added indicies for prototype
bugfix: use indivies to call activation values and prototype not by counting num cols

this is because when using the length of the number of cols, when a new
column is created, the cos values are off
added prop cos 95 and 97

the bugfix showed that cos sim is above 90 as soon as the agent is
updated.  this tries to find the threshold for agents that learne
prototype well and not
ignore ipython checkpoints
initial port of sse and cos_sim from r code into python

this will allow me to call the python analysis natively, and will be
much faster