We\'re beginning work on a couple of fully JavaScript-dependent web apps (our previous apps have been ASP.NET MVC, with JavaScript \'goodness\' sprinkled over-the-top).
In the end, this is how I've achieved it. It may not be to everyone's taste - but worked a treat for me.
Note: In all of our projects, static resources are in a root directory called 'Assets', so for example JavaScript is always in /Assets/js/ and CSS /Assets/css/.
Solution
When the project builds, it copies the imported files to \bin\Assets\js - the post-build event then takes a copy of those over to the project directory - in time for the site to use them.