As part of the process of migrating to checkout extensibility, Shopify may prompt you that the Shogun app needs updating ahead of the switchover for your store.
Shogun is Extensibility compatible; however, the necessary changes can only be made after you make the switch.
When you have successfully updated to Checkout Extensibility, a prompt will appear at the top of the Shogun dashboard that looks like this;
Clicking 'Update Permissions' will launch a second prompt that looks like this;
This will send you back to Shopify to approve new permissions that will ensure that Shogun Analytics, A/B testing, and Personalization continue to function correctly and collect conversions and sales data.