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Why are times represented using the TimeScope class in some places, and a datetime timestamp in others?

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Document and its child classes (Plan, Work Order, etc.) have several attributes (GrowerId, FarmId, FieldId, TimeScopes, etc.) that are also in the LoggedData and Summary objects that have an aggregation relationship with these Document child classes. Are LoggedData and Summary supposed to inherit the values of the parent Document?

No. The data shown in the document is supposed to be the UNION of the data in the child LoggedData / Summary objects. The original intent was for the lists of field references, etc. to serve as metadata that would help find documents of interest. The exception is the GrowerId, which is unique (the others are lists) and should be the same throughout the Document and its children.