Imagining if the signalling and presence information are handled, how, is it possible to use Webrtc datachannel as the underlying file transfer protocol instead of lync's own File transfer protocol (TFTP) to transfer file from a lync client(web app) to a non-lync client (web app with webrtc enabled)?
Lync provides Client interoperable programs. In that way it can be easily attached to any web application for presence information.
Client interoperability example:
Application: http://lyncpresence.orbitone.com/
Source: http://lyncwidget.codeplex.com/
Unified Program (includes interoperability of Lync server with all networks):
http://technet.microsoft.com/en-us/library/gg398996.aspx
http://technet.microsoft.com/en-in/office/ocs/bb735838.aspx
http://technet.microsoft.com/en-us/lync/gg131938.aspx