Indices now have a separate reindex() method because large changes to the index have to be supported.

Therefore, indices are no longer thread-safe. They don't need to be.

src/main/java/com/sk89q/worldguard/region/indices/FlatIndex.java

@@ -102,4 +102,9 @@ public synchronized Collection<Region> queryOverlapping(
     public synchronized int size() {
         return regions.size();
     }
+
+    @Override
+    public void reindex() {
+        // Whoo, nothing to do, because this index is so simple
+    }
 }

src/main/java/com/sk89q/worldguard/region/indices/PriorityRTreeIndex.java

@@ -21,6 +21,7 @@
 import com.sk89q.worldedit.Vector;
 import com.sk89q.worldguard.region.Region;
 import com.sk89q.worldguard.region.UnsupportedIntersectionException;
+import com.sk89q.worldguard.region.shapes.IndexableShape;
 import com.sk89q.worldguard.region.shapes.ShapeMBRConverter;
 
 import org.apache.commons.lang.Validate;
@@ -59,8 +60,6 @@ public synchronized void add(Region... region) {
         for (Region r : region) {
             regions.put(normalizeId(r.getId()), r);
         }
-        tree = new PRTree<Region>(converter, branchFactor);
-        tree.load(regions.values());
     }
 
     @Override
@@ -69,8 +68,6 @@ public synchronized void remove(String... id) {
         for (String i : id) {
             regions.remove(normalizeId(i));
         }
-        tree = new PRTree<Region>(converter, branchFactor);
-        tree.load(regions.values());
     }
 
     @Override
@@ -98,7 +95,7 @@ public synchronized Collection<Region> queryContains(
                 location.getY(), location.getZ(), location.getZ());
 
         for (Region region : tree.find(pointMBR)) {
-            if (region.contains(location) && !result.contains(region)) {
+            if (region.getShape().contains(location) && !result.contains(region)) {
                 result.add(region);
             }
         }
@@ -129,4 +126,10 @@ public synchronized int size() {
         return regions.size();
     }
 
+    @Override
+    public void reindex() {
+        tree = new PRTree<Region>(converter, branchFactor);
+        tree.load(regions.values());
+    }
+
 }

src/main/java/com/sk89q/worldguard/region/indices/RegionIndex.java

@@ -35,8 +35,8 @@
  * using the method {@link Region#shouldCache()}.
  * <p>
  * Region IDs are case in-sensitive and implementations must be aware of this when
- * querying by ID. Any casing can be used when looking up an ID. Implementations must
- * be thread-safe.
+ * querying by ID. Any casing can be used when looking up an ID. Implementations do NOT
+ * have to be thread-safe.
  */
 public interface RegionIndex {
 
@@ -100,6 +100,9 @@ Collection<Region> queryOverlapping(
      * Add the given region to this index. If a region already known by this index is
      * attempted to be added to this index, nothing will happen. Parents of the
      * given region will not be added automatically.
+     * <p>
+     * After making changes, {@link #reindex()} MUST be called in order to ensure
+     * maximum performance and index consistency.
      *
      * @param region the region to add
      */
@@ -109,6 +112,9 @@ Collection<Region> queryOverlapping(
      * Remove the region with the given ID from this index. If the region being removed
      * has children, they will not be removed automatically. Their parent will also
      * not be set to null automatically.
+     * <p>
+     * After making changes, {@link #reindex()} MUST be called in order to ensure
+     * maximum performance and index consistency.
      *
      * @param id the ID of the region to remove
      */
@@ -118,6 +124,9 @@ Collection<Region> queryOverlapping(
      * Remove a region from this index having the exact same ID, but possibly no
      * other equal attribute. If the region being removed as children, they will not be
      * removed automatically. Their parent will also not be set to null automatically.
+     * <p>
+     * After making changes, {@link #reindex()} MUST be called in order to ensure
+     * maximum performance and index consistency.
      *
      * @param region the region with the ID to match against
      */
@@ -176,4 +185,10 @@ Collection<Region> queryOverlapping(
      */
     int size();
 
+    /**
+     * After making a series of changes, this method should be called in order to
+     * perform any re-indexing activities.
+     */
+    void reindex();
+
 }