Program: 169666
Project: 169666
Buggy source:
@Override public boolean onPlayerRightClick(EntityPlayer player,int side,Pos hit){
  if (isServer()) {
    if (player.getHeldItem() != null) {
      if (getMissileItem() == null) {
        if (isItemValidForSlot(INPUT_SLOT,player.getHeldItem())) {
          if (InventoryUtility.addItemToSlot(player,this,INPUT_SLOT)) {
            updateMissile();
          }
 else {
            player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
          }
        }
 else {
          player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
        }
      }
 else       if (getMissile() != null) {
        IModule module=null;
        if (player.getHeldItem() != null)         module=((IModuleItem)player.getHeldItem().getItem()).getModule(player.getHeldItem());
        if (module instanceof Guidance) {
          if (getMissile().getGuidance() == null) {
            getMissile().setGuidance((Guidance)module);
            player.getHeldItem().stackSize--;
            if (player.getHeldItem().stackSize <= 0)             player.inventory.setInventorySlotContents(player.inventory.currentItem,null);
            player.inventoryContainer.detectAndSendChanges();
            updateMissileItem();
          }
 else {
            player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
          }
        }
 else         if (module instanceof RocketEngine) {
          player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
        }
 else         if (module instanceof Warhead) {
          player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
        }
 else {
          player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
        }
      }
    }
 else     if (player.isSneaking()) {
      InventoryUtility.removeItemFromSlot(player,this,INPUT_SLOT);
      updateMissile();
    }
 else     if (getMissile() != null && getMissile().getGuidance() != null) {
      ItemStack stack=getMissile().getGuidance().toStack();
      player.inventory.setInventorySlotContents(player.inventory.currentItem,stack);
      getMissile().setGuidance(null);
      updateMissileItem();
      player.inventoryContainer.detectAndSendChanges();
    }
  }
  return true;
}

Fixed version (ground truth):
@Override public boolean onPlayerRightClick(EntityPlayer player,int side,Pos hit){
  if (isServer()) {
    if (player.getHeldItem() != null) {
      if (getMissileItem() == null) {
        if (isItemValidForSlot(INPUT_SLOT,player.getHeldItem())) {
          if (InventoryUtility.addItemToSlot(player,this,INPUT_SLOT)) {
            updateMissile();
          }
 else {
            player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
          }
        }
 else {
          player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
        }
      }
 else       if (getMissile() != null && player.getHeldItem().getItem() instanceof IModule) {
        IModule module=null;
        if (player.getHeldItem() != null) {
          module=((IModuleItem)player.getHeldItem().getItem()).getModule(player.getHeldItem());
        }
        if (module instanceof Guidance) {
          if (getMissile().getGuidance() == null) {
            getMissile().setGuidance((Guidance)module);
            player.getHeldItem().stackSize--;
            if (player.getHeldItem().stackSize <= 0)             player.inventory.setInventorySlotContents(player.inventory.currentItem,null);
            player.inventoryContainer.detectAndSendChanges();
            updateMissileItem();
          }
 else {
            player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
          }
        }
 else         if (module instanceof RocketEngine) {
          player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
        }
 else         if (module instanceof Warhead) {
          player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
        }
 else {
          player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
        }
      }
    }
 else     if (player.isSneaking()) {
      InventoryUtility.removeItemFromSlot(player,this,INPUT_SLOT);
      updateMissile();
    }
 else     if (getMissile() != null && getMissile().getGuidance() != null) {
      ItemStack stack=getMissile().getGuidance().toStack();
      player.inventory.setInventorySlotContents(player.inventory.currentItem,stack);
      getMissile().setGuidance(null);
      updateMissileItem();
      player.inventoryContainer.detectAndSendChanges();
    }
  }
  return true;
}