Problem

JIRA is not starting even after displaying the following messages in the application and catalina.out log

17-Apr-2019 13:18:17.236 INFO [main] org.apache.catalina.startup.Catalina.start Server startup in 131668 ms

Diagnosis

Diagnostic Steps

After verifying the application log, we can notice that the web.xml file is modified with the message Modified Files: WEB-INF/web.xml. While we know that the file has been modified, to troubleshoot further we can add the following logging to gather additional information

Modify the logging.properties file in <jira_home>/atlassian-jira/WEB-INF/classes/ and add the following. This would enable catalina to log additional information while parsing the web.xml file

org.apache.catalina.core.ContainerBase.[Catalina].level = TRACE
org.apache.catalina.core.ContainerBase.[Catalina].handlers = java.util.logging.ConsoleHandler

Cause

We noticed after enabling the above logging that web.xml file had some additional filters from older JIRA version added which did not have the corresponding class files in the newer version. An error message similar to below would be seen. Then those filters identified by the log can be removed from the web.xml file.

17-Apr-2019 13:17:53.129 SEVERE [localhost-startStop-1] org.apache.catalina.core.StandardContext.filterStart Exception starting filter [prevent-ie-accept-css-vulnerability]
 java.lang.ClassNotFoundException: 

Resolution

Do not modify the web.xml file under <jira_installation>/atlassian-jira/WEB-INF/ unless there is a need for it or replace it from a different version of JIRA.