Separating the main "/system" folder out of WWW root for multiple web apps?

[eluser]taewoo[/eluser]
Hi all.
I have multiple web applications (that do totally different, unrelated things) written in CI. It seems to me the main CI "plumbing" should be removed from the WWW root since this stuff doesn't change (unless official versions of CI are released in which case update is done - but this occurs rarely).

Is there a "clean" way to host multiple applications using one CI copy/instance on my web server?