I installed the WAR version of Archiva into my tomcat instance... no problem so far.
I then attempted to delete the default "internal" repository. I hit the delete config and contents button.
At that moment I noticed that the repository directory was the tomcat home directory.
Archiva managed to completely delete my Tomcat installation.
To reproduce this, install it as a war, point a repo dir at your app server home, and hit the delete button (make sure you have a backup).