diff --git a/org.eclipse.jdt.launching/META-INF/MANIFEST.MF b/org.eclipse.jdt.launching/META-INF/MANIFEST.MF
index ed62dbc..4321b1a 100644
--- a/org.eclipse.jdt.launching/META-INF/MANIFEST.MF
+++ b/org.eclipse.jdt.launching/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@
 Bundle-ManifestVersion: 2
 Bundle-Name: %pluginName
 Bundle-SymbolicName: org.eclipse.jdt.launching; singleton:=true
-Bundle-Version: 3.4.1.qualifier
+Bundle-Version: 3.4.2.qualifier
 Bundle-Activator: org.eclipse.jdt.internal.launching.LaunchingPlugin
 Bundle-Vendor: %providerName
 Bundle-Localization: plugin
diff --git a/org.eclipse.jdt.launching/launching/org/eclipse/jdt/internal/launching/LaunchingPlugin.java b/org.eclipse.jdt.launching/launching/org/eclipse/jdt/internal/launching/LaunchingPlugin.java
index 22741be..493f1c6 100644
--- a/org.eclipse.jdt.launching/launching/org/eclipse/jdt/internal/launching/LaunchingPlugin.java
+++ b/org.eclipse.jdt.launching/launching/org/eclipse/jdt/internal/launching/LaunchingPlugin.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2000, 2008 IBM Corporation and others.
+ * Copyright (c) 2000, 2010 IBM Corporation and others.
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
  * which accompanies this distribution, and is available at
@@ -23,7 +23,6 @@
 import java.net.URL;
 import java.util.ArrayList;
 import java.util.HashMap;
-import java.util.Hashtable;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
@@ -33,29 +32,15 @@
 import javax.xml.parsers.FactoryConfigurationError;
 import javax.xml.parsers.ParserConfigurationException;
 
-import com.ibm.icu.text.MessageFormat;
-
-import org.osgi.framework.BundleContext;
-
-import org.w3c.dom.Document;
-import org.w3c.dom.Element;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-
-import org.xml.sax.InputSource;
-import org.xml.sax.SAXException;
-import org.xml.sax.helpers.DefaultHandler;
-
-import org.eclipse.debug.core.DebugEvent;
-import org.eclipse.debug.core.DebugPlugin;
-import org.eclipse.debug.core.IDebugEventSetListener;
-import org.eclipse.debug.core.ILaunch;
-import org.eclipse.debug.core.ILaunchConfiguration;
-import org.eclipse.debug.core.ILaunchConfigurationWorkingCopy;
-import org.eclipse.debug.core.ILaunchesListener;
-import org.eclipse.debug.core.model.IDebugTarget;
-import org.eclipse.debug.core.model.IProcess;
-
+import org.eclipse.core.resources.IMarker;
+import org.eclipse.core.resources.IResource;
+import org.eclipse.core.resources.IResourceChangeEvent;
+import org.eclipse.core.resources.IResourceChangeListener;
+import org.eclipse.core.resources.IResourceDelta;
+import org.eclipse.core.resources.ISaveContext;
+import org.eclipse.core.resources.ISaveParticipant;
+import org.eclipse.core.resources.IWorkspaceRunnable;
+import org.eclipse.core.resources.ResourcesPlugin;
 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.FileLocator;
 import org.eclipse.core.runtime.IConfigurationElement;
@@ -71,21 +56,18 @@
 import org.eclipse.core.runtime.Status;
 import org.eclipse.core.runtime.Preferences.PropertyChangeEvent;
 import org.eclipse.core.runtime.jobs.Job;
-
-import org.eclipse.core.resources.IMarker;
-import org.eclipse.core.resources.IResource;
-import org.eclipse.core.resources.IResourceChangeEvent;
-import org.eclipse.core.resources.IResourceChangeListener;
-import org.eclipse.core.resources.IResourceDelta;
-import org.eclipse.core.resources.ISaveContext;
-import org.eclipse.core.resources.ISaveParticipant;
-import org.eclipse.core.resources.IWorkspaceRunnable;
-import org.eclipse.core.resources.ResourcesPlugin;
-
+import org.eclipse.debug.core.DebugEvent;
+import org.eclipse.debug.core.DebugPlugin;
+import org.eclipse.debug.core.IDebugEventSetListener;
+import org.eclipse.debug.core.ILaunch;
+import org.eclipse.debug.core.ILaunchConfiguration;
+import org.eclipse.debug.core.ILaunchConfigurationWorkingCopy;
+import org.eclipse.debug.core.ILaunchesListener;
+import org.eclipse.debug.core.model.IDebugTarget;
+import org.eclipse.debug.core.model.IProcess;
 import org.eclipse.jdt.core.IClasspathEntry;
 import org.eclipse.jdt.core.IJavaProject;
 import org.eclipse.jdt.core.JavaCore;
-
 import org.eclipse.jdt.launching.IRuntimeClasspathEntry2;
 import org.eclipse.jdt.launching.IVMConnector;
 import org.eclipse.jdt.launching.IVMInstall;
@@ -95,6 +77,16 @@
 import org.eclipse.jdt.launching.environments.IExecutionEnvironment;
 import org.eclipse.jdt.launching.environments.IExecutionEnvironmentsManager;
 import org.eclipse.jdt.launching.sourcelookup.ArchiveSourceLocation;
+import org.osgi.framework.BundleContext;
+import org.w3c.dom.Document;
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+import org.w3c.dom.NodeList;
+import org.xml.sax.InputSource;
+import org.xml.sax.SAXException;
+import org.xml.sax.helpers.DefaultHandler;
+
+import com.ibm.icu.text.MessageFormat;
 
 public class LaunchingPlugin extends Plugin implements Preferences.IPropertyChangeListener, IVMInstallChangedListener, IResourceChangeListener, ILaunchesListener, IDebugEventSetListener {
 	
@@ -485,28 +477,8 @@
 			public void saving(ISaveContext context1) throws CoreException {
 				savePluginPreferences();
 			}
-			
 		});
-		// Exclude launch configurations from being copied to the output directory
-		String launchFilter = "*." + ILaunchConfiguration.LAUNCH_CONFIGURATION_FILE_EXTENSION; //$NON-NLS-1$
-		Hashtable optionsMap = JavaCore.getOptions();
-		String filters= (String)optionsMap.get(JavaCore.CORE_JAVA_BUILD_RESOURCE_COPY_FILTER);
-		boolean modified = false;
-		if (filters == null || filters.length() == 0) {
-			filters= launchFilter;
-			modified = true;
-		} else if (filters.indexOf(launchFilter) == -1) {
-			filters= filters + ',' + launchFilter;
-			modified = true;
-		}
 
-		if (modified) {
-			optionsMap.put(JavaCore.CORE_JAVA_BUILD_RESOURCE_COPY_FILTER, filters);
-			JavaCore.setOptions(optionsMap);
-		}
-
-		// set default preference values
-		getPluginPreferences().setDefault(JavaRuntime.PREF_CONNECT_TIMEOUT, JavaRuntime.DEF_CONNECT_TIMEOUT);
 		getPluginPreferences().addPropertyChangeListener(this);
 
 		JavaRuntime.addVMInstallChangedListener(this);
diff --git a/org.eclipse.jdt.launching/launching/org/eclipse/jdt/internal/launching/LaunchingPreferenceInitializer.java b/org.eclipse.jdt.launching/launching/org/eclipse/jdt/internal/launching/LaunchingPreferenceInitializer.java
new file mode 100644
index 0000000..b26d113
--- /dev/null
+++ b/org.eclipse.jdt.launching/launching/org/eclipse/jdt/internal/launching/LaunchingPreferenceInitializer.java
@@ -0,0 +1,62 @@
+/*******************************************************************************
+ * Copyright (c) 2008, 2010 IBM Corporation and others.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ *     IBM Corporation - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.jdt.internal.launching;
+
+import org.eclipse.core.runtime.preferences.AbstractPreferenceInitializer;
+import org.eclipse.core.runtime.preferences.DefaultScope;
+import org.eclipse.core.runtime.preferences.IEclipsePreferences;
+import org.eclipse.debug.core.ILaunchConfiguration;
+import org.eclipse.jdt.core.JavaCore;
+import org.eclipse.jdt.launching.JavaRuntime;
+import org.osgi.service.prefs.BackingStoreException;
+
+/**
+ * Initializes preferences for the JDT launching plug-in.
+ *
+ * @since 3.5
+ */
+public class LaunchingPreferenceInitializer extends AbstractPreferenceInitializer {
+
+	/* (non-Javadoc)
+	 * @see org.eclipse.core.runtime.preferences.AbstractPreferenceInitializer#initializeDefaultPreferences()
+	 */
+	public void initializeDefaultPreferences() {
+		DefaultScope scope = new DefaultScope();
+		IEclipsePreferences dnode = scope.getNode(LaunchingPlugin.ID_PLUGIN);
+		if(dnode == null) {
+			return;
+		}
+		dnode.putInt(JavaRuntime.PREF_CONNECT_TIMEOUT, JavaRuntime.DEF_CONNECT_TIMEOUT);
+		
+		try {
+			dnode.flush();
+		} catch (BackingStoreException e) {
+			LaunchingPlugin.log(e);
+		}
+				
+		// https://bugs.eclipse.org/bugs/show_bug.cgi?id=255381
+		// NOTE: only the pref's default value is initialized to avoid deadlock (we don't set the
+		// associated JavaCore options, as this can trigger a job to touch the project (see 
+		// bug https://bugs.eclipse.org/bugs/show_bug.cgi?id=260445)
+		String launchFilter = "*." + ILaunchConfiguration.LAUNCH_CONFIGURATION_FILE_EXTENSION; //$NON-NLS-1$
+		dnode = scope.getNode(JavaCore.PLUGIN_ID);
+		if(dnode == null) {
+			return;
+		}
+		dnode.put(JavaCore.CORE_JAVA_BUILD_RESOURCE_COPY_FILTER, launchFilter);
+		
+		try {
+			dnode.flush();
+		} catch (BackingStoreException e) {
+			LaunchingPlugin.log(e);
+		}
+	}
+}
diff --git a/org.eclipse.jdt.launching/plugin.xml b/org.eclipse.jdt.launching/plugin.xml
index 7a89a35..df2b5fd 100644
--- a/org.eclipse.jdt.launching/plugin.xml
+++ b/org.eclipse.jdt.launching/plugin.xml
@@ -193,6 +193,9 @@
    <extension
          point="org.eclipse.core.runtime.preferences">
       <modifier class="org.eclipse.jdt.internal.launching.JREPreferenceModifyListener"/>
+      <initializer
+            class="org.eclipse.jdt.internal.launching.LaunchingPreferenceInitializer">
+      </initializer>
    </extension>
    
    <extension point="org.eclipse.core.expressions.propertyTesters">