deleted unused config parameters
added new parameters (PrototypeGeneration, NumPrototypes) and re-arranged parameter order
deleted r_script variables and commented out code
do not need to track number of nodes in network bc it is in config file
number of prototypes come from config file now, before was hard-coded 1
prototype generation either from user or random from config file

code to generate prototype depending on the config file.  raises
ValueError if unknown type is entered
comment on what time -3 is.  the state when all agents are init

should all be 0's and None
ignore bkup_folder which saves lens experiments I want to keep
02-lens clean.sh script does not delete the README.md file
comments in config file
commented out prototype_string read form config, already read in beginning of script
read criterion and epsilon from config
changed interface for seed_agent_no_update

no longer takes the string from the config file, now takes a list and
epsilon value to seed.  parsing is taken care of earlier
changed interface for seed_agent to seed_agent_update

same reasoning as seed_agent_no_update
comments
move library(grid) to top of script instead of in multiplot function
ini file has new seep parameters as well as able to take list or range syntax

new sweep parameters: NumberOfAgents, Epsilon, Criterion
can now take list or range (aka fr, to, by)

too lazy to select specific lines so adding the other param changes as
well
delete old commented out code
changed permissions to clean.sh for execute (775)
added code comments that section off code