My previous answer was in a comment, but having given it a bit more thought I'd like to reply a bit more extensively.
My assumption is that you have one "master" application from which you want to send the push notifications. With that in mind, I think you have two options:
Option A Include the pushnotifications module in your master app and in all your other applications. Then set up requesthandlers in all of your applications to handle sending the request to from your overlooking app. So you would send a request for a notification from you master app to one of the requesthandlers in the other apps, which will then send the actual notification. This ensures opening the right app from the notification
Option B Make use of Action Buttons and set custom handlers in your index.html for handling whatever it is you want the button to do/sending them to the right application. Check my GitHub repository for more information on this subject