You need to be clear about what you are talking about here:
- Apache is a web-server
- Apache Tomcat is an application server (mostly just referred to as Tomcat)
- Apache is NOT installed with JIRA
- JIRA runs (mostly) on Tomcat, and that is bundled into all the installations.
- Tomcat is not configurable during installation because most users can use the settings Atlassian provide.
If you can't use their settings, then you fall into a group of people who need to spend the time configuring and understanding Tomcat, and that means changing Tomcat setting files on the file system. It's all done under the directory in which you installed JIRA
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