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You can add more than one instance of the same application to your Application Links suite. For example, you can include two Confluence sites into your suite of Application Links applications. This is described in More about Adding Applications.
There must be one primary instance of each application.
If there is only one instance of a particular application, the primary instance will by default be that single instance. If there are multiple instances of a particular application, the primary instance will by default be the one added first.
The primary instance is the default instance that is used if no project links are configured for a project.
You can manage your applications via either Confluence or JIRA.
Screenshot: Specifying a primary application instance
Adding and Synchronising Project Links via JIRA
Application Links Administration Guide
Application Links User Guide