Your app dependencies must be stored in /www/js/lib (js) and /www/css/lib (css).
Usually, dependencies are fetched with bower (in /bower_components) and added
to the libs on build.
For example, backbone is fetched with this command :
bower install --save backbone
Note that bower components are checked in git.
Currently, the build is performed with make build.
For example, Backbone is added in /www/js/lib with this command in the Makefile :
cp bower_components/backbone/backbone.js www/js/lib/
This way, the whole backbone directory isn't added to the assets of the built
apps.
To add your own dependency, simply add it to the build-app-dependencies rule in
the Makefile.
You can then configure the require path (and optionnaly shim) in js/core.js
(see js/core/core-require-conf.js for an example).
You'll need to add your dependencies in www/build.js, too, if you want them to
be found by r.js.