Just wanted to note that there are two threads covering the workspace subfolder suggestion, the other being recently commented on and located here:
What I wonder is how Coda hasn’t raised the priority on this as they use Coda for all their internal processes. My assumption is that they are using many workspaces, and thus organizing their documents under relevant workspaces. This doesn’t seem like a intuitive solution for regular users however who don’t want to pay for the same maker many times across workspaces, or manage billing across many workspaces.