I notice that emacs shell-mode colorizes certain strings in the output of a
command you run. For example most (though not all) words starting with - or
-- get colorized. You can see this if you run emacs --help. I don't see this
goofy colorization in term mode or eshell mode.

Can anyone explain what the deal is? A cursory look at the code in shell.el
didn't reveal anything, but I'm sure that somewhere emacs must be deciding
to add colors to the output.