I've recently become interested in embedded scripting languages and their usage, but it doesn't seem very applicable in the Java services world. It seems that by allowing scripting of a platform, you lose the ability to track changes to the system (do you store user defined scripts in a DB, file system, Git?). How have you used embedded scripting languages? What benefits did it provide? What costs?
I think embedding a scripting language can be very useful for allowing users of your software to write extensions/plugins. Usually they are stored on the file system, if the user wants to manage their custom extensions another with Git or something else then they are free to do so. You could also include a package manager (like Sublime Text).