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ls from the Shell mode?
This happens because ls is aliased to `ls --color' in your
shell init file. You have two alternatives to solve this:
EMACS variable in the
environment. When Emacs runs a subsidiary shell, it exports the
EMACS variable with the value t to that shell. You can
unalias ls when that happens, thus limiting the alias to your
interactive sessions.
ansi-color package (bundled with Emacs 21.1 and
later), which converts these ANSI escape sequences into colors.