Each directory has a RUNS file with method steps.
In general, this is what happens in each directory.
 
Link to poly surface.
ln -s /scratch/sft/tam/grid_gen/arctic/intermediate_scale/polys_intermediate/out_quad_lobster_var/poly_all_quads2.gmv poly_all_quads.gmv
ln -s /scratch/sft/tam/grid_gen/arctic/intermediate_scale/polys_intermediate/out_quad_lobster_var/poly_all_quads2.inp poly_all_quads.inp

Link to elevation surface.
ln -s /scratch/sft/tam/grid_gen/arctic/intermediate_scale/input_poly_data/lidar_site3_surf.inp lidar_site3_surf.inp

Copy files from fine scale work, these have the stack definitions we need
cp /scratch/sft2/lucia/grid_gen/arctic/arctic_fine_v3_C_1/lagrit_files/* lagrit_files_fine_scale

Apply elevations to merged poly surface
	lagrit < apply_elevations.lgi
	cp outx3dgen apply_elevations.out

Stack layers using poly surface as top
	lagrit < stack_layers.lgi
	cp outx3dgen stack_layers.out

Write final mesh files
Using scripts from fine scale, not the aggregate work which removes cells.
Modified to work for degenerate quads during extract, tag sides process
Be sure to check surf_sides.gmv to find zero vol faces attached to bottom
top and bottom facesets must have same number of faces
        lagrit < write_exo.lgi 
                 uses output_faceset.mlgi
        cp outx3dgen  write_exo.out

ncdump_lin64 mesh_fsets.exo > mesh_fsets_ascii.exo