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I guess what I’m asking is that if grouping JavaScript is considered good practice, why don’t more websites place the JavaScript and CSS directly into one HTML document?
Individual file caching.
External files have the advantage of being cached. Since scripts and styles rarely change (static) and/or are shared between pages, it’s better to just separate them from the page making the page lighter.
Instead of downloading 500kb of page data with embedded JS and CSS, why not load 5kb of the page, and load from the cache the 495kb worth of JS and CSS – saves you 495kb of bandwidth and avoids an additional 2 HTTP requests.
Although you could embed JS and CSS into the page, the page will most likely be dynamic. This will make the page load a new copy all the time, making each request very heavy.
Modular code
Imagine a WordPress site. They are built using a tom of widgets made by different developers around the world. Handling that many code stuffed in one page is possible, but unimaginable.
if some code just short circuited or just didn’t work on your site, it’s easier to take out that code linking the external file, rather than scouring the page for the related code and possibly accidentally remove code from another widget.
Separation of concerns