I\'m beginning to evaluate javascript module tools like RequireJS for javascript modularization. This seems useful, especially during development, so I don\'t need to recomp
First you have to compile your depency tree into one file using the r compiler. After that you can a striped down AMD loader like almond. At least you have to find a way to change the url in your index html.
Take a look at gruntjs which can automatize the whole thing, there a bunch task to like usemin that helps you with the process.