When you receive a new chat message, there is no notification, and if you don't scroll all the way down in the navigation side bar there is no clue you received it. This happened on TDWTF instance.
Hm that is correct (insomuch that it is a correct interpretation of what is happening)... on desktop we show the chat bubble, but these bubbles are hidden on mobile as there is a lack of screen real estate.
What would be your suggestion here from a design POV?
Idea 1: 2 entries (Notifications and Chats) under Unread in the Navigation pane, with a counter bubble, and clicking on them would scroll down to these itens.
Idea 2: Chats could be more attention grabbing, since someone maybe waiting for you to reply. Something on the left side of the hamburguer menu could be appropriate.
Idea 3: Copy facebook messsenger's idea of an overlay avatar notification for chats, that you can drag to another place, or throw out of the screen to dismiss.
Re: idea 2, we already have something left of the hamburger for active notifications, unfortunately.
and idea 3... good lord I hate the chat heads 馃槵
Another option:
Here's a mockup:

@pitaj How easy is it to swap the menus? Could that be made a toggleable option?
New menu has so many issues now. Better to make it work properly before thinking about toggleable options.
New menu has so many issues now.
I'd recommend you open a new issue for any bugs you're seeing regarding the new sidebar menu. It may not be in master but it'll still help us track them.
Swapping the menus is easy. The hardest part is probably adding the option in the first place.