Customizing Craft Commerce Template Paths
You'll need to keep any action URLs as commerce/, as these point to controller actions inside the Commerce plugin, not templates in your store directory. So if you find:

&lt;input type="hidden" name="action" value="store/cart/updateCart"&gt;


That will need to be restored to:

&lt;input type="hidden" name="action" value="commerce/cart/updateCart"&gt;