How i2b2 Wizard works - Important things you need to know
The figure above illustrates how i2b2 Wizard interacts with i2b2 and the overall Linux system. The large white rectangle in the upper left part shows the i2b2 Wizard directory, which contains wizard.sh (the i2b2 Wizard start script) and, besides others, a config directory. This config directory stores the current configuration of your i2b2 hive, i.e. information about all created i2b2 projects, users, passwords, ... everything that can be configured through i2b2 Wizard's menu system.
This configuration is used to configure the i2b2 hive source code during deployment (the source code is automatically extracted to /i2b2scr, then cofigured and deployed to /opt/jboss-XXX/ by i2b2 Wizard during setup, as shown in the figure above (right part). It is OK to delete /i2b2scr and /opt/jboss-XXX if something gets messed up, because i2b2 Wizard will automatically rebuild these directories whenever necessary.