Added large sparse matrix generation and redid configuration files

[taddyb]

what was done:

• better organized the config file so you know which variables belong to what part of the process
• added code that will generate a sparse connectivity matrix:
  • the code uses a loop that determines the index of it's upstream, and saves the pairs to disk
  • works with what is expected from dMC

testing:

• ran the whole script and generated output in a new location
• The output works when plugged into the routing code