The function "Build i2b2" from the main menu compiles and deploys the i2b2 Web Services. Normally, this function is triggered automatically when the configuration has been changed and JBoss is started via the menu.
If you're used to start JBoss outside of i2b2 Wizard (e.g. with start-i2b2.sh), running this function is necessary after you have created a new i2b2 project.