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March 19, 2018 edited
You can copy or delete these files as you wish. But in regards to deleting logs, this tends to make troubleshooting problems in Jira more difficult. The logs in the /var/atlassian/jira/log/ folder will typically automatically roll themselves in order to limit size.
However the logs generated directly by tomcat in the /opt/ folder cannot be rotated out-of-the-box for Jira. So I have seen a many catalina.out files that are several GB in size that can cause storage problems. I would recommend trying to follow the KB: How to rotate the Tomcat catalina log file. This way you can still keep some data while rotating the log so that the file does not grow to an enormous size.
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