[VnV][telemac3d] Update amr example with better choices for a few keywords

- TREATMENT OF NEGATIVE DEPTHS = 2 (new default value since release 9.0)
to improve mass conservation (water depth + temperature, water depth up to
machine accuracy)
- solver and accuracy for propagation set to default (GMRES + 1.E-8)
- accuracy for diffusion of tracers can be set to 1.E-15 without significant
increase of CPU time
- preconditioning for diffusion = 34 = 2*17 for tracers + velocities for
more efficiency (less iterations)
- solver and preconditioning for PPE = conjugate gradient (1) and 34
- non-hydrostatic version (new default since 8.0)