The /butcher command no longer kills NPCs, except when the -n flag is passed.

Also:
- Moved some code from BukkitWorld to LocalWorld.
- Replaced the "boolean killPets" argument by an "int flags" to provide extensibility
- Made the radius argument a double
- Basically rewrote the entire function
- Deprecated all old versions of killMobs

src/main/java/com/sk89q/worldedit/LocalWorld.java

@@ -32,6 +32,14 @@ import com.sk89q.worldedit.regions.Region;
  * @author sk89q
  */
 public abstract class LocalWorld {
+    /**
+     * Named flags to use as parameters to {@link LocalWorld#killMobs(Vector, int, int)}
+     */
+    public class KillFlags {
+        public static final int PETS = 1 << 0;
+        public static final int NPCS = 1 << 1;
+    }
+
     /**
      * Random generator.
      */
@@ -268,17 +276,35 @@ public abstract class LocalWorld {
      * @param radius
      * @return
      */
-    public abstract int killMobs(Vector origin, int radius);
+    @Deprecated
+    public int killMobs(Vector origin, int radius) {
+        return killMobs(origin, radius, false);
+    }
+
+    /**
+     * Kill mobs in an area.
+     * 
+     * @param origin
+     * @param radius -1 for all mobs
+     * @param flags various flags that determine what to kill
+     * @return
+     */
+    @Deprecated
+    public int killMobs(Vector origin, int radius, boolean killPets) {
+        return killMobs(origin, radius, killPets ? KillFlags.PETS : 0);
+    }
 
     /**
      * Kill mobs in an area.
      * 
      * @param origin
      * @param radius
-     * @param killPets
+     * @param killflags
      * @return
      */
-    public abstract int killMobs(Vector origin, int radius, boolean killPets);
+    public int killMobs(Vector origin, double radius, int flags) {
+        return killMobs(origin, (int) radius, (flags & KillFlags.PETS) != 0);
+    }
 
     /**
      * Remove entities in an area.

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

@@ -488,41 +488,43 @@ public class BukkitWorld extends LocalWorld {
 
     }
 
-    /**
-     * Kill mobs in an area, excluding tamed wolves.
-     * 
-     * @param origin
-     * @param radius -1 for all mobs
-     * @return
-     */
-    @Override
-    public int killMobs(Vector origin, int radius) {
-        return killMobs(origin, radius, false);
-    }
-
     /**
      * Kill mobs in an area.
      * 
-     * @param origin
-     * @param radius -1 for all mobs
-     * @param killPets true to kill tames wolves
+     * @param origin The center of the area to kill mobs in.
+     * @param radius Maximum distance to kill mobs at; radius < 0 means kill all mobs
+     * @param flags various flags that determine what to kill
      * @return
      */
     @Override
-    public int killMobs(Vector origin, int radius, boolean killPets) {
+    public int killMobs(Vector origin, double radius, int flags) {
+        boolean killPets = (flags & KillFlags.PETS) != 0;
+        boolean killNPCs = (flags & KillFlags.NPCS) != 0;
+
         int num = 0;
-        double radiusSq = Math.pow(radius, 2);
+        double radiusSq = radius * radius;
+
+        Location bukkitOrigin = BukkitUtil.toLocation(world, origin);
 
         for (LivingEntity ent : world.getLivingEntities()) {
+            if (ent instanceof HumanEntity) {
+                continue;
+            }
+
             if (!killPets && ent instanceof Tameable && ((Tameable) ent).isTamed()) {
                 continue; // tamed wolf
             }
-            if (ent instanceof LivingEntity && !(ent instanceof HumanEntity)) {
-                if (radius == -1
-                        || origin.distanceSq(BukkitUtil.toVector(ent.getLocation())) <= radiusSq) {
-                    ent.remove();
-                    ++num;
+
+            try {
+                // Temporary solution until org.bukkit.entity.NPC is widely deployed.
+                if (!killNPCs && Class.forName("org.bukkit.entity.NPC").isAssignableFrom(ent.getClass())) {
+                    continue;
                 }
+            } catch (ClassNotFoundException e) {}
+
+            if (radius < 0 || bukkitOrigin.distanceSquared(ent.getLocation()) <= radiusSq) {
+                ent.remove();
+                ++num;
             }
         }
 

src/main/java/com/sk89q/worldedit/commands/UtilityCommands.java

@@ -26,6 +26,7 @@ import com.sk89q.minecraft.util.commands.CommandPermissions;
 import com.sk89q.minecraft.util.commands.Logging;
 import static com.sk89q.minecraft.util.commands.Logging.LogMode.*;
 import com.sk89q.worldedit.*;
+import com.sk89q.worldedit.LocalWorld.KillFlags;
 import com.sk89q.worldedit.blocks.BaseBlock;
 import com.sk89q.worldedit.patterns.*;
 import com.sk89q.worldedit.regions.CuboidRegion;
@@ -344,11 +345,13 @@ public class UtilityCommands {
     @Command(
         aliases = { "butcher" },
         usage = "[radius]",
-        flags = "p",
+        flags = "pn",
         desc = "Kill all or nearby mobs",
         help =
             "Kills nearby mobs, or all mobs if you don't specify a radius.\n" +
-            "The -p flag makes /butcher also kill pets.",
+            "Flags:" +
+            "  -p also kill pets.\n" +
+            "  -n also kill NPCs.",
         min = 0,
         max = 1
     )
@@ -361,7 +364,12 @@ public class UtilityCommands {
         int radius = args.argsLength() > 0 ? Math.max(1, args.getInteger(0)) : -1;
 
         Vector origin = session.getPlacementPosition(player);
-        int killed = player.getWorld().killMobs(origin, radius, args.hasFlag('p'));
+
+        int flags = 0;
+        if (args.hasFlag('p')) flags |= KillFlags.PETS;
+        if (args.hasFlag('n')) flags |= KillFlags.NPCS;
+
+        int killed = player.getWorld().killMobs(origin, radius, flags);
         player.print("Killed " + killed + " mobs.");
     }