Deep clone fix to keep stylus nodes intact

This pull request is a fix for #101.

Since `paths` is the only value of `opts` that we mutate whose changes would affect the outside, I've added special handling for it so we don't lose the functionality introduced in 15fb57a81bfcbf927a84c14e364a2889128997d8.

@TeffenEllis it would be great if you could take a look and let me know if it works for your use case.