> I am trying to download a web site full of Java JSP's and 
> Servlets. It is also running an application server which 
> assigns sessions ID's. 
> 
> My first problem is getting past the login screen to the 
> https secure part of the site.

See 'Add URL'/'Capture URL'. This is not obvious to do 
(you'll have to change the proxy settings), but it 
sometimes work.

> The second problem is the session ID's, which are checked 
> with every new page you ask.

Normally cookies are handled automatically ; except when 
the site is reseting the session, or does not accept scan 
per levels (see related thread here) - in the worst case, 
the site will send a new cookie each time a page is 
requested, generating useless data. But this may work, too. 
It depends on the way the site is designed.