Merge branch 'azamat/mpas/scratch-file-io' (PR #1110)

Keep MPAS SCRATCH files open during init, run and finalization

Previously, SCRATCH files were opened and closed in each init_mct, run_mct and
final_mct call. With large number of MPI ranks that may
overwhelm a file system. This will instead open per-process temporary
files once in init_mct call and close once in final_mct call, keeping them
open in each run_mct call.

Fixes #1106
[BFB]