add the prototype to the output

for #66
comments for the columns in the output file
comment out r_script and r_status kwarg parameters
rename var from num_train_mutations to prototype_mutation_prob
prototypes will be a LensAgent class variable (list)
randomly creating a prototype
set the prototype as a Class variable
each agent gets a prototype

this is just incase multiple prototypes get generated
doc string documentation
parameter var chane from num_train_mutaitons to mutation_prob
num_train_mutations to mutation_prob in function body
implementing marks R code into python

replaces the older mutation method that samples the prototype and
changes it.  it now has independent probabilites for each unit of the
prototype
if to elif
remove r stuff from function parameters, and rename num to prob
delete old commented out code
remove the r_status part and use the python implementation only
hacky re-setting the state to prototype for seed and seed_no_update