What makes the workflows different? It sounds(based on the question title) like you might make it easier for yourself by issuing different Issue Types. It will make workflow management easier and allow you to visualize the difference a lot easier....
You need different issue types if you want different workflows in the same project.
Different projects can have different "story" workflows, but the configuration hangs off project and issue type, so you simply can't have different workflows for the same type in the same project.
...PermissionsStartOnly=true User=www-data Group=www-data ExecStart=/opt/jira/bin/startup.sh ExecStop=/opt/jira/bin/shutdown.sh TimeoutStartSec=120 TimeoutStopSec=600 PrivateTmp=true [Install] WantedBy...
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