possible fix and lots of other changes

src/net/citizensnpcs/Citizens.java

@@ -14,6 +14,7 @@ import net.citizensnpcs.npc.trait.CitizensCharacterManager;
 import net.citizensnpcs.npc.trait.CitizensTraitManager;
 import net.citizensnpcs.storage.Storage;
 import net.citizensnpcs.storage.flatfile.YamlStorage;
+import net.citizensnpcs.util.ByIdArray;
 import net.citizensnpcs.util.Messaging;
 
 import org.bukkit.Bukkit;
@@ -92,7 +93,6 @@ public class Citizens extends JavaPlugin {
     // TODO possibly separate this out some more
     private void setupNPCs() throws NPCLoadException {
         traitManager.registerTrait("location", SpawnLocation.class);
-        int spawned = 0;
         for (DataKey key : saves.getKey("npc").getIntegerSubKeys()) {
             int id = Integer.parseInt(key.name());
             if (!key.keyExists("name"))
@@ -121,19 +121,18 @@ public class Citizens extends JavaPlugin {
             }
 
             // Spawn the NPC
-            if (key.getBoolean("spawned")) {
+            if (key.getBoolean("spawned"))
                 npc.spawn(npc.getTrait(SpawnLocation.class).getLocation());
-                spawned++;
-            }
         }
-        Messaging.log("Loaded " + npcManager.size() + " NPCs (" + spawned + " spawned).");
+        Messaging.log("Loaded " + ((ByIdArray<NPC>) npcManager.getAllNPCs()).size() + " NPCs ("
+                + ((ByIdArray<NPC>) npcManager.getSpawnedNPCs()).size() + " spawned).");
     }
 
     private void saveNPCs() {
         for (NPC npc : npcManager.getAllNPCs()) {
             DataKey root = saves.getKey("npc." + npc.getId());
             root.setString("name", npc.getFullName());
-            root.setBoolean("spawned", npc.isSpawned());
+            root.setBoolean("spawned", npc.getBukkitEntity().isDead());
 
             // Save the character if it exists
             if (npc.getCharacter() != null) {
@@ -142,9 +141,8 @@ public class Citizens extends JavaPlugin {
             }
 
             // Save all existing traits
-            for (Trait trait : npc.getTraits()) {
+            for (Trait trait : npc.getTraits())
                 trait.save(root.getRelative(trait.getName()));
-            }
         }
         saves.save();
     }

src/net/citizensnpcs/EventListen.java

@@ -51,7 +51,8 @@ public class EventListen implements Listener {
             return;
 
         NPC npc = manager.getNPC(event.getEntity());
-        npc.getCharacter().onRightClick(npc, (Player) event.getTarget());
+        if (npc.getCharacter() != null)
+            npc.getCharacter().onRightClick(npc, (Player) event.getTarget());
     }
 
     /*

src/net/citizensnpcs/npc/CitizensNPCManager.java

@@ -27,8 +27,8 @@ import org.bukkit.entity.Entity;
 import org.bukkit.entity.Player;
 
 public class CitizensNPCManager implements NPCManager {
-    private final ByIdArray<NPC> spawned = ByIdArray.create();
+    private final ByIdArray<NPC> spawned = new ByIdArray<NPC>();
-    private final ByIdArray<NPC> byID = ByIdArray.create();
+    private final ByIdArray<NPC> byID = new ByIdArray<NPC>();
 
     @Override
     public NPC createNPC(String name) {
@@ -65,7 +65,7 @@ public class CitizensNPCManager implements NPCManager {
     @Override
     public Collection<NPC> getNPCs(Class<? extends Trait> trait) {
         List<NPC> npcs = new ArrayList<NPC>();
-        for (NPC npc : byID) {
+        for (NPC npc : getAllNPCs()) {
             if (npc.hasTrait(trait))
                 npcs.add(npc);
         }
@@ -88,8 +88,6 @@ public class CitizensNPCManager implements NPCManager {
     }
 
     public CraftNPC spawn(NPC npc, Location loc) {
-        if (spawned.contains(npc.getBukkitEntity().getEntityId()))
-            throw new IllegalStateException("The NPC with ID '" + npc.getId() + "' is already spawned.");
         WorldServer ws = getWorldServer(loc.getWorld());
         CraftNPC mcEntity = new CraftNPC(getMinecraftServer(ws.getServer()), ws, npc.getFullName(),
                 new ItemInWorldManager(ws));
@@ -103,8 +101,6 @@ public class CitizensNPCManager implements NPCManager {
     }
 
     public void despawn(NPC npc) {
-        if (!spawned.contains(npc.getBukkitEntity().getEntityId()))
-            throw new IllegalStateException("The NPC with ID '" + npc.getId() + "' is already despawned.");
         CraftNPC mcEntity = ((CitizensNPC) npc).getHandle();
         for (Player player : Bukkit.getOnlinePlayers())
             ((CraftPlayer) player).getHandle().netServerHandler.sendPacket(new Packet29DestroyEntity(mcEntity.id));
@@ -128,8 +124,4 @@ public class CitizensNPCManager implements NPCManager {
     private MinecraftServer getMinecraftServer(Server server) {
         return ((CraftServer) server).getServer();
     }
-
-    public int size() {
-        return byID.size();
-    }
 }

src/net/citizensnpcs/test/StorageTest.java

@@ -1,10 +1,10 @@
 package net.citizensnpcs.test;
 
-import org.junit.Test;
+//import org.junit.Test;
 
 public class StorageTest {
 
-    @Test
+   // @Test
     public void testYaml() {
 
     }

src/net/citizensnpcs/util/ByIdArray.java

@@ -46,7 +46,7 @@ public class ByIdArray<T> implements Iterable<T> {
     }
 
     private void recalcLowest() {
-        while (elementData.length > lowest && elementData[lowest++] == null)
+        while (elementData.length > lowest && highest > lowest && elementData[lowest++] == null)
             ;
     }
 
@@ -129,10 +129,6 @@ public class ByIdArray<T> implements Iterable<T> {
             elementData = Arrays.copyOf(elementData, highest + 1);
     }
 
-    public static <T> ByIdArray<T> create() {
-        return new ByIdArray<T>();
-    }
-
     public boolean contains(int index) {
         return elementData.length > index && elementData[index] != null;
     }