Comments, reorganized functions, small fixes

- added comments to functions
- moved functions around to better reflect the order in which they're
called
- removed a few unused variables
- replaced manual path already exists indexing systems in two places
with path_already_exists()

The data_accessioner.py works as follows (more or less):
DataAccessioner class initialized
self.initialize_accession_settings()
rec_traverse_dir()
remove_special_characters()
(recursive) rec_traverse_dir()
accession_bags_in_dir()
initialize_import_file()
is_excluded()
1. accession_file()
accession_bag()
2. accession_bag()
format_bag_name()
create_bag_structure()
is_excluded()
cleanse_bag_name()
create_relative_bag_dict()
(recursive) create_relative_bag_dict()
cleanse_dict()
(recursive) cleanse_dict()
path_already_exists()
write_rename_file()
traverse_bag_contents()
is_excluded()