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Am trying to migrate From rally to Jira in process i have tried to create a hierarchy to match the hierarchy in rally, According to our Jira portfolio hierarchy configuration. Can we create a separate hierarchy for different projects as we are working on various hierarchies for different products.
No, the hierarchy is shared across the entire Jira instance.
I don't know if it is relevant to your use case, but you can map different issue types to a single hierarchy level. By default you have
You can add additional levels above the Epic level and then map different issue types to those levels. But you cannot have Epics at one level in one project and at another level in another project.
For a bit more background, see Portfolio documentation.