Issue: Spotfire server upgrade fails and the below error appears in the upgrade tool.

Internal error.
java.lang.IllegalArgumentException: 'other' has different root

Check the upgrade-details.log and you can find the below error (Example)

INFO 2024-08-26T16:05:02,154 tools.upgrade.UpgradeManager: Successfully copied the bootstrap.xml file.
TRACE 2024-08-26T16:05:02,167 tools.upgrade.UpgradeManager: Entering method com.spotfire.server.tools.upgrade.UpgradeManager.copyFiles(UpgradeContext context)
DEBUG 2024-08-26T16:05:02,261 tools.upgrade.UpgradeManager: Found configured value 'E:\tibco\tss\12.1.0\tomcat\logs' for log.dir in C:\tibco\tss\12.1.0\tomcat\spotfire-config\log4j2-custom.xml
ERROR 2024-08-26T16:05:02,261 tools.upgrade.UpgradeManager: Internal error.
java.lang.IllegalArgumentException: 'other' has a different root

The error indicates that there are some modifications done to the "log4j2-custom.xml" file. For example, in the above log the path value of "log.dir" in "C:\tibco\tss\12.1.0\tomcat\spotfire-config\log4j2-custom.xml" has been modified as "E:\tibco\tss\12.1.0\tomcat\logs".  Revert to the default value that matches "logs", which resides in the same directory as Spotfire installation. Then restore the database backup which was taken before the upgrade and run the upgrade tool.