to use the gnu.getopt package.  can someone verify that the run.bat with
--help shows the correct program name.

the main reason why I did this was to allow for unique substrings to be used
for option names, plus it is easier to manage adding new options.  for
example, to set the configuration name, you can -c or --conf, or rather
anthing that is unique across all of the other long options.

the gnu.getopt package is small (and lgpl), so I did not see any issues with
making this change and including those classes in run.jar.  if there are any
issues please let me know, as I am not aware of them.

--jason


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