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This fixes #2, changing topojson.topology so that it no longer destroys the input objects; instead, shallow copies are made as needed.
This also fixes #3 by removing type reduction: for example, an input MultiPolygon geometry with only a single polygon is no longer reduced to a Polygon, and an input empty MultiLineString geometry is no longer reduced to a null geometry. The output type of a geometry object is always the same as its input type. You can remove null geometries using topojson.filter.
This will be a major version change, released as 3.0.
For the other changes in 3.0, see: