On my system, anything that changes is in /bin. For a catastrophe, I would reinstall the OS and environment and then restore data from the thumb drive.
EVERYTHING is stored as data on the u2 database. All javascript, css, html, php, and mysql is generated from this data through custom builds. No need to backup anything except the source data and the custom programs used to generate everything else. And all of that is within the IBM/u2/bin directory.
Have a disaster? Restore the environment, restore the u2 database & code, and rebuild everything else. I designed it for the development leverage. The ease of disaster recovery is just a bonus.
