Because JWrapper packages your java app in a consistent way and handles all the hassles like icons, app names, executable names, installation folders and elevation, we've been able to add a simple switch that lets your app deploy as a completely separate installation with its own name, versions and storage areas.
As of today's release just adding these options to the end of your JWrapper build:
will change the naming and installation of your app to reflect the added suffix (e.g. "Beta" or "Dev").
This allows you to run the production version of your own app (always useful for support purposes or maybe you just find your own app useful) alongside a developer version for testing and debugging.
It also allows you to very easily create a beta version and to distribute your beta version to customers and have them run it while keeping the production version around to use for critical work. They can install, upgrade, break, delete the beta version without ever affecting the production version of your app.
The alternate URL specifies an alternative Update URL allowing you to run beta or alternate versions with their own timelines and release cycles - for example a regularly updated beta build.