LimeWire has not modified the Gnutella protocol.

In LimeWire 1.4, we began both using and supplying the "metadata" inserted within query reply packets, as many oher Gnutella cleints do.

This metadata, however, does not represent a "new" protocol. It rather takes advantage of the flexibility built into the existing protocol (whether intentionally, or by accident), although individual Gnutella developers differ slightly in their opinion on this.

The protocol, including metadata, is documented very well in the clip2 document found at:

http://dss.clip2.com/GnutellaProtocol04.pdf.