More support for 3D biomes (#608)

* More support for 3D biomes

* Resolved merge conflicts

worldedit-bukkit/src/main/java/com/sk89q/worldedit/bukkit/BukkitWorld.java

@@ -31,7 +31,6 @@ import com.sk89q.worldedit.WorldEditException;
 import com.sk89q.worldedit.blocks.BaseItem;
 import com.sk89q.worldedit.blocks.BaseItemStack;
 import com.sk89q.worldedit.bukkit.adapter.BukkitImplAdapter;
-import com.sk89q.worldedit.entity.BaseEntity;
 import com.sk89q.worldedit.entity.Player;
 import com.sk89q.worldedit.internal.wna.WorldNativeAccess;
 import com.sk89q.worldedit.math.BlockVector2;
@@ -71,7 +70,6 @@ import java.util.List;
 import java.util.Locale;
 import java.util.Map;
 import java.util.Set;
-import javax.annotation.Nullable;
 
 import static com.google.common.base.Preconditions.checkNotNull;
 
@@ -543,6 +541,13 @@ public class BukkitWorld extends AbstractWorld {
         return false;
     }
 
+    @Override
+    public boolean fullySupports3DBiomes() {
+        // Supports if API does and we're not in the overworld
+        return HAS_3D_BIOMES && getWorld().getEnvironment() != World.Environment.NORMAL;
+    }
+
+    @SuppressWarnings("deprecation")
     @Override
     public BiomeType getBiome(BlockVector3 position) {
         if (HAS_3D_BIOMES) {
@@ -576,7 +581,7 @@ public class BukkitWorld extends AbstractWorld {
 
     @Override
     public boolean setBiome(int x, int y, int z, BiomeType biome) {
-        return setBiome(BlockVector2.at(x, z), biome);
+        return setBiome(BlockVector3.at(x, y, z), biome);
     }
 
     @Override

worldedit-core/src/main/java/com/boydti/fawe/beta/implementation/blocks/CharSetBlocks.java

@@ -7,7 +7,6 @@ import com.boydti.fawe.config.Settings;
 import com.boydti.fawe.object.collection.BlockVector3ChunkMap;
 import com.sk89q.jnbt.CompoundTag;
 import com.sk89q.worldedit.WorldEditException;
-import com.sk89q.worldedit.math.BlockVector2;
 import com.sk89q.worldedit.math.BlockVector3;
 import com.sk89q.worldedit.world.biome.BiomeType;
 import com.sk89q.worldedit.world.block.BlockStateHolder;
@@ -198,8 +197,8 @@ public class CharSetBlocks extends CharBlocks implements IChunkSet {
     }
 
     @Override
-    public boolean setBiome(BlockVector2 position, BiomeType biome) {
+    public boolean setBiome(BlockVector3 position, BiomeType biome) {
-        return setBiome(position.getX(),0, position.getZ(), biome);
+        return setBiome(position.getX(),position.getY(), position.getZ(), biome);
     }
 
     @Override

worldedit-core/src/main/java/com/boydti/fawe/beta/implementation/chunk/NullChunk.kt

@@ -82,6 +82,10 @@ object NullChunk : IQueueChunk<Nothing> {
 
     }
 
+    override fun fullySupports3DBiomes(): Boolean {
+        return false
+    }
+
     override fun setBlockLight(x: Int, y: Int, z: Int, value: Int) {
 
     }

worldedit-core/src/main/java/com/boydti/fawe/beta/implementation/filter/block/CharFilterBlock.java

@@ -11,7 +11,7 @@ import com.boydti.fawe.beta.implementation.blocks.CharGetBlocks;
 import com.sk89q.jnbt.CompoundTag;
 import com.sk89q.worldedit.WorldEditException;
 import com.sk89q.worldedit.extent.Extent;
-import com.sk89q.worldedit.math.BlockVector2;
+import com.sk89q.worldedit.math.BlockVector3;
 import com.sk89q.worldedit.regions.Region;
 import com.sk89q.worldedit.world.biome.BiomeType;
 import com.sk89q.worldedit.world.block.BaseBlock;
@@ -419,8 +419,8 @@ public class CharFilterBlock extends ChunkFilterBlock {
     }
 
     @Override
-    public boolean setBiome(BlockVector2 position, BiomeType biome) {
+    public boolean setBiome(BlockVector3 position, BiomeType biome) {
-        return setBiome(position.getX(), 0, position.getBlockZ(), biome);
+        return setBiome(position.getX(), position.getY(), position.getBlockZ(), biome);
     }
 
     @Override

worldedit-core/src/main/java/com/boydti/fawe/beta/implementation/filter/block/FilterBlock.java

@@ -150,12 +150,6 @@ public abstract class FilterBlock extends BlockVector3 implements Extent, TileEn
         return true;
     }
 
-    @Override
-    public boolean setBiome(Extent orDefault, BiomeType biome) {
-        setBiome(biome);
-        return true;
-    }
-
     @Override
     public int getOrdinal(Extent orDefault) {
         return getOrdinal();

worldedit-core/src/main/java/com/boydti/fawe/beta/implementation/processors/LimitExtent.java

@@ -16,7 +16,6 @@ import com.sk89q.worldedit.function.generator.GenBase;
 import com.sk89q.worldedit.function.generator.Resource;
 import com.sk89q.worldedit.function.mask.Mask;
 import com.sk89q.worldedit.function.pattern.Pattern;
-import com.sk89q.worldedit.math.BlockVector2;
 import com.sk89q.worldedit.math.BlockVector3;
 import com.sk89q.worldedit.regions.Region;
 import com.sk89q.worldedit.session.ClipboardHolder;
@@ -545,7 +544,7 @@ public class LimitExtent extends PassthroughExtent {
     }
 
     @Override
-    public BiomeType getBiome(BlockVector2 position) {
+    public BiomeType getBiome(BlockVector3 position) {
         limit.THROW_MAX_CHECKS();
         try {
             return getExtent().getBiome(position);
@@ -614,7 +613,7 @@ public class LimitExtent extends PassthroughExtent {
     }
 
     @Override
-    public boolean setBiome(BlockVector2 position, BiomeType biome) {
+    public boolean setBiome(BlockVector3 position, BiomeType biome) {
         limit.THROW_MAX_CHANGES();
         try {
             return getExtent().setBiome(position, biome);

worldedit-core/src/main/java/com/boydti/fawe/jnbt/anvil/MCAChunk.java

@@ -16,7 +16,6 @@ import com.sk89q.jnbt.ListTag;
 import com.sk89q.jnbt.NBTConstants;
 import com.sk89q.jnbt.NBTInputStream;
 import com.sk89q.jnbt.NBTOutputStream;
-import com.sk89q.worldedit.math.BlockVector2;
 import com.sk89q.worldedit.math.BlockVector3;
 import com.sk89q.worldedit.regions.Region;
 import com.sk89q.worldedit.registry.state.Property;
@@ -481,14 +480,14 @@ public class MCAChunk implements IChunk {
     }
 
     @Override
-    public boolean setBiome(BlockVector2 pos, BiomeType biome) {
+    public boolean setBiome(BlockVector3 pos, BiomeType biome) {
-        return this.setBiome(pos.getX(), 0, pos.getZ(), biome);
+        return this.setBiome(pos.getX(), pos.getY(), pos.getZ(), biome);
     }
 
     @Override
     public boolean setBiome(int x, int y, int z, BiomeType biome) {
         setModified();
-        biomes[x + (z << 4)] = biome;
+        biomes[x + (z << 4)] = biome; //TODO Support 3D Biomes
         return true;
     }
 

worldedit-core/src/main/java/com/boydti/fawe/object/HistoryExtent.java

@@ -7,7 +7,6 @@ import com.sk89q.worldedit.entity.Entity;
 import com.sk89q.worldedit.extent.AbstractDelegateExtent;
 import com.sk89q.worldedit.extent.Extent;
 import com.sk89q.worldedit.history.changeset.ChangeSet;
-import com.sk89q.worldedit.math.BlockVector2;
 import com.sk89q.worldedit.math.BlockVector3;
 import com.sk89q.worldedit.regions.Region;
 import com.sk89q.worldedit.util.Location;
@@ -96,7 +95,7 @@ public class HistoryExtent extends AbstractDelegateExtent {
     }
 
     @Override
-    public boolean setBiome(BlockVector2 position, BiomeType newBiome) {
+    public boolean setBiome(BlockVector3 position, BiomeType newBiome) {
         BiomeType oldBiome = this.getBiome(position);
         if (oldBiome.getId() != newBiome.getId()) {
             this.changeSet.addBiomeChange(position.getBlockX(), position.getBlockZ(), oldBiome, newBiome);
@@ -108,7 +107,7 @@ public class HistoryExtent extends AbstractDelegateExtent {
 
     @Override
     public boolean setBiome(int x, int y, int z, BiomeType newBiome) {
-        BiomeType oldBiome = this.getBiome(BlockVector2.at(x, z));
+        BiomeType oldBiome = this.getBiome(BlockVector3.at(x, y, z));
         if (oldBiome.getId() != newBiome.getId()) {
             this.changeSet.addBiomeChange(x, z, oldBiome, newBiome);
             return getExtent().setBiome(x, y, z, newBiome);

worldedit-core/src/main/java/com/boydti/fawe/object/brush/visualization/ImmutableVirtualWorld.java

@@ -4,7 +4,6 @@ import com.sk89q.worldedit.EditSession;
 import com.sk89q.worldedit.MaxChangedBlocksException;
 import com.sk89q.worldedit.WorldEditException;
 import com.sk89q.worldedit.blocks.BaseItemStack;
-import com.sk89q.worldedit.math.BlockVector2;
 import com.sk89q.worldedit.math.BlockVector3;
 import com.sk89q.worldedit.math.Vector3;
 import com.sk89q.worldedit.regions.Region;
@@ -28,7 +27,7 @@ public abstract class ImmutableVirtualWorld implements VirtualWorld {
     }
 
     @Override
-    public BiomeType getBiome(BlockVector2 position) {
+    public BiomeType getBiome(BlockVector3 position) {
         return BiomeTypes.FOREST;
     }
 

worldedit-core/src/main/java/com/boydti/fawe/object/brush/visualization/cfi/HeightMapMCAGenerator.java

@@ -1024,8 +1024,8 @@ public class HeightMapMCAGenerator extends MCAWriter implements StreamChange, Dr
     }
 
     @Override
-    public BiomeType getBiome(BlockVector2 position) {
+    public BiomeType getBiome(BlockVector3 position) {
-        return getBiomeType(position.getBlockX(), 0, position.getBlockZ());
+        return getBiomeType(position.getBlockX(), position.getBlockY(), position.getBlockZ());
     }
 
     @Override

worldedit-core/src/main/java/com/boydti/fawe/object/clipboard/EmptyClipboard.kt

@@ -45,7 +45,7 @@ object EmptyClipboard : Clipboard {
         return BlockTypes.AIR!!.defaultState
     }
 
-    override fun getBiome(position: BlockVector2): BiomeType? {
+    override fun getBiome(position: BlockVector3): BiomeType? {
         return null
     }
 
@@ -64,7 +64,11 @@ object EmptyClipboard : Clipboard {
         return false
     }
 
-    override fun setBiome(position: BlockVector2, biome: BiomeType): Boolean {
+    override fun setBiome(position: BlockVector3, biome: BiomeType): Boolean {
+        return false
+    }
+
+    override fun fullySupports3DBiomes(): Boolean {
         return false
     }
 

worldedit-core/src/main/java/com/boydti/fawe/object/extent/BlockTranslateExtent.java

@@ -3,7 +3,6 @@ package com.boydti.fawe.object.extent;
 import com.sk89q.worldedit.WorldEditException;
 import com.sk89q.worldedit.extent.AbstractDelegateExtent;
 import com.sk89q.worldedit.extent.Extent;
-import com.sk89q.worldedit.math.BlockVector2;
 import com.sk89q.worldedit.math.BlockVector3;
 import com.sk89q.worldedit.math.MutableBlockVector3;
 import com.sk89q.worldedit.world.biome.BiomeType;
@@ -36,8 +35,8 @@ public class BlockTranslateExtent extends AbstractDelegateExtent {
     }
 
     @Override
-    public boolean setBiome(BlockVector2 position, BiomeType biome) {
+    public boolean setBiome(BlockVector3 position, BiomeType biome) {
-        return super.setBiome(position.add(dx, dz), biome);
+        return super.setBiome(position.add(dx, dy, dz), biome);
     }
 
     @Override
@@ -46,8 +45,8 @@ public class BlockTranslateExtent extends AbstractDelegateExtent {
     }
 
     @Override
-    public BiomeType getBiome(BlockVector2 position) {
+    public BiomeType getBiome(BlockVector3 position) {
-        return super.getBiome(position.add(dx, dz));
+        return super.getBiome(position.add(dx, dy, dz));
     }
 
     @Override

worldedit-core/src/main/java/com/boydti/fawe/object/extent/FaweRegionExtent.java

@@ -93,7 +93,7 @@ public abstract class FaweRegionExtent extends ResettableExtent implements IBatc
     }
 
     @Override
-    public BiomeType getBiome(BlockVector2 position) {
+    public BiomeType getBiome(BlockVector3 position) {
         if (!contains(position)) {
             if (!limit.MAX_FAILS()) {
                 WEManager.IMP.cancelEditSafe(this, FaweCache.OUTSIDE_REGION);

worldedit-core/src/main/java/com/boydti/fawe/object/extent/NullExtent.java

@@ -19,7 +19,6 @@ import com.sk89q.worldedit.function.generator.Resource;
 import com.sk89q.worldedit.function.mask.Mask;
 import com.sk89q.worldedit.function.operation.Operation;
 import com.sk89q.worldedit.function.pattern.Pattern;
-import com.sk89q.worldedit.math.BlockVector2;
 import com.sk89q.worldedit.math.BlockVector3;
 import com.sk89q.worldedit.regions.Region;
 import com.sk89q.worldedit.session.ClipboardHolder;
@@ -110,7 +109,7 @@ public class NullExtent extends FaweRegionExtent implements IBatchProcessor {
     }
 
     @Override
-    public BiomeType getBiome(BlockVector2 position) {
+    public BiomeType getBiome(BlockVector3 position) {
         return BiomeTypes.THE_VOID;
     }
 
@@ -141,7 +140,7 @@ public class NullExtent extends FaweRegionExtent implements IBatchProcessor {
     }
 
     @Override
-    public boolean setBiome(BlockVector2 position, BiomeType biome) {
+    public boolean setBiome(BlockVector3 position, BiomeType biome) {
         return false;
     }
 

worldedit-core/src/main/java/com/boydti/fawe/object/extent/PositionTransformExtent.java

@@ -2,7 +2,6 @@ package com.boydti.fawe.object.extent;
 
 import com.sk89q.worldedit.WorldEditException;
 import com.sk89q.worldedit.extent.Extent;
-import com.sk89q.worldedit.math.BlockVector2;
 import com.sk89q.worldedit.math.BlockVector3;
 import com.sk89q.worldedit.math.MutableBlockVector3;
 import com.sk89q.worldedit.math.MutableVector3;
@@ -62,11 +61,11 @@ public class PositionTransformExtent extends ResettableExtent {
     }
 
     @Override
-    public BiomeType getBiome(BlockVector2 position) {
+    public BiomeType getBiome(BlockVector3 position) {
         mutable.mutX(position.getBlockX());
         mutable.mutZ(position.getBlockZ());
-        mutable.mutY(0);
+        mutable.mutY(position.getBlockY());
-        return super.getBiome(getPos(mutable).toBlockVector2());
+        return super.getBiome(getPos(mutable));
     }
 
     @Override
@@ -81,11 +80,11 @@ public class PositionTransformExtent extends ResettableExtent {
     }
 
     @Override
-    public boolean setBiome(BlockVector2 position, BiomeType biome) {
+    public boolean setBiome(BlockVector3 position, BiomeType biome) {
         mutable.mutX(position.getBlockX());
         mutable.mutZ(position.getBlockZ());
-        mutable.mutY(0);
+        mutable.mutY(position.getBlockY());
-        return super.setBiome(getPos(mutable).toBlockVector2(), biome);
+        return super.setBiome(getPos(mutable), biome);
     }
 
     public void setTransform(Transform transform) {

worldedit-core/src/main/java/com/boydti/fawe/object/extent/TemporalExtent.java

@@ -2,7 +2,6 @@ package com.boydti.fawe.object.extent;
 
 import com.sk89q.worldedit.extent.Extent;
 import com.sk89q.worldedit.extent.PassthroughExtent;
-import com.sk89q.worldedit.math.BlockVector2;
 import com.sk89q.worldedit.math.BlockVector3;
 import com.sk89q.worldedit.world.biome.BiomeType;
 import com.sk89q.worldedit.world.block.BaseBlock;
@@ -69,7 +68,7 @@ public class TemporalExtent extends PassthroughExtent {
     }
 
     @Override
-    public BiomeType getBiome(BlockVector2 position) {
+    public BiomeType getBiome(BlockVector3 position) {
         if (position.getX() == bx && position.getZ() == bz) {
             return biome;
         }

worldedit-core/src/main/java/com/boydti/fawe/object/function/block/BiomeCopy.java

@@ -3,31 +3,31 @@ package com.boydti.fawe.object.function.block;
 import com.sk89q.worldedit.WorldEditException;
 import com.sk89q.worldedit.extent.Extent;
 import com.sk89q.worldedit.function.RegionFunction;
-import com.sk89q.worldedit.math.BlockVector2;
 import com.sk89q.worldedit.math.BlockVector3;
-import com.sk89q.worldedit.math.MutableBlockVector2;
+import com.sk89q.worldedit.math.MutableBlockVector3;
 
 public class BiomeCopy implements RegionFunction {
 
     protected final Extent source;
     protected final Extent destination;
-    private final MutableBlockVector2 mPos2d;
+    private final MutableBlockVector3 mutableVector;
 
     public BiomeCopy(Extent source, Extent destination) {
         this.source = source;
         this.destination = destination;
-        this.mPos2d = new MutableBlockVector2();
+        this.mutableVector = new MutableBlockVector3();
-        this.mPos2d.setComponents(Integer.MIN_VALUE, Integer.MIN_VALUE);
+        this.mutableVector.setComponents(Integer.MIN_VALUE, Integer.MIN_VALUE, Integer.MIN_VALUE);
     }
 
     @Override
     public boolean apply(BlockVector3 position) throws WorldEditException {
         int x = position.getBlockX();
+        int y = position.getBlockY();
         int z = position.getBlockZ();
-        if (x != mPos2d.getBlockX() || z != mPos2d.getBlockZ()) {
+        if (x != mutableVector.getBlockX() || z != mutableVector.getBlockZ()|| y != mutableVector
-            mPos2d.setComponents(x, z);
+            .getBlockY()) {
-            BlockVector2 bv = mPos2d;
+            mutableVector.setComponents(x, y, z);
-            return destination.setBiome(bv, source.getBiome(bv));
+            return destination.setBiome(mutableVector, source.getBiome(mutableVector));
         }
         return false;
     }

worldedit-core/src/main/java/com/boydti/fawe/wrappers/WorldWrapper.java

@@ -281,12 +281,12 @@ public class WorldWrapper extends AbstractWorld {
     }
 
     @Override
-    public BiomeType getBiome(BlockVector2 position) {
+    public BiomeType getBiome(BlockVector3 position) {
         return parent.getBiome(position);
     }
 
     @Override
-    public boolean setBiome(BlockVector2 position, BiomeType biome) {
+    public boolean setBiome(BlockVector3 position, BiomeType biome) {
         return parent.setBiome(position, biome);
     }
 

worldedit-core/src/main/java/com/sk89q/worldedit/EditSession.java

@@ -96,7 +96,6 @@ import com.sk89q.worldedit.math.BlockVector3;
 import com.sk89q.worldedit.math.MathUtils;
 import com.sk89q.worldedit.math.MutableBlockVector2;
 import com.sk89q.worldedit.math.MutableBlockVector3;
-import com.sk89q.worldedit.math.Vector2;
 import com.sk89q.worldedit.math.Vector3;
 import com.sk89q.worldedit.math.interpolation.Interpolation;
 import com.sk89q.worldedit.math.interpolation.KochanekBartelsInterpolation;
@@ -763,7 +762,17 @@ public class EditSession extends PassthroughExtent implements AutoCloseable {
     }
 
     @Override
-    public boolean setBiome(BlockVector2 position, BiomeType biome) {
+    public boolean fullySupports3DBiomes() {
+        return this.getExtent().fullySupports3DBiomes();
+    }
+
+    @Override
+    public BiomeType getBiome(BlockVector3 position) {
+        return this.getExtent().getBiome(position);
+    }
+
+    @Override
+    public boolean setBiome(BlockVector3 position, BiomeType biome) {
         this.changes++;
         return this.getExtent().setBiome(position, biome);
     }
@@ -2916,8 +2925,6 @@ public class EditSession extends PassthroughExtent implements AutoCloseable {
     public int makeBiomeShape(final Region region, final Vector3 zero, final Vector3 unit, final BiomeType biomeType,
                               final String expressionString, final boolean hollow, final int timeout)
             throws ExpressionException, MaxChangedBlocksException {
-        final Vector2 zero2D = zero.toVector2();
-        final Vector2 unit2D = unit.toVector2();
 
         final Expression expression = Expression.compile(expressionString, "x", "z");
         expression.optimize();
@@ -2930,12 +2937,13 @@ public class EditSession extends PassthroughExtent implements AutoCloseable {
         final ArbitraryBiomeShape shape = new ArbitraryBiomeShape(region) {
             @Override
             protected BiomeType getBiome(int x, int y, int z, BiomeType defaultBiomeType) {
-                environment.setCurrentBlock(x, 0, z);
+                environment.setCurrentBlock(x, y, z);
-                double scaledX = (x - zero2D.getX()) / unit2D.getX();
+                double scaledX = (x - zero.getX()) / unit.getX();
-                double scaledZ = (z - zero2D.getZ()) / unit2D.getZ();
+                double scaledY = (x - zero.getY()) / unit.getX();
+                double scaledZ = (z - zero.getZ()) / unit.getZ();
 
                 try {
-                    if (expression.evaluate(timeout, scaledX, scaledZ) <= 0) {
+                    if (expression.evaluate(timeout, scaledX, scaledY, scaledZ) <= 0) {
                         return null;
                     }
 

worldedit-core/src/main/java/com/sk89q/worldedit/command/BiomeCommands.java

@@ -37,10 +37,8 @@ import com.sk89q.worldedit.function.mask.Mask;
 import com.sk89q.worldedit.function.mask.Mask2D;
 import com.sk89q.worldedit.function.operation.Operations;
 import com.sk89q.worldedit.function.visitor.FlatRegionVisitor;
-import com.sk89q.worldedit.math.BlockVector2;
 import com.sk89q.worldedit.math.BlockVector3;
 import com.sk89q.worldedit.regions.CuboidRegion;
-import com.sk89q.worldedit.regions.FlatRegion;
 import com.sk89q.worldedit.regions.Region;
 import com.sk89q.worldedit.regions.Regions;
 import com.sk89q.worldedit.util.Location;
@@ -132,12 +130,12 @@ public class BiomeCommands {
                 return;
             }
 
-            BiomeType biome = player.getWorld().getBiome(blockPosition.toVector().toBlockPoint().toBlockVector2());
+            BiomeType biome = player.getWorld().getBiome(blockPosition.toVector().toBlockPoint());
             biomes.add(biome);
 
             messageKey = "worldedit.biomeinfo.lineofsight";
         } else if (usePosition) {
-            BiomeType biome = player.getWorld().getBiome(player.getLocation().toVector().toBlockPoint().toBlockVector2());
+            BiomeType biome = player.getWorld().getBiome(player.getLocation().toVector().toBlockPoint());
             biomes.add(biome);
 
             messageKey = "worldedit.biomeinfo.position";
@@ -145,14 +143,8 @@ public class BiomeCommands {
             World world = player.getWorld();
             Region region = session.getSelection(world);
 
-            if (region instanceof FlatRegion) {
+            for (BlockVector3 pt : region) {
-                for (BlockVector2 pt : ((FlatRegion) region).asFlatRegion()) {
+                biomes.add(world.getBiome(pt));
-                    biomes.add(world.getBiome(pt));
-                }
-            } else {
-                for (BlockVector3 pt : region) {
-                    biomes.add(world.getBiome(pt.toBlockVector2()));
-                }
             }
 
             messageKey = "worldedit.biomeinfo.selection";

worldedit-core/src/main/java/com/sk89q/worldedit/extent/AbstractDelegateExtent.java

@@ -32,7 +32,6 @@ import com.sk89q.worldedit.entity.Entity;
 import com.sk89q.worldedit.extent.buffer.ForgetfulExtentBuffer;
 import com.sk89q.worldedit.function.operation.Operation;
 import com.sk89q.worldedit.function.operation.OperationQueue;
-import com.sk89q.worldedit.math.BlockVector2;
 import com.sk89q.worldedit.math.BlockVector3;
 import com.sk89q.worldedit.regions.Region;
 import com.sk89q.worldedit.util.Location;
@@ -40,15 +39,12 @@ import com.sk89q.worldedit.world.biome.BiomeType;
 import com.sk89q.worldedit.world.block.BaseBlock;
 import com.sk89q.worldedit.world.block.BlockState;
 import com.sk89q.worldedit.world.block.BlockStateHolder;
-
-import java.util.List;
-import java.util.UUID;
-
-import javax.annotation.Nullable;
 import org.jetbrains.annotations.Range;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
+import java.util.List;
+import java.util.UUID;
 import javax.annotation.Nullable;
 
 import static com.google.common.base.Preconditions.checkNotNull;
@@ -88,10 +84,21 @@ public class AbstractDelegateExtent implements Extent {
         return extent.getBlock(position.getX(), position.getY(), position.getZ());
     }
 
+    @Override
+    public BaseBlock getFullBlock(int x, int y, int z) {
+        return extent.getFullBlock(x, y, z);
+    }
+
+    @Override
+    public BaseBlock getFullBlock(BlockVector3 position) {
+        return extent.getFullBlock(position.getX(), position.getY(), position.getZ());
+    }
+
     /*
         Queue based methods
         TODO NOT IMPLEMENTED: IQueueExtent and such need to implement these
          */
+
     @Override
     public boolean isQueueEnabled() {
         return extent.isQueueEnabled();
@@ -122,10 +129,10 @@ public class AbstractDelegateExtent implements Extent {
             new ExtentTraverser<>(this).setNext(new ForgetfulExtentBuffer(extent));
         }
     }
-
     /*
      History
      */
+
     public void setChangeSet(AbstractChangeSet changeSet) {
         if (extent instanceof HistoryExtent) {
             HistoryExtent history = ((HistoryExtent) extent);
@@ -173,13 +180,13 @@ public class AbstractDelegateExtent implements Extent {
     }
 
     @Override
-    public BiomeType getBiome(BlockVector2 position) {
+    public boolean fullySupports3DBiomes() {
-        return extent.getBiome(position);
+        return extent.fullySupports3DBiomes();
     }
 
     @Override
-    public BaseBlock getFullBlock(int x, int y, int z) {
+    public BiomeType getBiome(BlockVector3 position) {
-        return extent.getFullBlock(x, y, z);
+        return extent.getBiome(position);
     }
 
     @Override
@@ -210,8 +217,8 @@ public class AbstractDelegateExtent implements Extent {
     }
 
     @Override
-    public boolean setBiome(BlockVector2 position, BiomeType biome) {
+    public boolean setBiome(BlockVector3 position, BiomeType biome) {
-        return extent.setBiome(position.getX(), 0, position.getZ(), biome);
+        return extent.setBiome(position.getX(), position.getY(), position.getZ(), biome);
     }
 
     @Override

worldedit-core/src/main/java/com/sk89q/worldedit/extent/ChangeSetExtent.java

@@ -22,12 +22,11 @@ package com.sk89q.worldedit.extent;
 import com.sk89q.worldedit.WorldEditException;
 import com.sk89q.worldedit.entity.BaseEntity;
 import com.sk89q.worldedit.entity.Entity;
-import com.sk89q.worldedit.history.change.BiomeChange;
+import com.sk89q.worldedit.history.change.BiomeChange3D;
 import com.sk89q.worldedit.history.change.BlockChange;
 import com.sk89q.worldedit.history.change.EntityCreate;
 import com.sk89q.worldedit.history.change.EntityRemove;
 import com.sk89q.worldedit.history.changeset.ChangeSet;
-import com.sk89q.worldedit.math.BlockVector2;
 import com.sk89q.worldedit.math.BlockVector3;
 import com.sk89q.worldedit.regions.Region;
 import com.sk89q.worldedit.util.Location;
@@ -68,9 +67,9 @@ public class ChangeSetExtent extends AbstractDelegateExtent {
     }
 
     @Override
-    public boolean setBiome(BlockVector2 position, BiomeType biome) {
+    public boolean setBiome(BlockVector3 position, BiomeType biome) {
         BiomeType previous = getBiome(position);
-        changeSet.add(new BiomeChange(position, previous, biome));
+        changeSet.add(new BiomeChange3D(position, previous, biome));
         return super.setBiome(position, biome);
     }
 

worldedit-core/src/main/java/com/sk89q/worldedit/extent/NullExtent.java

@@ -97,6 +97,11 @@ public class NullExtent implements Extent {
         return false;
     }
 
+    @Override
+    public boolean fullySupports3DBiomes() {
+        return false;
+    }
+
     @Override
     public boolean setTile(int x, int y, int z, CompoundTag tile) throws WorldEditException {
         return false;

worldedit-core/src/main/java/com/sk89q/worldedit/extent/OutputExtent.java

@@ -67,6 +67,22 @@ public interface OutputExtent {
 
     boolean setTile(int x, int y, int z, CompoundTag tile) throws WorldEditException;
 
+    /**
+     * Check if this extent fully supports 3D biomes.
+     *
+     * <p>
+     * If {@code false}, the extent only visually reads biomes from {@code y = 0}.
+     * The biomes will still be set in 3D, but the client will only see the one at
+     * {@code y = 0}. It is up to the caller to determine if they want to set that
+     * biome instead, or simply warn the actor.
+     * </p>
+     *
+     * @return if the extent fully supports 3D biomes
+     */
+    default boolean fullySupports3DBiomes() {
+        return true;
+    }
+
     /**
      * Set the biome.
      *
@@ -77,7 +93,7 @@ public interface OutputExtent {
      */
     @Deprecated
     default boolean setBiome(BlockVector2 position, BiomeType biome) {
-        return setBiome(position.getX(), 0, position.getBlockZ(), biome);
+        return setBiome(position.toBlockVector3(), biome);
     }
 
     @NonAbstractForCompatibility(
@@ -149,5 +165,4 @@ public interface OutputExtent {
      * @return an operation or null if there is none to execute
      */
     @Nullable Operation commit();
-
 }

worldedit-core/src/main/java/com/sk89q/worldedit/extent/buffer/ForgetfulExtentBuffer.java

@@ -23,7 +23,6 @@ import com.sk89q.worldedit.WorldEditException;
 import com.sk89q.worldedit.extent.AbstractDelegateExtent;
 import com.sk89q.worldedit.extent.Extent;
 import com.sk89q.worldedit.function.mask.Mask;
-import com.sk89q.worldedit.function.mask.Mask2D;
 import com.sk89q.worldedit.function.mask.Masks;
 import com.sk89q.worldedit.function.pattern.BiomePattern;
 import com.sk89q.worldedit.function.pattern.Pattern;
@@ -41,6 +40,7 @@ import com.sk89q.worldedit.world.block.BlockTypes;
 import java.util.Iterator;
 import java.util.LinkedHashMap;
 import java.util.Map;
+import java.util.stream.Collectors;
 
 import static com.google.common.base.Preconditions.checkNotNull;
 
@@ -54,13 +54,10 @@ import static com.google.common.base.Preconditions.checkNotNull;
 public class ForgetfulExtentBuffer extends AbstractDelegateExtent implements Pattern, BiomePattern {
 
     private final Map<BlockVector3, BaseBlock> buffer = new LinkedHashMap<>();
-    private final Map<BlockVector2, BiomeType> biomeBuffer = new LinkedHashMap<>();
+    private final Map<BlockVector3, BiomeType> biomeBuffer = new LinkedHashMap<>();
     private final Mask mask;
-    private final Mask2D biomeMask;
     private BlockVector3 min = null;
-    private BlockVector2 min2d = null;
     private BlockVector3 max = null;
-    private BlockVector2 max2d = null;
 
     /**
      * Create a new extent buffer that will buffer every change.
@@ -87,8 +84,6 @@ public class ForgetfulExtentBuffer extends AbstractDelegateExtent implements Pat
         super(delegate);
         checkNotNull(mask);
         this.mask = mask;
-        Mask2D bmask = mask.toMask2D();
-        this.biomeMask = bmask == null ? Masks.alwaysTrue2D() : bmask;
     }
 
     @Override
@@ -107,7 +102,7 @@ public class ForgetfulExtentBuffer extends AbstractDelegateExtent implements Pat
             max = max.getMaximum(location);
         }
 
-        if (mask.test( location)) {
+        if (mask.test(location)) {
             buffer.put(location, block.toBaseBlock());
             return true;
         } else {
@@ -116,22 +111,22 @@ public class ForgetfulExtentBuffer extends AbstractDelegateExtent implements Pat
     }
 
     @Override
-    public boolean setBiome(BlockVector2 position, BiomeType biome) {
+    public boolean setBiome(BlockVector3 position, BiomeType biome) {
         // Update minimum
-        if (min2d == null) {
+        if (min == null) {
-            min2d = position;
+            min = position;
         } else {
-            min2d = min2d.getMinimum(position);
+            min = min.getMinimum(position);
         }
 
         // Update maximum
-        if (max2d == null) {
+        if (max == null) {
-            max2d = position;
+            max = position;
         } else {
-            max2d = max2d.getMaximum(position);
+            max = max.getMaximum(position);
         }
 
-        if (biomeMask.test(position)) {
+        if (mask.test(position)) {
             biomeBuffer.put(position, biome);
             return true;
         } else {
@@ -142,25 +137,26 @@ public class ForgetfulExtentBuffer extends AbstractDelegateExtent implements Pat
     @Override
     public boolean setBiome(int x, int y, int z, BiomeType biome) {
         // Update minimum
-        if (min2d == null) {
+        if (min == null) {
-            min2d = BlockVector2.at(x, z);
+            min = BlockVector3.at(x, y, z);
         } else {
-            min2d = min2d.getMinimum(BlockVector2.at(x,z));
+            min = min.getMinimum(BlockVector3.at(x, y, z));
         }
 
         // Update maximum
-        if (max2d == null) {
+        if (max == null) {
-            max2d = BlockVector2.at(x,z);
+            max = BlockVector3.at(x, y, z);
         } else {
-            max2d = max2d.getMaximum(BlockVector2.at(x,z));
+            max = max.getMaximum(BlockVector3.at(x, y, z));
         }
 
-        if (biomeMask.test(BlockVector2.at(x,z))) {
+        if (mask.test(BlockVector3.at(x, y, z))) {
-            biomeBuffer.put(BlockVector2.at(x,z), biome);
+            biomeBuffer.put(BlockVector3.at(x, y, z), biome);
             return true;
         } else {
             return getExtent().setBiome(x, y, z, biome);
-        }    }
+        }
+    }
 
 
     @Override
@@ -174,7 +170,7 @@ public class ForgetfulExtentBuffer extends AbstractDelegateExtent implements Pat
     }
 
     @Override
-    public BiomeType apply(BlockVector2 pos) {
+    public BiomeType applyBiome(BlockVector3 pos) {
         BiomeType biome = biomeBuffer.get(pos);
         if (biome != null) {
             return biome;
@@ -222,7 +218,10 @@ public class ForgetfulExtentBuffer extends AbstractDelegateExtent implements Pat
 
             @Override
             public Iterable<BlockVector2> asFlatRegion() {
-                return biomeBuffer.keySet();
+                return biomeBuffer.keySet()
+                        .stream()
+                        .map(BlockVector3::toBlockVector2)
+                        .collect(Collectors.toSet());
             }
         };
     }

worldedit-core/src/main/java/com/sk89q/worldedit/extent/clipboard/BlockArrayClipboard.java

@@ -42,10 +42,10 @@ import org.jetbrains.annotations.NotNull;
 import java.util.Iterator;
 import java.util.List;
 import java.util.UUID;
+import java.util.stream.Collectors;
 import javax.annotation.Nullable;
 
 import static com.google.common.base.Preconditions.checkNotNull;
-import java.util.stream.Collectors;
 
 /**
  * Stores block data as a multi-dimensional array of {@link BlockState}s and
@@ -174,16 +174,17 @@ public class BlockArrayClipboard implements Clipboard {
     }
 
     @Override
-    public BiomeType getBiome(BlockVector2 position) {
+    public BiomeType getBiome(BlockVector3 position) {
-        BlockVector2 v = position.subtract(region.getMinimumPoint().toBlockVector2());
+        BlockVector3 v = position.subtract(region.getMinimumPoint());
-        return getParent().getBiomeType(v.getX(), 0, v.getZ());
+        return getParent().getBiomeType(v.getX(), v.getY(), v.getZ());
     }
 
     @Override
-    public boolean setBiome(BlockVector2 position, BiomeType biome) {
+    public boolean setBiome(BlockVector3 position, BiomeType biome) {
         int x = position.getBlockX() - origin.getX();
+        int y = position.getBlockY() - origin.getY();
         int z = position.getBlockZ() - origin.getZ();
-        return getParent().setBiome(x, 0, z, biome);
+        return getParent().setBiome(x, y, z, biome);
     }
 
     @Override

worldedit-core/src/main/java/com/sk89q/worldedit/extent/clipboard/Clipboard.java

@@ -41,7 +41,7 @@ import com.sk89q.worldedit.function.operation.Operations;
 import com.sk89q.worldedit.function.visitor.Order;
 import com.sk89q.worldedit.math.BlockVector2;
 import com.sk89q.worldedit.math.BlockVector3;
-import com.sk89q.worldedit.math.MutableBlockVector2;
+import com.sk89q.worldedit.math.MutableBlockVector3;
 import com.sk89q.worldedit.math.transform.Transform;
 import com.sk89q.worldedit.regions.Region;
 import com.sk89q.worldedit.regions.Regions;
@@ -311,16 +311,17 @@ public interface Clipboard extends Extent, Iterable<BlockVector3>, Closeable {
 
         pasteBiomes &= Clipboard.this.hasBiomes();
 
-        MutableBlockVector2 mpos2d = new MutableBlockVector2();
+        MutableBlockVector3 blockVector3 = new MutableBlockVector3();
-        mpos2d.setComponents(Integer.MIN_VALUE, Integer.MIN_VALUE);
+        blockVector3.setComponents(Integer.MIN_VALUE, Integer.MIN_VALUE, Integer.MIN_VALUE);
         for (BlockVector3 pos : this) {
             BaseBlock block = pos.getFullBlock(this);
             int xx = pos.getX() + relx;
-            int zz = pos.getZ() + relz;
+            int yy = pos.getZ() + relz;
+            int zz = pos.getY() + rely;
             if (hasBiomes() && pos.getBlockY() == 0) {
-                if (pasteBiomes && (xx != mpos2d.getBlockX() || zz != mpos2d.getBlockZ())) {
+                if (pasteBiomes && (xx != blockVector3.getBlockX() || zz != blockVector3.getBlockZ())) {
-                    mpos2d.setComponents(xx, zz);
+                    blockVector3.setComponents(xx, yy, zz);
-                    extent.setBiome(mpos2d, Clipboard.this.getBiome(BlockVector2.at(pos.getX(), pos.getZ())));
+                    extent.setBiome(blockVector3, Clipboard.this.getBiome(BlockVector3.at(pos.getX(), pos.getY(), pos.getZ())));
                 }
             }
             if (!pasteAir && block.getBlockType().getMaterial().isAir()) {

worldedit-core/src/main/java/com/sk89q/worldedit/extent/clipboard/io/FastSchematicWriter.java

@@ -37,7 +37,6 @@ import com.sk89q.worldedit.extension.platform.Capability;
 import com.sk89q.worldedit.extent.clipboard.BlockArrayClipboard;
 import com.sk89q.worldedit.extent.clipboard.Clipboard;
 import com.sk89q.worldedit.function.visitor.Order;
-import com.sk89q.worldedit.math.BlockVector2;
 import com.sk89q.worldedit.math.BlockVector3;
 import com.sk89q.worldedit.regions.Region;
 import com.sk89q.worldedit.world.biome.BiomeType;
@@ -287,7 +286,7 @@ public class FastSchematicWriter implements ClipboardWriter {
             int z0 = min.getBlockZ() + z;
             for (int x = 0; x < width; x++, i++) {
                 int x0 = min.getBlockX() + x;
-                BlockVector2 pt = BlockVector2.at(x0, z0);
+                BlockVector3 pt = BlockVector3.at(x0, min.getBlockY(), z0);
                 BiomeType biome = clipboard.getBiome(pt);
                 task.applyInt(i, biome.getInternalId());
             }

worldedit-core/src/main/java/com/sk89q/worldedit/extent/clipboard/io/SpongeSchematicWriter.java

@@ -35,7 +35,6 @@ import com.sk89q.worldedit.WorldEdit;
 import com.sk89q.worldedit.entity.BaseEntity;
 import com.sk89q.worldedit.extension.platform.Capability;
 import com.sk89q.worldedit.extent.clipboard.Clipboard;
-import com.sk89q.worldedit.math.BlockVector2;
 import com.sk89q.worldedit.math.BlockVector3;
 import com.sk89q.worldedit.math.Vector3;
 import com.sk89q.worldedit.regions.Region;
@@ -155,11 +154,7 @@ public class SpongeSchematicWriter implements ClipboardWriter {
                         values.remove("z");
 
                         values.put("Id", new StringTag(block.getNbtId()));
-                        values.put("Pos", new IntArrayTag(new int[]{
+                        values.put("Pos", new IntArrayTag(new int[] { x, y, z }));
-                                x,
-                                y,
-                                z
-                        }));
 
                         tileEntities.add(new CompoundTag(values));
                     }
@@ -218,7 +213,7 @@ public class SpongeSchematicWriter implements ClipboardWriter {
             int z0 = min.getBlockZ() + z;
             for (int x = 0; x < width; x++) {
                 int x0 = min.getBlockX() + x;
-                BlockVector2 pt = BlockVector2.at(x0, z0);
+                BlockVector3 pt = BlockVector3.at(x0, min.getBlockY(), z0);
                 BiomeType biome = clipboard.getBiome(pt);
 
                 String biomeKey = biome.getId();

worldedit-core/src/main/java/com/sk89q/worldedit/extent/world/BiomeQuirkExtent.java

@@ -0,0 +1,50 @@
+/*
+ * WorldEdit, a Minecraft world manipulation toolkit
+ * Copyright (C) sk89q <http://www.sk89q.com>
+ * Copyright (C) WorldEdit team and contributors
+ *
+ * This program is free software: you can redistribute it and/or modify it
+ * under the terms of the GNU Lesser General Public License as published by the
+ * Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but WITHOUT
+ * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or
+ * FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License
+ * for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package com.sk89q.worldedit.extent.world;
+
+import com.sk89q.worldedit.extent.AbstractDelegateExtent;
+import com.sk89q.worldedit.extent.Extent;
+import com.sk89q.worldedit.math.BlockVector3;
+import com.sk89q.worldedit.world.biome.BiomeType;
+
+/**
+ * Handles quirks when placing biomes.
+ */
+public class BiomeQuirkExtent extends AbstractDelegateExtent {
+
+    /**
+     * Create a new instance.
+     *
+     * @param extent the extent
+     */
+    public BiomeQuirkExtent(Extent extent) {
+        super(extent);
+    }
+
+    @Override
+    public boolean setBiome(BlockVector3 position, BiomeType biome) {
+        boolean success = false;
+        if (!fullySupports3DBiomes()) {
+            // Also place at Y = 0 for proper handling
+            success = super.setBiome(position.withY(0), biome);
+        }
+        return success || super.setBiome(position, biome);
+    }
+}

worldedit-core/src/main/java/com/sk89q/worldedit/function/biome/BiomeReplace.java

@@ -22,8 +22,10 @@ package com.sk89q.worldedit.function.biome;
 import com.sk89q.worldedit.WorldEditException;
 import com.sk89q.worldedit.extent.Extent;
 import com.sk89q.worldedit.function.FlatRegionFunction;
+import com.sk89q.worldedit.function.RegionFunction;
 import com.sk89q.worldedit.function.pattern.BiomePattern;
 import com.sk89q.worldedit.math.BlockVector2;
+import com.sk89q.worldedit.math.BlockVector3;
 import com.sk89q.worldedit.world.biome.BiomeType;
 
 import static com.google.common.base.Preconditions.checkNotNull;
@@ -31,10 +33,10 @@ import static com.google.common.base.Preconditions.checkNotNull;
 /**
  * Replaces the biome at the locations that this function is applied to.
  */
-public class BiomeReplace implements FlatRegionFunction {
+public class BiomeReplace implements FlatRegionFunction, RegionFunction {
 
     private final Extent extent;
-    private BiomePattern biome;
+    private final BiomePattern biome;
 
     /**
      * Create a new instance.
@@ -60,8 +62,17 @@ public class BiomeReplace implements FlatRegionFunction {
     }
 
     @Override
-    public boolean apply(BlockVector2 position) throws WorldEditException {
+    public boolean apply(BlockVector3 position) throws WorldEditException {
-        return extent.setBiome(position, biome.apply(position));
+        return extent.setBiome(position, biome.applyBiome(position));
     }
 
+    @Override
+    @Deprecated
+    public boolean apply(BlockVector2 position) throws WorldEditException {
+        boolean success = false;
+        for (int y = extent.getMinimumPoint().getY(); y <= extent.getMaximumPoint().getY(); y++) {
+            success |= apply(position.toBlockVector3(y));
+        }
+        return success;
+    }
 }

worldedit-core/src/main/java/com/sk89q/worldedit/function/biome/ExtentBiomeCopy.java

@@ -22,7 +22,9 @@ package com.sk89q.worldedit.function.biome;
 import com.sk89q.worldedit.WorldEditException;
 import com.sk89q.worldedit.extent.Extent;
 import com.sk89q.worldedit.function.FlatRegionFunction;
+import com.sk89q.worldedit.function.RegionFunction;
 import com.sk89q.worldedit.math.BlockVector2;
+import com.sk89q.worldedit.math.BlockVector3;
 import com.sk89q.worldedit.math.transform.Transform;
 import com.sk89q.worldedit.world.biome.BiomeType;
 
@@ -31,12 +33,12 @@ import static com.google.common.base.Preconditions.checkNotNull;
 /**
  * Copies the biome from one extent to another.
  */
-public class ExtentBiomeCopy implements FlatRegionFunction {
+public class ExtentBiomeCopy implements FlatRegionFunction, RegionFunction {
 
     private final Extent source;
     private final Extent destination;
-    private final BlockVector2 from;
+    private final BlockVector3 from;
-    private final BlockVector2 to;
+    private final BlockVector3 to;
     private final Transform transform;
 
     /**
@@ -47,8 +49,32 @@ public class ExtentBiomeCopy implements FlatRegionFunction {
      * @param destination the destination extent
      * @param to the destination offset
      * @param transform a transform to apply to positions (after source offset, before destination offset)
+     * @deprecated use {@link ExtentBiomeCopy#ExtentBiomeCopy(Extent, BlockVector3, Extent, BlockVector3, Transform)}
      */
+    @Deprecated
     public ExtentBiomeCopy(Extent source, BlockVector2 from, Extent destination, BlockVector2 to, Transform transform) {
+        checkNotNull(source);
+        checkNotNull(from);
+        checkNotNull(destination);
+        checkNotNull(to);
+        checkNotNull(transform);
+        this.source = source;
+        this.from = from.toBlockVector3();
+        this.destination = destination;
+        this.to = to.toBlockVector3();
+        this.transform = transform;
+    }
+
+    /**
+     * Make a new biome copy.
+     *
+     * @param source the source extent
+     * @param from the source offset
+     * @param destination the destination extent
+     * @param to the destination offset
+     * @param transform a transform to apply to positions (after source offset, before destination offset)
+     */
+    public ExtentBiomeCopy(Extent source, BlockVector3 from, Extent destination, BlockVector3 to, Transform transform) {
         checkNotNull(source);
         checkNotNull(from);
         checkNotNull(destination);
@@ -62,11 +88,23 @@ public class ExtentBiomeCopy implements FlatRegionFunction {
     }
 
     @Override
-    public boolean apply(BlockVector2 position) throws WorldEditException {
+    public boolean apply(BlockVector3 position) throws WorldEditException {
         BiomeType biome = source.getBiome(position);
-        BlockVector2 orig = position.subtract(from);
+        BlockVector3 orig = position.subtract(from);
-        BlockVector2 transformed = transform.apply(orig.toVector3(0)).toVector2().toBlockPoint();
+        BlockVector3 transformed = transform.apply(orig.toVector3())
+            .toBlockPoint()
+            .add(to);
 
-        return destination.setBiome(transformed.add(to), biome);
+        return destination.setBiome(transformed, biome);
+    }
+
+    @Override
+    @Deprecated
+    public boolean apply(BlockVector2 position) throws WorldEditException {
+        boolean success = false;
+        for (int y = destination.getMinimumPoint().getY(); y <= destination.getMaximumPoint().getY(); y++) {
+            success |= apply(position.toBlockVector3(y));
+        }
+        return success;
     }
 }

worldedit-core/src/main/java/com/sk89q/worldedit/function/operation/ForwardExtentCopy.java

@@ -39,7 +39,6 @@ import com.sk89q.worldedit.function.entity.ExtentEntityCopy;
 import com.sk89q.worldedit.function.mask.Mask;
 import com.sk89q.worldedit.function.mask.Masks;
 import com.sk89q.worldedit.function.visitor.EntityVisitor;
-import com.sk89q.worldedit.function.visitor.FlatRegionVisitor;
 import com.sk89q.worldedit.function.visitor.IntersectRegionFunction;
 import com.sk89q.worldedit.function.visitor.RegionVisitor;
 import com.sk89q.worldedit.math.BlockVector3;
@@ -85,6 +84,10 @@ public class ForwardExtentCopy implements Operation {
     private Transform currentTransform = null;
     private int affectedBlocks;
     private RegionFunction filterFunction;
+    private RegionVisitor lastBiomeVisitor;
+    private EntityVisitor lastEntityVisitor;
+    private int affectedBiomeCols;
+    private int affectedEntities;
 
     /**
      * Create a new copy using the region's lowest minimum point as the
@@ -99,10 +102,6 @@ public class ForwardExtentCopy implements Operation {
     public ForwardExtentCopy(Extent source, Region region, Extent destination, BlockVector3 to) {
         this(source, region, region.getMinimumPoint(), destination, to);
     }
-    private FlatRegionVisitor lastBiomeVisitor;
-    private EntityVisitor lastEntityVisitor;
-    private int affectedBiomeCols;
-    private int affectedEntities;
 
     /**
      * Create a new copy.

worldedit-core/src/main/java/com/sk89q/worldedit/function/pattern/BiomePattern.java

@@ -19,7 +19,10 @@
 
 package com.sk89q.worldedit.function.pattern;
 
+import com.sk89q.worldedit.internal.util.DeprecationUtil;
+import com.sk89q.worldedit.internal.util.NonAbstractForCompatibility;
 import com.sk89q.worldedit.math.BlockVector2;
+import com.sk89q.worldedit.math.BlockVector3;
 import com.sk89q.worldedit.world.biome.BiomeType;
 
 /**
@@ -31,7 +34,29 @@ public interface BiomePattern {
      * Return a {@link BiomeType} for the given position.
      *
      * @param position the position
-     * @return a block
+     * @return a biome
+     * @deprecated use {@link BiomePattern#applyBiome(BlockVector3)}
      */
-    BiomeType apply(BlockVector2 position);
+    @Deprecated
+    default BiomeType apply(BlockVector2 position) {
+        return applyBiome(position.toBlockVector3());
+    }
+
+    /**
+     * Return a {@link BiomeType} for the given position.
+     *
+     * @param position the position
+     * @return a biome
+     * @apiNote This must be overridden by new subclasses. See {@link NonAbstractForCompatibility}
+     *          for details
+     */
+    @NonAbstractForCompatibility(
+        delegateName = "apply",
+        delegateParams = { BlockVector2.class }
+    )
+    default BiomeType applyBiome(BlockVector3 position) {
+        DeprecationUtil.checkDelegatingOverride(getClass());
+
+        return apply(position.toBlockVector2());
+    }
 }

worldedit-core/src/main/java/com/sk89q/worldedit/history/change/BiomeChange.java

@@ -33,7 +33,9 @@ import static com.google.common.base.Preconditions.checkNotNull;
  * <p>This biome change does not have an {@link Extent} assigned to it because
  * one will be taken from the passed {@link UndoContext}. If the context
  * does not have an extent (it is null), cryptic errors may occur.</p>
+ * @deprecated use {@link BiomeChange3D}
  */
+@Deprecated
 public class BiomeChange implements Change {
 
     private final BlockVector2 position;
@@ -85,12 +87,12 @@ public class BiomeChange implements Change {
 
     @Override
     public void undo(UndoContext context) throws WorldEditException {
-        checkNotNull(context.getExtent()).setBiome(position, previous);
+        checkNotNull(context.getExtent()).setBiome(position.toBlockVector3(), previous);
     }
 
     @Override
     public void redo(UndoContext context) throws WorldEditException {
-        checkNotNull(context.getExtent()).setBiome(position, current);
+        checkNotNull(context.getExtent()).setBiome(position.toBlockVector3(), current);
     }
 
 }

worldedit-core/src/main/java/com/sk89q/worldedit/math/BlockVector3.java

@@ -22,7 +22,6 @@ package com.sk89q.worldedit.math;
 import com.sk89q.jnbt.CompoundTag;
 import com.sk89q.worldedit.extent.Extent;
 import com.sk89q.worldedit.math.transform.AffineTransform;
-import com.sk89q.worldedit.world.biome.BiomeType;
 import com.sk89q.worldedit.world.block.BaseBlock;
 import com.sk89q.worldedit.world.block.BlockState;
 
@@ -715,10 +714,6 @@ public abstract class BlockVector3 {
         return orDefault.setBlock(this, block);
     }
 
-    public boolean setBiome(Extent orDefault, BiomeType biome) {
-        return orDefault.setBiome(getX(), getY(), getZ(), biome);
-    }
-
     public int getOrdinal(Extent orDefault) {
         return getBlock(orDefault).getOrdinal();
     }

worldedit-core/src/main/java/com/sk89q/worldedit/math/DelegateBlockVector3.java

@@ -325,11 +325,6 @@ public class DelegateBlockVector3 extends BlockVector3 {
         return parent.setFullBlock(orDefault, block);
     }
 
-    @Override
-    public boolean setBiome(Extent orDefault, BiomeType biome) {
-        return parent.setBiome(orDefault, biome);
-    }
-
     @Override
     public int getOrdinal(Extent orDefault) {
         return parent.getOrdinal(orDefault);

worldedit-core/src/main/java/com/sk89q/worldedit/session/request/RequestExtent.java

@@ -26,7 +26,6 @@ import com.sk89q.worldedit.entity.BaseEntity;
 import com.sk89q.worldedit.entity.Entity;
 import com.sk89q.worldedit.extent.Extent;
 import com.sk89q.worldedit.function.operation.Operation;
-import com.sk89q.worldedit.math.BlockVector2;
 import com.sk89q.worldedit.math.BlockVector3;
 import com.sk89q.worldedit.regions.Region;
 import com.sk89q.worldedit.util.Location;
@@ -87,7 +86,7 @@ public class RequestExtent implements Extent {
     }
 
     @Override
-    public BiomeType getBiome(BlockVector2 position) {
+    public BiomeType getBiome(BlockVector3 position) {
         return getExtent().getBiome(position);
     }
 
@@ -102,19 +101,24 @@ public class RequestExtent implements Extent {
         return getExtent().setBlock(x, y, z, block);
     }
 
+    @Override
+    public boolean fullySupports3DBiomes() {
+        return getExtent().fullySupports3DBiomes();
+    }
+
     @Override
     public boolean setTile(int x, int y, int z, CompoundTag tile) throws WorldEditException {
         return getExtent().setTile(x, y, z, tile);
     }
 
     @Override
-    public boolean setBiome(BlockVector2 position, BiomeType biome) {
+    public boolean setBiome(BlockVector3 position, BiomeType biome) {
         return getExtent().setBiome(position, biome);
     }
 
     @Override
     public boolean setBiome(int x, int y, int z, BiomeType biome) {
-        return getExtent().setBiome(BlockVector2.at(x,z), biome);
+        return getExtent().setBiome(BlockVector3.at(x, y, z), biome);
     }
 
     @Override

worldedit-core/src/main/java/com/sk89q/worldedit/world/NullWorld.java

@@ -31,7 +31,6 @@ import com.sk89q.worldedit.blocks.BaseItemStack;
 import com.sk89q.worldedit.entity.BaseEntity;
 import com.sk89q.worldedit.entity.Entity;
 import com.sk89q.worldedit.entity.Player;
-import com.sk89q.worldedit.math.BlockVector2;
 import com.sk89q.worldedit.math.BlockVector3;
 import com.sk89q.worldedit.math.Vector3;
 import com.sk89q.worldedit.regions.Region;
@@ -94,9 +93,13 @@ public class NullWorld extends AbstractWorld {
     public boolean clearContainerBlockContents(BlockVector3 position) {
         return false;
     }
+    @Override
+    public boolean fullySupports3DBiomes() {
+        return false;
+    }
 
     @Override
-    public BiomeType getBiome(BlockVector2 position) {
+    public BiomeType getBiome(BlockVector3 position) {
         return BiomeTypes.THE_VOID;
     }
 
@@ -106,7 +109,7 @@ public class NullWorld extends AbstractWorld {
     }
 
     @Override
-    public boolean setBiome(BlockVector2 position, BiomeType biome) {
+    public boolean setBiome(BlockVector3 position, BiomeType biome) {
         return false;
     }
 
@@ -166,6 +169,11 @@ public class NullWorld extends AbstractWorld {
         return NullChunkGet.INSTANCE;
     }
 
+    @Override
+    public BlockState getBlock(BlockVector3 position) {
+        return this.getBlock(position.getBlockX(), position.getBlockY(), position.getBlockZ());
+    }
+
     @Override
     public BlockState getBlock(int x, int y, int z) {
         return BlockTypes.AIR.getDefaultState();

worldedit-core/src/main/java/com/sk89q/worldedit/world/biome/BiomeType.java

@@ -20,7 +20,7 @@
 package com.sk89q.worldedit.world.biome;
 
 import com.sk89q.worldedit.function.pattern.BiomePattern;
-import com.sk89q.worldedit.math.BlockVector2;
+import com.sk89q.worldedit.math.BlockVector3;
 import com.sk89q.worldedit.registry.Keyed;
 import com.sk89q.worldedit.registry.NamespacedRegistry;
 import com.sk89q.worldedit.registry.RegistryItem;
@@ -84,7 +84,7 @@ public class BiomeType implements RegistryItem, Keyed, BiomePattern {
     }
 
     @Override
-    public BiomeType apply(BlockVector2 position) {
+    public BiomeType applyBiome(BlockVector3 position) {
         return this;
     }
 }