fix(python/core): fix bug on Molecule::clear* call with active mutator

[jnooree]

Checklist

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Linked Issues

Link the tracking issue(s) of this PR, with the auto-close keywords here:

• Fixes [BUG] molecule clear* methods are unsafe when a mutator is active #289.

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[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 90.86%. Comparing base (12f7938) to head (207570d).

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #290      +/-   ##
==========================================
+ Coverage   90.84%   90.86%   +0.01%     
==========================================
  Files          37       37              
  Lines        8682     8699      +17     
==========================================
+ Hits         7887     7904      +17     
  Misses        795      795              

Files	Coverage Δ
python/include/nuri/python/core/core_module.h	92.16% <100.00%> (+0.38%)	⬆️
python/src/nuri/core/molecule.cpp	90.14% <100.00%> (-0.21%)	⬇️