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I've added the embedding that you suggest. Actually,
I had implemented something like this almost a year ago
included in the distribution as a script called 'embed'.
But it broke, and I didn't like how it looked. So
just last week I worked on it some more.
Currently it doesnt include the links for adding responses
below each embedded response, but that should be easy
to add. You can specify the depth of embedding you
want, and the depth of remaining subtrees displayed after each
response. There is more work to do on it, but I'll let
it go out as is.
I would disagree with a claim that annotations must
be embedded. Mere references, as in the tree of responses
at the bottom of a page are annotations too.
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Mostly implmented 
Embedding Responses within existing HTML file
(Doug Dunlop)
