`fre run`: input-stager (setup-workdir)

[singhd789]

fre run setup-workdir subtool (is stateDir needed?):

• will be creating workdir (mkdir) from path defined in YAML
• setting up INPUT and RESTART folders
• expanding namelists and copying file to workdir
• using fms-yaml-tools to combine tables and copying combined files to workDir

workDir:

• what goes into the workDir:
  • INPUT (netcdf files included in datasets in xml configs), RESTART --> setting up workDir structure
  • input.nml files --> creating expanded namelists; lines 690-705, lines 857-872
  • data table, diag table, field table, executable or container --> expand tables and executable
    • data, diag, and field table loading would use fms-yaml-tools
• should pass -y yamlfile and parse to find the directories defined (can define them in [settings.yaml][directories] section)

PROTOTYPE RUNTIME YAML: https://gitlab.gfdl.noaa.gov/Dana.Singh/am5xml/-/blob/runtime-yaml-prototyping/yaml_workflow/run/combined.yaml?ref_type=heads