Fixing a bug introduced by my earlier change adding in -s and -i command line arguments. I forgot to also update the Javascript which processes the command line arguments when I updated the bash command line processing. This didn't cause any problems unless you don't specify a main script to run (but just a before or after script). If you don't specify the main script it used the -i or -s value as the main script value.
Merge pull request #34 from dansoton/fix-bug-in-cli-args

Merging this change in as simple fix.