August 2014 bugs

@bradnerComputation Charles, please review these changes resolving #30  and #29 .  This also fixes other minor items and provides a couple new optional arguments -- please see commit comments for more details.

I added several automated tests to verify the changes.

If possible, please ask someone to spend some extra time manually testing the current state.  Now that we are at version 1.0 and will likely be publishing a paper highlighting the tool, I hope we can have some increased confidence in this code.

Thanks.