Is there a way to query or run a report that would show me the Workflow, Permission and Notification Scheme (Etc) for all Projects or a subset of Projects? Thank you! We are very Project heavy and I need to validate setups for hundreds of projects.
Have a look at the REST API docs. I think most of what your looking for is there.
Project details (workflow, roles, etc) - https://docs.atlassian.com/jira/REST/6.1.7/#d2e91
But I am not sure about notifications, permission schemes. You may need to interact with the UI for that using a tool like curl to potentiall automate the retreival of content.
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