The FreeNAS 10 middleware is a separate process which controls all aspects of a FreeNAS 10 instance's configuration and management. It can be talked to using the CLI (also part of this project) or a web application (see http://github.com/freenas/gui).
For documentation of the tools and processes for hacking on FreeNAS 10 overall, visit http://doc.freenas.org/10/devdocs.
You should not, however, be working directly in this repo if you simply wish to build and/or test the middleware. You should, instead, check out the http://github.com/freenas/freenas-build project which will automatically check out all sub-repositories (including this one) and do the right things to create / update a FreeNAS 10 development instance.