Bukkit perms are broken.

Or at least they don't work the way they (in my opinion) should. Take a
look at HierarchyPermission.java for a detailed explanation.

src/main/java/com/onarandombox/MultiverseCore/permissions/HierarchyPermission.java

@@ -0,0 +1,52 @@
+package com.onarandombox.MultiverseCore.permissions;
+
+import org.bukkit.Bukkit;
+import org.bukkit.permissions.Permission;
+import org.bukkit.permissions.Permissible;
+import org.bukkit.permissions.PermissionDefault;
+
+/**
+ * Provides improved parent-child relationships for permissions. This is the standard implementation of {@link PermissionNode}.
+ * <p>
+ * Apparently parents override their children in Bukkit:
+ * Let {@code permissionA} be a parent permission of {@code permissionB}, setting {@code permissionB} to {@code true}.
+ * Now a player has {@code permissionA=true} and {@code permissionB=false}. Result: Both are {@code true}.
+ * Another player has {@code permissionA=false} and {@code permissionB=true}. Result: Both are {@code false}.
+ * <p>
+ * This is completely useless for things like MV's world access permissions where you could for example want to deny
+ * access to all worlds by default, with a few exceptions.
+ * <p>
+ * This class takes over all the permission hierarchy checks and provides a way that makes sense. In the
+ * above examples, the effective permissions would be equal to the permissions that were set.
+ */
+public class HierarchyPermission implements PermissionNode {
+    private final PermissionNode parent;
+    private final Permission permission;
+
+    public HierarchyPermission(final PermissionNode parent, final String permission, final String description) {
+        this.parent = parent;
+        Permission p = Bukkit.getServer().getPluginManager().getPermission(permission);
+        if (p == null)
+            p = new Permission(permission, description, PermissionDefault.FALSE);
+        else {
+            p.getChildren().clear();
+            //p.recalculatePermissibles(); // Not necessary because it's done automatically after setting the default
+            p.setDefault(PermissionDefault.FALSE);
+        }
+        this.permission = p;
+    }
+
+    /**
+     * Checks whether a given {@link Permissible} has this {@link HierarchyPermission}.
+     *
+     * @param permissible The {@link Permissible} that might have the permission.
+     * @return Whether it has the permission.
+     */
+    public boolean has(Permissible permissible) {
+        if (permissible.isPermissionSet(permission))
+            return permissible.hasPermission(permission);
+
+        // ask the guy over there
+        return parent.has(permissible);
+    }
+}

src/main/java/com/onarandombox/MultiverseCore/permissions/PermissionCollection.java

@@ -0,0 +1,38 @@
+package com.onarandombox.MultiverseCore.permissions;
+
+import org.bukkit.permissions.Permissible;
+
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * Represents a permission node with dynamically created children.
+ */
+public class PermissionCollection {
+    private final PermissionNode root;
+    private final Map<String, PermissionNode> elements;
+    private final String prefix;
+    private final String description;
+
+    public PermissionCollection(PermissionNode parent, String prefix, String description) {
+        if (!prefix.endsWith("."))
+            throw new IllegalArgumentException("The prefix must end with a dot!");
+        this.root = new HierarchyPermission(parent, prefix + "*", description);
+        this.elements = new HashMap<String, PermissionNode>();
+        this.prefix = prefix;
+        this.description = description;
+    }
+
+    /**
+     * Checks whether a given {@link Permissible} has a specified element permission.
+     *
+     * @param p The {@link Permissible}.
+     * @param element The element.
+     * @return Whether the {@link Permissible} has the permission.
+     */
+    public boolean has(Permissible p, String element) {
+        if (!this.elements.containsKey(element))
+            this.elements.put(element, new HierarchyPermission(root, prefix + element, description));
+        return this.elements.get(element).has(p);
+    }
+}

src/main/java/com/onarandombox/MultiverseCore/permissions/PermissionNode.java

@@ -0,0 +1,30 @@
+package com.onarandombox.MultiverseCore.permissions;
+
+import org.bukkit.permissions.Permissible;
+
+/**
+ * A node in a permissions hierarchy.
+ *
+ * @see HierarchyPermission
+ */
+public interface PermissionNode {
+    static final class OperatorDefault implements PermissionNode {
+        @Override
+        public boolean has(final Permissible permissible) {
+            return permissible.isOp();
+        }
+    }
+
+    /**
+     * This {@link HierarchyPermission} depends on the operator state. Ops have it, non-ops don't.
+     */
+    PermissionNode OP_DEFAULT = new OperatorDefault();
+
+    /**
+     * Checks whether a given {@link Permissible} has this node.
+     *
+     * @param permissible The {@link Permissible} that might have the permission.
+     * @return Whether it has the permission.
+     */
+    boolean has(Permissible permissible);
+}

src/main/java/com/onarandombox/MultiverseCore/permissions/Permissions.java

@@ -0,0 +1,21 @@
+package com.onarandombox.MultiverseCore.permissions;
+
+/**
+ * Permission nodes.
+ */
+public class Permissions {
+    protected Permissions() {
+        throw new UnsupportedOperationException();
+    }
+
+    /**
+     * The {@code multiverse.*} permission.
+     */
+    public static final HierarchyPermission MV_ROOT = new HierarchyPermission(PermissionNode.OP_DEFAULT,
+            "multiverse.*", "Provides access to all Multiverse features.");
+
+    /**
+     * The {@code multiverse.access.*} family of permissions.
+     */
+    public static final PermissionCollection ACCESS = new PermissionCollection(MV_ROOT, "multiverse.access.", "World access");
+}

src/main/java/com/onarandombox/MultiverseCore/permissions/package-info.java

@@ -0,0 +1,4 @@
+/**
+ * Contains permissions utility classes.
+ */
+package com.onarandombox.MultiverseCore.permissions;

src/main/java/com/onarandombox/MultiverseCore/utils/MVPermissions.java

@@ -11,6 +11,7 @@ import com.onarandombox.MultiverseCore.MultiverseCore;
 import com.onarandombox.MultiverseCore.api.MVDestination;
 import com.onarandombox.MultiverseCore.api.MVWorldManager;
 import com.onarandombox.MultiverseCore.api.MultiverseWorld;
+import com.onarandombox.MultiverseCore.permissions.Permissions;
 import com.pneumaticraft.commandhandler.PermissionsInterface;
 import org.bukkit.ChatColor;
 import org.bukkit.Location;
@@ -103,18 +104,15 @@ public class MVPermissions implements PermissionsInterface {
             this.plugin.log(Level.FINEST, "EnforceAccess is OFF. Player was allowed in " + w.getAlias());
             return true;
         }
-        return this.hasPermission(p, "multiverse.access." + w.getName(), false);
+        return Permissions.ACCESS.has(p, w.getName());
     }
 
     private boolean canEnterLocation(Player p, Location l) {
-        if (l == null) {
+        if (l == null)
             return false;
-        }
+
         String worldName = l.getWorld().getName();
-        if (!this.plugin.getMVWorldManager().isMVWorld(worldName)) {
-            return false;
-        }
-        return this.hasPermission(p, "multiverse.access." + worldName, false);
+        return this.plugin.getMVWorldManager().isMVWorld(worldName) && Permissions.ACCESS.has(p, worldName);
     }
 
     /**