Lucas/geometry refactor

[lucas-flexcompute]

I tried to split our geometry primitives into separate files but there are a few interdependencies that seem impossible to avoid, so I ended up leaving Box, GeometryGroup and ClipOperation inside base.py.

• Box is required as a return type for bounding_box, which is only defined for the base Geometry.
• Geometry operations return GeometryGroup or ClipOperation, so those also have to be available for Geometry.

Furthermore, GeometryType and from_shapely are also problematic and were left on a separate file: utils.py. This file requires all geometry classes to define GeometryType.

• GeometryType can only be defined after all classes, but it it used by GeometryGroup and ClipOperation, so a cycle is inevitable here if we want any file separation.
• from_shapely should, ideally, be a method of Geometry because it can return different classes based on the shapely geometry, but it requires the construction of PolySlab, so it cannot depend only on base.py. Because we inevitably have a cyclic import due to GeometryType, I used the same cycle to define from_shapely outside base.py but wrap it inside Geometry.

The final organization is better than having a single file, but not as good as in the initial split (f08d821), which contained a lot more import cycles.