Program: 166004
Project: 166004
Buggy source:
@Override public ItemStack transferStackInSlot(EntityPlayer player,int index){
  ItemStack itemstack=null;
  Slot slot=(Slot)this.inventorySlots.get(index);
  if (slot != null && slot.getHasStack()) {
    ItemStack origStack=slot.getStack();
    itemstack=origStack.copy();
    if (factory.isSpecificItemSlot(index)) {
      if (!mergeItemStacks(origStack,SlotType.SLOT_PLAYERINV,true)) {
        if (!mergeItemStacks(origStack,SlotType.SLOT_PLAYERHOTBAR,false)) {
          return null;
        }
      }
      slot.onSlotChange(origStack,itemstack);
    }
 else     if (factory.isOutputSlot(index) || factory.isInputSlot(index) || factory.isContainerSlot(index)) {
      if (!mergeItemStacks(origStack,SlotType.SLOT_SPECIFICITEM,false)) {
        if (!mergeItemStacks(origStack,SlotType.SLOT_PLAYERINV,true)) {
          if (!mergeItemStacks(origStack,SlotType.SLOT_PLAYERHOTBAR,false)) {
            return null;
          }
        }
      }
      slot.onSlotChange(origStack,itemstack);
    }
 else     if (factory.isGhostSlot(index) || factory.isGhostOutputSlot(index)) {
      return null;
    }
 else     if (factory.isPlayerInventorySlot(index)) {
      if (!mergeItemStacks(origStack,SlotType.SLOT_SPECIFICITEM,false)) {
        if (!mergeItemStacks(origStack,SlotType.SLOT_INPUT,false)) {
          if (!mergeItemStacks(origStack,SlotType.SLOT_PLAYERHOTBAR,false)) {
            return null;
          }
        }
      }
    }
 else     if (factory.isPlayerHotbarSlot(index)) {
      if (!mergeItemStacks(origStack,SlotType.SLOT_SPECIFICITEM,false)) {
        if (!mergeItemStacks(origStack,SlotType.SLOT_INPUT,false)) {
          if (!mergeItemStacks(origStack,SlotType.SLOT_PLAYERINV,false)) {
            return null;
          }
        }
      }
    }
 else {
      RFTools.log("String_Node_Str" + index);
    }
    if (origStack.stackSize == 0) {
      slot.putStack(null);
    }
 else {
      slot.onSlotChanged();
    }
    if (origStack.stackSize == itemstack.stackSize) {
      return null;
    }
    slot.onPickupFromSlot(player,origStack);
  }
  return itemstack;
}

Fixed version (ground truth):
@Override public ItemStack transferStackInSlot(EntityPlayer player,int index){
  ItemStack itemstack=null;
  Slot slot=(Slot)this.inventorySlots.get(index);
  if (slot != null && slot.getHasStack()) {
    ItemStack origStack=slot.getStack();
    itemstack=origStack.copy();
    if (factory.isSpecificItemSlot(index)) {
      if (!mergeItemStacks(origStack,SlotType.SLOT_PLAYERINV,true)) {
        if (!mergeItemStacks(origStack,SlotType.SLOT_PLAYERHOTBAR,false)) {
          return null;
        }
      }
      slot.onSlotChange(origStack,itemstack);
    }
 else     if (factory.isOutputSlot(index) || factory.isInputSlot(index) || factory.isContainerSlot(index)) {
      if (!mergeItemStacks(origStack,SlotType.SLOT_SPECIFICITEM,false)) {
        if (!mergeItemStacks(origStack,SlotType.SLOT_PLAYERINV,true)) {
          if (!mergeItemStacks(origStack,SlotType.SLOT_PLAYERHOTBAR,false)) {
            return null;
          }
        }
      }
      slot.onSlotChange(origStack,itemstack);
    }
 else     if (factory.isGhostSlot(index) || factory.isGhostOutputSlot(index)) {
      return null;
    }
 else     if (factory.isPlayerInventorySlot(index)) {
      if (!mergeItemStacks(origStack,SlotType.SLOT_SPECIFICITEM,false)) {
        if (!mergeItemStacks(origStack,SlotType.SLOT_INPUT,false)) {
          if (!mergeItemStacks(origStack,SlotType.SLOT_PLAYERHOTBAR,false)) {
            return null;
          }
        }
      }
    }
 else     if (factory.isPlayerHotbarSlot(index)) {
      if (!mergeItemStacks(origStack,SlotType.SLOT_SPECIFICITEM,false)) {
        if (!mergeItemStacks(origStack,SlotType.SLOT_INPUT,false)) {
          if (!mergeItemStacks(origStack,SlotType.SLOT_PLAYERINV,false)) {
            return null;
          }
        }
      }
    }
 else {
      RFTools.log("String_Node_Str" + index);
    }
    if (origStack.stackSize == 0) {
      slot.putStack(null);
    }
 else {
      slot.onSlotChanged();
    }
    if (origStack.stackSize == itemstack.stackSize) {
      return null;
    }
    RFTools.log("String_Node_Str");
    slot.onPickupFromSlot(player,origStack);
  }
  return itemstack;
}