Handling external application with Codeigniter

[eluser]Phil Sturgeon[/eluser]
I assume the problem is you are using the default .htaccess with index.php removed and are recieving the CI 404 error when you attempt to view the chart?

Possibly not though, as you haven't really described the problem.

Either way, your files can be anywhere in the webroot, it doesn't matter. Your system folder should not be in the web root though, for security reasons.