Function best_ms1_for_each_ms2 

pub fn best_ms1_for_each_ms2(
    ms1: &[ClusterResult1D],
    ms2: &[ClusterResult1D],
    pairs: &[(usize, usize)],
    opts: &ScoreOpts,
) -> Vec<Option<usize>>

For each MS2, choose the best MS1 index (by score, then deterministic tie-breaks). Returns a Vec<Option> indexed by ms2_idx.