One way to do it is to have your own implementation of javax.ws.rs.ext.MessageBodyReader and javax.ws.rs.ext.MessageBodyWriter. The package where those implementations reside must be included in the <rest> module descriptor in the atlassian-plugin.xml. In those implementations you can instantiate an ObjectMapper and configure it the way you want.
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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