I thought it would be a good idea to have an empty qa-scripts.js file in the theme folder that the user can use to put his own scripts into.
In my q2a installations I am either: writing a plugin (but sometimes too much hassle for just 3 lines of JS), or: abusing the page.js file to store the code.
It would be great to have a save place for custom userscripts (like jquery libraries pasted into the file), just like the qa-styles.css