Okay, it's the end of the day -- here's the list of fixes that are on Wikimedia.org now. Assuming it still looks stable tomorrow, these will get pushed to enwiki tomorrow afternoon (PST):

* Alerts tab is the default when you open the flyout, unless you’ve only got new Messages notifications and no new Alerts.
* Bundling "created a new topic" Echo notifications, so you don’t get multiple notifications for the same board at once.
* "No formatting for notification" errors are reported, but not displayed in the notifications.
* When Flow notifications are turned off in preferences, user doesn't get notification for Flow mentions.
* Email notifications bundled per topic, limited to once every four hours.

The other items listed above are still being worked on, and the plan is to get those out later this week. Thanks to all of the people who've posted bug reports, and I apologize for the distractions and inconveniences with this release.