Refactor CUI for using pypolymlp

[atztogo]

The pypolymlp call, previously located deep within nested functions, has been moved to the top level of the main function in phono3py_script.py. This change ensures that the CUI can terminate after developing and storing MLPs if no subsequent steps are specified.

[codecov]

Codecov Report

Attention: Patch coverage is 56.08108% with 65 lines in your changes missing coverage. Please review.

Project coverage is 67.29%. Comparing base (47aaab5) to head (9587735).
Report is 36 commits behind head on develop.

Files with missing lines	Patch %	Lines
phono3py/cui/load.py	51.92%	25 Missing ⚠️
phono3py/cui/phono3py_script.py	68.75%	25 Missing ⚠️
phono3py/cui/create_force_constants.py	6.66%	14 Missing ⚠️
phono3py/cui/phono3py_argparse.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop     #332      +/-   ##
===========================================
- Coverage    67.54%   67.29%   -0.26%     
===========================================
  Files           71       72       +1     
  Lines        12720    12838     +118     
===========================================
+ Hits          8592     8639      +47     
- Misses        4128     4199      +71     

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