var Prototype = {
//....
  ScriptFragment: '<script[^>]*>([\\S\\s]*?)<\/script>',
//....
}

May be next code would a little better?

var Prototype = {
//....
  ScriptFragment: '<script[^>]*>(?:<!\\-\\-)?([\\S\\s]*?)(?:\\-\\->)?<
\/script>',
//....
}

and for:
  evalScripts: function() {
    return this.extractScripts().map(function(script) { return
eval(script) });
  },

  evalScripts: function() {
    return this.extractScripts().map(function(script) { return
window.eval(script) });
  },


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