1. "todo.list" file to track which segements still have to be done.
2. small and numbered list files to go through segements faster.
3. run_manager script which is the same as the script.bash file except that it takes a command line argument for the file containing the list of segments to go through
4. #TODO# remove bash.script and use run_manager.script instead.
5.progress.log to indicate which segments have been done