You can't deploy .war files on Atlassian Cloud - it's a managed service, not a hosting provider.
Atlassian no longer provide .war builds for their applications, it's strongly recommended that you deploy them with the installers.
But if you must use a .war, then all you need is a web application server like Tomcat, Glassfish, jboss etc.
I have multiple projects that use variations of the same base workflow. The variations depend on the requirements of the project or issue type. The variations mostly come in the form of new statuses ...
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