Improve failure handling, phonopy compatibility, and agent long-running tests

[Zikkying]

Improve workflow failure handling and phonopy compatibility

• Classify transient LAMMPS startup failures consistently.
• Collect debug artifacts when workflow retrieval fails.
• Fail earlier for fragile Gamma and Interstitial inputs.
• Improve compatibility with phonopy v4.
• Keep a fallback routine for phonopy v3.x.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 71.94%. Comparing base (028235f) to head (f977d8e).
⚠️ Report is 2 commits behind head on devel-1.3.0.

Additional details and impacted files

@@               Coverage Diff               @@
##           devel-1.3.0     #118      +/-   ##
===============================================
+ Coverage        69.62%   71.94%   +2.32%     
===============================================
  Files              102      103       +1     
  Lines            20396    21279     +883     
===============================================
+ Hits             14201    15310    +1109     
+ Misses            6195     5969     -226     

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