Refactoring. Moving to score/report/analyze

An overall theme for top level options has developed. It has turned into
score, report, and analyze. This commit does some refactoring to put
that in place. The analyze option has not yet been implemented. The
original cli options will remain in tact for one more release and have
been marked as deprecated.

Signed-off-by: Aaron Bedra <aaron@aaronbedra.com>