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The GitHub API now has an endpoint that will let you mark the ghost notification as done! This marks your first notification as done:
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Product Feedback
Body
Context
It's the second time I face an apparently known bug that creates "ghost" notifications: on the Notifications page, in the list of repositories a repository appears, but when selecting it to see its notifications, an empty table appears, even if it shows there is one unread notification.
Workaround
The GitHub support team suggested a hack to mark all notifications as read via the API, but this will only mark the ghost notification as read, not as done.
Issue
The repository will continue to appear in the list... And according to the support team it will disappear after 4 months because it seems that read notifications older than 4 months are not listed anymore in the Notifications page.
I confirm this works, but it means having that repository listed for 4 months...
It's frustrating and not practical to have that repository persist with a ghost read notification that we can't mark as done neither via the interface neither via the API
Proposal
As a workaround but quite logical to me, I'd suggest to simply remove all notifications related to a repository when un-watching it.
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