NodeJS package based application architecture

Question

I'm coming to NodeJS from other platforms and so far everything makes total sense. I'm starting to look at the different ways to structure applications/site, with the aim to get a sense of whats out there.

The one I'm currently stuck on is when you want to have different functionality in your app/site split into different packages (not simply different modules) - a similar approach which has been taken by Atom and mentioned briefly here.

I get that you can split the functionality into distinct packages and that usually these packages are small, but I'm missing the piece on how to glue it all together and trigger them to "execute". Are the any samples on this, reference implementation, guidance, etc?