One thing that troubled me in the initial version (and still troubles me in the upgrade - probably even more) is the client-side requirement to select the transmission with or without notifications. Perhaps this is just MY opinion/concern; but it seems to me that if there is a server-side workflow process depending on notifications of inbound files, then allowing the client to control that notification unnecessarily introduces potential points of failure. I think there should be a single send button/action on the client side and, if there is a supporting configuration in the control file, then notifications should be sent to the server; otherwise, they should not be sent.
I understand that there may be some folders that may contain some files that are not important for notifications and workflow processing; however, I believe there could be some server-side intelligence and soft-coding that we could configure that would enable us to filter out the notifications of transmissions for which we don't care. I think with all things considered, it would be better to over-notify to the server than to allow workflow processing problems from fat-finger mistakes or other human flubs on the client.
Hope this helps - thanks again for the enhanced version - I'm looking forward to the next set of enhancements!