CHEF-4612 Remove secret in favor of secret-file

* Attempting to use knife bootstrap --secret.. the documentation was a bit ambiguous in that I (and many others on my team) thought it would load argument passed as a file. Not that the string itself was the secret. Given that one shouldn't be passing a secret via STDIN, I've removed --secret from bootstrap and also from the tests. --secret-file is much less ambiguous. There was also another issue with -s being an alias to --secret because -s is already an alias for --server-url.