These are preliminary animated mockups. Subject to change.

List of Apps > List of Threads

Notifications are grouped by app, and threads are combined into single bubbles. There's also explicit expanding/collapsing in the popover to show the full content and reveal actions.

Expanding the Thread

Notification can expand if it contains a thread. In more busy configurations, the App header may scroll out of view.

Collapsed List: New Notification

When a new notification arrives into a collapsed stack, the message stack gets compacted, doesn't indicate real number of messages in thickness.