This is for issues created through non-JIRA emails:
In a fogbugz case(generated by non-fogbugz user email) you can either comment on it and only fogbugz users can see comments, or you can "reply" to the original email that the case was created with. Those non-fogbugz users get these replies but still cannot see any "comments".
Is there a way to get this functionality in JIRA?
It sounds to me like you may want to have a look at JIRA Service Desk. When you comment on an issue, you have the option to either make the comment internal, or viewable by the customer. Customers do not consume a license on your JIRA instance either, only your Service Desk agents. On a standard JIRA Core or JIRA Software instance, you do have options to restrict comments by Group or Role, but you have to set these up, and every JIRA user consumes a license.
Have a look here for more info, hope it helps!
I've tried Service Desk and it looks like only people set up in Jira (either as a customer or as a Jira user) can see comments. In Fogbugz, you are able to email the person who emailed in the issue, or comment internally. That customer is not set up in Fogbugz at all. Is this possible in Jira?
What happens in Service Desk is that your users (we call then Service Desk agents) are your licensed users. A customer either emails you, or logs a request vie your Service Desk portal. They're created within your JIRA system, but they do not require a license. When an agent replies to a comment, they have the option to keep the comment internal, or make it visible to the customer. If it's visible to the customer, they will receive an email to say a comment has been made on their request. They can either reply to the email directly, or go to the request via the Service Desk portal and respond there. Now the caveat. This is how the latest versions of Service Desk work. In previous versions, all your JIRA users had to be licensed for Service Desk. That's no longer the case in the latest versions, where you can use application access to decide which users can access which application (Service Desk, Software and Core). Your Service Desk customers will not count as users. Therefore it's possible to have 3 Service Desk agents (and only pay for 3 agents) but have them service tens, hundreds or even thousands of customers. Hope that makes it a little clearer?
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