Integrate ClimaComms logging updates #3532
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This PR tests out the latest logging features from ClimaComms, especially CliMA/ClimaComms.jl#104.
This adds a new config option
log_to_file = truewhich will enable ClimaComms.FileLogger, a logger that outputs to stdout and saves logs to disk inoutput_active/output.log. As part of this, MPI simulations will have an additional folderoutput_active/logsstoring the logs from each MPI process.TODO: remove
silence_non_root_processes, since this is also handled by ClimaComms now.