MIGRATION - Write as geometries

[jginternational]

This PR / branch will accumulate the migration of the different apps from the classic MDPA write to the new format as geometries

• [x] Fluid
• [x] Embedded Fluid #989
• [x] Geomechanics
• [x] Compressible flow #991
• [x] Convection diffussion #992
• [x] Structural #988
• [x] Buoyancy #986
• [x] Shallow water #995
• [x] Potential Flow #987
• [x] Free surface #990 ➡️ Wait for https://github.com/KratosMultiphysics/Kratos/issues/12564
• [ ] Conjugate heat transfer #994
• [ ] FSI #996 ➡️ Wait for https://github.com/KratosMultiphysics/Kratos/issues/12747
• [ ] MPM
• [ ] DAM
• [ ] PFEM Fluid
• [ ] DEM
• [ ] DEM PFEM
• [ ] Fluid DEM
• [ ] PFEM Melting