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It is strongly recommended that you do not install both licenses at once, as this might yield unwanted results. For example, consider that you have an Atlassian License with the support date expired and one valid cPrime License. In this case you cannot update the pluginapp, because the Atlassian License is checked first and its support date is expired.
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After generating the license key, all you have to do is access the Administration > Plugins section in your Jira instance and paste the key into the corresponding plugin app textbox.
For more information see UPM documentation.
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