Thing I'd worry about is there is already file-types such as WMA, WMV and mov etc that have interactive links. Unfortunately these have been abused and misused by spammers. Sometimes to malware infested web-sites. Flash and XML .. both have their dangers. Both leave heavy footprints AFAIK (under the surface). But Devs would know better. I might be wrong.

Using more than one protocol to transfer files for security reasons I believe is definitely one way to go. ie: part of a file is transferred using one protocol, another part another protocol. This helps to mask file-transfers, particularly if TLS or other encrypted approaches are used as are already used in torrent file-sharing. TLS has its limits to my knowledge. There are better approaches. For example, Azureus (Vuse) uses some suggestive highly protective approaches that I would like to be seen used within the Gnutella protocol.

Unless you are getting to more of a DC approach, but in an indirect way so to speak. I haven't used that network in years. It would need some kind of protection for the cloud owner/user. A mask of sorts. A guarantee of no form of identification of the owner of the files in the cloud or of any suspicion brought toward them in any such manner.