Documentation for JIRA 5.0. Documentation for other versions of JIRA is available too. 
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Please follow the JIRA general upgrade instructions, plus note the following:
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In addition to the above, please read the Upgrade Guide for every version you are skipping during the upgrade. The complete list of Upgrade Guides is available here.
Please note that older versions of the Crowd client, (i.e. version 1.2.1 or earlier), can interfere with the correct operation of the Trusted Applications feature. If you are enabling Trusted Applications and using Crowd, please ensure that your Crowd client is version 1.2.2 or later.