With V13 and going forward, the JRE is only included with the client components (full client and workbench-only). Server and agent machines will not have a SCM-specific copy of the JRE so they should not be a problem.
For the full client and workbench-only client, on all platforms except Windows, upgrading Java is not a problem. This can be done as needed. The Workbench-only clients are on Linux OS and MAC OS.
For the full client and workbench-only client on the Windows platforms, you will need to request an Efix in order to upgrade Java on these machines. As of now we don’t have a way to configure it so that Java can be upgraded as needed.