fix: apply remove_pbc to mixed configurations

[njzjz-bot]

Summary

• retain the existing deepmd/npy/mixed multi-system loader
• apply remove_pbc to every reconstructed chemical system when requested
• cover the original mixed-format configuration path with a non-periodic regression test

Tests

• PYTHONPATH=tests python -m unittest -v tests.conf.test_file_conf
• ruff format --check dpgen2/conf/file_conf.py tests/conf/test_file_conf.py
• isort --check-only dpgen2/conf/file_conf.py tests/conf/test_file_conf.py
• git diff --check

Closes #153

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 cd8563e.

📒 Files selected for processing (2)

• dpgen2/conf/file_conf.py
• tests/conf/test_file_conf.py

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 84.20%. Comparing base (fa4a4cf) to head (cd8563e).
⚠️ Report is 109 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #391      +/-   ##
==========================================
- Coverage   85.61%   84.20%   -1.41%     
==========================================
  Files          92      104      +12     
  Lines        4852     6110    +1258     
==========================================
+ Hits         4154     5145     +991     
- Misses        698      965     +267     

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