Hello Jamie Echlin,
at the moment lastest the script-runner is not complatible with JIRA 6.0m09-3 (EAP).
When you plan to fix this?
(Our workflow is very dependend of Script-Runner)
2.1.2 which is on marketplace now is mostly compatible with jira 6.
I say mostly because there are a few built-in scripts that have not been tested, mainly because I'm waiting for a compatible version of greenhopper.
But, you should test your scripts, some of them may need some tweaking due to API changes. I'll write something up when I have some suggestions.
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