Removes GetOpt::Long 2.36 dep, runs under 5.8.8.

This removes all calls to GetOptionsFromArray, so we can use
Getopt::Long 2.35, which is what ships with stock Perl 5.8.8.
Fixing some things I messed up during development.
Merge pull request #240 from mmcclimon/issue_225

Removes GetOpt::Long 2.36 dep, runs under 5.8.8 (issue #225)