Make sure all WorldEdit files are in the plugins/WorldEdit folder

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

@@ -21,23 +21,54 @@ package com.sk89q.worldedit.bukkit;
 
 import com.sk89q.util.yaml.YAMLProcessor;
 import com.sk89q.worldedit.util.YAMLConfiguration;
+import org.apache.commons.io.FileUtils;
 
-import java.util.logging.Logger;
+import java.io.File;
+import java.io.IOException;
 
 /**
- * YAMLConfiguration but with setting for no op permissions.
+ * YAMLConfiguration but with setting for no op permissions and plugin root data folder
  */
 public class BukkitConfiguration extends YAMLConfiguration {
 
     public boolean noOpPermissions = false;
+    private final WorldEditPlugin plugin;
 
-    public BukkitConfiguration(YAMLProcessor config, Logger logger) {
+    public BukkitConfiguration(YAMLProcessor config, WorldEditPlugin plugin) {
-        super(config, logger);
+        super(config, plugin.getLogger());
+        this.plugin = plugin;
     }
 
     @Override
     public void load() {
         super.load();
         noOpPermissions = config.getBoolean("no-op-permissions", false);
+        migrateLegacyFolders();
+    }
+
+    private void migrateLegacyFolders() {
+        migrate(scriptsDir, "craftscripts");
+        migrate(saveDir, "schematics");
+        migrate("drawings", "draw.js images");
+    }
+
+    private void migrate(String file, String name) {
+        File fromDir = new File(".", file);
+        File toDir = new File(getWorkingDirectory(), file);
+        if (fromDir.exists() & !toDir.exists()) {
+            try {
+                FileUtils.moveDirectory(fromDir, toDir);
+                plugin.getLogger().info("Migrated " + name + " folder '" + file +
+                        "' from server root to plugin data folder." );
+            } catch (IOException e) {
+                plugin.getLogger().warning("Error while migrating " + name + " folder: " +
+                        e.getMessage());
+            }
+        }
+    }
+
+    @Override
+    public File getWorkingDirectory() {
+        return plugin.getDataFolder();
     }
 }

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

@@ -27,7 +27,6 @@ import java.io.InputStream;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.jar.JarFile;
-import java.util.logging.Logger;
 import java.util.zip.ZipEntry;
 
 import com.sk89q.util.yaml.YAMLProcessor;
@@ -53,11 +52,6 @@ public class WorldEditPlugin extends JavaPlugin {
      */
     public static final String CUI_PLUGIN_CHANNEL = "WECUI";
 
-    /**
-     * WorldEdit messages get sent here.
-     */
-    private static final Logger logger = Logger.getLogger("Minecraft.WorldEdit");
-
     /**
      * The server interface that all server-related API goes through.
      */
@@ -100,7 +94,7 @@ public class WorldEditPlugin extends JavaPlugin {
 
         // Set up configuration and such, including the permissions
         // resolver
-        config = new BukkitConfiguration(new YAMLProcessor(new File(getDataFolder(), "config.yml"), true), logger);
+        config = new BukkitConfiguration(new YAMLProcessor(new File(getDataFolder(), "config.yml"), true), this);
         PermissionsResolverManager.initialize(this);
 
         // Load the configuration
@@ -161,7 +155,7 @@ public class WorldEditPlugin extends JavaPlugin {
                 if (copy == null) throw new FileNotFoundException();
                 input = file.getInputStream(copy);
             } catch (IOException e) {
-                logger.severe(getDescription().getName() + ": Unable to read default configuration: " + name);
+                getLogger().severe("Unable to read default configuration: " + name);
             }
             if (input != null) {
                 FileOutputStream output = null;
@@ -174,8 +168,7 @@ public class WorldEditPlugin extends JavaPlugin {
                         output.write(buf, 0, length);
                     }
 
-                    logger.info(getDescription().getName()
+                    getLogger().info("Default configuration file written: " + name);
-                            + ": Default configuration file written: " + name);
                 } catch (IOException e) {
                     e.printStackTrace();
                 } finally {

src/main/java/com/sk89q/worldedit/spout/SpoutConfiguration.java

@@ -0,0 +1,41 @@
+/*
+ * WorldEdit
+ * Copyright (C) 2012 sk89q <http://www.sk89q.com> and contributors
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU 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 General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ */
+
+package com.sk89q.worldedit.spout;
+
+import com.sk89q.util.yaml.YAMLProcessor;
+import com.sk89q.worldedit.util.YAMLConfiguration;
+
+import java.io.File;
+import java.util.logging.Logger;
+
+/**
+ * @author zml2008
+ */
+public class SpoutConfiguration extends YAMLConfiguration {
+    private final WorldEditPlugin plugin;
+    public SpoutConfiguration(YAMLProcessor config, WorldEditPlugin plugin) {
+        super(config, plugin.getLogger());
+        this.plugin = plugin;
+    }
+
+    @Override
+    public File getWorkingDirectory() {
+        return plugin.getDataFolder();
+    }
+}

src/main/java/com/sk89q/worldedit/spout/WorldEditListener.java

@@ -46,7 +46,7 @@ import java.util.regex.Pattern;
 /**
  * Handles all events thrown in relation to a Player
  */
-public class WorldEditPlayerListener implements Listener {
+public class WorldEditListener implements Listener {
     /**
      * Plugin.
      */
@@ -61,7 +61,7 @@ public class WorldEditPlayerListener implements Listener {
      *
      * @param plugin
      */
-    public WorldEditPlayerListener(WorldEditPlugin plugin) {
+    public WorldEditListener(WorldEditPlugin plugin) {
         this.plugin = plugin;
     }
 

src/main/java/com/sk89q/worldedit/spout/WorldEditPlugin.java

@@ -49,10 +49,6 @@ import java.util.zip.ZipEntry;
  * @author sk89q
  */
 public class WorldEditPlugin extends CommonPlugin implements Named {
-    /**
-     * WorldEdit messages get sent here.
-     */
-    private static final Logger logger = Logger.getLogger("Minecraft.WorldEdit");
 
     /**
      * The server interface that all server-related API goes through.
@@ -80,7 +76,7 @@ public class WorldEditPlugin extends CommonPlugin implements Named {
         final String pluginYmlVersion = getDescription().getVersion();
         final String manifestVersion = WorldEdit.getVersion();
 
-        logger.info("WorldEdit " + pluginYmlVersion + " enabled.");
+        getLogger().info("WorldEdit " + pluginYmlVersion + " enabled.");
         if (!manifestVersion.equalsIgnoreCase(pluginYmlVersion)) {
             WorldEdit.setVersion(manifestVersion + " (" + pluginYmlVersion + ")");
         }
@@ -93,7 +89,7 @@ public class WorldEditPlugin extends CommonPlugin implements Named {
 
         // Set up configuration and such, including the permissions
         // resolver
-        config = new YAMLConfiguration(new YAMLProcessor(new File(getDataFolder(), "config.yml"), true), logger);
+        config = new SpoutConfiguration(new YAMLProcessor(new File(getDataFolder(), "config.yml"), true), this);
 
         // Load the configuration
         loadConfiguration();
@@ -136,7 +132,7 @@ public class WorldEditPlugin extends CommonPlugin implements Named {
      * Register the events used by WorldEdit.
      */
     protected void registerEvents() {
-        getGame().getEventManager().registerEvents(new WorldEditPlayerListener(this), this);
+        getGame().getEventManager().registerEvents(new WorldEditListener(this), this);
     }
 
     /**
@@ -155,7 +151,7 @@ public class WorldEditPlugin extends CommonPlugin implements Named {
                 if (copy == null) throw new FileNotFoundException();
                 input = file.getInputStream(copy);
             } catch (IOException e) {
-                logger.severe(getDescription().getName() + ": Unable to read default configuration: " + name);
+                getLogger().severe("Unable to read default configuration: " + name);
             }
             if (input != null) {
                 FileOutputStream output = null;
@@ -168,22 +164,19 @@ public class WorldEditPlugin extends CommonPlugin implements Named {
                         output.write(buf, 0, length);
                     }
 
-                    logger.info(getDescription().getName()
+                    getLogger().info("Default configuration file written: " + name);
-                            + ": Default configuration file written: " + name);
                 } catch (IOException e) {
                     e.printStackTrace();
                 } finally {
                     try {
-                        if (input != null) {
+                        input.close();
-                            input.close();
+                    } catch (IOException ignore) {}
-                        }
-                    } catch (IOException e) {}
 
                     try {
                         if (output != null) {
                             output.close();
                         }
-                    } catch (IOException e) {}
+                    } catch (IOException ignore) {}
                 }
             }
         }

src/main/java/com/sk89q/worldedit/util/YAMLConfiguration.java

@@ -25,6 +25,7 @@ import com.sk89q.worldedit.LocalSession;
 import com.sk89q.worldedit.LogFormat;
 import com.sk89q.worldedit.snapshots.SnapshotRepository;
 
+import java.io.File;
 import java.io.IOException;
 import java.util.HashSet;
 import java.util.logging.FileHandler;
@@ -105,7 +106,8 @@ public class YAMLConfiguration extends LocalConfiguration {
         String logFile = config.getString("logging.file", "");
         if (!logFile.equals("")) {
             try {
-                logFileHandler = new FileHandler(logFile, true);
+                logFileHandler = new FileHandler(new File(getWorkingDirectory(),
+                        logFile).getAbsolutePath(), true);
                 logFileHandler.setFormatter(new LogFormat());
                 logger.addHandler(logFileHandler);
             } catch (IOException e) {