> My problem is that after a long time figuring out
> how to get the links from jsp files, I'm having
A mirror is not a copy. You can not get jsp files (server side code) from the
public side of a web server, only the html output.

> troubles with the file structure. I only wan't to
> download pdf and zip files, but winhttrack keeps
You must download the html to get the links.
-* +mime:text/html +*.pdf +*.zip

> saving all downloaded files on the main folder of
> the projects and I know that in the server they are
> not on the same folder.
> 
> Of course, Build options are set to "default" which
> is "site strcuture".

Not possible. Post the start of the log so we know exactly what settings and
url you're using.