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It looks like this issue has gone away with the new beta version of Xcode 12. Thanks for looking into this.
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My app is so old, the sqlite file is stored in the Documents directory and not the Library/"Application Support" directory as the new files are. I've created a struct for every entity in my core data and made the structs Codable. NSManagedObjects are not Codable. There were some issues as NSNumbers are not Codable, but I replaced those with Ints in the structures. I have written methods which stuff the structs from core data and have written methods which stuff the core data entities from the structs. I've also written methods to encode and decode the struct data using the JSON encoder/decoder. The plan is to grab the data from the old directory, put all of the core data objects into structs and then put the struct data into the new store file. That will sync the data. This will require a separate ManagedObjectContext for the old data. I also plan on saving the encoded data out for the user in iCloud Drive as backup files and will allow the user to restore their data from a backup file. Whew!
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It doesn't happen when the .wheels style is used. But it does in .automatic and .inline.
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I have uploaded my project. The title of the report is 'CompositionalLayout] Invalid absolute dimension, must be > 0.0. (Xcode 12)'.
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If you add a bool, or a uuid in my case, then you will have double entities. But you can then delete any entity without a uuid (or bool) and that should sync to the other devices. I don't know this for sure, but it seems reasonable.
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Try adding a UUID attribute to all of your entities in the model. You'll have to migrate, but that should be easy as it's only adding one attribute per entity. Then fetch every entity and add the UUID to every managed object. Then save. I have done this with a sample project and it seemed to work. You might want to try this on an experimental project first. Another way would be to have two managed object contexts and copy each one and save in the context with the CloudKit store. Although relationships are an issue.
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I'm thinking about creating a UUID attribute and adding that to every entity in my core data model. Then, I will fetch every entity and add the UUID to it. And then save. Hopefully, that will trigger a sync of the pre-existing data.
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Adding a UUID attribute for each entity in my model and setting a uuid worked for me. My pre-existing data synced as a result.
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This happens when running under iOS 13, but does not happen when running a simulator under iOS 12.2 for example. I've submitted a bug report.
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I hope you've mentioned this to Apple in a feedback.