Cannot be done in the way you describe.
You will have to include the script in every file and include logic that checks to see if this.hostContainer == undefined (meaning you're not in a browser).
OK; If I do have to touch every single file in order to add my document level script, is there a way to include a .js file (or equivalent) instead of hardcoding, so that if I have to change code later, I don't have to change it in hundreds of places? I could not find any such way.
If so, are there Reader version limitations I should be aware of?