Program: 165963
Project: 165963
Buggy source:
/** 
 * Merges provided ItemStack with the first available one in this inventory. It will return the amount of items that could not be merged. Also fills the undo buffer in case you want to undo the operation.
 */
public static int mergeItemStack(IInventory inventory,ItemStack result,int start,int stop,List<SlotModifier> undo){
  int k=start;
  ItemStack itemstack1;
  int itemsToPlace=result.stackSize;
  if (result.isStackable()) {
    while (itemsToPlace > 0 && (k < stop)) {
      itemstack1=inventory.getStackInSlot(k);
      if (itemstack1 != null && itemstack1.getItem() == result.getItem() && (!result.getHasSubtypes() || result.getItemDamage() == itemstack1.getItemDamage()) && ItemStack.areItemStackTagsEqual(result,itemstack1)) {
        int l=itemstack1.stackSize + itemsToPlace;
        if (l <= result.getMaxStackSize()) {
          if (undo != null) {
            undo.add(new SlotModifier(k,itemstack1.copy()));
          }
          itemsToPlace=0;
          itemstack1.stackSize=l;
          inventory.markDirty();
        }
 else         if (itemstack1.stackSize < result.getMaxStackSize()) {
          if (undo != null) {
            undo.add(new SlotModifier(k,itemstack1.copy()));
          }
          itemsToPlace-=result.getMaxStackSize() - itemstack1.stackSize;
          itemstack1.stackSize=result.getMaxStackSize();
          inventory.markDirty();
        }
      }
      ++k;
    }
  }
  if (itemsToPlace > 0) {
    k=start;
    while (k < stop) {
      itemstack1=inventory.getStackInSlot(k);
      if (itemstack1 == null) {
        if (undo != null) {
          undo.add(new SlotModifier(k,null));
        }
        inventory.setInventorySlotContents(k,result.copy());
        inventory.markDirty();
        itemsToPlace=0;
        break;
      }
      ++k;
    }
  }
  return itemsToPlace;
}

Fixed version (ground truth):
/** 
 * Merges provided ItemStack with the first available one in this inventory. It will return the amount of items that could not be merged. Also fills the undo buffer in case you want to undo the operation.
 */
public static int mergeItemStack(IInventory inventory,ItemStack result,int start,int stop,List<SlotModifier> undo){
  int k=start;
  ItemStack itemstack1;
  int itemsToPlace=result.stackSize;
  if (result.isStackable()) {
    while (itemsToPlace > 0 && (k < stop)) {
      itemstack1=inventory.getStackInSlot(k);
      if (itemstack1 != null && itemstack1.getItem() == result.getItem() && (!result.getHasSubtypes() || result.getItemDamage() == itemstack1.getItemDamage()) && ItemStack.areItemStackTagsEqual(result,itemstack1)) {
        int l=itemstack1.stackSize + itemsToPlace;
        if (l <= result.getMaxStackSize()) {
          if (undo != null) {
            undo.add(new SlotModifier(k,itemstack1.copy()));
          }
          itemsToPlace=0;
          itemstack1.stackSize=l;
          inventory.markDirty();
        }
 else         if (itemstack1.stackSize < result.getMaxStackSize()) {
          if (undo != null) {
            undo.add(new SlotModifier(k,itemstack1.copy()));
          }
          itemsToPlace-=result.getMaxStackSize() - itemstack1.stackSize;
          itemstack1.stackSize=result.getMaxStackSize();
          inventory.markDirty();
        }
      }
      ++k;
    }
  }
  if (itemsToPlace > 0) {
    k=start;
    while (k < stop) {
      itemstack1=inventory.getStackInSlot(k);
      if (itemstack1 == null) {
        if (undo != null) {
          undo.add(new SlotModifier(k,null));
        }
        ItemStack copy=result.copy();
        copy.stackSize=itemsToPlace;
        inventory.setInventorySlotContents(k,copy);
        inventory.markDirty();
        itemsToPlace=0;
        break;
      }
      ++k;
    }
  }
  return itemsToPlace;
}