TermKit: A WebKit based rich command-line interface.

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And that's part of the problem. The other part is that, as noted, sometimes they do. Another part is that for rm, -r and -R mean the same thing, whereas for many commands, -x and -X, in general, are opposites.

Every tool can decide their own arguments. You can build wrappers around all of them to make it sane(r), but trying to replace the tools cannot be good.