To debug and resolve issues with a Jira app not working reliably after an upgrade, you can use several methods. One effective way is to inspect the catalina.out logs for stack traces, as this file contains application server logs that can help identify errors and issues (option A). Another useful method is to set package com.atlassian to Trace logging level, which will provide detailed logging information that can help in diagnosing the problem at a granular level (option C). Setting the logging level to FATAL (option E) is not helpful for debugging because it only logs critical errors and omits useful information needed for debugging. Enabling the SQL log (option B) might be helpful in some contexts but is not directly relevant to app reliability issues. Adding the app to the logger (option D) might assist, but it is not as impactful as the chosen methods.