Backport some fixes for BTM

Conflicts:
	gradle.properties

gradle.properties

@@ -1,5 +1,5 @@
 mcversion=1.9.4
-forgeversion=12.17.0.1957
+forgeversion=12.17.0.1968
 mcp_mappings=snapshot_20160525
 
 jei_version=3.6.4.+
@@ -7,4 +7,4 @@ ic2_version=2.5.5-ex19
 
 version_major=5
 version_minor=0
-version_patch=20
+version_patch=24

gradle/wrapper/gradle-wrapper.properties

@@ -1,6 +1,6 @@
-#Mon Sep 14 12:28:28 PDT 2015
+#Tue Jun 21 15:23:47 PDT 2016
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-2.7-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-2.7-all.zip

src/main/java/forestry/Forestry.java

@@ -49,7 +49,7 @@ import forestry.plugins.PluginManager;
 		name = "Forestry",
 		version = Constants.VERSION,
 		guiFactory = "forestry.core.config.ForestryGuiConfigFactory",
-		dependencies = "required-after:Forge@[12.17.0.1949,);"
+		dependencies = "required-after:Forge@[12.17.0.1963,);"
 				+ "after:Buildcraft|Core@[7.2,);"
 				+ "after:BuildCraft|Energy@[7.2,);"
 				+ "after:ExtrabiomesXL;"

src/main/java/forestry/api/apiculture/IBeeHousing.java

@@ -5,6 +5,8 @@
  ******************************************************************************/
 package forestry.api.apiculture;
 
+import javax.annotation.Nonnull;
+
 import net.minecraft.util.math.Vec3d;
 import net.minecraft.world.World;
 import net.minecraft.world.biome.Biome;
@@ -32,6 +34,7 @@ public interface IBeeHousing extends IHousing, IErrorLogicSource {
 	 */
 	Iterable<IBeeListener> getBeeListeners();
 
+	@Nonnull
 	IBeeHousingInventory getBeeInventory();
 
 	IBeekeepingLogic getBeekeepingLogic();

src/main/java/forestry/api/arboriculture/ITree.java

@@ -84,7 +84,7 @@ public interface ITree extends IIndividual, ITreeGenData {
 	 * @return Integer denoting the size of the tree trunk.
 	 */
 	@Override
-	int getGirth(World world, BlockPos pos);
+	int getGirth();
 
 	/**
 	 * @return Growth conditions at the given position.

src/main/java/forestry/api/world/ITreeGenData.java

@@ -18,7 +18,7 @@ import forestry.api.arboriculture.ITreeGenome;
 
 public interface ITreeGenData {
 
-	int getGirth(World world, BlockPos pos);
+	int getGirth();
 
 	float getHeightModifier();
 

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

@@ -11,6 +11,7 @@
 package forestry.apiculture;
 
 import javax.annotation.Nonnull;
+import javax.annotation.Nullable;
 import java.io.IOException;
 import java.util.ArrayList;
 import java.util.Collection;
@@ -233,18 +234,20 @@ public class BeekeepingLogic implements IBeekeepingLogic, IStreamable {
 		if (beeType == EnumBeeType.PRINCESS) {
 			tickBreed();
 		} else if (beeType == EnumBeeType.QUEEN) {
-			queenWorkTick(queen);
+			queenWorkTick(queen, queenStack);
 		}
 	}
 
 	@Override
 	public void clearCachedValues() {
-		hasFlowersCache.clear();
-		queenCanWorkCache.clear();
-		canWork();
+		if (!housing.getWorldObj().isRemote) {
+			hasFlowersCache.clear();
+			queenCanWorkCache.clear();
+			canWork();
+		}
 	}
 
-	private void queenWorkTick(IBee queen) {
+	private void queenWorkTick(@Nullable IBee queen, @Nonnull ItemStack queenStack) {
 		if (queen == null) {
 			beeProgress = 0;
 			beeProgressMax = 0;
@@ -270,7 +273,8 @@ public class BeekeepingLogic implements IBeekeepingLogic, IStreamable {
 			// Write the changed queen back into the item stack.
 			NBTTagCompound nbttagcompound = new NBTTagCompound();
 			queen.writeToNBT(nbttagcompound);
-			housing.getBeeInventory().getQueen().setTagCompound(nbttagcompound);
+			queenStack.setTagCompound(nbttagcompound);
+			housing.getBeeInventory().setQueen(queenStack);
 		}
 
 		beeProgress = queen.getHealth();

src/main/java/forestry/apiculture/entities/EntityMinecartApiary.java

@@ -10,6 +10,7 @@
  ******************************************************************************/
 package forestry.apiculture.entities;
 
+import javax.annotation.Nonnull;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -36,8 +37,11 @@ import forestry.core.config.Config;
 import forestry.core.inventory.IInventoryAdapter;
 
 public class EntityMinecartApiary extends EntityMinecartBeeHousingBase implements IApiary {
+	@Nonnull
 	private static final IBeeModifier beeModifier = new ApiaryBeeModifier();
+	@Nonnull
 	private final IBeeListener beeListener = new ApiaryBeeListener(this);
+	@Nonnull
 	private final InventoryApiary inventory = new InventoryApiary(getAccessHandler());
 
 	@SuppressWarnings("unused")
@@ -64,6 +68,7 @@ public class EntityMinecartApiary extends EntityMinecartBeeHousingBase implement
 		return inventory;
 	}
 
+	@Nonnull
 	@Override
 	public IBeeHousingInventory getBeeInventory() {
 		return inventory;

src/main/java/forestry/apiculture/entities/EntityMinecartBeehouse.java

@@ -10,6 +10,7 @@
  ******************************************************************************/
 package forestry.apiculture.entities;
 
+import javax.annotation.Nonnull;
 import java.util.Collections;
 import java.util.List;
 
@@ -72,6 +73,7 @@ public class EntityMinecartBeehouse extends EntityMinecartBeeHousingBase {
 		return Collections.singleton(beeListener);
 	}
 
+	@Nonnull
 	@Override
 	public IBeeHousingInventory getBeeInventory() {
 		return beeInventory;

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

@@ -53,6 +53,7 @@ import forestry.core.utils.Translator;
 
 public class AlvearyController extends RectangularMultiblockControllerBase implements IAlvearyControllerInternal, IClimateControlled {
 
+	@Nonnull
 	private final InventoryBeeHousing inventory;
 	private final IBeekeepingLogic beekeepingLogic;
 
@@ -77,6 +78,7 @@ public class AlvearyController extends RectangularMultiblockControllerBase imple
 		this.beeModifiers.add(new AlvearyBeeModifier());
 	}
 
+	@Nonnull
 	@Override
 	public IBeeHousingInventory getBeeInventory() {
 		return inventory;

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

@@ -10,6 +10,7 @@
  ******************************************************************************/
 package forestry.apiculture.multiblock;
 
+import javax.annotation.Nonnull;
 import java.util.Collections;
 
 import net.minecraft.util.math.BlockPos;
@@ -45,6 +46,7 @@ public class FakeAlvearyController extends FakeMultiblockController implements I
 		return Collections.emptyList();
 	}
 
+	@Nonnull
 	@Override
 	public IBeeHousingInventory getBeeInventory() {
 		return FakeBeeHousingInventory.instance;

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

@@ -10,6 +10,7 @@
  ******************************************************************************/
 package forestry.apiculture.multiblock;
 
+import javax.annotation.Nonnull;
 import java.io.IOException;
 import java.util.List;
 
@@ -99,6 +100,7 @@ public abstract class TileAlveary extends MultiblockTileEntityForestry<Multibloc
 		return getMultiblockLogic().getController().getBeeListeners();
 	}
 
+	@Nonnull
 	@Override
 	public IBeeHousingInventory getBeeInventory() {
 		return getMultiblockLogic().getController().getBeeInventory();

src/main/java/forestry/apiculture/tiles/FakeBeeHousingInventory.java

@@ -1,10 +1,13 @@
 package forestry.apiculture.tiles;
 
+import javax.annotation.Nonnull;
+
 import net.minecraft.item.ItemStack;
 
 import forestry.api.apiculture.IBeeHousingInventory;
 
 public class FakeBeeHousingInventory implements IBeeHousingInventory {
+	@Nonnull
 	public static final FakeBeeHousingInventory instance = new FakeBeeHousingInventory();
 
 	private FakeBeeHousingInventory() {

src/main/java/forestry/apiculture/tiles/TileApiary.java

@@ -10,6 +10,7 @@
  ******************************************************************************/
 package forestry.apiculture.tiles;
 
+import javax.annotation.Nonnull;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
@@ -30,8 +31,11 @@ import forestry.apiculture.inventory.IApiaryInventory;
 import forestry.apiculture.inventory.InventoryApiary;
 
 public class TileApiary extends TileBeeHousingBase implements IApiary {
+	@Nonnull
 	private final IBeeModifier beeModifier = new ApiaryBeeModifier();
+	@Nonnull
 	private final IBeeListener beeListener = new ApiaryBeeListener(this);
+	@Nonnull
 	private final InventoryApiary inventory = new InventoryApiary(getAccessHandler());
 
 	public TileApiary() {
@@ -39,6 +43,7 @@ public class TileApiary extends TileBeeHousingBase implements IApiary {
 		setInternalInventory(inventory);
 	}
 
+	@Nonnull
 	@Override
 	public IBeeHousingInventory getBeeInventory() {
 		return inventory;

src/main/java/forestry/apiculture/tiles/TileBeeHouse.java

@@ -10,6 +10,7 @@
  ******************************************************************************/
 package forestry.apiculture.tiles;
 
+import javax.annotation.Nonnull;
 import java.util.Collections;
 
 import net.minecraft.entity.player.EntityPlayer;
@@ -24,9 +25,12 @@ import forestry.apiculture.gui.ContainerBeeHousing;
 import forestry.apiculture.gui.GuiBeeHousing;
 
 public class TileBeeHouse extends TileBeeHousingBase {
+	@Nonnull
 	private static final IBeeModifier beeModifier = new BeehouseBeeModifier();
 
+	@Nonnull
 	private final IBeeListener beeListener;
+	@Nonnull
 	private final InventoryBeeHousing beeInventory;
 
 	public TileBeeHouse() {
@@ -38,6 +42,7 @@ public class TileBeeHouse extends TileBeeHousingBase {
 		setInternalInventory(beeInventory);
 	}
 
+	@Nonnull
 	@Override
 	public IBeeHousingInventory getBeeInventory() {
 		return beeInventory;

src/main/java/forestry/apiculture/tiles/TileHive.java

@@ -293,6 +293,7 @@ public class TileHive extends TileEntity implements ITickable, IHiveTile, IActiv
 		return Collections.emptyList();
 	}
 
+	@Nonnull
 	@Override
 	public IBeeHousingInventory getBeeInventory() {
 		return inventory;

src/main/java/forestry/arboriculture/blocks/BlockArbDoor.java

@@ -101,7 +101,6 @@ public class BlockArbDoor extends BlockDoor implements IWoodTyped, IItemModelReg
 	}
 
 	@Override
-	@SideOnly(Side.CLIENT)
 	public ItemStack getItem(World worldIn, BlockPos pos, IBlockState state) {
 		return new ItemStack(getItem());
 	}

src/main/java/forestry/arboriculture/genetics/Tree.java

@@ -203,7 +203,7 @@ public class Tree extends Individual implements ITree, IPlantable {
 	}
 
 	@Override
-	public int getGirth(World world, BlockPos pos) {
+	public int getGirth() {
 		return genome.getGirth();
 	}
 

src/main/java/forestry/arboriculture/worldgen/WorldGenArboriculture.java

@@ -18,6 +18,7 @@ import java.util.List;
 import java.util.Random;
 import java.util.Set;
 
+import forestry.arboriculture.blocks.BlockSapling;
 import net.minecraft.util.math.BlockPos;
 import net.minecraft.world.World;
 
@@ -61,6 +62,7 @@ public abstract class WorldGenArboriculture extends WorldGenBase {
 		}
 
 		if (genPos != null) {
+			clearSaplings(world, genPos);
 			List<BlockPos> branchEnds = new ArrayList<>(generateTrunk(world, rand, wood, genPos));
 			Collections.sort(branchEnds, TopDownBlockPosComparator.INSTANCE);
 			generateLeaves(world, rand, leaf, branchEnds, genPos);
@@ -96,6 +98,18 @@ public abstract class WorldGenArboriculture extends WorldGenBase {
 	@Nullable
 	public abstract BlockPos getValidGrowthPos(World world, BlockPos pos);
 
+	public void clearSaplings(World world, BlockPos genPos) {
+		int treeGirth = tree.getGirth();
+		for (int x = 0; x < treeGirth; x++) {
+			for (int z = 0; z < treeGirth; z++) {
+				BlockPos saplingPos = genPos.add(x, 0, z);
+				if (world.getBlockState(saplingPos).getBlock() instanceof BlockSapling) {
+					world.setBlockToAir(saplingPos);
+				}
+			}
+		}
+	}
+
 	public boolean hasPods() {
 		return tree.allowsFruitBlocks();
 	}

src/main/java/forestry/arboriculture/worldgen/WorldGenCherry.java

@@ -47,12 +47,13 @@ public class WorldGenCherry extends WorldGenTree {
 
 	@Override
 	protected void generateLeaves(World world, Random rand, TreeBlockTypeLeaf leaf, List<BlockPos> branchEnds, BlockPos startPos) {
-		int leafSpawn = height + 1;
+		int leafSpawn = height + 2;
 		WorldGenHelper.generateCylinderFromTreeStartPos(world, leaf, startPos.add(0, leafSpawn--, 0), girth, girth, 1, WorldGenHelper.EnumReplaceMode.SOFT);
-		WorldGenHelper.generateCylinderFromTreeStartPos(world, leaf, startPos.add(0, leafSpawn, 0), girth, (float) 1 + girth, 1, WorldGenHelper.EnumReplaceMode.SOFT);
+		WorldGenHelper.generateCylinderFromTreeStartPos(world, leaf, startPos.add(0, leafSpawn, 0), girth, 1 + girth, 1, WorldGenHelper.EnumReplaceMode.SOFT);
 
 		for (BlockPos branchEnd : branchEnds) {
-			WorldGenHelper.generateCircle(world, rand, branchEnd, 4, 3, 2, leaf, 1.0f, WorldGenHelper.EnumReplaceMode.AIR);
+			WorldGenHelper.generateCircle(world, rand, branchEnd.up(), 3, 3, 1, leaf, 1.0f, WorldGenHelper.EnumReplaceMode.AIR);
+			WorldGenHelper.generateCircle(world, rand, branchEnd, 4, 3, 1, leaf, 1.0f, WorldGenHelper.EnumReplaceMode.AIR);
 		}
 	}
 }

src/main/java/forestry/arboriculture/worldgen/WorldGenEbony.java

@@ -31,11 +31,10 @@ public class WorldGenEbony extends WorldGenTree {
 	@Nonnull
 	@Override
 	public Set<BlockPos> generateTrunk(World world, Random rand, TreeBlockTypeLog wood, BlockPos startPos) {
-		int offset = (girth - 1) / 2;
 		int trunksGenerated = 0;
 
-		for (int x = -offset; x < -offset + girth; x++) {
-			for (int z = -offset; z < -offset + girth; z++) {
+		for (int x = 0; x < girth; x++) {
+			for (int z = 0; z < girth; z++) {
 				if (rand.nextFloat() < 0.6f) {
 					for (int y = 0; y < height; y++) {
 						WorldGenHelper.addBlock(world, startPos.add(x, y, z), wood, WorldGenHelper.EnumReplaceMode.ALL);
@@ -68,8 +67,8 @@ public class WorldGenEbony extends WorldGenTree {
 				h = height / 2 + rand.nextInt(height / 2);
 			}
 
-			int x_off = -girth + rand.nextInt(2 * girth);
-			int y_off = -girth + rand.nextInt(2 * girth);
+			int x_off = rand.nextInt(girth);
+			int y_off = rand.nextInt(girth);
 
 			BlockPos center = startPos.add(x_off, h, y_off);
 			int radius = 1 + rand.nextInt(girth);

src/main/java/forestry/arboriculture/worldgen/WorldGenTree.java

@@ -74,7 +74,7 @@ public abstract class WorldGenTree extends WorldGenArboriculture {
 	public final void preGenerate(World world, Random rand, BlockPos startPos) {
 		super.preGenerate(world, rand, startPos);
 		height = determineHeight(world, rand, baseHeight, heightVariation);
-		girth = tree.getGirth(world, startPos);
+		girth = tree.getGirth();
 	}
 
 	protected int modifyByHeight(World world, int val, int min, int max) {

src/main/java/forestry/core/blocks/BlockRegistryCore.java

@@ -69,5 +69,6 @@ public class BlockRegistryCore extends BlockRegistry {
 
 		// register some common oreDict names for our recipes
 		OreDictionary.registerOre(OreDictUtil.CRAFTING_TABLE_WOOD, Blocks.CRAFTING_TABLE);
+		OreDictionary.registerOre(OreDictUtil.TRAPDOOR_WOOD, Blocks.TRAPDOOR);
 	}
 }

src/main/java/forestry/core/gui/ContainerEscritoire.java

@@ -23,16 +23,11 @@ import forestry.core.tiles.EscritoireGame;
 import forestry.core.tiles.TileEscritoire;
 
 public class ContainerEscritoire extends ContainerTile<TileEscritoire> implements IGuiSelectable {
-
-	private final EntityPlayer player;
-
 	private long lastUpdate;
 
 	public ContainerEscritoire(EntityPlayer player, TileEscritoire tile) {
 		super(tile, player.inventory, 34, 153);
 
-		this.player = player;
-
 		// Analyze slot
 		addSlotToContainer(new SlotFiltered(this.tile, InventoryEscritoire.SLOT_ANALYZE, 97, 67).setPickupWatcher(this.tile).setStackLimit(1));
 
@@ -54,7 +49,7 @@ public class ContainerEscritoire extends ContainerTile<TileEscritoire> implement
 		long gameLastUpdate = tile.getGame().getLastUpdate();
 		if (lastUpdate != gameLastUpdate) {
 			lastUpdate = gameLastUpdate;
-			Proxies.net.sendToPlayer(new PacketGuiUpdate(tile), player);
+			sendPacketToListeners(new PacketGuiUpdate(tile));
 		}
 	}
 

src/main/java/forestry/core/gui/widgets/GameTokenWidget.java

@@ -91,6 +91,7 @@ public class GameTokenWidget extends Widget {
 
 	@Override
 	public void handleMouseClick(int mouseX, int mouseY, int mouseButton) {
+		game.choose(index);
 		Proxies.net.sendToServer(new PacketGuiSelectRequest(index, 0));
 	}
 }

src/main/java/forestry/core/items/ItemPipette.java

@@ -59,7 +59,6 @@ public class ItemPipette extends ItemForestry implements IToolPipette, IFluidCon
 			}
 
 			contained = new PipetteContents(new FluidStack(liquid, filled));
-			filled = liquid.amount;
 		} else {
 			if (contained.getContents().amount >= limit) {
 				return 0;
@@ -141,7 +140,7 @@ public class ItemPipette extends ItemForestry implements IToolPipette, IFluidCon
 			contained.getContents().amount -= drained;
 
 			if (contained.getContents().amount <= 0) {
-				pipette.setTagCompound(null);
+				pipette.setTagCompound(new NBTTagCompound());
 				pipette.setItemDamage(0);
 			} else {
 				NBTTagCompound nbttagcompound = new NBTTagCompound();

src/main/java/forestry/core/proxy/ProxyCommon.java

@@ -65,7 +65,7 @@ public class ProxyCommon {
 	public boolean isOp(EntityPlayer player) {
 		MinecraftServer server = FMLCommonHandler.instance().getMinecraftServerInstance();
 		UserListOpsEntry userlistopsentry = server.getPlayerList().getOppedPlayers().getEntry(player.getGameProfile());
-		return userlistopsentry.getPermissionLevel() >= server.getOpPermissionLevel();
+		return userlistopsentry != null && userlistopsentry.getPermissionLevel() >= server.getOpPermissionLevel();
 	}
 
 	public double getBlockReachDistance(EntityPlayer entityplayer) {

src/main/java/forestry/core/recipes/jei/ForestryRecipeCategory.java

@@ -6,8 +6,9 @@ import forestry.core.utils.Translator;
 
 import mezz.jei.api.gui.IDrawable;
 import mezz.jei.api.recipe.BlankRecipeCategory;
+import mezz.jei.api.recipe.IRecipeWrapper;
 
-public abstract class ForestryRecipeCategory extends BlankRecipeCategory {
+public abstract class ForestryRecipeCategory<T extends IRecipeWrapper> extends BlankRecipeCategory<T> {
 	@Nonnull
 	private final IDrawable background;
 	@Nonnull

src/main/java/forestry/core/recipes/jei/JEIUtils.java

@@ -1,72 +0,0 @@
-/*******************************************************************************
- * 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.jei;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Iterator;
-import java.util.List;
-
-import net.minecraft.block.Block;
-import net.minecraft.item.ItemStack;
-
-import net.minecraftforge.fluids.Fluid;
-import net.minecraftforge.fluids.FluidContainerRegistry;
-import net.minecraftforge.fluids.FluidStack;
-import net.minecraftforge.fluids.IFluidBlock;
-import net.minecraftforge.fluids.IFluidContainerItem;
-
-public class JEIUtils {
-
-	public static List<ItemStack> getItemVariations(ItemStack base) {
-		List<ItemStack> variations = new ArrayList<>();
-		base.getItem().getSubItems(base.getItem(), null, variations);
-		Iterator<ItemStack> itr = variations.iterator();
-		ItemStack stack;
-		while (itr.hasNext()) {
-			stack = itr.next();
-			if (!base.isItemEqual(stack) || !stack.hasTagCompound()) {
-				itr.remove();
-			}
-		}
-		if (variations.isEmpty()) {
-			return Collections.singletonList(base);
-		}
-		return variations;
-	}
-
-	public static FluidStack getFluidStack(ItemStack stack) {
-		if (stack != null) {
-			FluidStack fluidStack = null;
-			if (stack.getItem() instanceof IFluidContainerItem) {
-				fluidStack = ((IFluidContainerItem) stack.getItem()).getFluid(stack);
-			}
-			if (fluidStack == null) {
-				fluidStack = FluidContainerRegistry.getFluidForFilledItem(stack);
-			}
-			if (fluidStack == null && Block.getBlockFromItem(stack.getItem()) instanceof IFluidBlock) {
-				Fluid fluid = ((IFluidBlock) Block.getBlockFromItem(stack.getItem())).getFluid();
-				if (fluid != null) {
-					fluidStack = new FluidStack(fluid, Fluid.BUCKET_VOLUME);
-				}
-			}
-			return fluidStack;
-		}
-		return null;
-	}
-
-	public static boolean areFluidsSameType(FluidStack fluidStack1, FluidStack fluidStack2) {
-		if (fluidStack1 == null || fluidStack2 == null) {
-			return false;
-		}
-		return fluidStack1.getFluid() == fluidStack2.getFluid();
-	}
-}

src/main/java/forestry/core/render/RenderEscritoire.java

@@ -104,6 +104,8 @@ public class RenderEscritoire extends TileEntitySpecialRenderer<TileEscritoire>
 				rendermanager.doRenderEntity(dummyEntityItem, 0.0D, 0.0D, 0.0D, 0.0F, 0.0F, false);
 			}
 			GlStateManager.popMatrix();
+
+			dummyEntityItem.worldObj = null; // prevent leaking the world object
 		}
 	}
 }

src/main/java/forestry/core/tiles/EscritoireGameBoard.java

@@ -17,6 +17,7 @@ import java.util.Collections;
 import java.util.List;
 import java.util.Random;
 
+import forestry.api.genetics.IAllele;
 import net.minecraft.item.ItemStack;
 import net.minecraft.nbt.NBTTagCompound;
 import net.minecraft.nbt.NBTTagList;
@@ -72,10 +73,10 @@ public class EscritoireGameBoard implements INbtWritable, IStreamable {
 		tokenCount = getTokenCount(genome);
 
 		for (int i = 0; i < tokenCount / 2; i++) {
-			IIndividual token = root.templateAsIndividual(root.getRandomTemplate(rand));
-			ItemStack pair = root.getMemberStack(token, root.getIconType());
-			gameTokens.add(new EscritoireGameToken(pair));
-			gameTokens.add(new EscritoireGameToken(pair));
+			IAllele[] randomTemplate = root.getRandomTemplate(rand);
+			String speciesUid = randomTemplate[root.getSpeciesChromosomeType().ordinal()].getUID();
+			gameTokens.add(new EscritoireGameToken(speciesUid));
+			gameTokens.add(new EscritoireGameToken(speciesUid));
 		}
 		Collections.shuffle(gameTokens);
 		return true;

src/main/java/forestry/core/tiles/EscritoireGameToken.java

@@ -14,17 +14,19 @@ import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
 import java.io.IOException;
 
-import net.minecraft.item.ItemStack;
-import net.minecraft.nbt.NBTTagCompound;
-
 import forestry.api.core.INbtWritable;
 import forestry.api.genetics.AlleleManager;
+import forestry.api.genetics.IAllele;
+import forestry.api.genetics.IAlleleSpecies;
 import forestry.api.genetics.IIndividual;
+import forestry.api.genetics.ISpeciesRoot;
 import forestry.core.network.DataInputStreamForestry;
 import forestry.core.network.DataOutputStreamForestry;
 import forestry.core.network.IStreamable;
 import forestry.core.utils.ColourUtil;
 import forestry.core.utils.Translator;
+import net.minecraft.item.ItemStack;
+import net.minecraft.nbt.NBTTagCompound;
 
 public class EscritoireGameToken implements INbtWritable, IStreamable {
 
@@ -41,6 +43,8 @@ public class EscritoireGameToken implements INbtWritable, IStreamable {
 	private static final String[] OVERLAY_FAILED = new String[]{"errors/errored"};
 	private static final String[] OVERLAY_SELECTED = new String[]{"errors/unknown"};
 
+	@Nullable
+	private IIndividual tokenIndividual;
 	@Nullable
 	private ItemStack tokenStack;
 	@Nonnull
@@ -51,8 +55,8 @@ public class EscritoireGameToken implements INbtWritable, IStreamable {
 		// required for IStreamable serialization
 	}
 
-	public EscritoireGameToken(@Nullable ItemStack tokenStack) {
-		this.tokenStack = tokenStack;
+	public EscritoireGameToken(@Nullable String speciesUid) {
+		setTokenSpecies(speciesUid);
 	}
 
 	public EscritoireGameToken(@Nonnull NBTTagCompound nbttagcompound) {
@@ -61,8 +65,29 @@ public class EscritoireGameToken implements INbtWritable, IStreamable {
 			state = State.values()[stateOrdinal];
 		}
 
+		// legacy
 		if (nbttagcompound.hasKey("tokenStack")) {
 			tokenStack = ItemStack.loadItemStackFromNBT(nbttagcompound.getCompoundTag("tokenStack"));
+			ISpeciesRoot speciesRoot = AlleleManager.alleleRegistry.getSpeciesRoot(tokenStack);
+			tokenIndividual = speciesRoot.getMember(tokenStack);
+		}
+
+		if (nbttagcompound.hasKey("tokenSpecies")) {
+			String speciesUid = nbttagcompound.getString("tokenSpecies");
+			setTokenSpecies(speciesUid);
+		}
+	}
+
+	private void setTokenSpecies(String speciesUid) {
+		IAllele allele = AlleleManager.alleleRegistry.getAllele(speciesUid);
+		if (allele instanceof IAlleleSpecies) {
+			IAlleleSpecies species = (IAlleleSpecies) allele;
+			ISpeciesRoot root = species.getRoot();
+			IAllele[] template = root.getTemplate(speciesUid);
+			if (template != null) {
+				this.tokenIndividual = root.templateAsIndividual(template);
+				this.tokenStack = root.getMemberStack(this.tokenIndividual, root.getIconType());
+			}
 		}
 	}
 
@@ -108,12 +133,11 @@ public class EscritoireGameToken implements INbtWritable, IStreamable {
 	}
 
 	public int getTokenColour() {
-		if (tokenStack == null || !isVisible()) {
+		if (tokenIndividual == null || !isVisible()) {
 			return 0xffffff;
 		}
 
-		IIndividual individual = AlleleManager.alleleRegistry.getIndividual(tokenStack);
-		int iconColor = individual.getGenome().getPrimary().getSpriteColour(0);
+		int iconColor = tokenIndividual.getGenome().getPrimary().getSpriteColour(0);
 
 		if (state == State.MATCHED) {
 			return ColourUtil.multiplyRGBComponents(iconColor, 0.7f);
@@ -146,10 +170,8 @@ public class EscritoireGameToken implements INbtWritable, IStreamable {
 	public NBTTagCompound writeToNBT(NBTTagCompound nbttagcompound) {
 		nbttagcompound.setInteger("state", state.ordinal());
 
-		if (tokenStack != null) {
-			NBTTagCompound stackcompound = new NBTTagCompound();
-			tokenStack.writeToNBT(stackcompound);
-			nbttagcompound.setTag("tokenStack", stackcompound);
+		if (tokenIndividual != null) {
+			nbttagcompound.setString("tokenSpecies", tokenIndividual.getGenome().getPrimary().getUID());
 		}
 		return nbttagcompound;
 	}
@@ -158,12 +180,20 @@ public class EscritoireGameToken implements INbtWritable, IStreamable {
 	@Override
 	public void writeData(DataOutputStreamForestry data) throws IOException {
 		data.writeEnum(state, State.VALUES);
-		data.writeItemStack(tokenStack);
+		if (tokenIndividual != null) {
+			data.writeBoolean(true);
+			data.writeUTF(tokenIndividual.getGenome().getPrimary().getUID());
+		} else {
+			data.writeBoolean(false);
+		}
 	}
 
 	@Override
 	public void readData(DataInputStreamForestry data) throws IOException {
 		state = data.readEnum(State.VALUES);
-		tokenStack = data.readItemStack();
+		if (data.readBoolean()) {
+			String speciesUid = data.readUTF();
+			setTokenSpecies(speciesUid);
+		}
 	}
 }

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

@@ -14,11 +14,17 @@ import javax.annotation.Nonnull;
 import javax.annotation.Nullable;
 import java.util.List;
 
+import cofh.api.energy.IEnergyConnection;
+import cofh.api.energy.IEnergyReceiver;
+import forestry.core.network.packets.PacketFXSignal;
+import forestry.core.proxy.Proxies;
+import forestry.core.tiles.TileEngine;
 import net.minecraft.block.Block;
 import net.minecraft.block.BlockHorizontal;
 import net.minecraft.block.BlockOldLog;
 import net.minecraft.block.BlockPlanks;
 import net.minecraft.block.BlockStaticLiquid;
+import net.minecraft.block.properties.IProperty;
 import net.minecraft.block.state.IBlockState;
 import net.minecraft.init.Blocks;
 import net.minecraft.item.Item;
@@ -31,16 +37,8 @@ import net.minecraft.util.math.RayTraceResult;
 import net.minecraft.util.math.Vec3d;
 import net.minecraft.world.IBlockAccess;
 import net.minecraft.world.World;
-
 import net.minecraftforge.oredict.OreDictionary;
 
-import forestry.core.network.packets.PacketFXSignal;
-import forestry.core.proxy.Proxies;
-import forestry.core.tiles.TileEngine;
-
-import cofh.api.energy.IEnergyConnection;
-import cofh.api.energy.IEnergyReceiver;
-
 public abstract class BlockUtil {
 
 	private static final int slabWoodId = OreDictionary.getOreID("slabWood");
@@ -343,4 +341,17 @@ public abstract class BlockUtil {
 		}
 		return false;
 	}
+
+	@Nullable
+	public static <T extends Comparable<T>> IProperty<T> getProperty(Block block, String propertyName, Class<T> valueClass) {
+		for (IProperty<?> property : block.getDefaultState().getPropertyNames()) {
+			if (property.getName().equals(propertyName)) {
+				if (property.getValueClass().isAssignableFrom(valueClass)) {
+					//noinspection unchecked
+					return (IProperty<T>) property;
+				}
+			}
+		}
+		return null;
+	}
 }

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

@@ -34,6 +34,7 @@ public class OreDictUtil {
 	public static final String FENCE_GATE_WOOD = "fenceGateWood";
 	public static final String STAIR_WOOD = "stairWood";
 	public static final String DOOR_WOOD = "doorWood";
+	public static final String TRAPDOOR_WOOD = "trapdoorWood";
 	public static final String TREE_LEAVES = "treeLeaves";
 
 	public static final String EMPTIED_LETTER_ORE_DICT = "emptiedLetter";

src/main/java/forestry/factory/recipes/FermenterRecipe.java

@@ -29,6 +29,10 @@ public class FermenterRecipe implements IFermenterRecipe {
 		if (resource == null) {
 			throw new NullPointerException("Fermenter Resource cannot be null!");
 		}
+		
+		if (resource.getItem() == null) {
+			throw new NullPointerException("Fermenter Resource item cannot be null!");
+		}
 
 		if (output == null) {
 			throw new NullPointerException("Fermenter Output cannot be null!");

src/main/java/forestry/factory/recipes/jei/FactoryJeiPlugin.java

@@ -92,7 +92,7 @@ public class FactoryJeiPlugin extends BlankModPlugin {
 		registry.addRecipes(CarpenterRecipeMaker.getCarpenterRecipes());
 		registry.addRecipes(CentrifugeRecipeMaker.getCentrifugeRecipe());
 		registry.addRecipes(FabricatorRecipeMaker.getFabricatorRecipes());
-		registry.addRecipes(FermenterRecipeMaker.getFermenterRecipes());
+		registry.addRecipes(FermenterRecipeMaker.getFermenterRecipes(jeiHelpers.getStackHelper()));
 		registry.addRecipes(MoistenerRecipeMaker.getMoistenerRecipes());
 		registry.addRecipes(RainmakerRecipeMaker.getRecipes());
 		registry.addRecipes(SqueezerRecipeMaker.getSqueezerRecipes());

src/main/java/forestry/factory/recipes/jei/fermenter/FermenterRecipeCategory.java

@@ -23,7 +23,7 @@ import mezz.jei.api.gui.IGuiItemStackGroup;
 import mezz.jei.api.gui.IRecipeLayout;
 import mezz.jei.api.recipe.IRecipeWrapper;
 
-public class FermenterRecipeCategory extends ForestryRecipeCategory {
+public class FermenterRecipeCategory extends ForestryRecipeCategory<FermenterRecipeWrapper> {
 
 	private static final int resourceSlot = 0;
 	private static final int fuelSlot = 1;
@@ -62,7 +62,7 @@ public class FermenterRecipeCategory extends ForestryRecipeCategory {
 	}
 
 	@Override
-	public void setRecipe(@Nonnull IRecipeLayout recipeLayout, @Nonnull IRecipeWrapper recipeWrapper) {
+	public void setRecipe(@Nonnull IRecipeLayout recipeLayout, @Nonnull FermenterRecipeWrapper recipeWrapper) {
 		IGuiItemStackGroup guiItemStacks = recipeLayout.getItemStacks();
 		IGuiFluidStackGroup guiFluidStacks = recipeLayout.getFluidStacks();
 		
@@ -72,18 +72,15 @@ public class FermenterRecipeCategory extends ForestryRecipeCategory {
 		guiFluidStacks.init(inputTank, true, 1, 1, 16, 58, 3000, false, tankOverlay);
 		guiFluidStacks.init(outputTank, false, 91, 1, 16, 58, 3000, false, tankOverlay);
 		
-		FermenterRecipeWrapper wrapper = (FermenterRecipeWrapper) recipeWrapper;
-		
-		guiItemStacks.set(resourceSlot, wrapper.getFermentable());
+		guiItemStacks.set(resourceSlot, recipeWrapper.getFermentable());
 		List<ItemStack> fuels = new ArrayList<>();
 		for (FermenterFuel fuel : FuelManager.fermenterFuel.values()) {
 			fuels.add(fuel.item);
 		}
 		guiItemStacks.set(fuelSlot, fuels);
 		
-		guiFluidStacks.set(inputTank, wrapper.getFluidInputs());
-		guiFluidStacks.set(outputTank, wrapper.getFluidOutputs());
-		
+		guiFluidStacks.set(inputTank, recipeWrapper.getFluidInputs());
+		guiFluidStacks.set(outputTank, recipeWrapper.getFluidOutputs());
 	}
 
 }

src/main/java/forestry/factory/recipes/jei/fermenter/FermenterRecipeMaker.java

@@ -8,22 +8,29 @@ import net.minecraft.item.ItemStack;
 import forestry.api.recipes.IFermenterRecipe;
 import forestry.api.recipes.IVariableFermentable;
 import forestry.api.recipes.RecipeManagers;
-import forestry.core.recipes.jei.JEIUtils;
+import forestry.core.utils.Log;
+import forestry.factory.recipes.jei.FactoryJeiPlugin;
+
+import mezz.jei.api.recipe.IStackHelper;
 
 public class FermenterRecipeMaker {
 
 	private FermenterRecipeMaker() {
 	}
 	
-	public static List<FermenterRecipeWrapper> getFermenterRecipes() {
+	public static List<FermenterRecipeWrapper> getFermenterRecipes(IStackHelper stackHelper) {
 		List<FermenterRecipeWrapper> recipes = new ArrayList<>();
 		for (IFermenterRecipe recipe : RecipeManagers.fermenterManager.recipes()) {
-			if (recipe.getResource() != null && recipe.getResource().getItem() instanceof IVariableFermentable) {
-				for (ItemStack stack : JEIUtils.getItemVariations(recipe.getResource())) {
-					recipes.add(new FermenterRecipeWrapper(recipe, stack));
+			if (recipe.getResource() != null) {
+				if (recipe.getResource().getItem() instanceof IVariableFermentable) {
+					for (ItemStack stack : stackHelper.getSubtypes(recipe.getResource())) {
+						recipes.add(new FermenterRecipeWrapper(recipe, stack));
+					}
+				} else {
+					recipes.add(new FermenterRecipeWrapper(recipe, recipe.getResource()));
 				}
 			} else {
-				recipes.add(new FermenterRecipeWrapper(recipe, recipe.getResource()));
+				Log.error("Null resource for recipe");
 			}
 		}
 		return recipes;

src/main/java/forestry/farming/PluginFarming.java

@@ -42,6 +42,7 @@ import forestry.core.circuits.CircuitLayout;
 import forestry.core.config.Constants;
 import forestry.core.items.EnumElectronTube;
 import forestry.core.recipes.RecipeUtil;
+import forestry.core.utils.OreDictUtil;
 import forestry.farming.blocks.BlockMushroom;
 import forestry.farming.blocks.BlockRegistryFarming;
 import forestry.farming.blocks.EnumFarmBlockType;
@@ -207,7 +208,7 @@ public class PluginFarming extends BlankForestryPlugin {
 					"TDT",
 					'#', basic,
 					'T', "gearTin",
-					'D', Blocks.TRAPDOOR);
+					'D', OreDictUtil.TRAPDOOR_WOOD);
 
 			RecipeUtil.addRecipe(valve,
 					" # ",

src/main/java/forestry/greenhouse/PluginGreenhouse.java

@@ -27,6 +27,7 @@ import forestry.core.fluids.Fluids;
 import forestry.core.items.EnumElectronTube;
 import forestry.core.network.IPacketRegistry;
 import forestry.core.recipes.RecipeUtil;
+import forestry.core.utils.OreDictUtil;
 import forestry.greenhouse.blocks.BlockGreenhouseType;
 import forestry.greenhouse.blocks.BlockRegistryGreenhouse;
 import forestry.greenhouse.logics.GreenhouseLogicGreenhouseDoor;
@@ -91,7 +92,7 @@ public class PluginGreenhouse extends BlankForestryPlugin {
 				"TXT",
 				"#H#",
 				'X', blocks.getGreenhouseBlock(BlockGreenhouseType.PLAIN),
-				'H', Blocks.TRAPDOOR,
+				'H', OreDictUtil.TRAPDOOR_WOOD,
 				'#', "gearTin",
 				'T', PluginCore.items.tubes.get(EnumElectronTube.BRONZE, 1));
 		
@@ -100,7 +101,7 @@ public class PluginGreenhouse extends BlankForestryPlugin {
 				"#H#",
 				"TXT",
 				'X', blocks.getGreenhouseBlock(BlockGreenhouseType.PLAIN),
-				'H', Blocks.TRAPDOOR,
+				'H', OreDictUtil.TRAPDOOR_WOOD,
 				'#', "gearTin",
 				'T', PluginCore.items.tubes.get(EnumElectronTube.BRONZE, 1));
 		

src/main/java/forestry/lepidopterology/entities/EntityButterfly.java

@@ -231,7 +231,7 @@ public class EntityButterfly extends EntityCreature implements IEntityButterfly
 
 			BlockPos posBelow = pos.down();
 			IBlockState blockStateBelow = worldObj.getBlockState(posBelow);
-			Block blockBelow = blockState.getBlock();
+			Block blockBelow = blockStateBelow.getBlock();
 			if (blockBelow.isLeaves(blockStateBelow, worldObj, posBelow)) {
 				weight += 2.5f;
 			} else if (blockBelow instanceof BlockFence) {

src/main/java/forestry/lepidopterology/genetics/MothDefinition.java

@@ -33,7 +33,7 @@ import forestry.lepidopterology.genetics.alleles.AlleleButterflyCocoon;
 
 public enum MothDefinition implements IButterflyDefinition {
 	Brimstone(ButterflyBranchDefinition.Opisthograptis, "brimstone", "luteolata", new Color(0xffea40), true, 1.0f),
-	LatticedHeath(ButterflyBranchDefinition.Chiasmia, "latticeHeath", "clathrata", new Color(0xf2f0be), true, 0.5f) {
+	LatticedHeath(ButterflyBranchDefinition.Chiasmia, "latticedHeath", "clathrata", new Color(0xf2f0be), true, 0.5f) {
 		@Override
 		protected void setAlleles(IAllele[] alleles) {
 			AlleleHelper.instance.set(alleles, EnumButterflyChromosome.SIZE, EnumAllele.Size.SMALLEST);

src/main/java/forestry/lepidopterology/render/ModelButterflyItem.java

@@ -51,7 +51,7 @@ public class ModelButterflyItem extends BlankItemModel {
 		ImmutableMap.Builder<String, String> textures = ImmutableMap.builder();
 		textures.put("butterfly", butterfly.getGenome().getSecondary().getItemTexture());
 		IModel retexturedModel =  ModelProcessingHelper.retexture(modelButterfly, textures.build());
-		return new TRSRBakedModel(retexturedModel.bake(ModelRotation.X0_Y0, DefaultVertexFormats.ITEM, textureGetter), -0.03125F, 0.0F, -0.03125F, butterfly.getSize() * 1.5F);
+		return new TRSRBakedModel(retexturedModel.bake(ModelRotation.X0_Y0, DefaultVertexFormats.ITEM, textureGetter), -0.03125F, 0.5F, -0.03125F, butterfly.getSize() * 1.5F);
 	}
 
 	private class ButterflyItemOverrideList extends ItemOverrideList {

src/main/java/forestry/plugins/ForestryPluginUids.java

@@ -20,6 +20,8 @@ public class ForestryPluginUids {
 	public static final String BUILDCRAFT_STATEMENTS = "forestry.buildcraft.statements";
 	public static final String BUILDCRAFT_TRANSPORT = "forestry.buildcraft.transport";
 	public static final String CHISEL = "forestry.chisel";
+	public static final String ENDER_IO = "forestry.ender.io";
+	public static final String EXTRA_UTILITIES = "forestry.extra.utilities";
 	public static final String NATURA = "forestry.natura";
 	public static final String INDUSTRIALCRAFT2 = "forestry.industrialcraft2";
 }

src/main/java/forestry/plugins/compat/PluginBiomesOPlenty.java

@@ -14,14 +14,18 @@ import java.util.ArrayList;
 import java.util.List;
 
 import net.minecraft.block.Block;
+import net.minecraft.init.Blocks;
 import net.minecraft.item.Item;
 import net.minecraft.item.ItemStack;
+import net.minecraft.util.ResourceLocation;
 
 import net.minecraftforge.fml.common.event.FMLInterModComms;
+import net.minecraftforge.fml.common.registry.ForgeRegistries;
 import net.minecraftforge.fml.common.registry.GameRegistry;
 import net.minecraftforge.oredict.OreDictionary;
 
 import forestry.api.core.ForestryAPI;
+import forestry.api.farming.Farmables;
 import forestry.api.recipes.RecipeManagers;
 import forestry.api.storage.BackpackManager;
 import forestry.core.PluginCore;
@@ -31,6 +35,8 @@ import forestry.core.recipes.RecipeUtil;
 import forestry.core.utils.ItemStackUtil;
 import forestry.core.utils.Log;
 import forestry.core.utils.ModUtil;
+import forestry.farming.logic.FarmableBasicAgricraft;
+import forestry.farming.logic.FarmableGE;
 import forestry.plugins.BlankForestryPlugin;
 import forestry.plugins.ForestryPlugin;
 import forestry.plugins.ForestryPluginUids;
@@ -43,8 +49,6 @@ public class PluginBiomesOPlenty extends BlankForestryPlugin {
 	private static Block saplings;
 	private static Block colorizedSaplings;
 	private static Item food;
-	private static Item misc;
-	private static ItemStack persimmon;
 	private static int amount;
 
 	@Override
@@ -61,12 +65,9 @@ public class PluginBiomesOPlenty extends BlankForestryPlugin {
 	public void doInit() {
 		super.doInit();
 
-		saplings = GameRegistry.findBlock(BoP, "saplings");
-		colorizedSaplings = GameRegistry.findBlock(BoP, "colorizedSaplings");
-		food = GameRegistry.findItem(BoP, "food");
-		if (food != null) {
-			persimmon = new ItemStack(food, 1, 8);
-		}
+		saplings = ForgeRegistries.BLOCKS.getValue(new ResourceLocation(BoP, "saplings"));
+		colorizedSaplings = ForgeRegistries.BLOCKS.getValue(new ResourceLocation(BoP, "colorizedSaplings"));
+		food = ForgeRegistries.ITEMS.getValue(new ResourceLocation(BoP, "food"));
 
 		if (ForestryAPI.enabledPlugins.contains(ForestryPluginUids.APICULTURE)) {
 			addFlowers();
@@ -98,21 +99,21 @@ public class PluginBiomesOPlenty extends BlankForestryPlugin {
 		}
 
 		for (String key : saplingItemKeys) {
-			Item saplingItem = GameRegistry.findItem(BoP, key);
+			Item saplingItem = ForgeRegistries.ITEMS.getValue(new ResourceLocation(BoP, key));
 			String saplingName = ItemStackUtil.getItemNameFromRegistryAsString(saplingItem);
 			if (saplingName != null) {
 				FMLInterModComms.sendMessage(Constants.MOD_ID, "add-farmable-sapling", String.format("farmArboreal@%s.-1", saplingName));
 			}
 		}
-
-		if (ForestryAPI.enabledPlugins.contains(ForestryPluginUids.FARMING) && saplings != null && persimmon != null) {
-			//TODO BoP for 1.9: Add farmables
+		
+		//TODO BoP for 1.9: Add farmables
+//		if (ForestryAPI.enabledPlugins.contains(ForestryPluginUids.FARMING) && saplings != null && persimmon != null) {
 			//			Farmables.farmables.put("farmArboreal", new FarmableGenericSapling(saplings, 15, persimmon));
-		}
+//		}
 
-		Block boPTurnip = GameRegistry.findBlock(BoP, "turnip");
+		Block boPTurnip = ForgeRegistries.BLOCKS.getValue(new ResourceLocation(BoP, "turnip"));
 		if (ForestryAPI.enabledPlugins.contains(ForestryPluginUids.FARMING) && boPTurnip != null) {
-			Item boPTurnipSeeds = GameRegistry.findItem(BoP, "turnipSeeds");
+			Item boPTurnipSeeds = ForgeRegistries.ITEMS.getValue(new ResourceLocation(BoP, "turnipSeeds"));
 			ItemStack boPTurnipSeedStack = new ItemStack(boPTurnipSeeds, 1, 0);
 			if (boPTurnipSeeds != null) {
 				//TODO BoP for 1.9: Add farmable saplings
@@ -130,11 +131,11 @@ public class PluginBiomesOPlenty extends BlankForestryPlugin {
 	private static void addFermenterRecipes() {
 		int saplingYield = ForestryAPI.activeMode.getIntegerSetting("fermenter.yield.sapling");
 
-		if (saplings != null) {
+		if (saplings != Blocks.AIR) {
 			RecipeUtil.addFermenterRecipes(new ItemStack(saplings, 1, OreDictionary.WILDCARD_VALUE), saplingYield, Fluids.BIOMASS);
 		}
 
-		if (colorizedSaplings != null) {
+		if (colorizedSaplings != Blocks.AIR) {
 			RecipeUtil.addFermenterRecipes(new ItemStack(colorizedSaplings, 1, OreDictionary.WILDCARD_VALUE), saplingYield, Fluids.BIOMASS);
 		}
 	}
@@ -142,20 +143,18 @@ public class PluginBiomesOPlenty extends BlankForestryPlugin {
 	private static void addSqueezerRecipes() {
 		ItemStack mulch = new ItemStack(PluginCore.items.mulch);
 
-		misc = GameRegistry.findItem(BoP, "misc");
-		if (misc != null) {
-			ItemStack pinecone = new ItemStack(misc, 1, 13);
-			if (pinecone != null) {
-				RecipeManagers.squeezerManager.addRecipe(10, new ItemStack[]{pinecone}, Fluids.SEED_OIL.getFluid(3 * amount));
-			}
+		Item pinecone = ForgeRegistries.ITEMS.getValue(new ResourceLocation(BoP, "pinecone"));
+		if (pinecone != null) {
+			RecipeManagers.squeezerManager.addRecipe(10, new ItemStack[]{new ItemStack(pinecone)}, Fluids.SEED_OIL.getFluid(3 * amount));
 		}
 
 		if (food != null) {
 			RecipeManagers.squeezerManager.addRecipe(10, new ItemStack[]{new ItemStack(food)}, Fluids.JUICE.getFluid(50), mulch, 5);
 		}
 
+		Item persimmon = ForgeRegistries.ITEMS.getValue(new ResourceLocation(BoP, "persimmon"));
 		if (persimmon != null) {
-			RecipeManagers.squeezerManager.addRecipe(10, new ItemStack[]{persimmon}, Fluids.JUICE.getFluid(200), mulch, 20);
+			RecipeManagers.squeezerManager.addRecipe(10, new ItemStack[]{new ItemStack(persimmon)}, Fluids.JUICE.getFluid(200), mulch, 20);
 		}
 	}
 
@@ -234,7 +233,7 @@ public class PluginBiomesOPlenty extends BlankForestryPlugin {
 
 	private static void addBlocksToBackpack(String backpackUid, String... blockNames) {
 		for (String blockName : blockNames) {
-			Block block = GameRegistry.findBlock(BoP, blockName);
+			Block block = ForgeRegistries.BLOCKS.getValue(new ResourceLocation(BoP, blockName));
 			if (block != null) {
 				ItemStack blockStack = new ItemStack(block, 1, OreDictionary.WILDCARD_VALUE);
 				BackpackManager.backpackInterface.getBackpack(backpackUid).addValidItem(blockStack);

src/main/java/forestry/plugins/compat/PluginEnderIO.java

@@ -0,0 +1,70 @@
+package forestry.plugins.compat;
+
+import forestry.api.core.ForestryAPI;
+import forestry.core.config.Constants;
+import forestry.core.fluids.Fluids;
+import forestry.core.utils.ModUtil;
+import forestry.plugins.BlankForestryPlugin;
+import forestry.plugins.ForestryPlugin;
+import forestry.plugins.ForestryPluginUids;
+import net.minecraft.nbt.NBTTagCompound;
+import net.minecraftforge.fluids.Fluid;
+import net.minecraftforge.fml.common.event.FMLInterModComms;
+
+@ForestryPlugin(pluginID = ForestryPluginUids.ENDER_IO, name = "EnderIO", author = "mezz", url = Constants.URL, unlocalizedDescription = "for.plugin.enderIO.description")
+public class PluginEnderIO extends BlankForestryPlugin {
+
+	private static final String EnderIO = "EnderIO";
+
+	private static final String FLUID_FUEL_ADD = "fluidFuel:add";
+	private static final String FLUID_COOLANT_ADD = "fluidCoolant:add";
+
+	private static final String KEY_FLUID_NAME = "fluidName";
+	private static final String KEY_POWER_PER_CYCLE = "powerPerCycle";
+	private static final String KEY_TOTAL_BURN_TIME = "totalBurnTime";
+	private static final String KEY_COOLING_PER_MB = "coolingPerMb";
+
+	private static final float WATER_COOLING_PER_MB = 0.0023f;
+
+	@Override
+	public boolean isAvailable() {
+		return ModUtil.isModLoaded(EnderIO);
+	}
+
+	@Override
+	public String getFailMessage() {
+		return "EnderIO not found";
+	}
+
+	@Override
+	public void doInit() {
+		Fluid ethanol = Fluids.BIO_ETHANOL.getFluid();
+		if (ethanol != null) {
+			int ethanolBurnTime = Math.round(Constants.ENGINE_CYCLE_DURATION_ETHANOL * ForestryAPI.activeMode.getFloatSetting("fuel.ethanol.combustion"));
+			addFuel(ethanol, 40, ethanolBurnTime);
+		}
+
+		Fluid crushedIce = Fluids.ICE.getFluid();
+		if (crushedIce != null) {
+			addCoolant(crushedIce, Constants.ICE_COOLING_MULTIPLIER);
+		}
+	}
+
+	private static void addFuel(Fluid fluid, int powerPerCycle, int totalBurnTime) {
+		NBTTagCompound fuelTag = new NBTTagCompound();
+		fuelTag.setString(KEY_FLUID_NAME, fluid.getName());
+		fuelTag.setInteger(KEY_POWER_PER_CYCLE, powerPerCycle);
+		fuelTag.setInteger(KEY_TOTAL_BURN_TIME, totalBurnTime);
+
+		FMLInterModComms.sendMessage(EnderIO, FLUID_FUEL_ADD, fuelTag);
+	}
+
+	private static void addCoolant(Fluid fluid, float coolingMultiplier) {
+		float coolingPerMb = coolingMultiplier * WATER_COOLING_PER_MB;
+		NBTTagCompound coolantTag = new NBTTagCompound();
+		coolantTag.setString(KEY_FLUID_NAME, fluid.getName());
+		coolantTag.setFloat(KEY_COOLING_PER_MB, coolingPerMb);
+
+		FMLInterModComms.sendMessage(EnderIO, FLUID_COOLANT_ADD, coolantTag);
+	}
+}

src/main/java/forestry/plugins/compat/PluginExtraUtilities.java

@@ -0,0 +1,89 @@
+/*******************************************************************************
+ * 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.plugins.compat;
+
+import java.util.Collections;
+
+import forestry.api.circuits.ChipsetManager;
+import forestry.api.circuits.ICircuitLayout;
+import forestry.api.core.ForestryAPI;
+import forestry.api.farming.Farmables;
+import forestry.core.PluginCore;
+import forestry.core.circuits.Circuit;
+import forestry.core.config.Config;
+import forestry.core.config.Constants;
+import forestry.core.items.EnumElectronTube;
+import forestry.core.utils.BlockUtil;
+import forestry.core.utils.Log;
+import forestry.core.utils.ModUtil;
+import forestry.farming.circuits.CircuitFarmLogic;
+import forestry.farming.logic.FarmLogicEnder;
+import forestry.farming.logic.FarmableAgingCrop;
+import forestry.plugins.BlankForestryPlugin;
+import forestry.plugins.ForestryPlugin;
+import forestry.plugins.ForestryPluginUids;
+import net.minecraft.block.Block;
+import net.minecraft.block.properties.IProperty;
+import net.minecraft.init.Blocks;
+import net.minecraft.item.Item;
+import net.minecraft.item.ItemStack;
+import net.minecraft.util.ResourceLocation;
+import net.minecraftforge.fml.common.registry.ForgeRegistries;
+
+@ForestryPlugin(pluginID = ForestryPluginUids.EXTRA_UTILITIES, name = "ExtraUtilities", author = "Nirek", url = Constants.URL, unlocalizedDescription = "for.plugin.extrautilities.description")
+public class PluginExtraUtilities extends BlankForestryPlugin {
+
+	private static final String ExU = "ExtraUtils2";
+
+	@Override
+	public boolean isAvailable() {
+		return ModUtil.isModLoaded(ExU);
+	}
+
+	@Override
+	public String getFailMessage() {
+		return "ExtraUtilities not found";
+	}
+
+	@Override
+	public void doInit() {
+		super.doInit();
+
+		if (Config.isExUtilEnderLilyEnabled()) {
+			Block enderLillyBlock = ForgeRegistries.BLOCKS.getValue(new ResourceLocation("extrautils2", "EnderLilly"));
+			Item enderLillyItem = Item.getItemFromBlock(enderLillyBlock);
+			if (enderLillyBlock == Blocks.AIR) {
+				Log.error("Could not find ender lilly block.");
+			} else if (enderLillyItem == null) {
+				Log.error("Could not find ender lilly item.");
+			} else {
+				IProperty<Integer> growthProperty = BlockUtil.getProperty(enderLillyBlock, "growth", Integer.class);
+				if (growthProperty == null) {
+					Log.error("Could not find the growth property of ender lily.");
+				} else {
+					int harvestAge = Collections.max(growthProperty.getAllowedValues());
+					int replantAge = enderLillyBlock.getDefaultState().getValue(growthProperty);
+					Farmables.farmables.put("farmEnder", new FarmableAgingCrop(new ItemStack(enderLillyItem), enderLillyBlock, growthProperty, harvestAge, replantAge));
+					Circuit.farmEnderManaged = new CircuitFarmLogic("managedEnder", new FarmLogicEnder());
+				}
+			}
+		}
+	}
+
+	@Override
+	public void registerRecipes() {
+		super.registerRecipes();
+		if (ForestryAPI.enabledPlugins.contains(ForestryPluginUids.FARMING) && Circuit.farmEnderManaged != null) {
+			ICircuitLayout layoutManaged = ChipsetManager.circuitRegistry.getLayout("forestry.farms.managed");
+			ChipsetManager.solderManager.addRecipe(layoutManaged, PluginCore.items.tubes.get(EnumElectronTube.ENDER, 1), Circuit.farmEnderManaged);
+		}
+	}
+}

src/main/java/forestry/storage/PluginStorage.java

@@ -219,11 +219,12 @@ public class PluginStorage extends BlankForestryPlugin {
 				"stainedGlass[A-Z].*",
 				"stone",
 				"sandstone",
-				"plankWood",
-				"stairWood",
-				"slabWood",
+				OreDictUtil.PLANK_WOOD,
+				OreDictUtil.STAIR_WOOD,
+				OreDictUtil.SLAB_WOOD,
 				OreDictUtil.FENCE_WOOD,
 				OreDictUtil.FENCE_GATE_WOOD,
+				OreDictUtil.TRAPDOOR_WOOD,
 				"glass",
 				"paneGlass",
 				"torch",
@@ -350,7 +351,6 @@ public class PluginStorage extends BlankForestryPlugin {
 				new ItemStack(Blocks.PURPUR_SLAB),
 				new ItemStack(Blocks.END_BRICKS),
 				new ItemStack(Blocks.CARPET, 1, OreDictionary.WILDCARD_VALUE),
-				new ItemStack(Blocks.TRAPDOOR),
 				new ItemStack(Blocks.IRON_TRAPDOOR),
 				new ItemStack(Blocks.STONE_PRESSURE_PLATE),
 				new ItemStack(Blocks.WOODEN_PRESSURE_PLATE),