>  - note that for java classes, 
> there is a huge problem: httrack can't change the 
internal class structure files (no binary patch)

Yes, but here it really does find all the relevant classes!
I guess that in many casses people will hold a couple of 
classes in the same directory. So the only point is, that
 -N1003 puts everything it finds in the same flat directory 
as promised. I do this by hand (Perl) now, and it works.