Rework "feat: Python interfaces to geos from Makutu repo"

[alexbenedicto]

Following the revert of #47

The goal is to implement the best way possible the code provided by Makutu development team and @av-novikov in the pygeos repository.

3 main axis of development were highlighted:

• Unify with functionalities developed in mesh_doctor
• Use vtk library implemented methods when available
• Clean up every method to work in general cases