fix: preserve LAMMPS configuration indices

[njzjz-bot]

Summary

• copy caller configuration before normalization
• preserve an explicit conf_idx value
• add the empty workaround only when the key is absent
• cover the exported helper with an explicit index regression test

Tests

• PYTHONPATH=tests python -m unittest -v tests.exploration.test_make_task_group_from_config.TestMakeLmpTaskGroupFromConfig.test_npt_preserves_explicit_conf_idx tests.exploration.test_make_task_group_from_config.TestMakeLmpTaskGroupFromConfig.test_npt
• ruff format --check dpgen2/exploration/task/make_task_group_from_config.py tests/exploration/test_make_task_group_from_config.py
• isort --check-only dpgen2/exploration/task/make_task_group_from_config.py tests/exploration/test_make_task_group_from_config.py
• git diff --check

Closes #358

Coding agent: Codex
Codex version: codex-cli 0.149.0
Model: gpt-5.6-sol
Reasoning effort: xhigh

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📥 Commits

Reviewing files that changed from the base of the PR and between b05af11 and 4cf94ce.

📒 Files selected for processing (2)

• dpgen2/exploration/task/make_task_group_from_config.py
• tests/exploration/test_make_task_group_from_config.py

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[codecov]

Codecov Report

❌ Patch coverage is 50.00000% with 13 lines in your changes missing coverage. Please review.
✅ Project coverage is 84.20%. Comparing base (fa4a4cf) to head (4cf94ce).
⚠️ Report is 109 commits behind head on master.

Files with missing lines	Patch %	Lines
...n2/exploration/task/make_task_group_from_config.py	50.00%	13 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #384      +/-   ##
==========================================
- Coverage   85.61%   84.20%   -1.42%     
==========================================
  Files          92      104      +12     
  Lines        4852     6108    +1256     
==========================================
+ Hits         4154     5143     +989     
- Misses        698      965     +267     

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