Does the ability exist to set preferences on what notifications a specific User receives? E.g. if the User only wants to receive notifications for JIRA's that are assigned to them
No, the notifications are set by the notification scheme.
The user can set the format (text or html) and whether they get emails from their own actions (e.g. if the "edit" event sends mail to "all developers" and I edit something while I'm a developer, I can turn off the mail that says "hey, nic just edited this")
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