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In Debian systems the default keyboard layout is described in /etc/default/keyboard and it is shared between X and the console. –man

Colemak and other keyboard mods

Default keyboad is listed in /etc/default/keyboard:

# KEYBOARD CONFIGURATION FILE
# Consult the keyboard(5) manual page.

XKBMODEL="pc105"
XKBLAYOUT="gb"
XKBVARIANT="danmak"
XKBOPTIONS="ctrl:swapcaps"

BACKSPACE="guess"

X keyboards are configured in /usr/share/X11/xkb/, in the rules and symbols directories.

/usr/share/X11/xkb/symbols/gb can be linked to ~/config/gb. Likewise in symbols, base.xml and evdev.xml.

Caps lock and control

This has to be swapped on a per-desktop environment basis. KDE has various native options, Gnome requires a download of gnome-tweak-tool via apt-get.