Remove scene.groundPrimitives

I don't think there's a technical reason for `scene.primitives` and `scene.groundPrimitives` to be different collections anymore. It might just be legacy from when the classification pass didn't exist.

Start by tracing the definitions and references to scene.primitives and scene.groundPrimitives, then inspect how the classification pass uses them. Done means removing the separate groundPrimitives collection without breaking classification behavior and updating affected tests or callers.

Written by the indexing model from the issue text.