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Not surprisingly, jQuery has become the go-to example for developers looking to add an AMD definition to their library. As we know, jQuery's near ubiquity means that certain AMD recommendations are not practical for jQuery. Unfortunately, the jQuery named module registration is referenced with the (reasonable) assumption that it's representative of AMD best practices. For example discussions, see Leaflet/Leaflet#1364. Leaflet/Leaflet#1778, janl/mustache.js#333, janl/mustache.js#345 and d3/d3#1672.
I'm hoping an extra comment will make it clear that jQuery is a special case.