You have splitted Alerts vs Messages Notification systems. But there is a problem. For example, the alert "User:X thanks you for editing Y on page Z" does not have links from editing to diff page and to page Z. Also, browser right mouse menu "open in other tab/window" does not exist.
Thanks.
Description
Description
Event Timeline
Comment Actions
I use it too. And it still does not work for me. If I need the links I open the page with all notifications, the links are there as usual.
Comment Actions
This works the same in the old and the new systems: the entire notification is a link to the diff (and right-click works now), and the user name is a link to the user. The page is linked in Special:Notifications, but not in the popup; this has always been the case. Renaming the bug to reflect that.