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 6b01f29 and 23dee80.

📒 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 84.45%. Comparing base (6b01f29) to head (23dee80).

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #393      +/-   ##
==========================================
+ Coverage   84.43%   84.45%   +0.01%     
==========================================
  Files         104      104              
  Lines        6110     6110              
==========================================
+ Hits         5159     5160       +1     
+ Misses        951      950       -1     

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