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Let's say you are building a large application, and you expect to have tons of javascript on the site. Even if you separated the javascript into 1 file per page where javascript is used, you'd still have about 100 javascript files.
What is the best way to keep the file system organized, include these files on the page, and keep the code structure itself organized as well? All the while, having the option to keep things minified for production is important too.