We’ve created a Jira Datacenter plugin that uses TransformerFactory class and plugin creates new instances using the following implementation:
factory = TransformerFactory.newInstance("com.sun.org.apache.xalan.internal.xsltc.trax.TransformerFactoryImpl", null);
Initially, this setup functioned perfectly with Jira datacenter version 9.5.1. However, as we moved on to subsequent versions (post v9.5.1), an exception was encountered:
Provider com.sun.org.apache.xalan.internal.xsltc.trax.TransformerFactoryImpl not found
java.lang.ClassNotFoundException: com.sun.org.apache.xalan.internal.xsltc.trax.TransformerFactoryImpl not found by com.myapp.jira.plugin-server 
It’s important to note that this process is initiated by the Jira server itself through the use of PluginScheduler (com.atlassian.scheduler.compat). Interestingly, the very same process operates seamlessly when triggered manually. To get to the root of the issue, we are curious to ascertain whether there have been any modifications to the Java environment or other factors within Jira in the subsequent versions (post v9.5.1), as the problem exclusively occurs during scheduled jobs.