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/usr/share/crawl/settings/menu_colours.txt is in crawl-common 2:0.10.3-3.

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The actual contents of the file can be viewed below.

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# Changing colours of items in the inventory and other menus

menu := menu_colour
ae   := autopickup_exceptions

# Items currently not affecting you.
menu = darkgrey:(melded)

# Bad items
menu = lightred:.*bad_item.*

# Useless items, comes here to override artefacts etc.
menu = darkgrey:.*useless_item.*

: if you.race() == "Spriggan" then
menu = darkgrey:.*jewellery.*(sustenance)
ae   = >ring.*(sustenance)
:end

# Evil items
menu = $evil:.*evil_item.*

# Handle cursed and equipped items early to override other colour settings.
menu = lightred:.*equipped.* cursed
menu = red: (a|the) cursed
menu = inventory:lightgreen:.*equipped.*

# Important game items
#
menu = lightmagenta:.*misc.*rune( of Zot)?
menu = lightmagenta:.*orb.*Zot

# Artefacts
#
menu = white:.*artefact.*

#menu = white:.*identified.*artefact.*
#menu = lightblue:.*unidentified.*artefact.*

# Ego items
#
: if options.menu_colour_prefix_class then
menu = lightblue:(^identified armour.* pair of .* of )
menu = lightgrey:(^identified armour.* pair of )
menu = lightblue:(^identified (weapon|armour).* of )
menu = lightblue:(^identified weapon.* vampiric .*)
menu = lightblue:(^identified weapon.* anti-magic .*)

# Possible egos
menu = lightblue:^unidentified .*weapon.*(runed|glowing)
menu = lightblue:^unidentified .*armour.*(runed|glowing|embroidered|shiny|dyed)
:end

# Emergency items
menu = yellow:.*emergency_item.*

# Good items
menu = cyan:.*good_item.*
menu = cyan:.*misc.*[lL]antern

# Dangerous (but still useful) items
menu = $dangerous:.*dangerous_item.*

# Defaults for normal items
menu = green:uncursed