Summary

Some of configuration of Jira is stored in Jira installation directory. In order to change Jira's configuration it is required to modify existing configuration files.

Because those files can change with every Jira release, after upgrade admin should reapply every change in those configuration separately. This is complicated process and it's common practice to just replace the new configuration with the one copied from old Jira's installation.

Splitting the user configuration out of existing configuration files would simplify the upgrade experience and make it less possible for Jira to be incorrectly configured after upgrade.