Thank you for reaching out.
Could you please let us know more details about what exactly do you want to compare and clean?
Without those details, I believe that you can use Jira REST API to create a script that would return all the permission schemes details, that you can use to compare to each other.
Please, take a look at the documentation below to know what calls you can use to get the assigned/not-assigned permission scheme details and the roles/groups/users configured for each permission:
Let us know if you have any questions.
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