Does somebody know, how does the "Keyboard Preferences" / "Layout Options" 
feature of gnome work? I mean:
* does it run xmodmap behind the scene?
    * every time you change something in the "Keyboard Preferences" dialog
    * plus every time you start the session
* does it manipulate XKB layouts?
* something else?

I have not found any information about gnome concepts in this area on
the gnome web site. There are zillions of howtos on the web and part of
them partly works, but without knowing the big picture of this
multilayered keyboard layout system it is impossible to achieve a
reliably working solution.

[1] About XKB: http://www.charvolant.org/~doug/xkb/html/xkb.html
[2] About XKB and Xmodmap http://www.faqs.org/docs/Linux-mini/Intkeyb.html

But this sources are possibly obsolete? Not to say about more obscure
topics like proprietary keys, for example on my Thinkpad Notebook or
Keyboard shortcuts through xbindkeys, keytouch, gnome features and
others.

-- 
Gnome keyboard layout options (like remapping Caps Lock) are not reapplied 
after reboot
https://bugs.launchpad.net/bugs/173721
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Bugs, which is the bug contact for Ubuntu.

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