Isolate config and argument parsing

[juliasloan25]

Purpose

closes #678

To-do

• Add function to read in config file and job id
• Add function to parse input arguments (from config file)
  • Separate functions for coupler and atmos?
• Update atmos config function to not modify coupler (make these two independent)
• Remove atmos-related args from coupler configs, and move them into atmos configs
• Fix new driver warnings

Content

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• I have read and checked the items on the review checklist.