Yes. We have a tool called aurelia-bundler. You can use that to create any number of bundles you want from your source code. Our docs app, for example, is deployed as two bundles. One that contains aurelia and all 3rd party libraries and one that contains the application-specific code. You can read the docs on bundling here: aurelia.io/docs.html
We are constantly working on improving bundling. We have lots more features planned for the future.