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Fixed in 2017.1.X
Scenes looses references to scripts from "non Editor" plugins (assemblies)
1. Open project attached.
2. Open scene "FullDemo" (Assets\Koreographer\Demos\Scenes).
3. Press play.
Expected result: Scene will work without problems.
Actual result: Errors with "null reference" appears. Saving the scenes results in serialized data being removed from the scene files.
In Unity 5.6b5, the API Updater appears a bit earlier in the Package Import process. Unlike in b4, however, b5 (and all subsequent versions) always require that Unity be pushed to the background and then brought back to the foreground for the API Updater to report that it had completed the process. In these cases, whether you immediately open demo scenes before "finishing" the update process or after, the content is always broken.
Issue appeared because scripts have started pointing to the Editor version of the DLLs, rather than the Runtime version (the GUID in the FileID-and-GUID URI has changed).
Reproduced on: 5.6.0b5, 5.6.0b11, 2017.1.0a3.
Works fine on: 5.6.0b4.
Regression introduced in 5.6.0b5.
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