Docmentation Updates

All of the example scripts were rewritten as IPython notebooks. These
notebooks are then used to autogenerate example scripts as well as
Markdown for sphinx documentation.

In addition, the following changes were made:
 - qp example no longer specifies a solver
 - an extra MILP example added (NP complete from XKCD)
 - One single notebook for introduction describes core objects
 - All autogenerated example scripts in examples/ directory

The following minor bugfixes were made:
 - settings load mathjax over https
 - add ipynb_checkpoints to gitignore
 - latex preamble now loads amsmath and amssymb
 - remove extraneous docs such as cobra.version