phantomas
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Scope.js removes Array.prototype.toJSON
Ln:126 it's set as undefined but it's never restored. It was done for #482 but if any sites require that function then they can't use it since it's not overridden anywhere.
Took me a while to figure out why my site wasn't rendering correctly so it's a particularly nasty issue since it's quite subtle. I think we should be checking for Prototype (up to v1.7) and Mootools if they are the only things causing issues rather than removing it from the window global completely.