Added a new section 3.5 covering precisely this topic, pointing to more detailed
interception rules in 4.3.1 and encapsulation rules in 5.3.2. In particular,
added  a magic number to the Q-mode encapsulation in Section 5.3.2 to minimise
the risk of incorrect interception of UDP datagrams as GIST packets.

See http://nsis.srmr.co.uk/cgi-bin/roundup.cgi/nsis-ntlp-issues/issue184 for the
revised encapsulation text including the magic number (overlapping issue).

New section 3.5:

3.5.  Effect on Internet Transparency

   GIST relies on routers inside the network to intercept and process
   packets which would normally be transmitted end-to-end.  This
   processing may be non-transparent: messages may be forwarded with
   modifications, or not forwarded at all.  This interception applies
   only to the encapsulation used for messages which initially probe the
   network, for example along a flow path; all other GIST messages are
   handled only by the nodes to which they are directly addressed, i.e.
   as normal Internet traffic.

   Because this interception potentially breaks Internet transparency
   for packets which are nothing to do with GIST, the encapsulation used
   by GIST in this case (called Query-mode or Q-mode) has several
   features to avoid accidental collisions with other traffic:

   o  Q-mode messages are always sent as UDP traffic, and to a specific
      well-known port allocated by IANA.

   o  The first 32-bit word of the UDP datagram payload contains a magic
      number.

   Even if a node intercepts a packet as potentially a GIST message,
   unless it passes both these checks it will be ignored at the GIST
   level and forward transparently.  Further discussion of the reception
   process is in Section 4.3.1 and the encapsulation in Section 5.3.2.