We have to update the JIRA home documentation for the WAR/EAR JIRA version.
The recommended way to set the JIRA home directory is to edit the jira-application.properties file.
I suggest something like this:
"Specify the location of your JIRA Home Directory:
edit 'edit-webapp/WEB-INF/classes/jira-application.properties' and set the jira.home property to your JIRA home directory."

This has to happend BEFORE the customer builds the WAR/EAR file.