Fix broken data structure related to phonon_supercell_matrix etc #231
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When different supercell size for fc2 is used,
ph3.phonon_supercell_matrixisNone. This is implicitly used as the flag to invoke this mode, i.e., different supercell sizes for fc3 and fc2.This rule was not followed in a few places, not only in CUI logic for reading various types of inputs, but also in Yaml dumper and loader.
Probably a specific flag in boolean type should be prepared.