After a quick question in the Jekyll IRC chat room i was told to use the _data folder instead of using the main site config. The main site config is only read on startup while the data you store under the _data folder is watched.

You can create a filename.yml file in the _data folder and it will then be accessible in liquid and any ruby plugins you might have as site.data['filename']

Now my projects page is fully automated to complement my automatic deployment system.