Around 472, there was a change in the way we install Tomcat in a Linux server. You will see that there are two rpms that provide a tomcat installation:
which install two instances, one in /opt/netiq/common/tomcat/ and one in /opt/netiq/idm/tomcat/
IDM uses the later one. The difference with what we used to do is that in the past, the binaries and the configuration files for tomcat were in the same folder structure, which made it harder to upgrade the tomcat version.
We've seen a few times with systems upgraded from 4.6 that a few libraries are left behind from an old installation and Tomcat is not consuming the right libraries. The conflict is then between the contents of what you have in /opt/netiq/idm/tomcat/ and /opt/netiq/idm/apps/tomcat/