Several improvements to the handling of boxes

Description

Several changes:

• Cylinder boxes are now always along the direction defined by the first basis vector.
• Optimize box_shape_contains_points by using BLAS to change the point's coordinates.
• Make basis_vectors optional when initializing a box_shape.
• Rename box_shape basis_vectors to axes to make its meaning clearer.
• Add several missing private statements in the box modules.

Checklist

• I have checked that my code follows the Octopus coding standards
• I have added tests for all the new features added in this request.