When you’re replying, you can reply to the bottom of a thread (by using the blue button at the bottom) for a linear flow, or reply to a specific post (by clicking the reply arrow beside an individual post).
In both cases, replies are displayed in a linear, chronological order. It seems like there should be the ability to display these in a threaded/tree hierarchy like reddit. But there isn’t. The software authors seem pretty adamant about not providing this choice. So for right now, everything’s linear.