Program: 95675
Project: 95675
Buggy source:
public static String getDefaultMutations(){
  String data=mutationInstructions;
  data=data + '\n' + minecraftMutations;
  if (ConfigurationHandler.resourcePlants) {
    data=data + '\n' + agricraftMutations;
    if (OreDictHelper.oreCopper != null) {
      data=data + '\n' + copperMutation;
    }
    if (OreDictHelper.oreTin != null) {
      data=data + '\n' + tinMutation;
    }
    if (OreDictHelper.oreLead != null) {
      data=data + '\n' + leadMutation;
    }
    if (OreDictHelper.oreSilver != null) {
      data=data + '\n' + silverMutation;
    }
    if (OreDictHelper.oreAluminum != null) {
      data=data + '\n' + aluminumMutation;
    }
    if (OreDictHelper.oreNickel != null) {
      data=data + '\n' + nickelMutation;
    }
    if (OreDictHelper.orePlatinum != null) {
      data=data + '\n' + platinumMutation;
    }
    if (OreDictHelper.oreOsmium != null) {
      data=data + '\n' + osmiumMutation;
    }
  }
  if (ConfigurationHandler.integration_Botania) {
    data=data + '\n' + botaniaMutations;
  }
  if (ConfigurationHandler.integration_Nat && ConfigurationHandler.integration_HC && ModIntegration.LoadedMods.harvestcraft&& ModIntegration.LoadedMods.natura) {
    data=data + '\n' + harvestcraftMutations+ '\n'+ barleyNaturaMutations;
  }
 else {
    if (ConfigurationHandler.integration_HC && ModIntegration.LoadedMods.harvestcraft) {
      data=data + '\n' + harvestcraftMutations+ '\n'+ barleyHarvestCraftMutations;
    }
    if (ConfigurationHandler.integration_Nat && ModIntegration.LoadedMods.natura) {
      data=data + '\n' + naturaMutations;
    }
  }
  if (ConfigurationHandler.integration_WeeeFlowers && ModIntegration.LoadedMods.weeeFlowers) {
    data=data + '\n' + weeeFlowersMutations;
  }
  if (ConfigurationHandler.integration_PlantMegaPack && ModIntegration.LoadedMods.plantMegaPack) {
    data=data + '\n' + plantMegaPackMutations;
  }
  if (ConfigurationHandler.integration_Chococraft && ModIntegration.LoadedMods.chococraft) {
    if (ConfigurationHandler.integration_HC && ModIntegration.LoadedMods.harvestcraft) {
      data=data + '\n' + chococraft_harvestcraftMutations;
    }
 else {
      data=data + '\n' + chococraftMutations;
    }
  }
  return data;
}

Fixed version (ground truth):
public static String getDefaultMutations(){
  String data=mutationInstructions;
  data=data + '\n' + minecraftMutations;
  if (ConfigurationHandler.resourcePlants) {
    data=data + '\n' + agricraftMutations;
    if (OreDictHelper.oreCopper != null) {
      data=data + '\n' + copperMutation;
    }
    if (OreDictHelper.oreTin != null) {
      data=data + '\n' + tinMutation;
    }
    if (OreDictHelper.oreLead != null) {
      data=data + '\n' + leadMutation;
    }
    if (OreDictHelper.oreSilver != null) {
      data=data + '\n' + silverMutation;
    }
    if (OreDictHelper.oreAluminum != null) {
      data=data + '\n' + aluminumMutation;
    }
    if (OreDictHelper.oreNickel != null) {
      data=data + '\n' + nickelMutation;
    }
    if (OreDictHelper.orePlatinum != null) {
      data=data + '\n' + platinumMutation;
    }
    if (OreDictHelper.oreOsmium != null) {
      data=data + '\n' + osmiumMutation;
    }
  }
  if (ConfigurationHandler.integration_Botania) {
    data=data + '\n' + botaniaMutations;
  }
  if (ConfigurationHandler.integration_Nat && ConfigurationHandler.integration_HC && ModIntegration.LoadedMods.harvestcraft&& ModIntegration.LoadedMods.natura) {
    data=data + '\n' + harvestcraftMutations+ '\n'+ barleyNaturaMutations;
  }
 else {
    if (ConfigurationHandler.integration_HC && ModIntegration.LoadedMods.harvestcraft) {
      data=data + '\n' + harvestcraftMutations+ '\n'+ barleyHarvestCraftMutations;
    }
    if (ConfigurationHandler.integration_Nat && ModIntegration.LoadedMods.natura) {
      data=data + '\n' + naturaMutations;
    }
  }
  if (ConfigurationHandler.integration_WeeeFlowers && ModIntegration.LoadedMods.weeeFlowers) {
    data=data + '\n' + weeeFlowersMutations;
  }
  if (ConfigurationHandler.integration_PlantMegaPack && ModIntegration.LoadedMods.plantMegaPack) {
    data=data + '\n' + plantMegaPackMutations;
  }
  if (ConfigurationHandler.integration_Chococraft && ModIntegration.LoadedMods.chococraft) {
    if (ConfigurationHandler.integration_HC && ModIntegration.LoadedMods.harvestcraft) {
      data=data + '\n' + chococraft_harvestcraftMutations;
    }
 else {
      data=data + '\n' + chococraftMutations;
    }
  }
  if (ConfigurationHandler.integration_Psychedelicraft && ModIntegration.LoadedMods.psychedelicraft) {
    data=data + '\n' + psychedelicraftMutations;
  }
  return data;
}