When adding a new subsystem into an existing instance pkispawn will regenerate Tomcat configuration files such as serverCertNick.conf and server.xml. So if there are subsystem-specific settings in those files they will get replaced by the settings of the new subsystem.

For example the serverCertNick.conf on a CA may initially contain the following value:

Server-Cert cert-pki-ca

When KRA is added to the same instance it could change to this:

Server-Cert cert-pki-kra

One possible solution is to not regenerate Tomcat configuration files. This means the contents of those files are controlled by the first subsystem and if the second subsystem defines a different value it will get ignored, which may be confusing to the admin.

Another solution is to verify that the second subsystem does not define different values for the parameters that will go into Tomcat configuration files. Otherwise, the installation should fail.

Another possible solution is to split Tomcat configuration from subsystem configuration into separate deployment files. When adding a new subsystem to an existing instance only the subsystem configuration is required so the admin will not accidentally change the Tomcat configuration.