We are going to upgrade out JIRA instance from 6.2 to 6.4. what is the best method of upgrading plugins already installed on the existing system ? if i download the compatible version and put into plugins folder, would it be a problem ?

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In short the best way to do this is by downloading JIRA 6.4 and running the file, when prompted to choose between creating a new JIRA installation or upgrading an existing installation, choose theUpgrade an existing JIRA installation option.

Check out this link for all the details.

Check out this link for upgrade notes.

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