added command line parameter "-modules"

I have two overall comments:

1. Which command-line shells have you used to test this patch? At a minimum, please test against `bash`, `dash`, and `zsh`.
2. There is also a Windows version of this file, `jsdoc.cmd`. Is it possible for you to update that file as well? (If not, I won't block this pull request, but Windows users will have problems with your custom template.)