Some refactoring of the geometry module

Description

Move the content of the xyz_adjust module to either the geometry or to the centergeom utility. In the process, merged two different routines to calculate the center of mass (which was the reason why I did all this in the first place). Also removed an unused routine, made some cosmetic changes and changed several subroutines into functions.

News snippet

Some refactoring of the geometry module.

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.