Adding files for the code that deals with reading input. Might stay like this or maybe further separated. It is still big and complicated.
Adding dependency on load_data_for_complexity for preseq
Big organizational change to remove data reading code which is now in another file and also to put the option parsing in the individual modes. This will allow greater flexibility in making modes and keeping the main for determining which modes are useful. It will also allow additional modes to be built into other files if needed