We are building an app for web push notification but we are not able to add files to the root folder of the domain. To implement web push, two files need to be added to the root folder - manifest and service-worker. Shopify directly uploads all files to cdn and not on the root folder.
How can I find a work around for this one ?
You can't do this on Shopify. There ought to be a workaround within your app's code, but if there absolutely is not you could setup a lightweight AWS VM ($5/month) that runs an HTTP proxy to Shopify (for all other requests), and simply add those two files to the proxy.
We eventually figured out that it is not necessary to use the root folder for activating web push notifications. Here is how you can activate web push notifications on platforms which don't let you access the root folder.