Update historical configuration with latest payu changes

[blimlim]

This pull request completes the historical half of #40. It modifies the configuration with the following changes:

• Use new module settings for model executables
• Remove um_env.py file now that it has been replaced by the um_env.yaml file.
• Remove unused atmosphere configuration files Remove unused configuration files from atmosphere directory #27.
• Add/update the following settings in the config.yaml file:
  • Add commented out shortpath and project settings
  • Add sync settings with default false setting. Add comment explaining compatibility with postscripts
  • Add restart_freq setting with default value of 10YS.
  • Add runlog settings with default values.
  • Add manifest: reproduce: exe: True as in the OM2 configurations.
  • Increase walltime to 2:30 to guard against occasional slow simulations.

The settings have been chosen to match those used in the updated pre-industrial configuration via #42.

Also changed the target of this PR to the dev-historical+concentrations branch, which required the addition of files to make the QA checks pass.

[aidanheerdegen]

There seems to be some mismatch between the inputs for config.yaml and um_env.yaml

[aidanheerdegen]

LGTM

[aidanheerdegen]

LGTM