The Confluence installer is not able to migrate all configuration properties from server.xml to the upgraded installation. You have to do that manually and this is ok for me. However, after the installation it automatically starts Confluence which is going to fail, because it does start with the default context and port.
How can the installer be told not to start Confluence?
By defaul it is not possible for installer to not start Confluence, and in order for Confluence to start the upgrade process it need to necessary for Confluence to start.
I recommend you to try this method in order to upgrade your Confluence.
Hope it helps.
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