Okay, so — in short — the problem was that the command `/usr/lib/x86_64
-linux-gnu/libgtk-3-0/gtk-query-immodules-3.0 --update-cache` wasn't run
upon distro upgrade. Actually, I'm not sure if it's a distro bug or not,
because in my case the distro-upgrade came not quite fine. I was having
a PPA with latest GCC, which I didn't purge — that looks right, why
would I care if I'm using a binary distro anyway? However, after upgrade
Xorg didn't even start; long story short — libstdc++, for some reason,
didn't have some function which some apps were using. Reinstalling to
vanilla libstdc++ solved the problem. I did even see a bug about it
somewhere, but can't find it. But I can assume that some apps for distro
upgrade failed to run because of the library — as the bug with
$GTK_IM_MODULE not the only problem I encountered here. I'm seeing
things like missing tray icons, ignored preview options in Dolphin,
crashing vlc, and more.

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Touch seeded packages, which is subscribed to gtk+3.0 in Ubuntu.
https://bugs.launchpad.net/bugs/1598295

Title:
  $GTK_IM_MODULE ignored after upgrade

Status in GTK+:
  Confirmed
Status in gtk+3.0 package in Ubuntu:
  Triaged

Bug description:
  After upgrade trusty → xenial, Compose key stopped producing
  configured through ~/.XCompose characters for GTK3 only apps. To be
  sure that its the GTK problem, I created a simple GTK3 window with
  textbox, launched it like:

          $ GTK_IM_MODULE=xim XMODIFIERS=@im=none ./a

  and the textbox produces wrong characters for Compose key. (the
  variables are actually set globally, I wrote them here just for
  clarity).

  XCompose works fine for all other toolkit's apps, including GTK2 and
  Qt ones.

  1) The release of Ubuntu you are using, via 'lsb_release -rd' or
  System -> About Ubuntu

  $ lsb_release -rd
  Description:    Ubuntu 16.04 LTS
  Release:        16.04

  2) The version of the package you are using, via 'apt-cache policy pkgname' 
or by checking in Software Center
  $ apt-cache policy libgtk-3-0
  libgtk-3-0:
    Installed: 3.18.9-1ubuntu3
    Candidate: 3.18.9-1ubuntu3
    Version table:
   *** 3.18.9-1ubuntu3 500
          500 http://ru.archive.ubuntu.com/ubuntu xenial/main amd64 Packages
          100 /var/lib/dpkg/status

  3) What you expected to happen

  «Compose + - + space» would produce «— » in GTK3 apps.

  4) What happened instead

  «Compose + - + space» producing «~» in GTK3 apps.

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