What is main difference between Catilana.out and Jira.log files? what is the purpose for these files?
The main difference is that they're for two totally different things.
Jira is an Application that needs to be run by an "Application Server". Tomcat is an "Application Server".
Catalina.out is the log for Tomcat. It tells you what Tomcat is doing.
Atlassian-jira.log is the log for the application. It tells you what Jira is doing.
(Note that both of them live alongside similar, related logs in each directory, but the Server vs Application distinction is the same)
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