When storing a new model, the modeler API always keeps the raw data in third-party settings just because it doesn't want to store a separate config entity which would be orphaned in case the main entity is invalid and can't be stored. Or another reason is that when modeler API sets the raw data, the ID of the model may not be available yet.
When saving a new model and the configured storage method is set to a separate file, make sure it gets saved again so that this will be corrected.
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1.0
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Issue #3535238 by jurgenhaas: Saving new model always stores raw data in...
