Avoiding massive controller: where to put individual files

Firstly, have a nice choice with CI

for your massive php file is all stored in same folder (not root folder), so I purpose that you can modify your .htaccess file to ignore rewrite url for that folder. so you can have 2 systems (1 is CodeIgniter and 1 is your old AJAX gateway) in a same time.

This is an sample of .htacess file

RewriteEngine on
RewriteCond $1 !^(index\.php|images|robots\.txt|assets|YOUR_FOLDER_PATH_HERE)
RewriteRule ^(.*)$ /index.php/$1 [L]

hope that this is what you need

I truly appreciate your thoughtful response. However, I do intend in this project to adapt all of my code to proper CodeIgniter-based concepts. The old code utilizes Joomla code objects so it must be essentially rewritten. The question is not so much how I alter the URL mapping, but rather where do these files go in the directory structure of CI? They are not controllers. Do they belong in the library directory? Or core directory?