and mesa-utils-extra are both installed.

  I can't find a work around.  Perhaps there is something wrong with my
  install/upgrade?

  Everything else works fine, although the graphical transitions are no
  longer smooth.  But it would be nice to restore the expected behavior.

  I have attached the log of 'journalctl -b0'

  ProblemType: BugDistroRelease: Ubuntu 18.04
  Package: gnome-session 3.28.1-0ubuntu2
  ProcVersionSignature: Ubuntu 4.15.0-20.21-generic 4.15.17
  Uname: Linux 4.15.0-20-generic x86_64
  ApportVersion: 2.20.9-0ubuntu7
  Architecture: amd64
  CurrentDesktop: ubuntu:GNOME
  Date: Wed May  2 13:06:00 2018
  EcryptfsInUse: Yes
  InstallationDate: Installed on 2016-04-22 (739 days ago)
  InstallationMedia: Ubuntu 16.04 LTS "Xenial Xerus" - Release amd64 
(20160420.1)
  ProcEnviron:
   PATH=(custom, no user)
   XDG_RUNTIME_DIR=<set>
   LANG=en_US.UTF-8
   SHELL=/bin/bashSourcePackage: gnome-session
  UpgradeStatus: Upgraded to bionic on 2018-04-27 (5 days ago)

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