I've decompiled Thaumcraft into my workspace to find out how warded jars store essentia.

 

Of course, after decompiling I get a series of errors making my Thaumcraft unable to run in the workspace. I'm using Bearded-Octo-Nemesis to deobfuscate then jd-gui to decompile in to a source .zip which I then place into a Thaumcraft project. Is there a way to do this that doesn't give errors or am I just doing something wrong?

Decompiling is not a perfect science.  If you know what the errors are and know what you're trying to do, you can usually solve the problem.

I feared as much. I went and fixed some of it, but I'm surrently stuck on this little bit of code.

 

At         

} else if ((next instanceof ArrayList)) {for (ItemStack item : (ArrayList)next) {match = (match) || (checkItemEquals(item, slot));

I get an error: Type mismatch: cannot convert from element type Object to ItemStack.

 

 public ItemStack getCraftingResult(InventoryCrafting var1) {
     return this.output.copy();
  }

   public boolean matches(InventoryCrafting var1, World world)
   {
     ArrayList required = new ArrayList(this.input);
     for (int x = 0; x < var1.getSizeInventory(); x++)
     {
       ItemStack slot = var1.getStackInSlot(x);
       if (slot != null)
       {
         boolean inRecipe = false;
         Iterator req = required.iterator();
         while (req.hasNext())
         {
           boolean match = false;          
           Object next = req.next();
           if ((next instanceof ItemStack)) {
             match = checkItemEquals((ItemStack)next, slot);
           } else if ((next instanceof ArrayList)) {
             for (ItemStack item : (ArrayList)next) {
               match = (match) || (checkItemEquals(item, slot));
             }
           }
           if (match)
          {
             inRecipe = true;
             required.remove(next);
             break;
           }
         }
         if (!inRecipe) {
           return false;
        }
       }
     }
     return required.isEmpty();

Its the for loop.  Eclipse doesn't like

for(type var : array)

type loops.  You'll have to change it to a regular loop.

 

The code is technically valid, Eclipse just doesn't like it (it's a decompile-is-not-perfect issue).

Java compiler does type erasure.

It was probably ArrayList<ItemStack> in the original code.