craftbukkit/nms-patches/Slot.patch

--- a/net/minecraft/server/Slot.java
+++ b/net/minecraft/server/Slot.java
@@ -2,7 +2,7 @@
 
 public class Slot {
 
-    private final int index;
+    public final int index; // CraftBukkit - public
     public final IInventory inventory;
     public int rawSlotIndex;
     public int f;
@@ -45,6 +45,9 @@
     }
 
     public boolean hasItem() {
+        if (getItem() != null && getItem().count == 0) {
+            set(null);
+        }
         return this.getItem() != null;
     }