You'd be surprised how many people will download tools like that and trust that the tools do the job right. I've reviewed a couple of these tools over the last year or so and without fail, they all feel the need to mess around in the System folder. One even went as far as to start deleting bits of the old carbon framework because "all apps use cocoa these days".
Never, ever, ever.. did I say ever? Ever. Use tools like that. Not to be a dick, but if you can't afford to pay for a bigger harddisk, then don't go using tools that will "shrink" your system because often they'll shrink you right into a corner you can hardly get out of.
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