Add '--input / -i' as options and clean up documentation

[Amndeep7]

Instead of doing -x or -j or whatever, just simplify the situation and add/recommend -i since there are no other input files (though there are occasionally other arguments/options, but none of them use -i). First step would be to add the two as additional aliases to whatever's already there, and then in a later major version bump we can drop support for all the non i ones.

Also, the documentation needs to be cleaned up/improved in several regards: use the banner option from thor, clean up the english, sometimes it says --option_prefix even though it ought to be --option, etc.

[Bialogs]

I don't see us breaking compatibility with users existing workflows as a high priority. I understand the desire to simplify the interface but maybe there was little consideration given to existing users.