Would it be possible to support recursive graphs in protobuf-net, as a implementation-specific custom message extension? For example, if protobuf-net could automatically insert an "optional int32 uniqueID = 1000" field in to each message, it could store an auto-generated unique identifier for each object. Then, if you come across a previously serialized object, you need only read/write the uniqueID field and leave the other optional fields blank. The protobuf-net deserializer could output the previously constructed object. The uniqueIDs would only be valid for a defined scope, eg. one contiguous wire message.
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