How can we make sure that personal information in a PDF is secure? For example, a document that is only meant for the assignee or agent to see?
Could you explain what this has to do with Atlassian stuff?
If a document has been added to an issue as an attachment, then every user with enough permissions to see the issue will also be able to see its attachments.
So, you can either control who can view the issue, or add a link to the confidential document allocated in an external tool from which you can control who to share the file with.
You can password protect the PDF during creation, although that comes with the issue of how to deal with the password.
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