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ShapeIndex is not adding any value as a separate abstraction from
Model. Separating ShapeIndex from Model made building models much more verbose, interacting with shapes in a model more verbose, updating models verbose, and caused an awkward API if you need to access things like knowledge indexes but only have access to a ShapeIndex (knowledge indexes are only on models). This commit first deprecates all ShapeIndex APIs and provides alternatives that are to be used instead. In some cases, the alternative, Model based APIs, still call into the deprecated ShapeIndex APIs. This is because a Model always has a ShapeIndex but a ShapeIndex is not a model, and it cuts down on code duplication. In the next version bump (likely 0.10.0), we will remove the ShapeIndex APIs altogether.
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