Tricky Multi-site config

[eluser]TheFuzzy0ne[/eluser]
Yes, it's possible. This is why you shouldn't ever edit the core. In your case, you can just move the system directory to somewhere that's easily accessible by all of your apps, perhaps the Web root, or just outside the Web root. Then edit your index.php for all your apps to reflect the new application and system directories. You can also put your application directories out of the Web root if you choose to do so. The only thing that needs to be in your Web root, is the index.php.

EDIT: Here's an example directory structure:

+-system
+-app1
| +-application
+-app2
| +-application
+-app3
| +-application
+-htdocs
+-app1
| +-index.php
+-app2
| +-index.php
+-app3
+-index.php