Codeigniter はソース パス全体を圧縮します。
宛先フォルダーのみを圧縮する方法は?
この可能性を
$folder_in_zip = "/"; //root directory of the new zip file
$path = 'games/SDK/com/';
$this->zip->get_files_from_folder($path, $folder_in_zip);
$path = 'games/wheel/';
$this->zip->get_files_from_folder($path, $folder_in_zip);
$this->zip->download('my_backup.zip');
再帰なし
<?php if (!defined('BASEPATH')) exit('No direct script access allowed.');
class MY_Zip extends CI_Zip 
{   
    /**
     * Read a directory and add it to the zip using the new filepath set.
     *
     * This function recursively reads a folder and everything it contains (including
     * sub-folders) and creates a zip based on it.  You must specify the new directory structure.
     * The original structure is thrown out.
     *
     * @access  public
     * @param   string  path to source
     * @param   string  new directory structure
     */
    function get_files_from_folder($directory, $put_into, $recursion = false) 
    {
        if ($handle = opendir($directory)) 
        {
            while (false !== ($file = readdir($handle))) 
            {
                if (is_file($directory.$file)) 
                {
                    $fileContents = file_get_contents($directory.$file);
                    $this->add_data($put_into.$file, $fileContents);
                } 
                elseif ($recursion and $file != '.' and $file != '..' and is_dir($directory.$file)) {
                    $this->add_dir($put_into.$file.'/');
                    $this->get_files_from_folder($directory.$file.'/', $put_into.$file.'/', $recursion);
                }
            }//end while
        }//end if
        closedir($handle);
    }
}
この質問からのこの抜粋