Vertex renumbering for negative volumes not fully taken into account

[lukasdreyer]

Bug report

Describe the bug
Vertex renumbering due to negative volumes is not taken into account for face-neighbor computation.
Only the tree_vertices array is switched, not the node_indices which is passed vertex_indices to t8_cmesh_msh_file_find_neighbors and used to compute face indices of neighboring elements for t8_cmesh_set_join.

Additionally, only switching vertices 0 and 4 for pyramids does not seem correct.

Also see:

#1220 and #865

Estimated priority
Which of these is most applicable (remove the others):

"Priority: high" Should be solved as soon as possible