Since version 6.2.0 of Jira Misc Workflow Extensions app, there is vendor-supplied integration between the app and Configuration Manager.
Script Runner support:
Configuration Manager for Jira currently supports all post functions, validators and transitions provided by Script Runner. This means that when these scripted items have references to other configuration objects (e.g. a property for a custom field, role, status, resolution, etc.) Configuration Manager will resolve these references and handle them appropriately during deployment – i.e. they will be properly matched or created on the target system. Configuration Manager does not move the script files themselves.