docs: explain LAMMPS exploration extra files

[njzjz-bot]

Summary

• document input_extra_files for generated lmp-md task groups
• show the DP-ZBL use_srtab table-file configuration
• verify the normalized stage configuration copies the file content into each exploration task by basename

Tests

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

Closes #304

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 b472b34.

📒 Files selected for processing (2)

• docs/input.md
• tests/exploration/test_make_task_group_from_config.py

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.24%. Comparing base (fa4a4cf) to head (b472b34).
⚠️ Report is 109 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #393      +/-   ##
==========================================
- Coverage   85.61%   84.24%   -1.37%     
==========================================
  Files          92      104      +12     
  Lines        4852     6107    +1255     
==========================================
+ Hits         4154     5145     +991     
- Misses        698      962     +264     

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