Custom JavaScript

Is there way to link custom JavaScript to app.html? For example, I want to overwrite the shiny.instances.js to remove the confirm alert for restarting the current instance. I am using containerized ShinyProxy with custom app.html and login.html already.

For now, I am using embedded JS in the head of app.html. Would be great to be able to have the 227 line code in a separate file though!