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Note that the Application Links plugin is bundled and shipped with the Atlassian applications. You cannot install it yourself. Applications Links is bundled with FishEye 2.4, Confluence 3.5, JIRA 4.3, and all later versions of those applications. In addition, Bamboo 3.1 is compatible with AppLinks. You can configure JIRA-to-Bamboo links via the JIRA administration screens.
The Quick Start Guide provides instructions on how to set up the most common application link configuration.
The administrator's guide is for administrators who want to configure application links for the applications. The guide contains information on adding a new application link, configuring the authentication for an application link, setting up project links and more.
These resources are for developers who want to develop with the Application Links plugin. Take a look at the Development Hub.