I left the index.js file essentially as it was, just a way to invoke the built in APIs as a one time task by editing the file
I put everything new in /api/, and tried to do the whole swagger thing. I think I'm happy with it, but I'm not sure its what you would have done. As far as I can tell, the quickstart guide you sent me was for the "swagger-tools" package, but the "swagger project create" cli you talked about sets your project up with a totally different set of swagger middleware, "swagger-express-mw" or something. swagger-tools seemed to work fine so here it is.
Okay, here it is. Some notes: