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The Shopify terms state that if your application accesses the Shopify API and is used by two or more merchants, then you have to give 20% to Shopify.

Do you have any references on there being an exception for apps not installed through the store ? I would be very interested.

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It could be they got special permission for that, I'm not the owner

You make a private app for each customer.

This has been _specifically_ called out in Shopify's recent emails to partners. If the private apps are essentially all the same, it's considered abusing private apps and they may come down on you at some point. Private apps, in Shopify's eyes, are for something like a consultant whom is building one-off apps for clients, not as a way to avoid the store.

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