Docmentation Update: Examples as Notebooks

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
cglpk solver failing raises informative exception

The error code and error message are included in the RuntimeError,
instead of simply a failed assertion.
all of cobra core passes pep8

This is mostly whitespace and other small chagnes, such as rearranging
unnecessary list comprehensions to loops.