MooTools will not work with most javascript libraries. The following list is just a really short example of what MooTools will not work with.
What if you write your own library? Well, if you use any Class names such as Fx or Class or function names like $, you'll find your code or MooTools code borked. In addition to that, if you use native properties of _proto_, the prototypes in JavaScript, MooTools probably will break your code since MooTools modifies a lot of prototype stuff.
The MooTools Team has a good reason for making MooTools work this way.
There are other things, of course, but these are major ideas that the Team follows.
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