Fixes + Improvements

*WORK IN PROGRESS*

Currently we're running into a number of hard to diagnose problems with fuggetaboutit.  Accordingly this pull request will make some changes to try and trackdown issues/make things less fragile.  Specifically this pull request will:

  * Make persistence less fragile and more inspectable by moving from custom binary files to json + npy files.
  * Factor out tornado specific bits to make testing and interactive exploration easier.
  * Add a more comprehensive test suite.