Refactor empty packages to modules

[atteggiani]

Fixes #20 and Fixes #22

• [x] Refactored amami/loggers/__init__.py to amami/loggers.py
• [x] Refactored amami/misc_utils/__init__.py to amami/helpers.py
• [x] Refactored amami/um_utils/__init__.py to amami/um_utils.py
• [x] Refactored amami/stash_utils/__init__.py to amami/stash_utils.py and moved amami/stash_utils/atm_stashlist.py toamami/_atm_stashlist.py`
• [x] Refactored amami main entry point, from amami/amami.py:main() to amami/__initi__.py:mani() and deleted amami/amami.py
• [x] Updated the docs for amami -h removing the modify command