That’s what I use the App Connector plugin for. I have created a sub-app on a subdomain (data.mydomain.com) where I store data I’d like to have available on all of my sub-apps. As for changes to each unique sub-app, you can make many adjustments to the workflows in the primary app editor so that certain functions are available to each user account or users of a sub-app. I’d say build out an “available features” workflow that limits what adjustments people can make to the app based on certain variables set on their user account.
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