Program: 164288
Project: 164288
Buggy source:
public Item transmute(){
  CellEmitter.get(pos).burst(Speck.factory(Speck.BUBBLE),3);
  Splash.at(pos,0xFFFFFF,3);
  float chances[]=new float[items.size()];
  int count=0;
  if (items.size() == 2 && items.get(0) instanceof Seed && items.get(1) instanceof Blandfruit) {
    Sample.INSTANCE.play(Assets.SND_PUFF);
    CellEmitter.center(pos).burst(Speck.factory(Speck.EVOKE),3);
    Blandfruit result=new Blandfruit();
    result.cook((Seed)items.get(0));
    destroy();
    return result;
  }
  int index=0;
  for (  Item item : items) {
    if (item instanceof Seed) {
      count+=item.quantity;
      chances[index++]=item.quantity;
    }
 else {
      count=0;
      break;
    }
  }
  AlchemistsToolkit.alchemy alchemy=Dungeon.hero.buff(AlchemistsToolkit.alchemy.class);
  int bonus=alchemy != null ? alchemy.level() : -1;
  if (bonus != -1 ? alchemy.tryCook(count) : count >= SEEDS_TO_POTION) {
    CellEmitter.get(pos).burst(Speck.factory(Speck.WOOL),6);
    Sample.INSTANCE.play(Assets.SND_PUFF);
    Item potion;
    if (Random.Int(count + bonus) == 0) {
      CellEmitter.center(pos).burst(Speck.factory(Speck.EVOKE),3);
      destroy();
      Statistics.potionsCooked++;
      Badges.validatePotionsCooked();
      potion=Generator.random(Generator.Category.POTION);
    }
 else {
      Seed proto=(Seed)items.get(Random.chances(chances));
      Class<? extends Item> itemClass=proto.alchemyClass;
      destroy();
      Statistics.potionsCooked++;
      Badges.validatePotionsCooked();
      if (itemClass == null) {
        potion=Generator.random(Generator.Category.POTION);
      }
 else {
        try {
          potion=itemClass.newInstance();
        }
 catch (        Exception e) {
          return null;
        }
      }
    }
    if (bonus > 0)     if (Random.Int(1000 / bonus) == 0)     return new PotionOfExperience();
    while (potion instanceof PotionOfHealing && Random.Int(15) - Dungeon.limitedDrops.cookingHP.count >= 0)     potion=Generator.random(Generator.Category.POTION);
    if (potion instanceof PotionOfHealing)     Dungeon.limitedDrops.cookingHP.count++;
    return potion;
  }
 else {
    return null;
  }
}

Fixed version (ground truth):
public Item transmute(){
  CellEmitter.get(pos).burst(Speck.factory(Speck.BUBBLE),3);
  Splash.at(pos,0xFFFFFF,3);
  float chances[]=new float[items.size()];
  int count=0;
  if (items.size() == 2 && items.get(0) instanceof Seed && items.get(1) instanceof Blandfruit) {
    Sample.INSTANCE.play(Assets.SND_PUFF);
    CellEmitter.center(pos).burst(Speck.factory(Speck.EVOKE),3);
    Blandfruit result=new Blandfruit();
    result.cook((Seed)items.get(0));
    destroy();
    return result;
  }
  int index=0;
  for (  Item item : items) {
    if (item instanceof Seed) {
      count+=item.quantity;
      chances[index++]=item.quantity;
    }
 else {
      count=0;
      break;
    }
  }
  AlchemistsToolkit.alchemy alchemy=Dungeon.hero.buff(AlchemistsToolkit.alchemy.class);
  int bonus=alchemy != null ? alchemy.level() : -1;
  if (bonus != -1 ? alchemy.tryCook(count) : count >= SEEDS_TO_POTION) {
    CellEmitter.get(pos).burst(Speck.factory(Speck.WOOL),6);
    Sample.INSTANCE.play(Assets.SND_PUFF);
    Item potion;
    if (Random.Int(count + bonus) == 0) {
      CellEmitter.center(pos).burst(Speck.factory(Speck.EVOKE),3);
      destroy();
      Statistics.potionsCooked++;
      Badges.validatePotionsCooked();
      potion=Generator.random(Generator.Category.POTION);
    }
 else {
      Seed proto=(Seed)items.get(Random.chances(chances));
      Class<? extends Item> itemClass=proto.alchemyClass;
      destroy();
      Statistics.potionsCooked++;
      Badges.validatePotionsCooked();
      if (itemClass == null) {
        potion=Generator.random(Generator.Category.POTION);
      }
 else {
        try {
          potion=itemClass.newInstance();
        }
 catch (        Exception e) {
          return null;
        }
      }
    }
    if (bonus > 0)     if (Random.Int(1000 / bonus) == 0)     return new PotionOfExperience();
    while (potion instanceof PotionOfHealing && Random.Int(10) < Dungeon.limitedDrops.cookingHP.count)     potion=Generator.random(Generator.Category.POTION);
    if (potion instanceof PotionOfHealing)     Dungeon.limitedDrops.cookingHP.count++;
    return potion;
  }
 else {
    return null;
  }
}