I would like to see something similar to JIRA when repling to comments. In JIRA, replies are always linked to the comment I replied to (visualised by an intend). Currently only the author of the commented is @mentioned.
It would be more visible which comments are replies and which not so discussions (comments and according replies) would will be more visually coherent. The cool thing within JIRA also is that you can collapse these discussions.
Keep up the awesome work :)