Is it best practices to split an index file into three files for html, css and JavaScript?

It depends a little bit on what kind of set up you're working in but generally I would split those out into individual files, yes.

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I don't think Astro supports it but I may be 100% wrong bc I hardly know what I'm doing

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Yep, I'm back to my 800 line index file

I do have an api.js file, but it is no longer working after my morning mayhem, so I may do it the right way now

In astro you usually have components, a css, and little to no js files.

I haven't worked in Astro yet but I have to imagine it supports code splitting...