Overhaul setup.py and metadata

* Removes the `setup.py` file, replacing it with a `prepare_deploy.py` script that has the same functionality.
  Users / developers can now run or convert the files with:

      python prepare_deploy.py --run

  and

      python prepare_deploy.py --convert

  (or do both simultaneously).

* When notebook files are run, they are output to a separate file (same filename but prepended with `_run_`). This makes it easier for testing, because you can now just do `git clean -f` after running the notebooks to clean up the repo.

* The `metadata.cfg` files have been vanquished from this land. We now require IPython > 2.0, and use the build-in notebook metadata.

* I've updated README, CONTRIBUTING, and added a DEPLOY file, and made them markdown instead of ReST because ReST hurts my brain.

cc @eteq