Validation Error: Invalid Bundle. The bundle at … contains disallowed file ‘Frameworks’

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Turns out the error is related to using Swift (both the app and the extension make use of Swift).

For the app, I had to set:

Embedded Content Contains Swift Code: YES

and for the extension:

Embedded Content Contains Swift Code: NO

Xcode 8 and 9

Looks like this has been renamed to Always Embed Swift Standard Libraries in Xcode 8 and 9. So, for the app:

Always Embed Swift Standard Libraries: YES

and for the extension:

Always Embed Swift Standard Libraries: NO

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