Currently we only have "reply" button for inline comments but not for the "main" comments (posted through the comment box at the bottom of the page).
The problem: if we have a pretty long diff, whenever we want to reply to a comment, we have to scroll all the way down to the bottom to write the reply, and if we want to go back to look at the previous comment again, then scroll all the way up... then down again. This can get pretty annoying sometimes.
We have thought about a few solutions (alternatives include moving the comment box to the top before the actual code), adding a reply button seems easiest and most reasonable.