[closes #25] - Not perfect, but there's now a bit more consistency to the variable indexes that are used.
Corrected a typo.
[#19] - Changed over to using Python's logging module.

By default, stdout printing will not be enabled anymore unless the user adds a logging handler. For users unfamiliar with Python's logging module, added an enableStdOut() method to DirectoryTools to enable basic stdout logging.
Corrected a Doxygen typo.
Adjusted unit tests for [#19].
Updated Doxygen documentation after [#19]