Crop repo fix

Using Pyvista for creation of the dgr repo: with the argument crinkle=true for the clip filter, this ensures that elements will remain for the repo even for coarse meshes. Previously it could happen, that the creation via RemoveMeshElements resulted in an empty mesh, breaking the workflow. so...robustness++ One side effect is, that the repo will now always be a bit to large, depending on the discretization (before it was always a bit to small).

Also moved the remaining calls to OGS-tools (which couldn't be replaced with pyvista) to the snakefile, to reduce nesting of shell->python->shell->...