Mostly AI-Enhanced Improvements

- Refactoring.
- Added log_d(), log_i(), log_w(), log_e(); used them instead of raw print().
- Improved log and prompt messages.
- Replaced `hashlib.blake2b` with `nacl.hashlib.blake2b`.
- Added docstrings and comments.
- Improved error handling; handled nonce counter overflow and EORError on every input().
- Changed the numbering of input options.
- Added limitations for input options: 1023 for passphrase size, 2^60 for output file size (in action 8), and 10^18 for maximum padding percentage.
- Applied strip() for integer and boolean input options.
- Improved type hinting using the features of Python 3.9; the minimum required version of Python is now 3.9.