(refactoring) Clear separation of phonopy instances for phelel and for extra phonon

[atztogo]

Note: This is a major refactoring and so errors might be introduced.

Extra-phonon (e.g., different supercell size from that of phelel supercell) is rarely used, so in the future, this feature may be removed. The aim of this PR is to isolate extra-phonon related stuffs in Phelel class.

• self._phelel_phonon is used both for phelel dataset and phonon with the same supercell size
• self._phonon is used for the extra-phonon.
• Getter and setter of self.force_constants access self._phelel_phonon.force_constants if self._phonon is None, else self._phonon.force_constants
• Getter of self.nac_params accesses self._phelel_phonon.nac_params. Setter of self.nac_params accesses self._phelel_phonon.nac_params and, if self._phonon is not None, self._phonon.nac_params.

[codecov-commenter]

Codecov Report

Attention: Patch coverage is 76.31579% with 27 lines in your changes missing coverage. Please review.

Project coverage is 72.19%. Comparing base (3159f2e) to head (b45f30f).
Report is 35 commits behind head on develop.

Files with missing lines	Patch %	Lines
src/phelel/api_phelel.py	78.48%	17 Missing ⚠️
src/phelel/interface/vasp/derivatives.py	66.66%	6 Missing ⚠️
src/phelel/base/Dij_qij.py	50.00%	1 Missing ⚠️
src/phelel/base/local_potential.py	83.33%	1 Missing ⚠️
src/phelel/file_IO.py	75.00%	1 Missing ⚠️
src/phelel/interface/phelel_yaml.py	50.00%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##           develop      #52      +/-   ##
===========================================
- Coverage    73.21%   72.19%   -1.02%     
===========================================
  Files           77       81       +4     
  Lines         5500     5687     +187     
===========================================
+ Hits          4027     4106      +79     
- Misses        1473     1581     +108     

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.