Program: 169611
Project: 169611
Buggy source:
@Override public boolean onPlayerRightClick(EntityPlayer player,int side,Pos hit){
  if (player.getHeldItem() != null && player.getHeldItem().getItem() == Items.stick) {
    if (Engine.runningAsDev) {
      if (isServer()) {
        player.addChatComponentMessage(new ChatComponentText("String_Node_Str" + getMissile()));
      }
      return true;
    }
  }
  if (getMissile() == null) {
    if (player.getHeldItem() != null && player.getHeldItem().getItem() instanceof IModularMissileItem) {
      if (isServer()) {
        Missile missile=MissileModuleBuilder.INSTANCE.buildMissile(player.getHeldItem());
        if (missile != null) {
          if (canAcceptMissile(missile)) {
            ItemStack copy=player.getHeldItem().copy();
            copy.stackSize=1;
            this.setInventorySlotContents(0,copy);
            if (!player.capabilities.isCreativeMode) {
              if (player.getHeldItem().stackSize <= 0) {
                copy=player.getHeldItem().copy();
                copy.stackSize--;
                if (copy.stackSize <= 0) {
                  player.inventory.setInventorySlotContents(player.inventory.currentItem,null);
                }
 else {
                  player.inventory.setInventorySlotContents(player.inventory.currentItem,copy);
                }
              }
              player.inventoryContainer.detectAndSendChanges();
            }
          }
 else {
            player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
          }
        }
 else {
          player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
        }
      }
      return true;
    }
    if (StandardMissileCrafting.isPartOfRecipe(player.getHeldItem())) {
      if (recipe == null) {
        triggerCraftingMode();
        this.recipe=new StandardMissileCrafting();
        player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
      }
      ItemStack heldItem=player.getHeldItem();
      if (heldItem != null) {
        if (isServer()) {
          heldItem=heldItem.copy();
          if (recipe.canAddItem(heldItem)) {
            if (!recipe.addItem(heldItem)) {
              if (!recipe.isFinished()) {
                player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
              }
 else {
                player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
              }
            }
 else             if (!InventoryUtility.stacksMatchExact(player.getHeldItem(),heldItem)) {
              if (heldItem.stackSize <= 0) {
                heldItem=null;
              }
              player.inventory.setInventorySlotContents(player.inventory.currentItem,heldItem);
              player.inventoryContainer.detectAndSendChanges();
              sendDescPacket();
            }
          }
 else {
            player.addChatComponentMessage(recipe.getCurrentRecipeChat());
          }
          return true;
        }
 else         if (Block.getBlockFromItem(player.getHeldItem().getItem()) == null) {
          if (isServer()) {
            player.addChatComponentMessage(recipe.getCurrentRecipeChat());
          }
          return true;
        }
      }
    }
  }
  return false;
}

Fixed version (ground truth):
@Override public boolean onPlayerRightClick(EntityPlayer player,int side,Pos hit){
  if (player.getHeldItem() != null && player.getHeldItem().getItem() == Items.stick) {
    if (Engine.runningAsDev) {
      if (isServer()) {
        player.addChatComponentMessage(new ChatComponentText("String_Node_Str" + getMissile()));
      }
      return true;
    }
  }
  if (getMissile() == null) {
    if (player.getHeldItem() != null && player.getHeldItem().getItem() instanceof IModularMissileItem) {
      if (isServer()) {
        Missile missile=MissileModuleBuilder.INSTANCE.buildMissile(player.getHeldItem());
        if (missile != null) {
          if (canAcceptMissile(missile)) {
            ItemStack copy=player.getHeldItem().copy();
            copy.stackSize=1;
            this.setInventorySlotContents(0,copy);
            if (!player.capabilities.isCreativeMode) {
              player.getHeldItem().stackSize--;
              if (player.getHeldItem().stackSize <= 0) {
                player.inventory.setInventorySlotContents(player.inventory.currentItem,null);
              }
              player.inventoryContainer.detectAndSendChanges();
            }
          }
 else {
            player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
          }
        }
 else {
          player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
        }
      }
      return true;
    }
    if (StandardMissileCrafting.isPartOfRecipe(player.getHeldItem())) {
      if (recipe == null) {
        triggerCraftingMode();
        this.recipe=new StandardMissileCrafting();
        player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
      }
      ItemStack heldItem=player.getHeldItem();
      if (heldItem != null) {
        if (isServer()) {
          heldItem=heldItem.copy();
          if (recipe.canAddItem(heldItem)) {
            if (!recipe.addItem(heldItem)) {
              if (!recipe.isFinished()) {
                player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
              }
 else {
                player.addChatComponentMessage(new ChatComponentText("String_Node_Str"));
              }
            }
 else             if (!InventoryUtility.stacksMatchExact(player.getHeldItem(),heldItem)) {
              if (heldItem.stackSize <= 0) {
                heldItem=null;
              }
              player.inventory.setInventorySlotContents(player.inventory.currentItem,heldItem);
              player.inventoryContainer.detectAndSendChanges();
              sendDescPacket();
            }
          }
 else {
            player.addChatComponentMessage(recipe.getCurrentRecipeChat());
          }
          return true;
        }
 else         if (Block.getBlockFromItem(player.getHeldItem().getItem()) == null) {
          if (isServer()) {
            player.addChatComponentMessage(recipe.getCurrentRecipeChat());
          }
          return true;
        }
      }
    }
  }
  return false;
}