using helpers with multiple applications

[eluser]buggzzy[/eluser]
Hi,
I'm trying to get my configuration to run. Here is my structure:

Code:

domainname.com
-> codeigniter
   -> system
-> docroot
   -> index.php (header Location to default app)
   -> app1
      -> index.php
   -> app2
      -> index.php
-> applications
   -> app1
   -> app2

Now the problem are the helper classes like url helper. The function site_url returns something like that "index.php/app1". Is it possible to get the helper functions work correctly with this config? I think it's always a problem if changes to the folder structure are done, isn't it?

Thanks