More tests. Substitutions now work, and a fix is included. *sigh* Closes too many bugs to count.

src/main/java/net/minecraftforge/fml/common/LoadController.java

@@ -199,6 +199,10 @@ public class LoadController
         return activeContainer != null ? activeContainer : findActiveContainerFromStack();
     }
 
+    void forceActiveContainer(ModContainer container)
+    {
+        activeContainer = container;
+    }
     @Subscribe
     public void propogateStateMessage(FMLEvent stateEvent)
     {

src/main/java/net/minecraftforge/fml/common/Loader.java

@@ -38,6 +38,7 @@ import net.minecraftforge.common.capabilities.CapabilityManager;
 import net.minecraftforge.fml.common.LoaderState.ModState;
 import net.minecraftforge.fml.common.ModContainer.Disableable;
 import net.minecraftforge.fml.common.ProgressManager.ProgressBar;
+import net.minecraftforge.fml.common.discovery.ASMDataTable;
 import net.minecraftforge.fml.common.discovery.ModDiscoverer;
 import net.minecraftforge.fml.common.event.FMLInterModComms;
 import net.minecraftforge.fml.common.event.FMLLoadEvent;
@@ -488,11 +489,24 @@ public class Loader
         return instance().mods != null ? ImmutableList.copyOf(instance().mods) : ImmutableList.<ModContainer>of();
     }
 
+    /**
+     * Used to setup a testharness with a single dummy mod instance for use with various testing hooks
+     * @param dummycontainer A dummy container that will be returned as "active" for all queries
+     */
+    public void setupTestHarness(ModContainer dummycontainer)
+    {
+        modController = new LoadController(this);
+        mods = Lists.newArrayList(dummycontainer);
+        modController.transition(LoaderState.LOADING, false);
+        modController.transition(LoaderState.CONSTRUCTING, false);
+        ObjectHolderRegistry.INSTANCE.findObjectHolders(new ASMDataTable());
+        modController.forceActiveContainer(dummycontainer);
+    }
     /**
      * Called from the hook to start mod loading. We trigger the
      * {@link #identifyMods()} and Constructing, Preinitalization, and Initalization phases here. Finally,
      * the mod list is frozen completely and is consider immutable from then on.
-     * @param injectedModContainers
+     * @param injectedModContainers containers to inject
      */
     public void loadMods(List<String> injectedModContainers)
     {

src/main/java/net/minecraftforge/fml/common/registry/FMLControlledNamespacedRegistry.java

@@ -65,6 +65,10 @@ public class FMLControlledNamespacedRegistry<I extends IForgeRegistryEntry<I>> e
      * Persistent substitutions are the mechanism to allow mods to override specific behaviours with new behaviours.
      */
     private final BiMap<ResourceLocation, I> persistentSubstitutions = HashBiMap.create();
+    /**
+     * Substitution originals - these are the originals that are being substituted
+     */
+    private final BiMap<ResourceLocation, I> substitutionOriginals = HashBiMap.create();
     /**
      * This is the current active substitution set for a particular world. It will change as worlds come and go.
      */
@@ -602,6 +606,11 @@ public class FMLControlledNamespacedRegistry<I extends IForgeRegistryEntry<I>> e
             I sub = getPersistentSubstitutions().get(nameToReplace);
             getExistingDelegate(original).changeReference(sub);
             activeSubstitutions.put(nameToReplace, sub);
+            int id = getIDForObjectBypass(original);
+            // force the new object into the existing map
+            addObjectRaw(id, nameToReplace, sub);
+            // Track the original in the substitution originals collection
+            substitutionOriginals.put(nameToReplace, original);
             return original;
         }
         return null;
@@ -747,7 +756,11 @@ public class FMLControlledNamespacedRegistry<I extends IForgeRegistryEntry<I>> e
                 remappedIds.put(itemName, new Integer[] {currId, newId});
             }
             I obj = currentRegistry.getRaw(itemName);
-
+            // If we have an object in the originals set, we use that for initial adding - substitute activation will readd the substitute if neceessary later
+            if (currentRegistry.substitutionOriginals.containsKey(itemName))
+            {
+                obj = currentRegistry.substitutionOriginals.get(itemName);
+            }
             add(newId, itemName, obj);
         }
     }