Change to a flag system rather than order of parameters so that more features can be added

[JacobDB]

I think in order to make this script more flexible for future features, it'd be good to change the way this takes in settings so that it uses flags instead of a specific order of parameters.

For example, in order to implement #25, it'd be great to do something like virtualhost create localhost --user=www-data:www-data.

Other possible options could be:

• --alias=www.example.localhost
• --ssl_cert=/path/to/certificate.crt
• --ssl_key=/path/to/key.key
• --skip-test-file
• --skip-hosts