#830 fix farm crash when Plugin Arboriculture is disabled

application.properties

@@ -2,4 +2,4 @@ mcversion=1.7.10
 forgeversion=10.13.3.1370-1.7.10
 version_major=4
 version_minor=0
-version_patch=3
+version_patch=5

src/main/java/forestry/apiculture/BeekeepingLogic.java

@@ -73,8 +73,8 @@ public class BeekeepingLogic implements IBeekeepingLogic, IStreamable {
 
 	public BeekeepingLogic(IBeeHousing housing) {
 		this.housing = housing;
-		this.beeModifier = new BeeHousingModifier(housing);
-		this.beeListener = new BeeHousingListener(housing);
+		this.beeModifier = BeeManager.beeRoot.createBeeHousingModifier(housing);
+		this.beeListener = BeeManager.beeRoot.createBeeHousingListener(housing);
 	}
 
 	// / SAVING & LOADING

src/main/java/forestry/apiculture/flowers/FlowerRegistry.java

@@ -38,6 +38,7 @@ import net.minecraftforge.oredict.OreDictionary;
 
 import cpw.mods.fml.common.registry.GameRegistry;
 
+import forestry.api.apiculture.BeeManager;
 import forestry.api.apiculture.FlowerManager;
 import forestry.api.apiculture.IBee;
 import forestry.api.apiculture.IBeeGenome;
@@ -47,7 +48,6 @@ import forestry.api.genetics.IFlower;
 import forestry.api.genetics.IFlowerGrowthRule;
 import forestry.api.genetics.IFlowerRegistry;
 import forestry.api.genetics.IIndividual;
-import forestry.apiculture.BeeHousingModifier;
 import forestry.core.utils.vect.MutableVect;
 import forestry.core.utils.vect.Vect;
 import forestry.plugins.PluginManager;
@@ -142,7 +142,7 @@ public final class FlowerRegistry implements IFlowerRegistry {
 		Set<IFlower> acceptedFlowers = this.registeredFlowers.get(flowerType);
 		World world = beeHousing.getWorld();
 
-		IBeeModifier beeModifier = new BeeHousingModifier(beeHousing);
+		IBeeModifier beeModifier = BeeManager.beeRoot.createBeeHousingModifier(beeHousing);
 
 		Vect area = getArea(bee.getGenome(), beeModifier);
 		Vect housingPos = new Vect(beeHousing.getCoordinates()).add(-area.x / 2, -area.y / 2, -area.z / 2);

src/main/java/forestry/apiculture/genetics/Bee.java

@@ -52,7 +52,6 @@ import forestry.api.genetics.IFlowerProvider;
 import forestry.api.genetics.IIndividual;
 import forestry.api.genetics.IMutation;
 import forestry.api.genetics.IPollinatable;
-import forestry.apiculture.BeeHousingModifier;
 import forestry.arboriculture.genetics.pollination.FakePollinatable;
 import forestry.arboriculture.genetics.pollination.ICheckPollinatable;
 import forestry.core.config.Config;
@@ -253,7 +252,7 @@ public class Bee extends IndividualLiving implements IBee {
 
 		Set<IErrorState> errorStates = new HashSet<IErrorState>();
 
-		IBeeModifier beeModifier = new BeeHousingModifier(housing);
+		IBeeModifier beeModifier = BeeManager.beeRoot.createBeeHousingModifier(housing);
 
 		// / Rain needs tolerant flyers
 		if (world.isRaining() && !genome.getTolerantFlyer() && BiomeHelper.canRainOrSnow(biome) && !beeModifier.isSealed()) {
@@ -458,7 +457,7 @@ public class Bee extends IndividualLiving implements IBee {
 			setIsNatural(false);
 		}
 
-		IBeeModifier beeHousingModifier = new BeeHousingModifier(housing);
+		IBeeModifier beeHousingModifier = BeeManager.beeRoot.createBeeHousingModifier(housing);
 		IBeeModifier beeModeModifier = mode.getBeeModifier();
 
 		// Bee genetic speed * beehousing * beekeeping mode
@@ -630,7 +629,7 @@ public class Bee extends IndividualLiving implements IBee {
 	@Override
 	public IIndividual retrievePollen(IBeeHousing housing) {
 
-		IBeeModifier beeModifier = new BeeHousingModifier(housing);
+		IBeeModifier beeModifier = BeeManager.beeRoot.createBeeHousingModifier(housing);
 
 		int chance = Math.round(genome.getFlowering() * beeModifier.getFloweringModifier(getGenome(), 1f));
 
@@ -673,7 +672,7 @@ public class Bee extends IndividualLiving implements IBee {
 	@Override
 	public boolean pollinateRandom(IBeeHousing housing, IIndividual pollen) {
 
-		IBeeModifier beeModifier = new BeeHousingModifier(housing);
+		IBeeModifier beeModifier = BeeManager.beeRoot.createBeeHousingModifier(housing);
 
 		int chance = (int) (genome.getFlowering() * beeModifier.getFloweringModifier(getGenome(), 1f));
 
@@ -720,7 +719,7 @@ public class Bee extends IndividualLiving implements IBee {
 	@Override
 	public void plantFlowerRandom(IBeeHousing housing) {
 
-		IBeeModifier beeModifier = new BeeHousingModifier(housing);
+		IBeeModifier beeModifier = BeeManager.beeRoot.createBeeHousingModifier(housing);
 
 		int chance = Math.round(genome.getFlowering() * beeModifier.getFloweringModifier(getGenome(), 1f));
 

src/main/java/forestry/apiculture/genetics/BeeHelper.java

@@ -33,6 +33,8 @@ import forestry.api.apiculture.IApiaristTracker;
 import forestry.api.apiculture.IBee;
 import forestry.api.apiculture.IBeeGenome;
 import forestry.api.apiculture.IBeeHousing;
+import forestry.api.apiculture.IBeeListener;
+import forestry.api.apiculture.IBeeModifier;
 import forestry.api.apiculture.IBeeMutation;
 import forestry.api.apiculture.IBeeRoot;
 import forestry.api.apiculture.IBeekeepingLogic;
@@ -42,6 +44,8 @@ import forestry.api.genetics.IAllele;
 import forestry.api.genetics.IChromosomeType;
 import forestry.api.genetics.IIndividual;
 import forestry.api.genetics.IMutation;
+import forestry.apiculture.BeeHousingListener;
+import forestry.apiculture.BeeHousingModifier;
 import forestry.apiculture.BeekeepingLogic;
 import forestry.core.config.ForestryItem;
 import forestry.core.genetics.SpeciesRoot;
@@ -326,6 +330,16 @@ public class BeeHelper extends SpeciesRoot implements IBeeRoot {
 		return new BeekeepingLogic(housing);
 	}
 
+	@Override
+	public IBeeModifier createBeeHousingModifier(IBeeHousing housing) {
+		return new BeeHousingModifier(housing);
+	}
+
+	@Override
+	public IBeeListener createBeeHousingListener(IBeeHousing housing) {
+		return new BeeHousingListener(housing);
+	}
+
 	@Override
 	public IChromosomeType[] getKaryotype() {
 		return EnumBeeChromosome.values();

src/main/java/forestry/apiculture/genetics/BeeMutation.java

@@ -21,7 +21,6 @@ import forestry.api.apiculture.IBeeModifier;
 import forestry.api.apiculture.IBeeMutationCustom;
 import forestry.api.apiculture.IBeeRoot;
 import forestry.api.genetics.IAllele;
-import forestry.apiculture.BeeHousingModifier;
 import forestry.core.genetics.mutations.Mutation;
 
 public class BeeMutation extends Mutation implements IBeeMutationCustom {
@@ -48,7 +47,7 @@ public class BeeMutation extends Mutation implements IBeeMutationCustom {
 			return 0;
 		}
 
-		IBeeModifier beeHousingModifier = new BeeHousingModifier(housing);
+		IBeeModifier beeHousingModifier = BeeManager.beeRoot.createBeeHousingModifier(housing);
 		IBeeModifier beeModeModifier = BeeManager.beeRoot.getBeekeepingMode(world).getBeeModifier();
 
 		processedChance *= beeHousingModifier.getMutationModifier(genome0, genome1, processedChance);

src/main/java/forestry/apiculture/genetics/BeekeepingMode.java

@@ -16,13 +16,13 @@ import java.util.Random;
 
 import net.minecraft.world.World;
 
+import forestry.api.apiculture.BeeManager;
 import forestry.api.apiculture.DefaultBeeModifier;
 import forestry.api.apiculture.IBee;
 import forestry.api.apiculture.IBeeGenome;
 import forestry.api.apiculture.IBeeHousing;
 import forestry.api.apiculture.IBeeModifier;
 import forestry.api.apiculture.IBeekeepingMode;
-import forestry.apiculture.BeeHousingModifier;
 
 public class BeekeepingMode implements IBeekeepingMode {
 
@@ -84,7 +84,7 @@ public class BeekeepingMode implements IBeekeepingMode {
 			return false;
 		}
 
-		IBeeModifier beeModifier = new BeeHousingModifier(housing);
+		IBeeModifier beeModifier = BeeManager.beeRoot.createBeeHousingModifier(housing);
 
 		return queen.getGeneration() > 96 + rand.nextInt(6) + rand.nextInt(6) &&
 				rand.nextFloat() < 0.02f * beeModifier.getGeneticDecay(queen.getGenome(), 1f);
@@ -92,7 +92,7 @@ public class BeekeepingMode implements IBeekeepingMode {
 
 	@Override
 	public boolean isOverworked(IBee queen, IBeeHousing housing) {
-		IBeeModifier beeModifier = new BeeHousingModifier(housing);
+		IBeeModifier beeModifier = BeeManager.beeRoot.createBeeHousingModifier(housing);
 
 		float productionModifier = beeModifier.getProductionModifier(queen.getGenome(), 1f);
 		if (productionModifier > 16) {
@@ -106,7 +106,7 @@ public class BeekeepingMode implements IBeekeepingMode {
 	
 	@Override
 	public boolean isDegenerating(IBee queen, IBee offspring, IBeeHousing housing) {
-		IBeeModifier beeModifier = new BeeHousingModifier(housing);
+		IBeeModifier beeModifier = BeeManager.beeRoot.createBeeHousingModifier(housing);
 
 		float mutationModifier = beeModifier.getMutationModifier(queen.getGenome(), queen.getMate(), 1.0f);
 		if (mutationModifier > 10) {

src/main/java/forestry/apiculture/genetics/alleles/AlleleEffectNone.java

@@ -12,12 +12,12 @@ package forestry.apiculture.genetics.alleles;
 
 import net.minecraft.util.AxisAlignedBB;
 
+import forestry.api.apiculture.BeeManager;
 import forestry.api.apiculture.IAlleleBeeEffect;
 import forestry.api.apiculture.IBeeGenome;
 import forestry.api.apiculture.IBeeHousing;
 import forestry.api.apiculture.IBeeModifier;
 import forestry.api.genetics.IEffectData;
-import forestry.apiculture.BeeHousingModifier;
 import forestry.core.genetics.alleles.AlleleCategorized;
 import forestry.core.utils.vect.MutableVect;
 import forestry.core.utils.vect.Vect;
@@ -51,7 +51,7 @@ public class AlleleEffectNone extends AlleleCategorized implements IAlleleBeeEff
 	}
 
 	protected Vect getModifiedArea(IBeeGenome genome, IBeeHousing housing) {
-		IBeeModifier beeModifier = new BeeHousingModifier(housing);
+		IBeeModifier beeModifier = BeeManager.beeRoot.createBeeHousingModifier(housing);
 		float territoryModifier = beeModifier.getTerritoryModifier(genome, 1f);
 
 		MutableVect area = new MutableVect(genome.getTerritory());
@@ -71,7 +71,7 @@ public class AlleleEffectNone extends AlleleCategorized implements IAlleleBeeEff
 	}
 
 	protected AxisAlignedBB getBounding(IBeeGenome genome, IBeeHousing housing) {
-		IBeeModifier beeModifier = new BeeHousingModifier(housing);
+		IBeeModifier beeModifier = BeeManager.beeRoot.createBeeHousingModifier(housing);
 		float territoryModifier = beeModifier.getTerritoryModifier(genome, 1.0f);
 
 		MutableVect area = new MutableVect(genome.getTerritory());

src/main/java/forestry/apiculture/multiblock/AlvearyController.java

@@ -35,7 +35,6 @@ import forestry.api.core.EnumHumidity;
 import forestry.api.core.EnumTemperature;
 import forestry.api.core.IClimateControlled;
 import forestry.apiculture.BeeHousingInventory;
-import forestry.apiculture.BeeHousingModifier;
 import forestry.core.access.EnumAccess;
 import forestry.core.inventory.IInventoryAdapter;
 import forestry.core.multiblock.CoordTriplet;
@@ -384,7 +383,7 @@ public class AlvearyController extends RectangularMultiblockControllerBase imple
 
 	@Override
 	public EnumTemperature getTemperature() {
-		IBeeModifier beeModifier = new BeeHousingModifier(this);
+		IBeeModifier beeModifier = BeeManager.beeRoot.createBeeHousingModifier(this);
 		if (beeModifier.isHellish() && tempChange >= 0) {
 			return EnumTemperature.HELLISH;
 		}

src/main/java/forestry/core/network/PacketId.java

@@ -20,6 +20,7 @@ public enum PacketId {
 	FX_SIGNAL,
 
 	WORKTABLE_MEMORY_UPDATE,
+	WORKTABLE_NEI_SELECT,
 
 	HABITAT_BIOME_POINTER,
 	CANDLE,

src/main/java/forestry/core/recipes/nei/CustomOverlayHandler.java

@@ -0,0 +1,80 @@
+/*******************************************************************************
+ * Copyright (c) 2011-2014 SirSengir.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the GNU Lesser Public License v3
+ * which accompanies this distribution, and is available at
+ * http://www.gnu.org/licenses/lgpl-3.0.txt
+ *
+ * Various Contributors including, but not limited to:
+ * SirSengir (original work), CovertJaguar, Player, Binnie, MysteriousAges
+ ******************************************************************************/
+package forestry.core.recipes.nei;
+
+import java.util.List;
+
+import net.minecraft.client.gui.inventory.GuiContainer;
+import net.minecraft.item.ItemStack;
+import net.minecraft.nbt.NBTTagCompound;
+import net.minecraft.nbt.NBTTagList;
+
+import forestry.core.network.PacketId;
+import forestry.core.network.PacketNBT;
+import forestry.core.proxy.Proxies;
+
+import codechicken.nei.LayoutManager;
+import codechicken.nei.OffsetPositioner;
+import codechicken.nei.PositionedStack;
+import codechicken.nei.api.DefaultOverlayRenderer;
+import codechicken.nei.api.IOverlayHandler;
+import codechicken.nei.api.IStackPositioner;
+import codechicken.nei.recipe.IRecipeHandler;
+
+/**
+ * @author bdew
+ */
+public class CustomOverlayHandler implements IOverlayHandler {
+	private final int xOffs;
+	private final int yOffs;
+	private final boolean forceShift;
+
+	public CustomOverlayHandler(int xOffs, int yOffs, boolean forceShift) {
+		this.xOffs = xOffs;
+		this.yOffs = yOffs;
+		this.forceShift = forceShift;
+	}
+
+	@Override
+	public void overlayRecipe(GuiContainer cont, IRecipeHandler recipe, int recipeIndex, boolean shift) {
+		List<PositionedStack> ingr = recipe.getIngredientStacks(recipeIndex);
+
+		if (shift || forceShift) {
+			NBTTagList stacksnbt = new NBTTagList();
+
+			for (PositionedStack pstack : ingr) {
+				if (pstack != null) {
+					// This is back-asswards but i don't see a better way :(
+					int x = (pstack.relx - 25) / 18;
+					int y = (pstack.rely - 6) / 18;
+
+					ItemStack stack = pstack.item;
+					NBTTagCompound stacknbt = stack.writeToNBT(new NBTTagCompound());
+					stacknbt.setInteger("slot", y * 3 + x);
+					stacksnbt.appendTag(stacknbt);
+				}
+
+				ItemStack stack = recipe.getResultStack(recipeIndex).items[0];
+				NBTTagCompound stacknbt = stack.writeToNBT(new NBTTagCompound());
+				stacknbt.setInteger("slot", 9);
+				stacksnbt.appendTag(stacknbt);
+			}
+
+			NBTTagCompound data = new NBTTagCompound();
+			data.setTag("stacks", stacksnbt);
+
+			Proxies.net.sendToServer(new PacketNBT(PacketId.WORKTABLE_NEI_SELECT, data));
+		} else {
+			IStackPositioner positioner = new OffsetPositioner(xOffs, yOffs);
+			LayoutManager.overlayRenderer = new DefaultOverlayRenderer(ingr, positioner);
+		}
+	}
+}

src/main/java/forestry/core/recipes/nei/ItemFilterForestry.java

@@ -0,0 +1,57 @@
+/*******************************************************************************
+ * Copyright (c) 2011-2014 SirSengir.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the GNU Lesser Public License v3
+ * which accompanies this distribution, and is available at
+ * http://www.gnu.org/licenses/lgpl-3.0.txt
+ *
+ * Various Contributors including, but not limited to:
+ * SirSengir (original work), CovertJaguar, Player, Binnie, MysteriousAges
+ ******************************************************************************/
+package forestry.core.recipes.nei;
+
+import net.minecraft.item.Item;
+import net.minecraft.item.ItemBlock;
+import net.minecraft.item.ItemStack;
+
+import forestry.core.config.Constants;
+
+import codechicken.nei.api.ItemFilter;
+
+/**
+ * @author bdew
+ */
+public class ItemFilterForestry implements ItemFilter {
+	private final boolean items;
+
+	public ItemFilterForestry(Boolean items) {
+		this.items = items;
+	}
+
+	@Override
+	public boolean matches(ItemStack item) {
+		if (item == null || item.getItem() == null) {
+			return false;
+		}
+
+		if (item.getItem() instanceof ItemBlock && items) {
+			return false;
+		}
+
+		if (!(item.getItem() instanceof ItemBlock) && !items) {
+			return false;
+		}
+
+		String itemName = Item.itemRegistry.getNameForObject(item.getItem());
+		if (itemName == null) {
+			return false;
+		}
+
+		String[] s = itemName.split(":");
+		if (s.length <= 1) {
+			return false;
+		}
+
+		return s[0].equals(Constants.MOD);
+	}
+}

src/main/java/forestry/core/recipes/nei/ItemFilterGenetic.java

@@ -0,0 +1,54 @@
+/*******************************************************************************
+ * Copyright (c) 2011-2014 SirSengir.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the GNU Lesser Public License v3
+ * which accompanies this distribution, and is available at
+ * http://www.gnu.org/licenses/lgpl-3.0.txt
+ *
+ * Various Contributors including, but not limited to:
+ * SirSengir (original work), CovertJaguar, Player, Binnie, MysteriousAges
+ ******************************************************************************/
+package forestry.core.recipes.nei;
+
+import net.minecraft.item.ItemStack;
+
+import forestry.api.genetics.IIndividual;
+import forestry.api.genetics.ISpeciesRoot;
+
+import codechicken.nei.api.ItemFilter;
+
+/**
+ * @author bdew
+ */
+public class ItemFilterGenetic implements ItemFilter {
+	private final ISpeciesRoot root;
+	private final int type;
+	private final boolean analyzedOnly;
+
+	public ItemFilterGenetic(ISpeciesRoot root, int type, boolean analyzedOnly) {
+		this.root = root;
+		this.type = type;
+		this.analyzedOnly = analyzedOnly;
+	}
+
+	private boolean isMember(ItemStack item) {
+		if (type >= 0) {
+			return root.isMember(item, type);
+		} else {
+			return root.isMember(item);
+		}
+	}
+
+	@Override
+	public boolean matches(ItemStack item) {
+		if (analyzedOnly) {
+			if (!isMember(item)) {
+				return false;
+			}
+			IIndividual individual = root.getMember(item);
+			return individual.isAnalyzed() || !individual.isSecret();
+		} else {
+			return isMember(item);
+		}
+	}
+}

src/main/java/forestry/core/recipes/nei/ItemFilterOther.java

@@ -0,0 +1,30 @@
+/*******************************************************************************
+ * Copyright (c) 2011-2014 SirSengir.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the GNU Lesser Public License v3
+ * which accompanies this distribution, and is available at
+ * http://www.gnu.org/licenses/lgpl-3.0.txt
+ *
+ * Various Contributors including, but not limited to:
+ * SirSengir (original work), CovertJaguar, Player, Binnie, MysteriousAges
+ ******************************************************************************/
+package forestry.core.recipes.nei;
+
+import net.minecraft.item.ItemStack;
+
+import forestry.api.genetics.AlleleManager;
+
+/**
+ * @author bdew
+ */
+public class ItemFilterOther extends ItemFilterForestry {
+
+	public ItemFilterOther(Boolean items) {
+		super(items);
+	}
+
+	@Override
+	public boolean matches(ItemStack item) {
+		return super.matches(item) && !AlleleManager.alleleRegistry.isIndividual(item);
+	}
+}

src/main/java/forestry/core/recipes/nei/NEIIntegrationConfig.java

@@ -10,7 +10,15 @@
  ******************************************************************************/
 package forestry.core.recipes.nei;
 
+import net.minecraftforge.oredict.OreDictionary;
+
+import forestry.api.apiculture.BeeManager;
+import forestry.api.apiculture.EnumBeeType;
+import forestry.api.arboriculture.EnumGermlingType;
+import forestry.api.arboriculture.TreeManager;
+import forestry.api.lepidopterology.EnumFlutterType;
 import forestry.core.utils.Log;
+import forestry.factory.gui.GuiWorktable;
 import forestry.factory.recipes.nei.NEIHandlerBottler;
 import forestry.factory.recipes.nei.NEIHandlerCarpenter;
 import forestry.factory.recipes.nei.NEIHandlerCentrifuge;
@@ -19,6 +27,7 @@ import forestry.factory.recipes.nei.NEIHandlerFermenter;
 import forestry.factory.recipes.nei.NEIHandlerMoistener;
 import forestry.factory.recipes.nei.NEIHandlerSqueezer;
 import forestry.factory.recipes.nei.NEIHandlerStill;
+import forestry.plugins.PluginLepidopterology;
 
 import codechicken.nei.api.API;
 import codechicken.nei.api.IConfigureNEI;
@@ -39,6 +48,24 @@ public class NEIIntegrationConfig implements IConfigureNEI {
 		registerHandler(new NEIHandlerMoistener());
 		registerHandler(new NEIHandlerSqueezer());
 		registerHandler(new NEIHandlerStill());
+
+		CustomOverlayHandler handler = new CustomOverlayHandler(-14, 14, true);
+		API.registerGuiOverlayHandler(GuiWorktable.class, handler, "crafting");
+
+		API.addSubset("Forestry.Bees.Princesses", new ItemFilterGenetic(BeeManager.beeRoot, EnumBeeType.PRINCESS.ordinal(), true));
+		API.addSubset("Forestry.Bees.Drones", new ItemFilterGenetic(BeeManager.beeRoot, EnumBeeType.DRONE.ordinal(), true));
+		API.addSubset("Forestry.Bees.Larvae", new ItemFilterGenetic(BeeManager.beeRoot, EnumBeeType.LARVAE.ordinal(), true));
+
+		API.addSubset("Forestry.Trees.Saplings", new ItemFilterGenetic(TreeManager.treeRoot, EnumGermlingType.SAPLING.ordinal(), true));
+		API.addSubset("Forestry.Trees.Pollen", new ItemFilterGenetic(TreeManager.treeRoot, EnumGermlingType.POLLEN.ordinal(), true));
+
+		API.addSubset("Forestry.Butterflies.Butterflies", new ItemFilterGenetic(PluginLepidopterology.butterflyInterface, EnumFlutterType.BUTTERFLY.ordinal(), true));
+		API.addSubset("Forestry.Butterflies.Caterpillars", new ItemFilterGenetic(PluginLepidopterology.butterflyInterface, EnumFlutterType.CATERPILLAR.ordinal(), true));
+		API.addSubset("Forestry.Butterflies.Serum", new ItemFilterGenetic(PluginLepidopterology.butterflyInterface, EnumFlutterType.SERUM.ordinal(), true));
+
+		API.addSubset("Forestry.Bees.Combs", OreDictionary.getOres("beeComb"));
+		API.addSubset("Forestry.Blocks", new ItemFilterOther(false));
+		API.addSubset("Forestry.Items", new ItemFilterOther(true));
 	}
 
 	protected static void registerHandler(IRecipeHandlerBase handler) {
@@ -54,7 +81,7 @@ public class NEIIntegrationConfig implements IConfigureNEI {
 
 	@Override
 	public String getVersion() {
-		return "1.0.0";
+		return "1.1.0";
 	}
 
 }

src/main/java/forestry/core/recipes/nei/SetRecipeCommandHandler.java

@@ -0,0 +1,60 @@
+/*******************************************************************************
+ * Copyright (c) 2011-2014 SirSengir.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the GNU Lesser Public License v3
+ * which accompanies this distribution, and is available at
+ * http://www.gnu.org/licenses/lgpl-3.0.txt
+ *
+ * Various Contributors including, but not limited to:
+ * SirSengir (original work), CovertJaguar, Player, Binnie, MysteriousAges
+ ******************************************************************************/
+package forestry.core.recipes.nei;
+
+import java.util.HashMap;
+import java.util.Map;
+
+import net.minecraft.entity.player.EntityPlayerMP;
+import net.minecraft.inventory.Container;
+import net.minecraft.inventory.Slot;
+import net.minecraft.item.ItemStack;
+import net.minecraft.nbt.NBTTagCompound;
+import net.minecraft.nbt.NBTTagList;
+
+/**
+ * @author bdew
+ */
+public class SetRecipeCommandHandler {
+	private final Class<? extends Container> containerClass;
+	private final Class<? extends Slot> slotClass;
+
+	public SetRecipeCommandHandler(Class<? extends Container> containerClass, Class<? extends Slot> slotClass) {
+		this.containerClass = containerClass;
+		this.slotClass = slotClass;
+	}
+
+	public void handle(NBTTagCompound data, EntityPlayerMP player) {
+		NBTTagList stacks = data.getTagList("stacks", 10);
+		Container cont = player.openContainer;
+		if (!containerClass.isInstance(cont)) {
+			return;
+		}
+
+		Map<Integer, ItemStack> stmap = new HashMap<Integer, ItemStack>();
+		for (int i = 0; i < stacks.tagCount(); i++) {
+			NBTTagCompound itemdata = stacks.getCompoundTagAt(i);
+			stmap.put(itemdata.getInteger("slot"), ItemStack.loadItemStackFromNBT(itemdata));
+		}
+		for (Object slotobj : cont.inventorySlots) {
+			if (!slotClass.isInstance(slotobj)) {
+				continue;
+			}
+
+			Slot slot = (Slot) slotobj;
+			if (stmap.containsKey(slot.getSlotIndex())) {
+				slot.putStack(stmap.get(slot.getSlotIndex()));
+			} else {
+				slot.putStack(null);
+			}
+		}
+	}
+}

src/main/java/forestry/core/utils/GeneticsUtil.java

@@ -195,20 +195,19 @@ public class GeneticsUtil {
 		exclude.add(species);
 
 		for (IMutation mutation : species.getRoot().getPaths(species, speciesChromosome)) {
-			if (!exclude.contains(mutation.getAllele0())) {
-				int otherAdvance = getGeneticAdvancement(mutation.getAllele0(), exclude, speciesChromosome);
-				if (otherAdvance > highest) {
-					highest = otherAdvance;
-				}
-			}
-			if (!exclude.contains(mutation.getAllele1())) {
-				int otherAdvance = getGeneticAdvancement(mutation.getAllele1(), exclude, speciesChromosome);
-				if (otherAdvance > highest) {
-					highest = otherAdvance;
-				}
-			}
+			highest = getHighestAdvancement(mutation.getAllele0(), highest, exclude, speciesChromosome);
+			highest = getHighestAdvancement(mutation.getAllele1(), highest, exclude, speciesChromosome);
 		}
 
 		return 1 + highest;
 	}
+
+	private static int getHighestAdvancement(IAlleleSpecies mutationSpecies, int highest, Set<IAlleleSpecies> exclude, IChromosomeType speciesChromosome) {
+		if (exclude.contains(mutationSpecies) || AlleleManager.alleleRegistry.isBlacklisted(mutationSpecies.getUID())) {
+			return highest;
+		}
+
+		int otherAdvance = getGeneticAdvancement(mutationSpecies, exclude, speciesChromosome);
+		return otherAdvance > highest ? otherAdvance : highest;
+	}
 }

src/main/java/forestry/factory/network/PacketHandlerFactory.java

@@ -13,13 +13,20 @@ package forestry.factory.network;
 import java.io.IOException;
 
 import net.minecraft.entity.player.EntityPlayer;
+import net.minecraft.entity.player.EntityPlayerMP;
 
+import forestry.core.gui.slots.SlotCraftMatrix;
 import forestry.core.network.DataInputStreamForestry;
 import forestry.core.network.IPacketHandler;
 import forestry.core.network.PacketId;
+import forestry.core.network.PacketNBT;
+import forestry.core.recipes.nei.SetRecipeCommandHandler;
+import forestry.factory.gui.ContainerWorktable;
 
 public class PacketHandlerFactory implements IPacketHandler {
 
+	private static final SetRecipeCommandHandler worktableNEISelectHandler = new SetRecipeCommandHandler(ContainerWorktable.class, SlotCraftMatrix.class);
+
 	@Override
 	public boolean onPacketData(PacketId packetID, DataInputStreamForestry data, EntityPlayer player) throws IOException {
 
@@ -28,6 +35,11 @@ public class PacketHandlerFactory implements IPacketHandler {
 				PacketWorktableMemoryUpdate.onPacketData(data);
 				return true;
 			}
+			case WORKTABLE_NEI_SELECT: {
+				PacketNBT packet = new PacketNBT(data);
+				worktableNEISelectHandler.handle(packet.getTagCompound(), (EntityPlayerMP) player);
+				return true;
+			}
 		}
 
 		return false;

src/main/java/forestry/factory/tiles/TileWorktable.java

@@ -175,11 +175,14 @@ public class TileWorktable extends TileBase implements ICrafterWorktable {
 		ItemStack[] set = InventoryUtil.getStacks(currentRecipe.getMatrix(), SLOT_CRAFTING_1, SLOT_CRAFTING_COUNT);
 		ItemStack[] removed = InventoryUtil.removeSets(this, 1, set, SLOT_INVENTORY_1, SLOT_INVENTORY_COUNT, player, false, true, true);
 
+		if (removed == null) {
+			return false;
+		}
+
 		for (int i = 0; i < removed.length; i++) {
 			craftingInventory.setInventorySlotContents(i, removed[i]);
 		}
-
-		return removed != null;
+		return true;
 	}
 
 	@Override

src/main/java/forestry/plugins/PluginFarming.java

@@ -93,8 +93,10 @@ public class PluginFarming extends ForestryPlugin {
 
 		Farmables.farmables.put("farmArboreal", new ArrayList<IFarmable>());
 		Farmables.farmables.get("farmArboreal").add(new FarmableVanillaSapling());
-		Farmables.farmables.get("farmArboreal").add(new FarmableGE());
-
+		if (PluginManager.Module.ARBORICULTURE.isEnabled()) {
+			Farmables.farmables.get("farmArboreal").add(new FarmableGE());
+		}
+		
 		Farmables.farmables.put("farmOrchard", new ArrayList<IFarmable>());
 		Farmables.farmables.get("farmOrchard").add(new FarmableBasicFruit(Blocks.wheat, 7));
 		Farmables.farmables.get("farmOrchard").add(new FarmableBasicFruit(Blocks.potatoes, 7));