This is an attempt for fix #1 . I'm sure that there were many ways to do this but here's a summary of my changes:

• The FileStager class in staging.py no longer sets the default as True for remove_original, this is now done in defaults.py
• A --keep-original argument was added which sets the remove_original value to be False. I tried a few ways of doing this and this seemed like the least worst method.
• Some re-arragement of arguments in staging.py had to be done so that the args with defaults came last.
• Seeing as the FileStager class was only initiated in _stage_file, I took the perhaps incorrect route of adding remove_original value to files_iterable which allowed the information to eventually be present when initialising FileStager

In terms of testing - On Windows I used staging to move a folder to one other output directory. Adding --keep-original resulted in my source staging remaining intact, while removing this option resulted in the default behaiour prior to this patch - the source files are deleted after successful completion.