Using shorten is a similar process as using shntool. You just tell Terminal what you want shorten to do. Typing shorten -h will bring up the help screen:

-x will obviously extract SHNs that are specified in your file path (remember the cd, ls and pwd commands).
I've composed a page that details the batch processing of WAV and SHN files which can be found here.
Well, I hope these documents have been some help to my fellow Mac brethren. I hope eventually someone will create a GUI similiar to Carbon Shorten with all of the features our Windows counterparts have, but until then, give this a try sometime.
http://www.hornig.net/shorten.html
http://www.etree.org/linux.html
Dave Mallick, Jason Jordan, Joshua Harriman, Mike Kelleher, Scott Brown, Doug Hornig (if it wasn't for him we would STILL be in the dark about shorten on our favorite platform!) and of course, all of those Mac seeders out there!
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Disclaimer: you have my permission to link to these pages however, please ask for my permission if you would like to include it all or in part on any web site or software package.