I have a lot of projects using the same Field Configurations and so cannot change them. However, I do occasionally want to make an exception in some project and make a field that is required (according to the FC) optional.
Is there a way to do this using Script Runner?
No, the field configurations are handled by the internals of JIRA.
The Script Runner can execute code that can blank out mandatory fields as part of a script, but it can't bypass it in the UI, because of the structure. When you open up a create/edit page, JIRA hands the browser an indicator that the field is mandatory to tell the user that it's needed. When the user submits their data, the data goes to the internals, which check the field config and hand back a failure if a mandatory field is empty. There's no way to insert any scripting in that process.
If you reverse the concept though, then yes, you can do it. Make the field optional in the field configs, but then use a "behaviour" to make it mandatory when you want it to be mandatory. Script Runner can do this because it can hand the browser code that makes the field mandatory in the browser, before the field config check.
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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