This is a relatively minor update, but one I've been meaning to do for a long time. By default, comment notifications will now be automatically marked as read if you interact with the comment (currently, by: voting on it, replying to it, labelling it, or bookmarking it). This will happen regardless of where you take the interaction, so if you're viewing the thread itself and interact with comments that you also had notifications for, they will be marked read.
When you're on the unread notifications page, even though actions are resulting in the comments being marked read, they won't disappear like they do if you click the "mark as read" button manually. This is so that you can take multiple actions if you want (such as voting and then replying). However, if you reload the page, they will disappear.
If you don't like this behavior and would prefer to continue marking all comments as read manually, you can go to the Settings page and disable "Automatically mark notifications read when you interact with the source comment".
I've bumped everyone back up to 10 invite codes as well, which you can get from the Invite page.