We want to maintain single workflow scheme which can contain two different workflows for a single issue type.
The ideal scenario which we are trying to achieve is to allow certain projects to edit those project specific workflows and the other generic workflow which are shared among other should not be editable.
Is there a way we can have this done
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No, you cannot do this, the whole point of the issue type is that it enables configuration points, such as "which workflow to use". Multiple workflows for a single issue type would be nonsense, it would actually be "choose workflow based on something other than issue type", which makes the issue type pretty pointless.
You can do it by project of course. The workflow scheme says "in this project, use these workflows for these issue types", so if you give different projects different schemes, you can say stuff like "in project A, use workflow Z for bugs, and in project B, use workflow X for bugs"
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