Segregate Atlas UI Theme and Custom Theme

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Hi everyone, I was wondering whether it is possible to segregate the Atlas UI theme and your custom themes. The idea behind this is being able to update the Atlas UI Module while keeping the changes made by your customization.   The problem right now is, that you can only set one UI resource package: It also says in the documentation that "[.…] it will automatically overwrite the project’s theme folder with its own theme files." So currently I do not really see how to efficiently keep your custom style with new versions of the Atlas UI. Also it would be nice to be able to combine multiple custom styles or distribute styles for specific use cases through the app store.
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I’m also interested in this topic and wondering if you have learned anything best practices you can share?

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