Injecting extra scripts to a Cordova project at build time

I have an ember project which I build both into dist/ and cordova/www so that I can share the code between the web version and the hybrid mobile app.

Since the code is shared I need a way to inject a javascript file into the index.html but only when using ember-cli to build for cordova or to use an environment variable to check if the app is running on web or mobile and decide which code to execute.