> Same issue on sites with navigation generated by 
Javascript. 
>  Often it will fail -- in HTTrack and search engines.

Yes, and the main problem is because javascript files can 
be accessed from multiple sources.

Example: if you have

/foo/index.html
/foo/image.gif
/bar/deeper/index.html
/bar/deeper/image.gif

And from the two html files, a call to a "/bar.js", which 
loads the image "image.gif"
In /foo/index.html, this will result in 
loading /foo/image.gif. And 
in /bar/deeper/index.html, /bar/deeper/image.gif.

I'll have to find a workaround -- maybe setting 
the "working directory" to the caller one ; hoping that the 
filenames will correctly match if the case above is 
encountered.