Fix MMCIF roundtrip writing, closes #190

[diegozea]

Summary

• align MMCIF printing defaults with reader expectations so write_file produces label-based mmCIF output
• add a read/write/read roundtrip test for MMCIFFile to guard against regressions

Testing

• julia --project -e 'push!(LOAD_PATH, "test"); using MIToSTests; MIToSTests.retest("PDB"); MIToSTests.retest("PDB")'

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Codex Task

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 96.97%. Comparing base (4a26a3d) to head (3ba0bdb).
⚠️ Report is 1 commits behind head on master.

Additional details and impacted files

@@           Coverage Diff           @@
##           master     #191   +/-   ##
=======================================
  Coverage   96.97%   96.97%           
=======================================
  Files          64       64           
  Lines        4861     4861           
=======================================
  Hits         4714     4714           
  Misses        147      147           

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[coveralls]

coverage: 97.156%. remained the same
when pulling 49bd91a on codex/add-roundtrip-test-for-mmciffile
into 4a26a3d on master.