Some more code clean up.

This would be better if I knew more Ruby.

- Some more clean up, before trying to restructure things so this is an
actual Gem
- Rename Scan_and_parse to Scanner
- Move some error checking to the main() method, as that seems like the
more appropriate place for it.
- Keep required gems sorted.
- Remove old commented out code.
- Allow the user to load a different vulnerable apps CSV file.
- The main function now just does options parsing and validation, the
Scanner knows how to run itself. Logic about validating options is
pulled out of the Scanner class and into the main function.