MCTruthClassifier: Switch to using MC::isNucleus helper function from TruthUtils

This merge request migrates MCTruthClassifier to use the helper functions and constants from TruthUtils/AtlasPID.h related to nuclei. A key point here is whether protons should be considered as nuclei in each case. PDG considers protons nuclei, but does not give them an additional pdg id above 1000000000. MC::isNucleus() returns true for MC::PROTON, but the existing logic in MCTruthClassifier skips this case sometimes.

Leaving it as draft for now as while migrating the code, I noticed some other suspect logic which should be checked and patched in separate MRs if necessary.