You would move all the ZenCart files that are in /your_shop_folder......to the root of your site.

then edit 2 configure.php files
/includes/configure.php
/admin/includes/configure.php

these files contain references to your current folder in the form /your_folder/
Code:
  define('DIR_WS_CATALOG', '/shop/');
  define('DIR_WS_HTTPS_CATALOG', '/shop/')
you correct all occurences that reference the folder removing the shop/ entries so in the above example you end up with
Code:
  define('DIR_WS_CATALOG', '/');
  define('DIR_WS_HTTPS_CATALOG', '/')
Save these and replace the correct file to the reapective location.