Getting "application" folder out of "system"

[eluser]Thorpe Obazee[/eluser]
[quote author="jdfwarrior" date="1243244937"]
What he's saying is.. is that its not relative to the system folder. In another installation I had. I removed application from system and renamed it app, and renamed system to ci. I went to index.php and just updated the names, I didn't change path to show that the app folder wasn't in the system folder. You dont have to put ../ in from of it.[/quote]

I think Fuzzy was asking about what the guy means by 'compatibility issues' in the previous post.