make root & relativeTo options relative to source tree

Previously the options would be relative to the current working directory, which didn't really make any sense.

I also used the opportunity to only create one instance of CleanCSS.
@shinnn This is indeed kinda hacky but we need `readTree` before we can know the directory.

Looking at it again, I realize that it should be `read` that is used instead. That way we don't depend on implementation specific details of the filter plugin.