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.
Follow SBML Rerversibility tag guidelines

SBML requires that an irreversible rection never be negative. However,
cobrapy's definition of reversibility is more consistent with the
biochemical definition that flux flows both ways. Therefore, set the
SBML reversibility flag when writing out a file by using the criteria of
lower_bound < 0 instead of the Reaction.reversibility property.

This fixes #114.