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You need to have administrator rights to run them and you need to take care when updating your projects.

Following simple example shows how you can mess the Jira install: you have an existing project, several issue types, and you set up a new issue type scheme which does not contain all the issue types previously in the project. The result is undefined, and most probably Jira will complain and / or will throw exceptions because the set issue type scheme routine does not migrate the existing issues with non-existent types.