cumulative gene deletions and gene substring names

Solve the problem of shorter gene games substituting in for longer ones
when the name is a substring of the longer one without using costly
regular expressions.

Cumulative gene deletions now work correctly and are the default
behavior.
automatically detect glpk path from glpsol

Similar to the approach used by pyglpk.

Makes installation of cglpk easier when installed in non-standard
locations.
doc updates

https mathjax

merge multiple intro notebooks into one for intro

replace building model example with notebook

add ipynb_checkpoints to gitignore

minor bugfixes