Update pre-industrial configuration with latest payu updates

[blimlim]

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

• Remove um_env.py file now that it has been replaced by the um_env.yaml file.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 5.
  • Add runlog and platform settings with default values.
  • Add manifest: reproduce: exe: True as in the OM2 configurations.

It would be great to get a check over these changes, especially to confirm that the default values for several of the new config.yaml settings are suitable for ESM1.5.

[blimlim]

I'll wait until #38 is merged and update this branch with the changes before trying to merge.

[aidanheerdegen]

Some changes, some comments and some questions.

[aidanheerdegen]

Sorry! One more change required it seems.

[aidanheerdegen]

All good to merge, thanks @blimlim!

[blimlim]

Thanks for the review! There will be a similar one soon with the same changes for the historical configuration. I've added in all the changes from the discussion here and so hopefully that one won't be too involved!