Program: 95763
Project: 95763
Buggy source:
public void crossOver(){
  boolean change=false;
  ItemSeeds result=null;
  int resultMeta=0;
  int mutationId=0;
  Block req=null;
  int reqMeta=0;
  double chance=0;
  TileEntityCrop[] neighbours=this.findNeighbours();
  if (Math.random() > ConfigurationHandler.mutationChance) {
    int index=(int)Math.floor(Math.random() * neighbours.length);
    if (neighbours[index] != null && neighbours[index].seed != null && neighbours[index].isMature()) {
      result=(ItemSeeds)neighbours[index].seed;
      resultMeta=neighbours[index].seedMeta;
      chance=SeedHelper.getSpreadChance(result,resultMeta);
    }
  }
 else {
    Mutation[] crossOvers=MutationHandler.getCrossOvers(neighbours);
    if (crossOvers != null && crossOvers.length > 0) {
      int index=(int)Math.floor(Math.random() * crossOvers.length);
      if (crossOvers[index].result.getItem() != null) {
        result=(ItemSeeds)crossOvers[index].result.getItem();
        resultMeta=crossOvers[index].result.getItemDamage();
        mutationId=crossOvers[index].id;
        req=crossOvers[index].requirement;
        reqMeta=crossOvers[index].requirementMeta;
        chance=crossOvers[index].chance;
      }
    }
  }
  if (result != null && SeedHelper.isValidSeed(result,resultMeta) && this.canMutate(result,resultMeta,mutationId,req,reqMeta)) {
    if (Math.random() < chance) {
      this.crossCrop=false;
      int[] stats=MutationHandler.getStats(neighbours);
      this.setPlant(stats[0],stats[1],stats[2],false,result,resultMeta);
      change=true;
    }
  }
  if (change) {
    this.markDirty();
  }
}

Fixed version (ground truth):
public void crossOver(){
  boolean change=false;
  ItemSeeds result=null;
  int resultMeta=0;
  int mutationId=0;
  Block req=null;
  int reqMeta=0;
  double chance=0;
  TileEntityCrop[] neighbours=this.findNeighbours();
  if (Math.random() > ConfigurationHandler.mutationChance) {
    int index=(int)Math.floor(Math.random() * neighbours.length);
    if (neighbours[index] != null && neighbours[index].seed != null && neighbours[index].isMature()) {
      result=(ItemSeeds)neighbours[index].seed;
      resultMeta=neighbours[index].seedMeta;
      chance=SeedHelper.getSpreadChance(result,resultMeta);
    }
  }
 else {
    Mutation[] crossOvers=MutationHandler.getCrossOvers(neighbours);
    if (crossOvers != null && crossOvers.length > 0) {
      int index=(int)Math.floor(Math.random() * crossOvers.length);
      if (crossOvers[index].result.getItem() != null) {
        result=(ItemSeeds)crossOvers[index].result.getItem();
        resultMeta=crossOvers[index].result.getItemDamage();
        mutationId=crossOvers[index].id;
        req=crossOvers[index].requirement;
        reqMeta=crossOvers[index].requirementMeta;
        chance=crossOvers[index].chance;
      }
    }
  }
  if (result != null && SeedHelper.isValidSeed(result,resultMeta) && this.canMutate(result,resultMeta,mutationId,req,reqMeta)) {
    if (Math.random() < chance) {
      this.crossCrop=false;
      int[] stats=MutationHandler.getStats(neighbours);
      this.setPlant(stats[0],stats[1],stats[2],false,result,resultMeta);
      change=true;
    }
  }
  if (change) {
    markDirtyAndMarkForUpdate();
  }
}