How to set persistent keyboard layout for X Windows in Kali Linux?

Question

I want to set permanent Japanese keyboard layout for X Windows in Kali Linux (Rolling Edition 2016.1, testing with kali-2016.1 Vagrant box).

Setting Japanese keyboard manually through All Settings -> Region and Language -> Input Sources works ok and is persistent. I want to provision the same settings through a script.

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For ad-hoc configuration I run:

setxkbmap -layout jp

which works until user logoff. It does change the layout, however it does not add/change Input Source in settings panel.

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For persistent configuration I tried the following (with no success):

• I created directory /etc/X11/xorg.conf.d/ and /etc/X11/xorg.conf.d/00-keyboard.conf with the following content:

  Section "InputClass"
          Identifier "system-keyboard"
          MatchIsKeyboard "on"
          Option "XkbLayout" "jp"
          Option "XkbModel" ""
          Option "XkbVariant" ""
          Option "XkbOptions" ""
  EndSection
  

  But it has no effect.

• I tried running:

  localectl --no-convert set-x11-keymap jp
  

  which supposedly should create 00-keyboard.conf, but although it ends with no error, it does not create the file.

Settings for console work ok (Japanese layout is active when typing username at the logon screen). My /etc/default/keyboard is:

XKBLAYOUT=jp
BACKSPACE=guess

And I have also setting in vconsole.conf:

KEYMAP=jp106

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How can I set persistent keyboard layout from CLI?