Adding TODOs and cleaning up code a bit

renamed:    code/TODO -> code/GOALS -- our lofty goals for the project
new file:   code/LIBRARIES -- list of required python libs
modified:   code/TODO -- automatically generated list of TODO comments in code
modified:   code/models/createMatrix.R -- does not need a file anymore
modified:   code/models/model.py -- many small clean-ups
modified:   code/models/randomModel.py -- a few small clean-ups/renamings
new file:   code/todomaker.sh -- generate the TODO list automagically