I have got the item I need to damage after using in a crafting table:

package elementum;

import net.minecraft.client.renderer.texture.IconRegister;
import net.minecraft.item.Item;
import net.minecraft.item.ItemStack;
import net.minecraft.util.Icon;
import cpw.mods.fml.relauncher.Side;
import cpw.mods.fml.relauncher.SideOnly;

public class ItemForgingHammer extends Item
{
    private ItemStack emptyItem = null;

public ItemForgingHammer(int id) {
	super(id);
	maxStackSize = 1;
	setMaxDamage(31);
}

@Override
    public boolean hasContainerItem() {
            return true;
    }

    public void setEmptyItem(ItemStack ei) {
            this.emptyItem = ei;
    }

    public boolean doesContainerItemLeaveCraftingGrid(ItemStack par1ItemStack) {
            return false;
    }

    @Override
    public ItemStack getContainerItemStack(ItemStack stack) {
            int dmg = stack.getItemDamage();
            if (dmg == 32) {
                    return new ItemStack(stack.getItem(), 0, 32);
            }
            ItemStack tr = copyStack(stack, 1);
            tr.setItemDamage(dmg + 2);
            return tr;
    }

    public static ItemStack copyStack(ItemStack stack, int n) {
            return new ItemStack(stack.itemID, n, stack.getItemDamage());
    }

@SideOnly(Side.CLIENT)
public void registerIcons(IconRegister par1IconRegister)
{
	this.itemIcon = par1IconRegister.registerIcon(Elementum.modid + ":" + this.getUnlocalizedName().substring(5));
}

}

 

Here's the crafting recpie:

GameRegistry.addRecipe(new ItemStack(ironPlate), new Object[]{
            "X","Y", 'X', new ItemStack(Elementum.forgingHammer,1,-1), 'Y', Item.ingotIron
     });

The problem is that it doesn't want to craft after it's been used only once.

Here is my github:

 

https://github.com/f1rSt1k/f1rSt1kCraft/blob/master/f1rSt1k/items/ItemsContainerItem.java

 

And recipe:

 

GameRegistry.addShapelessRecipe(new ItemStack(foodDough, 2, 0), new Object[] {new ItemStack(Items.itemMortarWithPestle, 1, OreDictionary.WILDCARD_VALUE), Item.wheat});

Probably because your crafting recipe is set to only use the undamaged item.

(Edit: I don't know how the OreDictionary.WILDCARD_VALUE is intended to work with recipes like this, tbh)