Tomcat just played a nice trick on me and wired out my webapps/root directory full of years' worth of digital photography with no recent backups. I am not amused. I was simply trying to upgrade from Tomcat 5.5.1 to 5.5.4 so I uninstalled 5.5.1, it prompted me whether I wished to remove the entire directory, I hit NO because I knew I had made modifications since installation but I guess it *assumed* webapps/root was unmodified and wiped it out. Guys, you should really fix this sort of thing. Either do a simple check to see whether webapps/root has been modified or don't delete anything inside webapps to begin with. Please! I'm setting this issue to a higher priority because it involved data loss.
Modification done for Tomcat 5.0.30 and 5.5.5, because other newbies are likely to use the ROOT directory in the same manner. But please do start taking regular backups, and do consider using a real webapp instead of the ROOT hard- coded name.