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 6b01f29 and 4e11709.

📒 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 84.44%. Comparing base (6b01f29) to head (4e11709).

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #391   +/-   ##
=======================================
  Coverage   84.43%   84.44%           
=======================================
  Files         104      104           
  Lines        6110     6113    +3     
=======================================
+ Hits         5159     5162    +3     
  Misses        951      951           

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