The jira-application.properties file is a potential source of problems.

• Some of the properties are difficult to configure correctly (for instance jira.date.time.picker.java.format/jira.date.time.picker.javascript.format).
• It is also difficult to determine which of those properties you have changed in your installation, so you can apply the changes when you upgrade.
• We also see customers that forget to update these properties during an upgrade, which can be quite problematic (a typical example is forgetting to update the jira.projectkey.pattern property, which results into users not being able to see issues that do not much the current pattern)

I think most of those properties should be stored in the database, with Jira providing a user interface to modify them. That means that we could do proper validation of the entries, and the values would persist during upgrades.