Set the correct URL under admin -> system -> general configuration
It should be set to the url your users will be accessing the system under. A lot of people run Atlassian stuff behind proxies, but that rule stands - your users will be using a proxied url, so you set the base url to the proxied url, not the url of the JIRA server.
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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