Thanks for the design complement. We have 2 undergraduates do the redesign for a term project last fall.

In terms of the multiple jars, think of JIST like an onion.
JIST-BASE - No Plugins
JIST - Only Plugins in the JIST-Plugins repository
JIST-CRUISE - All available plugins

For example: If you are working on modifying something in the plugins repository, then you want to get the base so that the JAR doesn't conflict with your eclipse. If you are developing outside of the shared cvs or are just a user, then you want "JIST-CRUISE".