> In those cases where a Web's links point to itself,
> but using a trunucated host name ("bob.com" instead
> of "www.bob.com"), is there a way to rewrite such
> links to "reunite" these files under the propoerly
> formed host name?
Try the URL Hack option.  From the help doc:

%u  url hacks: various hacks to limit duplicate URLs (strip //,
www.foo.com==foo.com..) (--urlhack)