Remove IPython dependence, define and implement Application schema

Restructured the framework for accomplishing automated updates using `start.py` and `process.cfg` and removed the dependence on IPython. This means we won't be able to parallelize core-wise on a single machine, but at least the code is in a working state.

Defined the Application schema inside `lib/alchemy/schema.py` and added code to commit Application objects to the database. There is a lot of repeated code, which is bad style, but this late in the game, it's more important to have working code than beautiful code.