Hey there,
I am making an app for in-store pickup shipping for my store apstore-21.myshopify.com it will very similar to this app https://apps.shopify.com/click-and-collect for this I need to add a javascript file on checkout pages.
I've read Shopify API documentations and many forums on this topics but couldn't found any way, however I got a solution here http://freakdesign.com.au/blogs/news/18544989-adding-javascript-to-shopify-checkout. They basically using Google Analytics script box to add script tag on checkout pages. I figured out click-and-collect app is also using this way to add its js to checkout pages. I am not sure if this is the only way to add a javascript file to checkout pages or I can achieve this using Shopify API.or any other way.