Inside of the extension builder, when an error occurs that's part of an Ajax call (such as adding a Jar to the project), the error message is show in green and the entire HTML page response is being displayed in the error box.
Implement some error handling to flag the processing as successful or unsuccessful and control how the error is passed back for display. If not already, a log file or something might be necessary to store the "full" error including stack trace and such.c