Oh its totally a client UX thing. Many clients flatten responses. The threading is preserved in the JSON side of things. But many clients dont render the threading.
You can see a "hint" at the threading by checking who is tagged in the reply list usually or by clicking on a message to expand its thread and only its thread.
@freemo Very interesting, do you know if threads are preserved in the metadata if you remove the mentions?
@weston yes should be. every comment has an explicit parent.
@freemo @weston that makes so much more sense ... back with bbs and irc days -- especially irc -- non-threaded conversations could descend the public channel into chaos. If more than a handful of people jump into a conversation, you're re-reading a wall of text to make sense of the overall conversation.
You would eventually get the person who was scrolled back in their buffer and type & send their reply to very old information...
@freemo It could be an issue with client UX then. There are definitely sometimes I reply and my response is in the thread with others, but other times I somehow have forked it and the thread only contains my post and the original post.