Overhall CLI

[je-cook]

Description

Rewrites the CLI to use click and orchestrates all cli modules under the process cli function

Checklist

I confirm that I have completed the following checks:

• My changes follow the PROCESS style guide
• I have justified any large differences in the regression tests caused by this pull request in the comments.
• I have added new tests where appropriate for the changes I have made.
• If I have had to change any existing unit or integration tests, I have justified this change in the pull request comments.
• If I have made documentation changes, I have checked they render correctly.
• I have added documentation for my change, if appropriate.

[codecov-commenter]

Codecov Report

❌ Patch coverage is 16.21339% with 801 lines in your changes missing coverage. Please review.
✅ Project coverage is 47.84%. Comparing base (6d036d5) to head (ddbf2c1).
⚠️ Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
process/core/io/plot/plot_stress_tf.py	0.00%	265 Missing ⚠️
process/core/io/plot/sankey.py	11.60%	160 Missing ⚠️
process/core/io/plot/cli.py	0.00%	58 Missing ⚠️
process/core/io/plot/costs/costs_bar.py	0.00%	52 Missing ⚠️
process/core/io/in_dat/create.py	0.00%	45 Missing ⚠️
process/core/io/plot/plot_scans.py	0.00%	44 Missing ⚠️
process/core/io/plot/costs/cli.py	0.00%	37 Missing ⚠️
process/core/io/mfile/cli.py	0.00%	27 Missing ⚠️
process/core/io/mfile/mfile_comparison.py	0.00%	27 Missing ⚠️
process/core/io/plot/plot_proc.py	72.83%	22 Missing ⚠️
... and 6 more

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4105      +/-   ##
==========================================
+ Coverage   47.18%   47.84%   +0.65%     
==========================================
  Files         138      142       +4     
  Lines       29280    28855     -425     
==========================================
- Hits        13817    13805      -12     
+ Misses      15463    15050     -413     

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