Rocket Chat is currently down for an upgrade to 1.0.0.
it will be back up shortly.
So here’s what happened, the gist of it is that I should have read closer before I updated:
No need to actually look at that but basically, Rocket Chat now requires you use OpLog/Replica sets, which are usually for high-availability (HA) setups, which ours is not, hence why I never bothered to set it up. So this broke our setup until I configured it – which I did.
The upshot is that 1.0.0 of Rocket chat is released 
– with message threading!!!