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

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