The Shopify skeleton theme seems to be deprecated and it doesn't have any JS and I can't find a recent one..
Can you guys give me some suggestions? Thanks!
You can use Debut theme, this theme is best for all purpose, its contain ajax add to cart Js too.
This naked theme was a good choice for us when we redesigned. It is also not supported though, and I believe it was based off skeleton.
You can get the functions you want and some examples of how they're used here
Here's all the functions, but you can pick and choose what you want: