Documentation for JIRA 4.1. Documentation for other versions of JIRA is available too. 
For information on Atlassian's recommendation on JIRA and Confluence installation, see Installing Confluence and JIRA Together.
You may also wish to read Integrating Jira and Confluence for helpful information on integrating JIRA and Confluence.
Do not deploy multiple Atlassian applications in a single Tomcat container
Deploying multiple Atlassian applications in a single Tomcat container is not supported. We do not test this configuration and upgrading any of the applications (even for point releases) is likely to break it. There are also a number of known issues with this configuration (see this FAQ for more information).
We also strongly recommend that you do not deploy multiple Atlassian applications in a single Tomcat container for a number of practical reasons. Firstly, you will need to shut down Tomcat to upgrade any application and secondly, if one application crashes, the other applications running in the Tomcat container will be inaccessible.
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