[eluser]Randy Casburn[/eluser]
[quote author="callumd" date="1225600483"]Randy -> I am assuming that the path to index.php is the "root" folder, yes?[/quote]
Bad assumption. You'll need an index.php file for each application folder you create. Or, in other words, for each application you create.
[quote author="callumd" date="1225600483"]If so, why does the default "installation" of CodeIgniter hang the system folder off the root directory?[/quote]
Because the CodeIgniter developers cannot read our minds. CI is very flexible in how it allows us to do our layouts. There are many, many ways to accomplish what I've shown you here. Many others do things differently. The CI developers cannot determine in advance which to choose, and at the same time have been gracious enough not to force us all into one solution.
[quote author="callumd" date="1225600483"]As part of the CodeIgniter set up process, am I supposed to grab the application folder, and move it up one level in the tree structure?[/quote]
No, as part of your development process you are supposed to decide if you want to provide a secure software installation in an environment full of miscreants, pirates, and nasties that may be interested in destroying your data, server, or stealing your information. If you do, then you should move both the CodeIgniter system directory and your application directories to a file system location that is outside your webserver's DOCROOT and not accessible by your webserver's user account.
I hope that answers your question.
Randy