To clarify a few things.
I'm technically working on my own project. Its a fork, that is it does the same thing, but its an alternate implementation. So I will do things to a separate repository that won't be completely compatible. I'm doing it because I want a good web project to play with a few technologies I've been wanting to play with. Any work I complete related to this project can be used by you however you see fit. For instance, if my fork were to pass yours in functionality with less complexity, you have my express permission to incorporate it into the your project.
Since you are having such a problem with getting Java to communicate with your client side Javascript, I provided a simple Javascript server (back-end is synonymous here). When I say server, I mean the code that makes a machine behave like a server. The point of the Javascript server was to show you how you can accomplish those same tasks in Javascript. It is incompatible with your Java work though, commiting to it would require abandoning Java on the server. Technically you can get the two servers to communicate with eachother, but it would likely involve solving your current issues, and introduce a lot of unnecessary complexity. You may be able to use some Java technologies with the Javascript server, but thats likely to reintroduce issues getting Java and Javascript to work.
The server I provided can be used by you as you see fit, the repository too. If you aren't sure which direction to go with, feel free to develop them both side-by-side for a while. My fork will take place in a different repository.
Things you can do...
Install a driver for your database. Looks like there is one named mysql (type: npm install --save mysql).
Here is a page on it.This will allow you to connect to your MySQL database.
Since this server will be incompatible with your Java server, you will need to investigate to how to reimplement functionality you already have. Consider a little bit of effort here an investigation into which server you want to keep. I would also try and implement some of the routes your client side needs, and see if you can get it communicating.
Things I will be doing with my fork...
I will be adding a database (Cassandra in my case) to my fork. Next I will see if I can get
Browserify to serve (bundle, build, ship, whatever) a client side Durandal app to the browser (when a browser makes a request of the server, how else would the client side run?).
After that I will have a simple full stack application. From there I would implement most of the required functionality on the back-end. Test it using curl where applicable. Then implement the client side to provide an interface that utilizes the back-end restful API. At this point we have a partially functioning Agora implementation. Further iteration would refine it.