Improved comments and logging

[crichgriffin]

Actual code changes:

• fixed r_path in the pipeline scripts

• fixed parsing of the booleans in the argument parsing (some were still being parsed as strings)
  Here is an example change:
  parser.add_argument('--use_muon', default=False, type=check_for_bool, help='')
  instead of
  parser.add_argument('--use_muon', default=False, help='')
  and below in the script check_for_bool(args.use_muon) (this bit got forgotten sometimes)

Logging improvements:

• fixed [preprocess] how to run pre-filtered objects #15
• Added a lot of "done" flags at the end of the scripts,
• Change L.set level to info for all scripts (some were on debug)

[crichgriffin]

I have double checked all of these files