Status update (3/31): The server is solid. The search index is caught up. We fixed the most visible of the instances of HTML codes appearing on client sites (we'll do a more thorough cleanup of the XML templates soon). Permissions issues appear to be resolved. All is well with the world. We still have 7 moderate issues (non-blocking but ugly) and 20 low priority issues. We'll solve all of those in due time, at which point we can start tackling wishlist items.
Thank you everyone for your forbearance and apologies for the frustrations — this is the second such crisis we've endured with what otherwise has been a very stable system, and we've learned a lot which we intend to put toward avoiding these sorts of ground-up relaunches in the future. Every developer at GT probably has at least an inkling of the idea that the best way to relive every bug you've ever solved is to start over from scratch. We know it in our bones by now.
If you have issues you want to see addressed, the Mercury issue queue is the best place to go. You can follow issues and see when we have updates or solutions. If you have an issue that is not already the queue, you can add it directly there or email email@example.com. Our apologies to anyone who has been submitting issues to the support request form and wondering why we weren't responding—the site was not sending us emails about these.
FYI: If you created an item recently and noticed keywords or other tags have disappeared from it, this was a side effect of fixing the issue that was causing taxonomy terms to spontaneously clone themselves. You might need to re-add the missing tags.
Drupal 9+ Mercury Reader users: Eric Neville solved some issues with the reader module. Grab 2.13 asap (Composer should pick it up).
Drupal 7 Mercury Reader users: Michael Sheldon was kind enough to patch a number of issues with the Drupal 7 version of Mercury Reader which caused it to be unhappy with the new system. The new version is available here: https://github.gatech.edu/ICWebTeam/hg_reader-7.x/releases/tag/v2.20