more fixes related to tools with uses

src/main/java/com/raoulvdberge/refinedstorage/apiimpl/autocrafting/task/CraftingStep.java

@@ -83,6 +83,7 @@ public abstract class CraftingStep implements ICraftingStep {
     @Override
     public boolean canStartProcessing(IItemStackList items, IFluidStackList fluids) {
         items = items.copy(); // So we can edit the list
+        items.clean();// Clean the list so the zero stacks aren't there
 
         for (ItemStack stack : getToInsert()) {
             ItemStack actualStack = items.get(stack, IComparer.COMPARE_DAMAGE | IComparer.COMPARE_NBT | (pattern.isOredict() ? IComparer.COMPARE_OREDICT : 0));

src/main/java/com/raoulvdberge/refinedstorage/apiimpl/autocrafting/task/CraftingStepCraft.java

@@ -30,6 +30,9 @@ public class CraftingStepCraft extends CraftingStep {
         // So we can edit the lists
         items = items.copy();
         fluids = fluids.copy();
+        // Clean the lists so the zero stacks aren't there
+        items.clean();
+        fluids.clear();
 
         int compare = IComparer.COMPARE_DAMAGE | IComparer.COMPARE_NBT | (pattern.isOredict() ? IComparer.COMPARE_OREDICT : 0);
         for (ItemStack stack : getToInsert()) {

src/main/java/com/raoulvdberge/refinedstorage/apiimpl/autocrafting/task/CraftingTask.java

@@ -73,6 +73,7 @@ public class CraftingTask implements ICraftingTask {
     @Override
     public void calculate() {
         IItemStackList networkList = network.getItemStorageCache().getList().copy();
+        networkList.clean(); // Remove the zero stacks
         IItemStackList toInsert = API.instance().createItemStackList();
 
         toCraft.add(ItemHandlerHelper.copyStackWithSize(requested, quantity));