Feature/refactor gfs init

[HenryRWinterbottom]

Description

This PR provides an application to initialize the FV3 GFS run-time path, with the exception of the tables and input.nml. The creation of the tables is a simple addition. The implementation of input.nml requires additional discussions with the core development team.

Type of Change

• New feature (non-breaking change which adds functionality)
• This change requires a documentation update

How Has This Been Tested?

Currently the only testing methodology has been via evaluation of the directory tree. Full unit-tests will be need to be defined and will compose a future PR.

Checklist

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• I have commented my code, particularly in hard-to-understand areas
• My changes need updates to the documentation. I have made corresponding changes to the documentation
• My changes generate no new warnings
• New and existing tests pass with my changes
• Any dependent changes have been merged and published

Notes

The following variables should be added to run-time configuration (e.g., environment) to provide additional flexibility for model_configure:

• calendar; current default is julian;
• output_1st_tstep_rst; current default is .false.;
• quilting; this determination is made somewhere at the configuration and task (e.g., jobs and scripts) levels; for this draft PR a quilting value, as a function of cubed-sphere resolution has been added to the grid configuration class pygfs.utils.grids.FV3GFS;
• new variables, filename_base_atm and filename_base_sfc have been defined within model_configure; the default values remain as atm and sfc, respectively.

The model_configure file has been entirely templated and should not require user modifications. All modifications are made at the run-time and configuration level. We strongly suggest that this is at least a component of the creation of input.nml.

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