Add/Confirm Command-Line Argument Verification

[gkapfham]

While I understand that #2 indicates that the command-arguments are fully verified, it is not yet clear that they are fully verified and that error messages are displayed if the arguments are incorrect in any way. We should perform additional testing to ensure the robustness of the parsing of the command-line arguments. There should also be clear calls to the verification functions in the main module. Finally, we should try to further simplify the main module so that it is easier to test and understand.

[ilikerustoo]

@huangs1 After we document and work through the details of how GatorGrouper works, I may be able to tackle this issue.