[496582] Consider preferences scope hierarchy

Make sure we use either the platform's IPreferencesService or the
relevant IPreferenceStore when reading and writing preferences
everywhere in EMFCompare.

Bug: 496582
Change-Id: I2cbdf6f9356eafba867f0473f680429d0ae6cd35
Also-by: Mathias Schaefer <mschaefer@eclipsesource.com>
Also-by: Philip Langer <planger@eclipsesource.com>
Signed-off-by: Laurent Delaigue <laurent.delaigue@obeo.fr>

34 files changed, 411 insertions, 594 deletions

diff --git a/plugins/org.eclipse.emf.compare.egit/src/org/eclipse/emf/compare/egit/internal/match/EGitMatchEngineFactory.java b/plugins/org.eclipse.emf.compare.egit/src/org/eclipse/emf/compare/egit/internal/match/EGitMatchEngineFactory.java
index 25e6a2a43..ea07a3093 100644
--- a/plugins/org.eclipse.emf.compare.egit/src/org/eclipse/emf/compare/egit/internal/match/EGitMatchEngineFactory.java
+++ b/plugins/org.eclipse.emf.compare.egit/src/org/eclipse/emf/compare/egit/internal/match/EGitMatchEngineFactory.java
@@ -66,7 +66,7 @@ public class EGitMatchEngineFactory extends DefaultRCPMatchEngineFactory {
 	 */
 	@Override
 	public IMatchEngine getMatchEngine() {
-		final UseIdentifiers useUdentifier = getUseIdentifierValue(getConfiguration());
+		final UseIdentifiers useUdentifier = getUseIdentifierValue();
 		final Collection<IResourceMatchingStrategy> strategies = Sets.newLinkedHashSet();
 		strategies.add(new LocationMatchingStrategy());
 		return DefaultMatchEngine.create(useUdentifier,
diff --git a/plugins/org.eclipse.emf.compare.ide.ui.tests.framework/src/org/eclipse/emf/compare/ide/ui/tests/framework/AbstractCompareStatement.java b/plugins/org.eclipse.emf.compare.ide.ui.tests.framework/src/org/eclipse/emf/compare/ide/ui/tests/framework/AbstractCompareStatement.java
index 005ba218c..d019bf7b4 100644
--- a/plugins/org.eclipse.emf.compare.ide.ui.tests.framework/src/org/eclipse/emf/compare/ide/ui/tests/framework/AbstractCompareStatement.java
+++ b/plugins/org.eclipse.emf.compare.ide.ui.tests.framework/src/org/eclipse/emf/compare/ide/ui/tests/framework/AbstractCompareStatement.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2016 Obeo.
+ * Copyright (c) 2016 Obeo 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
@@ -7,10 +7,10 @@
  * 
  * Contributors:
  *     Obeo - initial API and implementation
+ *     Mathias Schaefer - preferences refactoring
  *******************************************************************************/
 package org.eclipse.emf.compare.ide.ui.tests.framework;
 
-import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
@@ -20,12 +20,13 @@ import org.eclipse.core.runtime.IExtension;
 import org.eclipse.core.runtime.IExtensionPoint;
 import org.eclipse.core.runtime.IExtensionRegistry;
 import org.eclipse.core.runtime.Platform;
-import org.eclipse.core.runtime.preferences.IEclipsePreferences;
+import org.eclipse.core.runtime.preferences.InstanceScope;
 import org.eclipse.emf.compare.ide.ui.internal.EMFCompareIDEUIPlugin;
 import org.eclipse.emf.compare.ide.ui.internal.preferences.EMFCompareUIPreferences;
 import org.eclipse.emf.compare.rcp.EMFCompareRCPPlugin;
 import org.eclipse.emf.compare.rcp.internal.preferences.EMFComparePreferences;
 import org.eclipse.jface.preference.IPreferenceStore;
+import org.eclipse.ui.preferences.ScopedPreferenceStore;
 import org.junit.runners.model.FrameworkMethod;
 import org.junit.runners.model.Statement;
 
@@ -65,6 +66,24 @@ public abstract class AbstractCompareStatement extends Statement {
 	private static final String CONFLICT_EXTENSION_POINT_ID = EMFCompareRCPPlugin.PLUGIN_ID + ID_SEPARATOR
 			+ EMFCompareRCPPlugin.CONFLICT_DETECTOR_PPID;
 
+	/** The default disabled match engines. */
+	private static final List<String> DEFAULT_DISABLED_MATCH_ENGINES = Collections.emptyList();
+
+	/** The default diff engine. */
+	private static final String DEFAULT_DIFF_ENGINE = "org.eclipse.emf.compare.rcp.default.diffEngine"; //$NON-NLS-1$
+
+	/** The default eq engine. */
+	private static final String DEFAULT_EQ_ENGINE = "org.eclipse.emf.compare.rcp.default.equiEngine"; //$NON-NLS-1$
+
+	/** The default req engine. */
+	private static final String DEFAULT_REQ_ENGINE = "org.eclipse.emf.compare.rcp.default.reqEngine"; //$NON-NLS-1$
+
+	/** The default conflict detector. */
+	private static final String DEFAULT_CONFLICT_DETECTOR = "org.eclipse.emf.compare.rcp.fast.conflictDetector"; //$NON-NLS-1$
+
+	/** The default disabled post-processors. */
+	private static final List<String> DEFAULT_DISABLED_POST_PROCESSORS = Collections.emptyList();
+
 	/** The test class. */
 	protected final Object testObject;
 
@@ -72,8 +91,8 @@ public abstract class AbstractCompareStatement extends Statement {
 	protected final FrameworkMethod test;
 
 	/** The EMFCompare preferences. */
-	private final IEclipsePreferences emfComparePreferences = EMFCompareRCPPlugin.getDefault()
-			.getEMFComparePreferences();
+	private final IPreferenceStore rcpPreferenceStore = new ScopedPreferenceStore(InstanceScope.INSTANCE,
+			EMFCompareRCPPlugin.PLUGIN_ID);
 
 	/** The EMFCompare UI preferences. */
 	private final IPreferenceStore uiPreferenceStore = EMFCompareIDEUIPlugin.getDefault()
@@ -103,24 +122,6 @@ public abstract class AbstractCompareStatement extends Statement {
 	/** The default resolution strategy. */
 	private String defaultResolutionStrategy = "WORKSPACE"; //$NON-NLS-1$
 
-	/** The default disabled match engines. */
-	private List<String> defaultDisabledMatchEngines = new ArrayList<String>();
-
-	/** The default diff engine. */
-	private String defaultDiffEngine = "org.eclipse.emf.compare.rcp.default.diffEngine"; //$NON-NLS-1$
-
-	/** The default eq engine. */
-	private String defaultEqEngine = "org.eclipse.emf.compare.rcp.default.equiEngine"; //$NON-NLS-1$
-
-	/** The default req engine. */
-	private String defaultReqEngine = "org.eclipse.emf.compare.rcp.default.reqEngine"; //$NON-NLS-1$
-
-	/** The default conflict detector. */
-	private String defaultConflictDetector = "org.eclipse.emf.compare.rcp.fast.conflictDetector"; //$NON-NLS-1$
-
-	/** The default disabled post-processors. */
-	private List<String> defaultDisabledPostProcessors = new ArrayList<String>();
-
 	/**
 	 * Constructor for the classic (no Git) comparison statement.
 	 * 
@@ -144,6 +145,7 @@ public abstract class AbstractCompareStatement extends Statement {
 		this.reqEngine = configuration.getReqEngine();
 		this.conflictDetector = configuration.getConflictDetector();
 		this.disabledPostProcessors = configuration.getDisabledPostProcessors();
+		setEMFComparePreferencesDefaults();
 	}
 
 	/**
@@ -164,19 +166,32 @@ public abstract class AbstractCompareStatement extends Statement {
 	}
 
 	/**
-	 * Restore preferences as they were before the test.
+	 * Set the default values to use for all test-relevant preference settings.
 	 */
-	protected void restoreEMFComparePreferences() {
-		uiPreferenceStore.setValue(EMFCompareUIPreferences.RESOLUTION_SCOPE_PREFERENCE,
+	private void setEMFComparePreferencesDefaults() {
+		uiPreferenceStore.setDefault(EMFCompareUIPreferences.RESOLUTION_SCOPE_PREFERENCE,
 				defaultResolutionStrategy);
-		emfComparePreferences.put(EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES,
-				join(defaultDisabledMatchEngines, PREFERENCES_SEPARATOR));
-		emfComparePreferences.put(EMFComparePreferences.DIFF_ENGINES, defaultDiffEngine);
-		emfComparePreferences.put(EMFComparePreferences.EQUI_ENGINES, defaultEqEngine);
-		emfComparePreferences.put(EMFComparePreferences.REQ_ENGINES, defaultReqEngine);
-		emfComparePreferences.put(EMFComparePreferences.CONFLICTS_DETECTOR, defaultConflictDetector);
-		emfComparePreferences.put(EMFComparePreferences.DISABLED_POST_PROCESSOR,
-				join(defaultDisabledPostProcessors, PREFERENCES_SEPARATOR));
+		rcpPreferenceStore.setDefault(EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES,
+				join(DEFAULT_DISABLED_MATCH_ENGINES, PREFERENCES_SEPARATOR));
+		rcpPreferenceStore.setDefault(EMFComparePreferences.DIFF_ENGINES, DEFAULT_DIFF_ENGINE);
+		rcpPreferenceStore.setDefault(EMFComparePreferences.EQUI_ENGINES, DEFAULT_EQ_ENGINE);
+		rcpPreferenceStore.setDefault(EMFComparePreferences.REQ_ENGINES, DEFAULT_REQ_ENGINE);
+		rcpPreferenceStore.setDefault(EMFComparePreferences.CONFLICTS_DETECTOR, DEFAULT_CONFLICT_DETECTOR);
+		rcpPreferenceStore.setDefault(EMFComparePreferences.DISABLED_POST_PROCESSOR,
+				join(DEFAULT_DISABLED_POST_PROCESSORS, PREFERENCES_SEPARATOR));
+	}
+
+	/**
+	 * Restore preferences as if they were unset by the user.
+	 */
+	protected void restoreEMFComparePreferences() {
+		uiPreferenceStore.setToDefault(EMFCompareUIPreferences.RESOLUTION_SCOPE_PREFERENCE);
+		rcpPreferenceStore.setToDefault(EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES);
+		rcpPreferenceStore.setToDefault(EMFComparePreferences.DIFF_ENGINES);
+		rcpPreferenceStore.setToDefault(EMFComparePreferences.EQUI_ENGINES);
+		rcpPreferenceStore.setToDefault(EMFComparePreferences.REQ_ENGINES);
+		rcpPreferenceStore.setToDefault(EMFComparePreferences.CONFLICTS_DETECTOR);
+		rcpPreferenceStore.setToDefault(EMFComparePreferences.DISABLED_POST_PROCESSOR);
 	}
 
 	/**
@@ -206,19 +221,11 @@ public abstract class AbstractCompareStatement extends Statement {
 	 * Set the match engine preference.
 	 */
 	private void setMatchPreference() {
-		String disabMatchEngine = emfComparePreferences.get(
-				EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES,
-				join(defaultDisabledMatchEngines, PREFERENCES_SEPARATOR));
-		defaultDisabledMatchEngines.clear();
-		for (String matchEngine : disabMatchEngine.split(PREFERENCES_SEPARATOR)) {
-			defaultDisabledMatchEngines.add(matchEngine);
-		}
-
 		List<String> matchEngineNames = Collections.emptyList();
 		for (Class<?> matchEngine : disabledMatchEngines) {
 			matchEngineNames.add(matchEngine.getCanonicalName());
 		}
-		emfComparePreferences.put(EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES,
+		rcpPreferenceStore.setValue(EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES,
 				join(matchEngineNames, PREFERENCES_SEPARATOR));
 	}
 
@@ -229,7 +236,7 @@ public abstract class AbstractCompareStatement extends Statement {
 		IExtensionRegistry extensionRegistry = Platform.getExtensionRegistry();
 		IExtensionPoint extensionPoint = extensionRegistry.getExtensionPoint(DIFF_EXTENSION_POINT_ID);
 		IExtension[] extensions = extensionPoint.getExtensions();
-		String diffEngineId = defaultDiffEngine;
+		String diffEngineId = null;
 		for (IExtension iExtension : extensions) {
 			for (IConfigurationElement iConfig : iExtension.getConfigurationElements()) {
 				if (iConfig.getAttribute(EXTENSION_POINT_CLASS_SELECTOR)
@@ -239,9 +246,9 @@ public abstract class AbstractCompareStatement extends Statement {
 				}
 			}
 		}
-
-		defaultDiffEngine = emfComparePreferences.get(EMFComparePreferences.DIFF_ENGINES, defaultDiffEngine);
-		emfComparePreferences.put(EMFComparePreferences.DIFF_ENGINES, diffEngineId);
+		if (diffEngineId != null) {
+			rcpPreferenceStore.setValue(EMFComparePreferences.DIFF_ENGINES, diffEngineId);
+		}
 	}
 
 	/**
@@ -251,7 +258,7 @@ public abstract class AbstractCompareStatement extends Statement {
 		IExtensionRegistry extensionRegistry = Platform.getExtensionRegistry();
 		IExtensionPoint extensionPoint = extensionRegistry.getExtensionPoint(EQ_EXTENSION_POINT_ID);
 		IExtension[] extensions = extensionPoint.getExtensions();
-		String eqEngineId = defaultEqEngine;
+		String eqEngineId = null;
 		for (IExtension iExtension : extensions) {
 			for (IConfigurationElement iConfig : iExtension.getConfigurationElements()) {
 				if (iConfig.getAttribute(EXTENSION_POINT_CLASS_SELECTOR)
@@ -261,9 +268,9 @@ public abstract class AbstractCompareStatement extends Statement {
 				}
 			}
 		}
-
-		defaultEqEngine = emfComparePreferences.get(EMFComparePreferences.EQUI_ENGINES, defaultEqEngine);
-		emfComparePreferences.put(EMFComparePreferences.EQUI_ENGINES, eqEngineId);
+		if (eqEngineId != null) {
+			rcpPreferenceStore.setValue(EMFComparePreferences.EQUI_ENGINES, eqEngineId);
+		}
 	}
 
 	/**
@@ -273,7 +280,7 @@ public abstract class AbstractCompareStatement extends Statement {
 		IExtensionRegistry extensionRegistry = Platform.getExtensionRegistry();
 		IExtensionPoint extensionPoint = extensionRegistry.getExtensionPoint(REQ_EXTENSION_POINT_ID);
 		IExtension[] extensions = extensionPoint.getExtensions();
-		String reqEngineId = defaultReqEngine;
+		String reqEngineId = null;
 		for (IExtension iExtension : extensions) {
 			for (IConfigurationElement iConfig : iExtension.getConfigurationElements()) {
 				if (iConfig.getAttribute(EXTENSION_POINT_CLASS_SELECTOR)
@@ -283,9 +290,9 @@ public abstract class AbstractCompareStatement extends Statement {
 				}
 			}
 		}
-
-		defaultReqEngine = emfComparePreferences.get(EMFComparePreferences.REQ_ENGINES, defaultReqEngine);
-		emfComparePreferences.put(EMFComparePreferences.REQ_ENGINES, reqEngineId);
+		if (reqEngineId != null) {
+			rcpPreferenceStore.setValue(EMFComparePreferences.REQ_ENGINES, reqEngineId);
+		}
 	}
 
 	/**
@@ -295,7 +302,7 @@ public abstract class AbstractCompareStatement extends Statement {
 		IExtensionRegistry extensionRegistry = Platform.getExtensionRegistry();
 		IExtensionPoint extensionPoint = extensionRegistry.getExtensionPoint(CONFLICT_EXTENSION_POINT_ID);
 		IExtension[] extensions = extensionPoint.getExtensions();
-		String conflictDetectorId = defaultConflictDetector;
+		String conflictDetectorId = null;
 		for (IExtension iExtension : extensions) {
 			for (IConfigurationElement iConfig : iExtension.getConfigurationElements()) {
 				if (iConfig.getAttribute(EXTENSION_POINT_CLASS_SELECTOR)
@@ -305,28 +312,20 @@ public abstract class AbstractCompareStatement extends Statement {
 				}
 			}
 		}
-
-		defaultConflictDetector = emfComparePreferences.get(EMFComparePreferences.CONFLICTS_DETECTOR,
-				defaultConflictDetector);
-		emfComparePreferences.put(EMFComparePreferences.CONFLICTS_DETECTOR, conflictDetectorId);
+		if (conflictDetectorId != null) {
+			rcpPreferenceStore.setValue(EMFComparePreferences.CONFLICTS_DETECTOR, conflictDetectorId);
+		}
 	}
 
 	/**
 	 * Set the post-processors preference.
 	 */
 	private void setPostProcessorPreference() {
-		String disabPostProcessors = emfComparePreferences.get(EMFComparePreferences.DISABLED_POST_PROCESSOR,
-				join(defaultDisabledPostProcessors, PREFERENCES_SEPARATOR));
-		defaultDisabledPostProcessors.clear();
-		for (String postProcessor : disabPostProcessors.split(PREFERENCES_SEPARATOR)) {
-			defaultDisabledPostProcessors.add(postProcessor);
-		}
-
 		List<String> postProcessorNames = Collections.emptyList();
 		for (Class<?> postProcessor : disabledPostProcessors) {
 			postProcessorNames.add(postProcessor.getCanonicalName());
 		}
-		emfComparePreferences.put(EMFComparePreferences.DISABLED_POST_PROCESSOR,
+		rcpPreferenceStore.setValue(EMFComparePreferences.DISABLED_POST_PROCESSOR,
 				join(postProcessorNames, PREFERENCES_SEPARATOR));
 	}
 
diff --git a/plugins/org.eclipse.emf.compare.ide.ui/src/org/eclipse/emf/compare/ide/ui/internal/handler/AbstractCompareHandler.java b/plugins/org.eclipse.emf.compare.ide.ui/src/org/eclipse/emf/compare/ide/ui/internal/handler/AbstractCompareHandler.java
index a82d4a3f2..5d3e0aedf 100644
--- a/plugins/org.eclipse.emf.compare.ide.ui/src/org/eclipse/emf/compare/ide/ui/internal/handler/AbstractCompareHandler.java
+++ b/plugins/org.eclipse.emf.compare.ide.ui/src/org/eclipse/emf/compare/ide/ui/internal/handler/AbstractCompareHandler.java
@@ -17,7 +17,6 @@ import java.util.Iterator;
 import org.eclipse.compare.CompareConfiguration;
 import org.eclipse.compare.CompareEditorInput;
 import org.eclipse.core.commands.AbstractHandler;
-import org.eclipse.core.runtime.preferences.IEclipsePreferences;
 import org.eclipse.emf.common.command.CommandStack;
 import org.eclipse.emf.common.notify.AdapterFactory;
 import org.eclipse.emf.common.notify.Notifier;
@@ -58,12 +57,6 @@ public abstract class AbstractCompareHandler extends AbstractHandler {
 
 	protected static CompareEditorInput createCompareEditorInput(IWorkbenchPart part,
 			AdapterFactory adapterFactory, Notifier left, Notifier right, Notifier origin) {
-		return createCompareEditorInput(part, adapterFactory, left, right, origin, null);
-	}
-
-	protected static CompareEditorInput createCompareEditorInput(IWorkbenchPart part,
-			AdapterFactory adapterFactory, Notifier left, Notifier right, Notifier origin,
-			IEclipsePreferences enginePreferences) {
 		CompareEditorInput input = null;
 
 		final ICompareEditingDomain editingDomain = createEMFCompareEditingDomain(part, left, right, origin);
@@ -76,20 +69,8 @@ public abstract class AbstractCompareHandler extends AbstractHandler {
 		matchEngineFactoryRegistry.add(eObjectMatchEngineFactory);
 
 		final Builder builder = EMFCompare.builder();
-		final IEclipsePreferences preferences;
-		if (enginePreferences == null) {
-			preferences = EMFCompareRCPPlugin.getDefault().getEMFComparePreferences();
-		} else {
-			preferences = enginePreferences;
-		}
-		if (preferences != null) {
-			EMFCompareBuilderConfigurator engineProvider = new EMFCompareBuilderConfigurator(preferences,
-					matchEngineFactoryRegistry, EMFCompareRCPPlugin.getDefault().getPostProcessorRegistry());
-			engineProvider.configure(builder);
-		} else {
-			builder.setMatchEngineFactoryRegistry(matchEngineFactoryRegistry)
-					.setPostProcessorRegistry(EMFCompareRCPPlugin.getDefault().getPostProcessorRegistry());
-		}
+		EMFCompareBuilderConfigurator engineProvider = EMFCompareBuilderConfigurator.createDefault();
+		engineProvider.configure(builder);
 		EMFCompare comparator = builder.build();
 
 		IComparisonScope scope = new DefaultComparisonScope(left, right, origin);
diff --git a/plugins/org.eclipse.emf.compare.ide.ui/src/org/eclipse/emf/compare/ide/ui/internal/handler/EMFComparisonSourceActionHandler.java b/plugins/org.eclipse.emf.compare.ide.ui/src/org/eclipse/emf/compare/ide/ui/internal/handler/EMFComparisonSourceActionHandler.java
index ebc350122..802917678 100644
--- a/plugins/org.eclipse.emf.compare.ide.ui/src/org/eclipse/emf/compare/ide/ui/internal/handler/EMFComparisonSourceActionHandler.java
+++ b/plugins/org.eclipse.emf.compare.ide.ui/src/org/eclipse/emf/compare/ide/ui/internal/handler/EMFComparisonSourceActionHandler.java
@@ -28,7 +28,6 @@ import org.eclipse.core.resources.IStorage;
 import org.eclipse.core.runtime.IAdapterManager;
 import org.eclipse.core.runtime.NullProgressMonitor;
 import org.eclipse.core.runtime.Platform;
-import org.eclipse.core.runtime.preferences.IEclipsePreferences;
 import org.eclipse.emf.common.command.CommandStack;
 import org.eclipse.emf.common.notify.AdapterFactory;
 import org.eclipse.emf.common.notify.Notifier;
@@ -183,16 +182,8 @@ public class EMFComparisonSourceActionHandler extends AbstractHandler {
 		final EMFCompareConfiguration configuration = new EMFCompareConfiguration(new CompareConfiguration());
 
 		final Builder builder = EMFCompare.builder();
-		final IEclipsePreferences preferences = EMFCompareRCPPlugin.getDefault().getEMFComparePreferences();
 
-		final EMFCompareBuilderConfigurator engineProvider;
-		if (preferences != null) {
-			engineProvider = new EMFCompareBuilderConfigurator(preferences,
-					EMFCompareRCPPlugin.getDefault().getMatchEngineFactoryRegistry(),
-					EMFCompareRCPPlugin.getDefault().getPostProcessorRegistry());
-		} else {
-			engineProvider = EMFCompareBuilderConfigurator.createDefault();
-		}
+		final EMFCompareBuilderConfigurator engineProvider = EMFCompareBuilderConfigurator.createDefault();
 		engineProvider.configure(builder);
 		final EMFCompare comparator = builder.build();
 
diff --git a/plugins/org.eclipse.emf.compare.rcp.tests/src/org/eclipse/emf/compare/rcp/tests/MatchEngineFactoryRegistryWrapperTest.java b/plugins/org.eclipse.emf.compare.rcp.tests/src/org/eclipse/emf/compare/rcp/tests/MatchEngineFactoryRegistryWrapperTest.java
index 4bbff66ef..50fae0d0c 100644
--- a/plugins/org.eclipse.emf.compare.rcp.tests/src/org/eclipse/emf/compare/rcp/tests/MatchEngineFactoryRegistryWrapperTest.java
+++ b/plugins/org.eclipse.emf.compare.rcp.tests/src/org/eclipse/emf/compare/rcp/tests/MatchEngineFactoryRegistryWrapperTest.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2014, 2015 Obeo.
+ * Copyright (c) 2014, 2016 Obeo 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
@@ -7,6 +7,7 @@
  * 
  * Contributors:
  *     Obeo - initial API and implementation
+ *     Mathias Schaefer - preferences refactoring
  *******************************************************************************/
 package org.eclipse.emf.compare.rcp.tests;
 
@@ -16,19 +17,16 @@ import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertSame;
 import static org.junit.Assert.assertTrue;
 
-import com.google.common.base.Joiner;
-import com.google.common.collect.Lists;
-
 import java.io.IOException;
 import java.util.Collection;
 import java.util.Collections;
 
-import org.eclipse.core.runtime.preferences.IEclipsePreferences;
 import org.eclipse.core.runtime.preferences.InstanceScope;
 import org.eclipse.emf.compare.EMFCompare;
 import org.eclipse.emf.compare.match.IMatchEngine;
 import org.eclipse.emf.compare.match.IMatchEngine.Factory;
 import org.eclipse.emf.compare.match.impl.MatchEngineFactoryImpl;
+import org.eclipse.emf.compare.rcp.EMFCompareRCPPlugin;
 import org.eclipse.emf.compare.rcp.internal.extension.IItemDescriptor;
 import org.eclipse.emf.compare.rcp.internal.extension.impl.ItemRegistry;
 import org.eclipse.emf.compare.rcp.internal.extension.impl.ItemUtil;
@@ -42,6 +40,9 @@ import org.junit.Before;
 import org.junit.Test;
 import org.osgi.service.prefs.BackingStoreException;
 
+import com.google.common.base.Joiner;
+import com.google.common.collect.Lists;
+
 /**
  * Test class for {@link MatchEngineFactoryRegistryWrapper}.
  * 
@@ -52,8 +53,6 @@ public class MatchEngineFactoryRegistryWrapperTest {
 
 	private MatchEngineFactoryRegistryWrapper registryWrapper;
 
-	private IEclipsePreferences preferences;
-
 	/**
 	 * Creates a comparison scope from Ecore model.
 	 * 
@@ -65,21 +64,15 @@ public class MatchEngineFactoryRegistryWrapperTest {
 		return new DefaultComparisonScope(ecoreData.getLeft(), ecoreData.getRight(), ecoreData.getOrigin());
 	}
 
-	// For Helios compatibility.
-	@SuppressWarnings("deprecation")
 	@Before
 	public void setUp() throws BackingStoreException {
-		ItemRegistry<Factory> registry = new ItemRegistry<IMatchEngine.Factory>();
-		// Mock preference node.
-		preferences = new InstanceScope()
-				.getNode("org.eclipse.emf.compare.tests.rcp.MatchEngineFactoryRegistryWrapperTest");
-		preferences.clear();
-		registryWrapper = new MatchEngineFactoryRegistryWrapper(registry, preferences);
+		ItemRegistry<Factory> registry = new ItemRegistry<>();
+		registryWrapper = new MatchEngineFactoryRegistryWrapper(registry);
 	}
 
 	@After
 	public void tearDown() throws BackingStoreException {
-		preferences.clear();
+		InstanceScope.INSTANCE.getNode(EMFCompareRCPPlugin.PLUGIN_ID).clear();
 	}
 
 	/**
@@ -274,12 +267,12 @@ public class MatchEngineFactoryRegistryWrapperTest {
 		IComparisonScope scope = createComparisonScope();
 		assertSame(registryWrapper.getHighestRankingMatchEngineFactory(scope), factory3);
 
-		disableEngine(preferences, EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES,
+		disableEngine(EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES,
 				Collections.singleton(factory3.getClass().getName()));
 		assertSame(registryWrapper.getHighestRankingMatchEngineFactory(scope), factory2);
 		assertTrue(!registryWrapper.getMatchEngineFactories(scope).contains(factory3));
 
-		disableEngine(preferences, EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES,
+		disableEngine(EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES,
 				Lists.newArrayList(factory3.getClass().getName(), factory2.getClass().getName()));
 		assertSame(registryWrapper.getHighestRankingMatchEngineFactory(scope), factory);
 		assertTrue(!registryWrapper.getMatchEngineFactories(scope).contains(factory2));
@@ -319,18 +312,17 @@ public class MatchEngineFactoryRegistryWrapperTest {
 	/**
 	 * Disables engine in preferences.
 	 * 
-	 * @param preference
-	 *            {@link IEclipsePreferences}
 	 * @param key
 	 * @param toDisable
-	 *            {@link Collection} of {@link IItemDescriptor} to disable.
+	 *            {@link Collection} of {@link IItemDescriptor} to disable, null or empty to enable all
+	 *            engines.
 	 */
-	private void disableEngine(IEclipsePreferences preference, String key, Collection<String> toDisable) {
+	private void disableEngine(String key, Collection<String> toDisable) {
 		if (toDisable != null && !toDisable.isEmpty()) {
 			String newPreferenceValue = Joiner.on(ItemUtil.PREFERENCE_DELIMITER).join(toDisable);
-			preference.put(key, newPreferenceValue);
+			InstanceScope.INSTANCE.getNode(EMFCompareRCPPlugin.PLUGIN_ID).put(key, newPreferenceValue);
 		} else {
-			preference.remove(key);
+			InstanceScope.INSTANCE.getNode(EMFCompareRCPPlugin.PLUGIN_ID).remove(key);
 		}
 	}
 
diff --git a/plugins/org.eclipse.emf.compare.rcp.ui.tests/META-INF/MANIFEST.MF b/plugins/org.eclipse.emf.compare.rcp.ui.tests/META-INF/MANIFEST.MF
index 25f269019..5c0b5b90c 100644
--- a/plugins/org.eclipse.emf.compare.rcp.ui.tests/META-INF/MANIFEST.MF
+++ b/plugins/org.eclipse.emf.compare.rcp.ui.tests/META-INF/MANIFEST.MF
@@ -13,7 +13,8 @@ Require-Bundle: org.eclipse.core.runtime,
  org.eclipse.emf.compare.rcp;bundle-version="2.1.0",
  org.eclipse.emf.compare.rcp.ui;bundle-version="3.0.0",
  org.eclipse.jface,
- org.eclipse.emf.compare.ide.ui.tests.framework
+ org.eclipse.emf.compare.ide.ui.tests.framework,
+ org.eclipse.ui.workbench
 Bundle-RequiredExecutionEnvironment: JavaSE-1.7
 Bundle-Vendor: %providerName
 Import-Package: com.google.common.base;version="[11.0.0,16.0.0)",
diff --git a/plugins/org.eclipse.emf.compare.rcp.ui.tests/src/org/eclipse/emf/compare/rcp/ui/tests/match/RCPMatchEngineFactoryRegistryTest.java b/plugins/org.eclipse.emf.compare.rcp.ui.tests/src/org/eclipse/emf/compare/rcp/ui/tests/match/RCPMatchEngineFactoryRegistryTest.java
index d4d4dc595..4c9368e00 100644
--- a/plugins/org.eclipse.emf.compare.rcp.ui.tests/src/org/eclipse/emf/compare/rcp/ui/tests/match/RCPMatchEngineFactoryRegistryTest.java
+++ b/plugins/org.eclipse.emf.compare.rcp.ui.tests/src/org/eclipse/emf/compare/rcp/ui/tests/match/RCPMatchEngineFactoryRegistryTest.java
@@ -17,14 +17,12 @@ import static org.junit.Assert.assertNull;
 import static org.junit.Assert.assertSame;
 import static org.junit.Assert.assertTrue;
 
-import com.google.common.base.Joiner;
-import com.google.common.collect.Lists;
-
 import java.io.IOException;
 import java.util.Collection;
 import java.util.Collections;
 
 import org.eclipse.core.runtime.preferences.IEclipsePreferences;
+import org.eclipse.core.runtime.preferences.InstanceScope;
 import org.eclipse.emf.compare.EMFCompare;
 import org.eclipse.emf.compare.match.IMatchEngine;
 import org.eclipse.emf.compare.match.IMatchEngine.Factory;
@@ -38,11 +36,15 @@ import org.eclipse.emf.compare.rcp.internal.preferences.EMFComparePreferences;
 import org.eclipse.emf.compare.rcp.ui.tests.match.data.EcoreInputData;
 import org.eclipse.emf.compare.scope.DefaultComparisonScope;
 import org.eclipse.emf.compare.scope.IComparisonScope;
+import org.eclipse.ui.preferences.ScopedPreferenceStore;
 import org.junit.After;
 import org.junit.Before;
 import org.junit.Test;
 import org.osgi.service.prefs.BackingStoreException;
 
+import com.google.common.base.Joiner;
+import com.google.common.collect.Lists;
+
 /**
  * Test class for {@link MatchEngineFactoryRegistryWrapper}.
  * 
@@ -53,7 +55,7 @@ public class RCPMatchEngineFactoryRegistryTest {
 
 	private IMatchEngine.Factory.Registry registryWrapper;
 
-	private IEclipsePreferences preferences;
+	private ScopedPreferenceStore preferenceStore;
 
 	/**
 	 * Creates a comparison scope from Ecore model.
@@ -68,13 +70,15 @@ public class RCPMatchEngineFactoryRegistryTest {
 
 	@Before
 	public void setUp() throws BackingStoreException {
-		preferences = EMFCompareRCPPlugin.getDefault().getEMFComparePreferences();
+		preferenceStore = new ScopedPreferenceStore(InstanceScope.INSTANCE, EMFCompareRCPPlugin.PLUGIN_ID);
 		registryWrapper = EMFCompareRCPPlugin.getDefault().getMatchEngineFactoryRegistry();
 	}
 
 	@After
 	public void tearDown() throws BackingStoreException {
-		preferences.clear();
+		for (IEclipsePreferences prefs : preferenceStore.getPreferenceNodes(false)) {
+			prefs.clear();
+		}
 	}
 
 	/**
@@ -258,12 +262,12 @@ public class RCPMatchEngineFactoryRegistryTest {
 		IComparisonScope scope = createComparisonScope();
 		assertSame(registryWrapper.getHighestRankingMatchEngineFactory(scope), factory3);
 
-		disableEngine(preferences, EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES,
+		disableEngine(EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES,
 				Collections.singleton(factory3.getClass().getName()));
 		assertSame(registryWrapper.getHighestRankingMatchEngineFactory(scope), factory2);
 		assertTrue(!registryWrapper.getMatchEngineFactories(scope).contains(factory3));
 
-		disableEngine(preferences, EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES,
+		disableEngine(EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES,
 				Lists.newArrayList(factory3.getClass().getName(), factory2.getClass().getName()));
 		assertSame(registryWrapper.getHighestRankingMatchEngineFactory(scope), factory);
 		assertTrue(!registryWrapper.getMatchEngineFactories(scope).contains(factory2));
@@ -303,18 +307,16 @@ public class RCPMatchEngineFactoryRegistryTest {
 	/**
 	 * Disables engine in preferences.
 	 * 
-	 * @param preference
-	 *            {@link IEclipsePreferences}
 	 * @param key
 	 * @param toDisable
 	 *            {@link Collection} of {@link IItemDescriptor} to disable.
 	 */
-	private void disableEngine(IEclipsePreferences preference, String key, Collection<String> toDisable) {
+	private void disableEngine(String key, Collection<String> toDisable) {
 		if (toDisable != null && !toDisable.isEmpty()) {
 			String newPreferenceValue = Joiner.on(ItemUtil.PREFERENCE_DELIMITER).join(toDisable);
-			preference.put(key, newPreferenceValue);
+			preferenceStore.setValue(key, newPreferenceValue);
 		} else {
-			preference.remove(key);
+			preferenceStore.setToDefault(key);
 		}
 	}
 
diff --git a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/EMFCompareRCPUIPlugin.java b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/EMFCompareRCPUIPlugin.java
index 49f3a8c96..bbfef3e6d 100644
--- a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/EMFCompareRCPUIPlugin.java
+++ b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/EMFCompareRCPUIPlugin.java
@@ -1,5 +1,5 @@
 /******************************************************************************
- * Copyright (c) 2012, 2015 Obeo.
+ * Copyright (c) 2012, 2016 Obeo 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
@@ -7,6 +7,7 @@
  * 
  * Contributors:
  *     Obeo - initial API and implementation
+ *     Mathias Schaefer - preferences refactoring
  *******************************************************************************/
 package org.eclipse.emf.compare.rcp.ui;
 
@@ -19,6 +20,9 @@ import org.eclipse.core.runtime.IExtensionRegistry;
 import org.eclipse.core.runtime.IStatus;
 import org.eclipse.core.runtime.Platform;
 import org.eclipse.core.runtime.Status;
+import org.eclipse.core.runtime.preferences.ConfigurationScope;
+import org.eclipse.core.runtime.preferences.DefaultScope;
+import org.eclipse.core.runtime.preferences.IScopeContext;
 import org.eclipse.core.runtime.preferences.InstanceScope;
 import org.eclipse.emf.compare.rcp.EMFCompareRCPPlugin;
 import org.eclipse.emf.compare.rcp.extension.AbstractRegistryEventListener;
@@ -42,11 +46,12 @@ import org.eclipse.emf.compare.rcp.ui.internal.structuremergeviewer.groups.impl.
 import org.eclipse.emf.compare.rcp.ui.structuremergeviewer.filters.IDifferenceFilter;
 import org.eclipse.emf.compare.rcp.ui.structuremergeviewer.groups.IDifferenceGroupProvider;
 import org.eclipse.emf.compare.rcp.ui.structuremergeviewer.groups.extender.IDifferenceGroupExtender;
+import org.eclipse.jface.preference.IPreferenceStore;
 import org.eclipse.jface.resource.ImageDescriptor;
 import org.eclipse.swt.graphics.Image;
 import org.eclipse.ui.plugin.AbstractUIPlugin;
+import org.eclipse.ui.preferences.ScopedPreferenceStore;
 import org.osgi.framework.BundleContext;
-import org.osgi.service.prefs.Preferences;
 
 /**
  * The activator class controls the plug-in life cycle.
@@ -118,17 +123,6 @@ public class EMFCompareRCPUIPlugin extends AbstractUIPlugin {
 	private ContentMergeViewerCustomizationRegistry contentMergeViewerCustomizationRegistry;
 
 	/**
-	 * Instance scope for preferences.
-	 * <p>
-	 * Do not use singleton to respect Helios compatibility
-	 * </p>
-	 * 
-	 * @see org.eclipse.core.runtime.preferences.InstanceScope#INSTANCE
-	 */
-	@SuppressWarnings("deprecation")
-	private InstanceScope instanceScope = new InstanceScope();
-
-	/**
 	 * The constructor.
 	 */
 	public EMFCompareRCPUIPlugin() {
@@ -147,8 +141,8 @@ public class EMFCompareRCPUIPlugin extends AbstractUIPlugin {
 		IExtensionRegistry extensionRegistry = Platform.getExtensionRegistry();
 
 		groupItemRegistry = new ItemRegistry<IDifferenceGroupProvider.Descriptor>();
-		DifferenceGroupManager groupManager = new DifferenceGroupManager(getEMFCompareUIPreferences(),
-				groupItemRegistry);
+		DifferenceGroupManager groupManager = new DifferenceGroupManager(groupItemRegistry,
+				getPreferenceStore());
 		groupProviderRegistry = new DifferenceGroupRegistryImpl(groupManager, groupItemRegistry);
 		groupProviderRegistryListener = new DifferenceGroupProviderExtensionRegistryListener(PLUGIN_ID,
 				GROUP_PROVIDER_PPID, getLog(), groupItemRegistry);
@@ -156,7 +150,7 @@ public class EMFCompareRCPUIPlugin extends AbstractUIPlugin {
 		extensionRegistry.addListener(groupProviderRegistryListener, PLUGIN_ID + "." + GROUP_PROVIDER_PPID); //$NON-NLS-1$
 		groupProviderRegistryListener.readRegistry(extensionRegistry);
 
-		filterManager = new DifferenceFilterManager(getEMFCompareUIPreferences());
+		filterManager = new DifferenceFilterManager(getPreferenceStore());
 		filterRegistry = new DifferenceFilterRegistryImpl(filterManager);
 		filterRegistryListener = new DifferenceFilterExtensionRegistryListener(PLUGIN_ID,
 				FILTER_PROVIDER_PPID, getLog(), filterManager);
@@ -384,9 +378,13 @@ public class EMFCompareRCPUIPlugin extends AbstractUIPlugin {
 	}
 
 	/**
-	 * @return the preferences related to EMF Compare RCP UI plugin.
+	 * Provide this plug-in's preference store, which searches values in {@link InstanceScope}, then
+	 * {@link ConfigurationScope}, and then {@link DefaultScope}.
 	 */
-	public Preferences getEMFCompareUIPreferences() {
-		return instanceScope.getNode(PLUGIN_ID);
+	@Override
+	public IPreferenceStore getPreferenceStore() {
+		ScopedPreferenceStore store = (ScopedPreferenceStore)super.getPreferenceStore();
+		store.setSearchContexts(new IScopeContext[] {InstanceScope.INSTANCE, ConfigurationScope.INSTANCE });
+		return store;
 	}
 }
diff --git a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/configuration/ui/AbstractConfigurationUI.java b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/configuration/ui/AbstractConfigurationUI.java
index 159e7058a..f08b0eb26 100644
--- a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/configuration/ui/AbstractConfigurationUI.java
+++ b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/configuration/ui/AbstractConfigurationUI.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2014 Obeo.
+ * Copyright (c) 2014, 2017 Obeo.
  * 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
@@ -10,6 +10,9 @@
  *******************************************************************************/
 package org.eclipse.emf.compare.rcp.ui.internal.configuration.ui;
 
+import static com.google.common.base.Preconditions.checkNotNull;
+
+import org.eclipse.jface.preference.IPreferenceStore;
 import org.eclipse.swt.widgets.Composite;
 import org.osgi.service.prefs.Preferences;
 
@@ -20,9 +23,8 @@ import org.osgi.service.prefs.Preferences;
  * @author <a href="mailto:arthur.daussy@obeo.fr">Arthur Daussy</a>
  */
 public abstract class AbstractConfigurationUI extends Composite {
-
-	/** {@link Preferences} holding the configuration. */
-	private final Preferences pref;
+	/** The preference store. */
+	private final IPreferenceStore store;
 
 	/**
 	 * Constructor.
@@ -31,22 +33,12 @@ public abstract class AbstractConfigurationUI extends Composite {
 	 *            Parent {@link Composite}.
 	 * @param style
 	 *            Style of this {@link Composite}
-	 * @param pref
-	 *            {@link Preferences} holding the configuration reprenseted by this composite.
+	 * @param store
+	 *            The {@link IPreferenceStore} to use for preferences, cannot be <code>null</code>
 	 */
-	public AbstractConfigurationUI(Composite parent, int style, Preferences pref) {
+	public AbstractConfigurationUI(Composite parent, int style, IPreferenceStore store) {
 		super(parent, style);
-		this.pref = pref;
-
-	}
-
-	/**
-	 * {@link AbstractConfigurationUI#pref}
-	 * 
-	 * @return
-	 */
-	protected Preferences getPreference() {
-		return pref;
+		this.store = checkNotNull(store);
 	}
 
 	/**
@@ -65,4 +57,13 @@ public abstract class AbstractConfigurationUI extends Composite {
 	 */
 	public abstract void resetDefault();
 
+	/**
+	 * Get the preference store used by this object.
+	 * 
+	 * @return The preference store used by this object.
+	 */
+	protected IPreferenceStore getPreferenceStore() {
+		return store;
+	}
+
 }
diff --git a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/configuration/ui/IConfigurationUIFactory.java b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/configuration/ui/IConfigurationUIFactory.java
index 71c61d1a7..3f0070681 100644
--- a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/configuration/ui/IConfigurationUIFactory.java
+++ b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/configuration/ui/IConfigurationUIFactory.java
@@ -10,8 +10,8 @@
  *******************************************************************************/
 package org.eclipse.emf.compare.rcp.ui.internal.configuration.ui;
 
+import org.eclipse.jface.preference.IPreferenceStore;
 import org.eclipse.swt.widgets.Composite;
-import org.osgi.service.prefs.Preferences;
 
 /**
  * Factory for {@link AbstractConfigurationUI}.
@@ -27,10 +27,10 @@ public interface IConfigurationUIFactory {
 	 *            Parent composite.
 	 * @param style
 	 *            Style of the new {@link AbstractConfigurationUI}
-	 * @param pref
-	 *            {@link Preferences} to store configuration.
+	 * @param store
+	 *            {@link IPreferenceStore} to store configuration.
 	 * @return Configuration UI
 	 */
-	AbstractConfigurationUI createUI(Composite parent, int style, Preferences pref);
+	AbstractConfigurationUI createUI(Composite parent, int style, IPreferenceStore store);
 
 }
diff --git a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/configuration/ui/match/DefaultMatchEngineConfiguatorUIFactory.java b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/configuration/ui/match/DefaultMatchEngineConfiguatorUIFactory.java
index dc3edf4dd..66898f343 100644
--- a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/configuration/ui/match/DefaultMatchEngineConfiguatorUIFactory.java
+++ b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/configuration/ui/match/DefaultMatchEngineConfiguatorUIFactory.java
@@ -13,8 +13,8 @@ package org.eclipse.emf.compare.rcp.ui.internal.configuration.ui.match;
 import org.eclipse.emf.compare.rcp.internal.match.DefaultRCPMatchEngineFactory;
 import org.eclipse.emf.compare.rcp.ui.internal.configuration.ui.AbstractConfigurationUI;
 import org.eclipse.emf.compare.rcp.ui.internal.configuration.ui.IConfigurationUIFactory;
+import org.eclipse.jface.preference.IPreferenceStore;
 import org.eclipse.swt.widgets.Composite;
-import org.osgi.service.prefs.Preferences;
 
 /**
  * IConfiguratorUIFactory for {@link DefaultRCPMatchEngineFactory}
@@ -23,12 +23,9 @@ import org.osgi.service.prefs.Preferences;
  */
 public class DefaultMatchEngineConfiguatorUIFactory implements IConfigurationUIFactory {
 
-	/**
-	 * {@inheritDoc}
-	 */
-	public AbstractConfigurationUI createUI(Composite parent, int style, Preferences pref) {
+	public AbstractConfigurationUI createUI(Composite parent, int style, IPreferenceStore store) {
 		DefaultMatchEngineConfiguratorUI composite = new DefaultMatchEngineConfiguratorUI(parent, style,
-				pref);
+				store);
 		composite.createContent();
 		return composite;
 	}
diff --git a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/configuration/ui/match/DefaultMatchEngineConfiguratorUI.java b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/configuration/ui/match/DefaultMatchEngineConfiguratorUI.java
index e5f4c480c..6c7683ea9 100644
--- a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/configuration/ui/match/DefaultMatchEngineConfiguratorUI.java
+++ b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/configuration/ui/match/DefaultMatchEngineConfiguratorUI.java
@@ -21,13 +21,13 @@ import org.eclipse.emf.compare.rcp.ui.internal.EMFCompareRCPUIMessages;
 import org.eclipse.emf.compare.rcp.ui.internal.configuration.ui.AbstractConfigurationUI;
 import org.eclipse.emf.compare.utils.UseIdentifiers;
 import org.eclipse.jface.databinding.swt.SWTObservables;
+import org.eclipse.jface.preference.IPreferenceStore;
 import org.eclipse.swt.SWT;
 import org.eclipse.swt.layout.GridData;
 import org.eclipse.swt.layout.GridLayout;
 import org.eclipse.swt.widgets.Button;
 import org.eclipse.swt.widgets.Composite;
 import org.eclipse.swt.widgets.Label;
-import org.osgi.service.prefs.Preferences;
 
 /**
  * {@link AbstractConfigurationUI} for {@link DefaultRCPMatchEngineFactory}.
@@ -49,8 +49,8 @@ public class DefaultMatchEngineConfiguratorUI extends AbstractConfigurationUI {
 
 	private DataHolder dataHolder;
 
-	public DefaultMatchEngineConfiguratorUI(Composite parent, int style, Preferences pref) {
-		super(parent, style, pref);
+	public DefaultMatchEngineConfiguratorUI(Composite parent, int style, IPreferenceStore store) {
+		super(parent, style, store);
 	}
 
 	@Override
@@ -80,7 +80,7 @@ public class DefaultMatchEngineConfiguratorUI extends AbstractConfigurationUI {
 		neverButton
 				.setText(EMFCompareRCPUIMessages.getString("DefaultMatchEngineConfiguratorUI.never.label")); //$NON-NLS-1$
 
-		UseIdentifiers defaultValue = DefaultRCPMatchEngineFactory.getUseIdentifierValue(getPreference());
+		UseIdentifiers defaultValue = DefaultRCPMatchEngineFactory.getUseIdentifierValue();
 		dataHolder = new DataHolder(defaultValue);
 
 		bindData();
@@ -109,9 +109,9 @@ public class DefaultMatchEngineConfiguratorUI extends AbstractConfigurationUI {
 	public void storeConfiguration() {
 		UseIdentifiers value = dataHolder.getValue();
 		if (value != DefaultRCPMatchEngineFactory.DEFAULT_USE_IDENTIFIER_ATRIBUTE) {
-			getPreference().put(DefaultRCPMatchEngineFactory.USE_IDENTIFIER_ATTR, value.toString());
+			getPreferenceStore().setValue(DefaultRCPMatchEngineFactory.USE_IDENTIFIER_ATTR, value.toString());
 		} else {
-			getPreference().remove(DefaultRCPMatchEngineFactory.USE_IDENTIFIER_ATTR);
+			getPreferenceStore().setToDefault(DefaultRCPMatchEngineFactory.USE_IDENTIFIER_ATTR);
 		}
 	}
 
@@ -135,7 +135,7 @@ public class DefaultMatchEngineConfiguratorUI extends AbstractConfigurationUI {
 		}
 		dataHolder.setValue(DefaultRCPMatchEngineFactory.DEFAULT_USE_IDENTIFIER_ATRIBUTE);
 		try {
-			getPreference().remove(DefaultRCPMatchEngineFactory.USE_IDENTIFIER_ATTR);
+			getPreferenceStore().setToDefault(DefaultRCPMatchEngineFactory.USE_IDENTIFIER_ATTR);
 		} catch (IllegalStateException e) {
 			Throwables.propagate(e);
 		}
diff --git a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/AdapterFactoriesPreferencePage.java b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/AdapterFactoriesPreferencePage.java
index fee8a93ce..fcb60c2df 100644
--- a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/AdapterFactoriesPreferencePage.java
+++ b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/AdapterFactoriesPreferencePage.java
@@ -23,6 +23,8 @@ import java.util.Collections;
 import java.util.Comparator;
 import java.util.List;
 
+import org.eclipse.core.runtime.preferences.ConfigurationScope;
+import org.eclipse.core.runtime.preferences.IScopeContext;
 import org.eclipse.core.runtime.preferences.InstanceScope;
 import org.eclipse.emf.compare.internal.adapterfactory.RankedAdapterFactoryDescriptor;
 import org.eclipse.emf.compare.rcp.EMFCompareRCPPlugin;
@@ -69,10 +71,9 @@ public class AdapterFactoriesPreferencePage extends PreferencePage implements IW
 	private CheckboxTableViewer adapterFactoryDescriptorViewer;
 
 	public void init(IWorkbench workbench) {
-		// Do not use InstanceScope.Instance to be compatible with Helios.
-		@SuppressWarnings("deprecation")
-		ScopedPreferenceStore store = new ScopedPreferenceStore(new InstanceScope(),
+		ScopedPreferenceStore store = new ScopedPreferenceStore(InstanceScope.INSTANCE,
 				EMFCompareRCPPlugin.PLUGIN_ID);
+		store.setSearchContexts(new IScopeContext[] {InstanceScope.INSTANCE, ConfigurationScope.INSTANCE });
 		setPreferenceStore(store);
 	}
 
@@ -109,8 +110,7 @@ public class AdapterFactoriesPreferencePage extends PreferencePage implements IW
 			adapterFactoryDescriptorViewer.setSelection(new StructuredSelection(descriptors.get(0)), true);
 		}
 
-		List<String> disabledDescriptors = EMFComparePreferences.getDisabledAdapterFacotryDescriptorIds(
-				EMFCompareRCPPlugin.getDefault().getEMFComparePreferences());
+		List<String> disabledDescriptors = EMFComparePreferences.getDisabledAdapterFactoryDescriptorIds();
 
 		initViewer(disabledDescriptors);
 	}
diff --git a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/EditorPreferencePage.java b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/EditorPreferencePage.java
index fa95fc859..61341f0d4 100644
--- a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/EditorPreferencePage.java
+++ b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/EditorPreferencePage.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2014 Obeo.
+ * Copyright (c) 2014, 2016 Obeo 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
@@ -7,9 +7,11 @@
  * 
  * Contributors:
  *     Obeo - initial API and implementation
+ *     Mathias Schaefer - preferences refactoring
  *******************************************************************************/
 package org.eclipse.emf.compare.rcp.ui.internal.preferences;
 
+import org.eclipse.emf.compare.rcp.ui.EMFCompareRCPUIPlugin;
 import org.eclipse.emf.compare.rcp.ui.internal.EMFCompareRCPUIMessages;
 import org.eclipse.emf.compare.rcp.ui.internal.mergeviewer.CompareColorImpl;
 import org.eclipse.jface.layout.GridLayoutFactory;
@@ -43,7 +45,7 @@ public class EditorPreferencePage extends PreferencePage implements IWorkbenchPr
 	}
 
 	public void init(IWorkbench workbench) {
-
+		setPreferenceStore(EMFCompareRCPUIPlugin.getDefault().getPreferenceStore());
 	}
 
 	@Override
diff --git a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/EnginesPreferencePage.java b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/EnginesPreferencePage.java
index dce91d0b4..e7e220e74 100644
--- a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/EnginesPreferencePage.java
+++ b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/EnginesPreferencePage.java
@@ -22,7 +22,8 @@ import java.util.Map.Entry;
 import java.util.Set;
 
 import org.eclipse.core.runtime.IStatus;
-import org.eclipse.core.runtime.preferences.IEclipsePreferences;
+import org.eclipse.core.runtime.preferences.ConfigurationScope;
+import org.eclipse.core.runtime.preferences.IScopeContext;
 import org.eclipse.core.runtime.preferences.InstanceScope;
 import org.eclipse.emf.compare.conflict.IConflictDetector;
 import org.eclipse.emf.compare.diff.IDiffEngine;
@@ -43,8 +44,12 @@ import org.eclipse.emf.compare.rcp.ui.internal.configuration.ui.IConfigurationUI
 import org.eclipse.emf.compare.rcp.ui.internal.preferences.impl.InteractiveUIContent;
 import org.eclipse.emf.compare.rcp.ui.internal.preferences.impl.InteractiveUIContent.InteractiveUIBuilder;
 import org.eclipse.emf.compare.req.IReqEngine;
+import org.eclipse.jface.dialogs.MessageDialog;
 import org.eclipse.jface.preference.PreferencePage;
 import org.eclipse.jface.resource.ImageDescriptor;
+import org.eclipse.jface.viewers.CheckStateChangedEvent;
+import org.eclipse.jface.viewers.CheckboxTableViewer;
+import org.eclipse.jface.viewers.ICheckStateListener;
 import org.eclipse.swt.SWT;
 import org.eclipse.swt.layout.FillLayout;
 import org.eclipse.swt.layout.GridData;
@@ -57,8 +62,6 @@ import org.eclipse.swt.widgets.TabItem;
 import org.eclipse.ui.IWorkbench;
 import org.eclipse.ui.IWorkbenchPreferencePage;
 import org.eclipse.ui.preferences.ScopedPreferenceStore;
-import org.osgi.service.prefs.BackingStoreException;
-import org.osgi.service.prefs.Preferences;
 
 /**
  * Preference page for engines preferences
@@ -98,10 +101,9 @@ public class EnginesPreferencePage extends PreferencePage implements IWorkbenchP
 	}
 
 	public void init(IWorkbench workbench) {
-		// Do not use InstanceScope.Instance to be compatible with Helios.
-		@SuppressWarnings("deprecation")
-		ScopedPreferenceStore store = new ScopedPreferenceStore(new InstanceScope(),
+		ScopedPreferenceStore store = new ScopedPreferenceStore(InstanceScope.INSTANCE,
 				EMFCompareRCPPlugin.PLUGIN_ID);
+		store.setSearchContexts(new IScopeContext[] {InstanceScope.INSTANCE, ConfigurationScope.INSTANCE });
 		setPreferenceStore(store);
 	}
 
@@ -133,8 +135,6 @@ public class EnginesPreferencePage extends PreferencePage implements IWorkbenchP
 	 *            Registry holding engines.
 	 * @param enginePreferenceKey
 	 *            Preference key use to store preferences
-	 * @param pref
-	 *            {@link IEclipsePreferences} holding preferences.
 	 * @param tabComposite
 	 *            Holding composite.
 	 * @param dataHolder
@@ -144,10 +144,8 @@ public class EnginesPreferencePage extends PreferencePage implements IWorkbenchP
 	 * @return {@link InteractiveUIContent} for a specific type of engine.
 	 */
 	private <T> InteractiveUIContent createEngineUIBuilder(IItemRegistry<T> registry,
-			String enginePreferenceKey, IEclipsePreferences pref, Composite tabComposite,
-			DataHolder<T> dataHolder) {
-		IItemDescriptor<T> defaultEngine = ItemUtil.getDefaultItemDescriptor(registry, enginePreferenceKey,
-				pref);
+			String enginePreferenceKey, Composite tabComposite, DataHolder<T> dataHolder) {
+		IItemDescriptor<T> defaultEngine = ItemUtil.getDefaultItemDescriptor(registry, enginePreferenceKey);
 		InteractiveUIBuilder<T> uiBuilder = new InteractiveUIBuilder<T>(tabComposite, registry);
 		uiBuilder.setSimple(true).setDefaultCheck(Collections.singleton(defaultEngine))
 				.setDefaultSelection(defaultEngine).setHoldingData(dataHolder);
@@ -162,15 +160,14 @@ public class EnginesPreferencePage extends PreferencePage implements IWorkbenchP
 	private void createConflictDetectorTab(TabFolder tabFolder) {
 		IItemRegistry<IConflictDetector> conflictDetectorDescriptorRegistry = EMFCompareRCPPlugin.getDefault()
 				.getConflictDetectorDescriptorRegistry();
+
 		// Create tab structure
 		Composite tabComposite = createTabSkeleton(tabFolder,
 				EMFCompareRCPUIMessages.getString("EnginesPreferencePage.conflictDetector.tab.label"), //$NON-NLS-1$
 				EMFCompareRCPUIMessages.getString("EnginesPreferencePage.conflictDetectorIntro.text"));//$NON-NLS-1$
 
 		InteractiveUIContent interactiveContent = createEngineUIBuilder(conflictDetectorDescriptorRegistry,
-				EMFComparePreferences.CONFLICTS_DETECTOR,
-				EMFCompareRCPPlugin.getDefault().getEMFComparePreferences(), tabComposite,
-				conflictsDetectorData);
+				EMFComparePreferences.CONFLICTS_DETECTOR, tabComposite, conflictsDetectorData);
 
 		// Save for reset default
 		interactiveUis.put(EMFComparePreferences.CONFLICTS_DETECTOR, interactiveContent);
@@ -190,8 +187,7 @@ public class EnginesPreferencePage extends PreferencePage implements IWorkbenchP
 				EMFCompareRCPUIMessages.getString("EnginesPreferencePage.reqEngineIntro.text")); //$NON-NLS-1$
 
 		InteractiveUIContent interactiveContent = createEngineUIBuilder(reqEngineDescriptorRegistry,
-				EMFComparePreferences.REQ_ENGINES,
-				EMFCompareRCPPlugin.getDefault().getEMFComparePreferences(), tabComposite, reqEngineData);
+				EMFComparePreferences.REQ_ENGINES, tabComposite, reqEngineData);
 
 		// Save for reset default
 		interactiveUis.put(EMFComparePreferences.REQ_ENGINES, interactiveContent);
@@ -211,8 +207,7 @@ public class EnginesPreferencePage extends PreferencePage implements IWorkbenchP
 				EMFCompareRCPUIMessages.getString("EnginesPreferencePage.equiEngineIntro.text")); //$NON-NLS-1$
 
 		InteractiveUIContent interactiveContent = createEngineUIBuilder(equiEngineDescriptorRegistry,
-				EMFComparePreferences.EQUI_ENGINES,
-				EMFCompareRCPPlugin.getDefault().getEMFComparePreferences(), tabComposite, equiEngineData);
+				EMFComparePreferences.EQUI_ENGINES, tabComposite, equiEngineData);
 
 		// Save for reset default
 		interactiveUis.put(EMFComparePreferences.EQUI_ENGINES, interactiveContent);
@@ -232,8 +227,7 @@ public class EnginesPreferencePage extends PreferencePage implements IWorkbenchP
 				EMFCompareRCPUIMessages.getString("EnginesPreferencePage.diffEngineIntro.text")); //$NON-NLS-1$
 
 		InteractiveUIContent interactiveContent = createEngineUIBuilder(diffEngineDescriptorRegistry,
-				EMFComparePreferences.DIFF_ENGINES,
-				EMFCompareRCPPlugin.getDefault().getEMFComparePreferences(), tabComposite, diffEngineData);
+				EMFComparePreferences.DIFF_ENGINES, tabComposite, diffEngineData);
 
 		// Save for reset default
 		interactiveUis.put(EMFComparePreferences.DIFF_ENGINES, interactiveContent);
@@ -258,17 +252,36 @@ public class EnginesPreferencePage extends PreferencePage implements IWorkbenchP
 				.getMatchEngineConfiguratorRegistry();
 		String matchEnginePreferenceKey = EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES;
 
-		Set<IItemDescriptor<Factory>> activeItems = ItemUtil
-				.getActiveItems(matchEngineFactoryDescriptorRegistry, matchEnginePreferenceKey);
+		Set<IItemDescriptor<Factory>> activeItems = ItemUtil.getActiveItems(
+				matchEngineFactoryDescriptorRegistry, EMFCompareRCPPlugin.PLUGIN_ID,
+				matchEnginePreferenceKey);
 
 		InteractiveUIBuilder<IMatchEngine.Factory> builder = new InteractiveUIBuilder<IMatchEngine.Factory>(
 				tabComposite, matchEngineFactoryDescriptorRegistry);
 		builder.setConfiguratorUIRegistry(configuratorUIRegistry).setDefaultCheck(activeItems)
-				.setConfigurationNodeKey(EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES)
+				.setConfigurationNodeKey(matchEnginePreferenceKey)
 				.setDefaultSelection(defaultMatchEngineDescriptor).setHoldingData(matchEnginesData);
-		// Save for reset default
-		interactiveUis.put(matchEnginePreferenceKey, builder.build());
+		// Forbid unchecking all match engines
+		InteractiveUIContent uiContent = builder.build();
+		uiContent.getViewer().addCheckStateListener(new ICheckStateListener() {
+			public void checkStateChanged(CheckStateChangedEvent event) {
+				Object element = event.getElement();
+				if (!event.getChecked()) {
+					// Prevent from nothing checked
+					if (((CheckboxTableViewer)event.getSource()).getCheckedElements().length == 0) {
+						((CheckboxTableViewer)event.getSource()).setCheckedElements(new Object[] {element });
+						MessageDialog.openWarning(getShell(),
+								EMFCompareRCPUIMessages
+										.getString("InteractiveUIContent.incorrectSelection.title"), //$NON-NLS-1$
+								EMFCompareRCPUIMessages
+										.getString("InteractiveUIContent.incorrectSelection.message")); //$NON-NLS-1$
+					}
+				}
 
+			}
+		});
+		// Save for reset default
+		interactiveUis.put(matchEnginePreferenceKey, uiContent);
 	}
 
 	/**
@@ -296,34 +309,8 @@ public class EnginesPreferencePage extends PreferencePage implements IWorkbenchP
 
 	@Override
 	public boolean performOk() {
-
 		setEnginesPreferences();
-
 		storeConfigurations();
-
-		if (TracingConstant.CONFIGURATION_TRACING_ACTIVATED) {
-			StringBuilder traceMessage = new StringBuilder("Engines preference serialization:\n"); //$NON-NLS-1$
-			String prefDelimiter = " :\n"; //$NON-NLS-1$
-			String newLine = "\n"; //$NON-NLS-1$
-			traceMessage.append(EMFComparePreferences.DIFF_ENGINES).append(prefDelimiter)
-					.append(getPreferenceStore().getString(EMFComparePreferences.DIFF_ENGINES))
-					.append(newLine);
-			traceMessage.append(EMFComparePreferences.EQUI_ENGINES).append(prefDelimiter)
-					.append(getPreferenceStore().getString(EMFComparePreferences.EQUI_ENGINES))
-					.append(newLine);
-			traceMessage.append(EMFComparePreferences.REQ_ENGINES).append(prefDelimiter)
-					.append(getPreferenceStore().getString(EMFComparePreferences.REQ_ENGINES))
-					.append(newLine);
-			traceMessage.append(EMFComparePreferences.CONFLICTS_DETECTOR).append(prefDelimiter)
-					.append(getPreferenceStore().getString(EMFComparePreferences.CONFLICTS_DETECTOR))
-					.append(newLine);
-			traceMessage.append(EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES).append(prefDelimiter)
-					.append(getPreferenceStore()
-							.getString(EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES))
-					.append(newLine);
-
-			EMFCompareRCPPlugin.getDefault().log(IStatus.INFO, traceMessage.toString());
-		}
 		return super.performOk();
 	}
 
@@ -364,37 +351,29 @@ public class EnginesPreferencePage extends PreferencePage implements IWorkbenchP
 				configurator.storeConfiguration();
 			}
 		}
-
 		if (TracingConstant.CONFIGURATION_TRACING_ACTIVATED) {
-			StringBuilder traceMessage = new StringBuilder("Configuration serialization:\n"); //$NON-NLS-1$
+			StringBuilder traceMessage = new StringBuilder("Engines preference serialization:\n"); //$NON-NLS-1$
 			String prefDelimiter = " :\n"; //$NON-NLS-1$
 			String newLine = "\n"; //$NON-NLS-1$
-			String nodeLabel = "Node "; //$NON-NLS-1$
-			String doubleDotLabel = " : "; //$NON-NLS-1$
-			String emptyLabel = "EMPTY"; //$NON-NLS-1$
-			for (Entry<String, InteractiveUIContent> interactiveContentEntry : interactiveUis.entrySet()) {
-				String itemTypeId = interactiveContentEntry.getKey();
-				for (Entry<String, AbstractConfigurationUI> configuratorEntry : interactiveContentEntry
-						.getValue().getConfigurators().entrySet()) {
-					String itemToConfigureId = configuratorEntry.getKey();
-					Preferences storeNode = ItemUtil.getConfigurationPreferenceNode(itemTypeId,
-							itemToConfigureId);
-					traceMessage.append(nodeLabel).append(storeNode.absolutePath()).append(prefDelimiter);
-					try {
-						for (String propertyKey : storeNode.keys()) {
-							traceMessage.append(propertyKey).append(doubleDotLabel)
-									.append(storeNode.get(propertyKey, emptyLabel)).append(newLine);
-						}
-					} catch (BackingStoreException e) {
-						e.printStackTrace();
-						traceMessage.append("Error in tracing ").append(storeNode.absolutePath()); //$NON-NLS-1$
-					}
-				}
-			}
+			traceMessage.append(EMFComparePreferences.DIFF_ENGINES).append(prefDelimiter)
+					.append(getPreferenceStore().getString(EMFComparePreferences.DIFF_ENGINES))
+					.append(newLine);
+			traceMessage.append(EMFComparePreferences.EQUI_ENGINES).append(prefDelimiter)
+					.append(getPreferenceStore().getString(EMFComparePreferences.EQUI_ENGINES))
+					.append(newLine);
+			traceMessage.append(EMFComparePreferences.REQ_ENGINES).append(prefDelimiter)
+					.append(getPreferenceStore().getString(EMFComparePreferences.REQ_ENGINES))
+					.append(newLine);
+			traceMessage.append(EMFComparePreferences.CONFLICTS_DETECTOR).append(prefDelimiter)
+					.append(getPreferenceStore().getString(EMFComparePreferences.CONFLICTS_DETECTOR))
+					.append(newLine);
+			traceMessage.append(EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES).append(prefDelimiter)
+					.append(getPreferenceStore()
+							.getString(EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES))
+					.append(newLine);
 
 			EMFCompareRCPPlugin.getDefault().log(IStatus.INFO, traceMessage.toString());
 		}
-
 	}
 
 	@Override
diff --git a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/FiltersPreferencePage.java b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/FiltersPreferencePage.java
index c38167856..b94a8d872 100644
--- a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/FiltersPreferencePage.java
+++ b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/FiltersPreferencePage.java
@@ -30,7 +30,6 @@ import org.eclipse.core.databinding.DataBindingContext;
 import org.eclipse.core.databinding.beans.PojoProperties;
 import org.eclipse.core.databinding.observable.set.IObservableSet;
 import org.eclipse.core.runtime.IStatus;
-import org.eclipse.core.runtime.preferences.InstanceScope;
 import org.eclipse.emf.compare.rcp.internal.extension.IItemDescriptor;
 import org.eclipse.emf.compare.rcp.internal.tracer.TracingConstant;
 import org.eclipse.emf.compare.rcp.ui.EMFCompareRCPUIPlugin;
@@ -66,7 +65,6 @@ import org.eclipse.swt.widgets.TabFolder;
 import org.eclipse.swt.widgets.TabItem;
 import org.eclipse.ui.IWorkbench;
 import org.eclipse.ui.IWorkbenchPreferencePage;
-import org.eclipse.ui.preferences.ScopedPreferenceStore;
 
 /**
  * Preference page for {@link IDifferenceFilter}.
@@ -109,12 +107,7 @@ public class FiltersPreferencePage extends PreferencePage implements IWorkbenchP
 	private String synchronizationBehaviorValue;
 
 	public void init(IWorkbench workbench) {
-		// Do not use InstanceScope.Instance to be compatible with Helios.
-		@SuppressWarnings("deprecation")
-		ScopedPreferenceStore store = new ScopedPreferenceStore(new InstanceScope(),
-				EMFCompareRCPUIPlugin.PLUGIN_ID);
-		setPreferenceStore(store);
-
+		setPreferenceStore(EMFCompareRCPUIPlugin.getDefault().getPreferenceStore());
 	}
 
 	@Override
diff --git a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/GroupsPreferencePage.java b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/GroupsPreferencePage.java
index e4fa48457..408fae996 100644
--- a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/GroupsPreferencePage.java
+++ b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/GroupsPreferencePage.java
@@ -21,7 +21,6 @@ import com.google.common.collect.ImmutableList;
 import java.util.List;
 
 import org.eclipse.core.runtime.IStatus;
-import org.eclipse.core.runtime.preferences.InstanceScope;
 import org.eclipse.emf.compare.rcp.internal.extension.IItemDescriptor;
 import org.eclipse.emf.compare.rcp.internal.tracer.TracingConstant;
 import org.eclipse.emf.compare.rcp.ui.EMFCompareRCPUIPlugin;
@@ -49,7 +48,6 @@ import org.eclipse.swt.widgets.TabFolder;
 import org.eclipse.swt.widgets.TabItem;
 import org.eclipse.ui.IWorkbench;
 import org.eclipse.ui.IWorkbenchPreferencePage;
-import org.eclipse.ui.preferences.ScopedPreferenceStore;
 
 /**
  * Preference page for group providers.
@@ -87,8 +85,8 @@ public class GroupsPreferencePage extends PreferencePage implements IWorkbenchPr
 
 	/** {@link DifferenceGroupManager}. */
 	private DifferenceGroupManager groupManager = new DifferenceGroupManager(
-			EMFCompareRCPUIPlugin.getDefault().getEMFCompareUIPreferences(),
-			EMFCompareRCPUIPlugin.getDefault().getItemDifferenceGroupProviderRegistry());
+			EMFCompareRCPUIPlugin.getDefault().getItemDifferenceGroupProviderRegistry(),
+			EMFCompareRCPUIPlugin.getDefault().getPreferenceStore());
 
 	/**
 	 * Gets the preference key for synchronization behavior.
@@ -105,16 +103,8 @@ public class GroupsPreferencePage extends PreferencePage implements IWorkbenchPr
 		}
 	}
 
-	/**
-	 * {@inheritDoc}
-	 */
 	public void init(IWorkbench workbench) {
-		// Do not use InstanceScope.Instance to be compatible with Helios.
-		@SuppressWarnings("deprecation")
-		ScopedPreferenceStore store = new ScopedPreferenceStore(new InstanceScope(),
-				EMFCompareRCPUIPlugin.PLUGIN_ID);
-		setPreferenceStore(store);
-
+		setPreferenceStore(EMFCompareRCPUIPlugin.getDefault().getPreferenceStore());
 	}
 
 	@Override
diff --git a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/LoggingPreferencePage.java b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/LoggingPreferencePage.java
index 33237038b..b9c6d8b50 100644
--- a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/LoggingPreferencePage.java
+++ b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/LoggingPreferencePage.java
@@ -8,6 +8,7 @@
  * Contributors:
  *     Obeo - initial API and implementation
  *     Simon Delisle - bug 495753
+ *     Mathias Schaefer - preferences refactoring
  *******************************************************************************/
 package org.eclipse.emf.compare.rcp.ui.internal.preferences;
 
@@ -21,9 +22,14 @@ import static org.eclipse.emf.compare.rcp.internal.preferences.EMFComparePrefere
 import static org.eclipse.emf.compare.rcp.internal.preferences.EMFComparePreferences.LOG_LEVEL_KEY;
 
 import java.io.File;
+import java.io.IOException;
 import java.util.Arrays;
 
-import org.eclipse.core.runtime.preferences.IEclipsePreferences;
+import org.eclipse.core.runtime.Platform;
+import org.eclipse.core.runtime.preferences.ConfigurationScope;
+import org.eclipse.core.runtime.preferences.IPreferencesService;
+import org.eclipse.core.runtime.preferences.IScopeContext;
+import org.eclipse.core.runtime.preferences.InstanceScope;
 import org.eclipse.emf.compare.rcp.EMFCompareRCPPlugin;
 import org.eclipse.emf.compare.rcp.ui.internal.EMFCompareRCPUIMessages;
 import org.eclipse.jface.layout.GridLayoutFactory;
@@ -44,6 +50,7 @@ import org.eclipse.swt.widgets.Label;
 import org.eclipse.swt.widgets.Text;
 import org.eclipse.ui.IWorkbench;
 import org.eclipse.ui.IWorkbenchPreferencePage;
+import org.eclipse.ui.preferences.ScopedPreferenceStore;
 import org.osgi.service.prefs.BackingStoreException;
 
 /**
@@ -96,7 +103,10 @@ public class LoggingPreferencePage extends PreferencePage implements IWorkbenchP
 	 * {@inheritDoc}
 	 */
 	public void init(IWorkbench workbench) {
-		// Nothing to do
+		ScopedPreferenceStore store = new ScopedPreferenceStore(InstanceScope.INSTANCE,
+				EMFCompareRCPPlugin.PLUGIN_ID);
+		store.setSearchContexts(new IScopeContext[] {InstanceScope.INSTANCE, ConfigurationScope.INSTANCE });
+		setPreferenceStore(store);
 	}
 
 	@Override
@@ -153,30 +163,31 @@ public class LoggingPreferencePage extends PreferencePage implements IWorkbenchP
 		return gd;
 	}
 
-	protected void savePreferences() throws BackingStoreException {
-		IEclipsePreferences prefs = EMFCompareRCPPlugin.getDefault().getEMFComparePreferences();
-		prefs.put(LOG_FILENAME_KEY, fileField.getText());
+	protected void savePreferences() throws BackingStoreException, IOException {
+		getPreferenceStore().setValue(LOG_FILENAME_KEY, fileField.getText());
 		String item = levelCombo.getItem(levelCombo.getSelectionIndex());
-		prefs.put(LOG_LEVEL_KEY, item);
-		prefs.put(LOG_BACKUP_COUNT_KEY, maxBackupField.getText());
-		prefs.put(LOG_FILE_MAX_SIZE_KEY, maxSizeField.getText());
-		prefs.flush();
+		getPreferenceStore().setValue(LOG_LEVEL_KEY, item);
+		getPreferenceStore().setValue(LOG_BACKUP_COUNT_KEY, maxBackupField.getText());
+		getPreferenceStore().setValue(LOG_FILE_MAX_SIZE_KEY, maxSizeField.getText());
 	}
 
 	protected void resetPreferences() {
-		IEclipsePreferences prefs = EMFCompareRCPPlugin.getDefault().getEMFComparePreferences();
-		prefs.put(LOG_FILENAME_KEY, ""); //$NON-NLS-1$
-		prefs.put(LOG_LEVEL_KEY, "OFF"); //$NON-NLS-1$
-		prefs.putInt(LOG_BACKUP_COUNT_KEY, LOG_BACKUP_DEFAULT);
-		prefs.putInt(LOG_FILE_MAX_SIZE_KEY, LOG_FILE_SIZE_DEFAULT);
+		getPreferenceStore().setToDefault(LOG_FILENAME_KEY);
+		getPreferenceStore().setToDefault(LOG_LEVEL_KEY);
+		getPreferenceStore().setToDefault(LOG_BACKUP_COUNT_KEY);
+		getPreferenceStore().setToDefault(LOG_FILE_MAX_SIZE_KEY);
 	}
 
 	protected void refreshWidgets() {
-		IEclipsePreferences prefs = EMFCompareRCPPlugin.getDefault().getEMFComparePreferences();
-		String fileName = prefs.get(LOG_FILENAME_KEY, LOG_FILE_DEFAULT);
-		String level = prefs.get(LOG_LEVEL_KEY, LOG_LEVEL_DEFAULT);
-		int maxBackupCount = prefs.getInt(LOG_BACKUP_COUNT_KEY, LOG_BACKUP_DEFAULT);
-		int maxSizeInMB = prefs.getInt(LOG_FILE_MAX_SIZE_KEY, LOG_FILE_SIZE_DEFAULT);
+		IPreferencesService prefsService = Platform.getPreferencesService();
+		String fileName = prefsService.getString(EMFCompareRCPPlugin.PLUGIN_ID, LOG_FILENAME_KEY,
+				LOG_FILE_DEFAULT, null);
+		String level = prefsService.getString(EMFCompareRCPPlugin.PLUGIN_ID, LOG_LEVEL_KEY, LOG_LEVEL_DEFAULT,
+				null);
+		int maxBackupCount = prefsService.getInt(EMFCompareRCPPlugin.PLUGIN_ID, LOG_BACKUP_COUNT_KEY,
+				LOG_BACKUP_DEFAULT, null);
+		int maxSizeInMB = prefsService.getInt(EMFCompareRCPPlugin.PLUGIN_ID, LOG_FILE_MAX_SIZE_KEY,
+				LOG_FILE_SIZE_DEFAULT, null);
 		levelCombo.select(Arrays.asList(LOG_LEVELS).indexOf(level));
 		levelCombo.pack();
 		fileField.setText(fileName);
@@ -190,7 +201,7 @@ public class LoggingPreferencePage extends PreferencePage implements IWorkbenchP
 			savePreferences();
 			refreshWidgets();
 			return super.performOk();
-		} catch (BackingStoreException e) {
+		} catch (IOException | BackingStoreException e) {
 			return false;
 		}
 	}
diff --git a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/PostProcessorPreferencePage.java b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/PostProcessorPreferencePage.java
index 19ebe1dc5..2a74ea95f 100644
--- a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/PostProcessorPreferencePage.java
+++ b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/PostProcessorPreferencePage.java
@@ -19,6 +19,8 @@ import com.google.common.collect.Sets.SetView;
 import java.util.Set;
 
 import org.eclipse.core.runtime.IStatus;
+import org.eclipse.core.runtime.preferences.ConfigurationScope;
+import org.eclipse.core.runtime.preferences.IScopeContext;
 import org.eclipse.core.runtime.preferences.InstanceScope;
 import org.eclipse.emf.compare.postprocessor.IPostProcessor;
 import org.eclipse.emf.compare.postprocessor.IPostProcessor.Descriptor;
@@ -88,10 +90,9 @@ public class PostProcessorPreferencePage extends PreferencePage implements IWork
 	 * {@inheritDoc}
 	 */
 	public void init(IWorkbench workbench) {
-		// Do not use InstanceScope.Instance to be compatible with Helios.
-		@SuppressWarnings("deprecation")
-		ScopedPreferenceStore store = new ScopedPreferenceStore(new InstanceScope(),
+		ScopedPreferenceStore store = new ScopedPreferenceStore(InstanceScope.INSTANCE,
 				EMFCompareRCPPlugin.PLUGIN_ID);
+		store.setSearchContexts(new IScopeContext[] {InstanceScope.INSTANCE, ConfigurationScope.INSTANCE });
 		setPreferenceStore(store);
 	}
 
@@ -107,7 +108,8 @@ public class PostProcessorPreferencePage extends PreferencePage implements IWork
 		IItemRegistry<IPostProcessor.Descriptor> postProcessorRegistryDescriptor = EMFCompareRCPPlugin
 				.getDefault().getPostProcessorDescriptorRegistry();
 		Set<IItemDescriptor<Descriptor>> activesPostProcessor = ItemUtil.getActiveItems(
-				postProcessorRegistryDescriptor, EMFComparePreferences.DISABLED_POST_PROCESSOR);
+				postProcessorRegistryDescriptor, EMFCompareRCPPlugin.PLUGIN_ID,
+				EMFComparePreferences.DISABLED_POST_PROCESSOR);
 		InteractiveUIBuilder<Descriptor> postProcessorUIBuilder = new InteractiveUIBuilder<IPostProcessor.Descriptor>(
 				container, postProcessorRegistryDescriptor);
 		Set<IItemDescriptor<Descriptor>> descriptors = Sets
diff --git a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/impl/InteractiveUIContent.java b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/impl/InteractiveUIContent.java
index dfd4e44f8..d9eb047b9 100644
--- a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/impl/InteractiveUIContent.java
+++ b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/preferences/impl/InteractiveUIContent.java
@@ -23,6 +23,10 @@ import java.util.Set;
 import org.eclipse.core.databinding.DataBindingContext;
 import org.eclipse.core.databinding.beans.PojoProperties;
 import org.eclipse.core.databinding.observable.set.IObservableSet;
+import org.eclipse.core.runtime.preferences.ConfigurationScope;
+import org.eclipse.core.runtime.preferences.IScopeContext;
+import org.eclipse.core.runtime.preferences.InstanceScope;
+import org.eclipse.emf.compare.rcp.EMFCompareRCPPlugin;
 import org.eclipse.emf.compare.rcp.internal.extension.IItemDescriptor;
 import org.eclipse.emf.compare.rcp.internal.extension.IItemRegistry;
 import org.eclipse.emf.compare.rcp.internal.extension.impl.ItemUtil;
@@ -34,6 +38,7 @@ import org.eclipse.jface.databinding.viewers.IViewerObservableSet;
 import org.eclipse.jface.databinding.viewers.ViewersObservables;
 import org.eclipse.jface.dialogs.MessageDialog;
 import org.eclipse.jface.layout.GridLayoutFactory;
+import org.eclipse.jface.preference.IPreferenceStore;
 import org.eclipse.jface.viewers.ArrayContentProvider;
 import org.eclipse.jface.viewers.CheckStateChangedEvent;
 import org.eclipse.jface.viewers.CheckboxTableViewer;
@@ -53,6 +58,7 @@ import org.eclipse.swt.widgets.Display;
 import org.eclipse.swt.widgets.Group;
 import org.eclipse.swt.widgets.Label;
 import org.eclipse.swt.widgets.Shell;
+import org.eclipse.ui.preferences.ScopedPreferenceStore;
 import org.osgi.service.prefs.Preferences;
 
 /**
@@ -157,12 +163,13 @@ public final class InteractiveUIContent {
 	 *            Id of the item to configure
 	 * @param configuratorfactory
 	 *            Factory for the configuration
-	 * @param pref
+	 * @param store
 	 *            Preference store that will hold this {@link IConfigurationUIFactory} value.
 	 */
-	public void addConfigurator(String id, IConfigurationUIFactory configuratorfactory, Preferences pref) {
+	public void addConfigurator(String id, IConfigurationUIFactory configuratorfactory,
+			IPreferenceStore store) {
 		AbstractConfigurationUI configurator = configuratorfactory.createUI(configurationComposite, SWT.NONE,
-				pref);
+				store);
 		configurators.put(id, configurator);
 	}
 
@@ -241,7 +248,7 @@ public final class InteractiveUIContent {
 	 * 
 	 * @return The viewer.
 	 */
-	private CheckboxTableViewer getViewer() {
+	public CheckboxTableViewer getViewer() {
 		return viewer;
 	}
 
@@ -619,8 +626,13 @@ public final class InteractiveUIContent {
 				String itemId = item.getID();
 				IConfigurationUIFactory configuratorFactory = configurationUIRegistry.get(itemId);
 				if (configuratorFactory != null) {
-					Preferences pref = ItemUtil.getConfigurationPreferenceNode(configurationNodeKey, itemId);
-					interactiveUI.addConfigurator(itemId, configuratorFactory, pref);
+					// Preferences pref = ItemUtil.getConfigurationPreferenceNode(configurationNodeKey,
+					// itemId);
+					ScopedPreferenceStore store = new ScopedPreferenceStore(InstanceScope.INSTANCE,
+							EMFCompareRCPPlugin.PLUGIN_ID);
+					store.setSearchContexts(
+							new IScopeContext[] {InstanceScope.INSTANCE, ConfigurationScope.INSTANCE });
+					interactiveUI.addConfigurator(itemId, configuratorFactory, store);
 				}
 			}
 		}
diff --git a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/structuremergeviewer/actions/FilterAction.java b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/structuremergeviewer/actions/FilterAction.java
index 1fba012c5..c1a4afe5e 100644
--- a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/structuremergeviewer/actions/FilterAction.java
+++ b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/structuremergeviewer/actions/FilterAction.java
@@ -14,7 +14,6 @@ import com.google.common.collect.Sets;
 
 import java.util.Set;
 
-import org.eclipse.core.runtime.preferences.InstanceScope;
 import org.eclipse.emf.compare.rcp.ui.EMFCompareRCPUIPlugin;
 import org.eclipse.emf.compare.rcp.ui.internal.EMFCompareRCPUIMessages;
 import org.eclipse.emf.compare.rcp.ui.internal.preferences.FiltersPreferencePage;
@@ -26,10 +25,9 @@ import org.eclipse.jface.action.Action;
 import org.eclipse.jface.action.IAction;
 import org.eclipse.jface.dialogs.IDialogConstants;
 import org.eclipse.jface.dialogs.MessageDialogWithToggle;
+import org.eclipse.jface.preference.IPreferenceStore;
 import org.eclipse.swt.widgets.Event;
 import org.eclipse.swt.widgets.Shell;
-import org.eclipse.ui.preferences.ScopedPreferenceStore;
-import org.osgi.service.prefs.Preferences;
 
 /**
  * These will be the actual actions displayed in the filter menu. Their sole purpose is to provide a Predicate
@@ -52,7 +50,7 @@ public class FilterAction extends Action {
 	private final StructureMergeViewerFilter structureMergeViewerFilter;
 
 	/** Preferences holding the value of the synchronization behavior of filters. */
-	private final Preferences preferences;
+	private final IPreferenceStore preferences;
 
 	/** {@link DifferenceFilterManager}. */
 	private final DifferenceFilterManager filterManager;
@@ -72,7 +70,7 @@ public class FilterAction extends Action {
 		super(text, IAction.AS_CHECK_BOX);
 		this.structureMergeViewerFilter = structureMergeViewerFilter;
 		this.filter = filter;
-		this.preferences = EMFCompareRCPUIPlugin.getDefault().getEMFCompareUIPreferences();
+		this.preferences = EMFCompareRCPUIPlugin.getDefault().getPreferenceStore();
 		this.filterManager = EMFCompareRCPUIPlugin.getDefault().getDifferenceFilterManager();
 	}
 
@@ -96,8 +94,10 @@ public class FilterAction extends Action {
 	 *            Event.
 	 */
 	private void handleSynchronization(Event event) {
-		String sync = preferences.get(FiltersPreferencePage.SYNCHRONIZATION_BEHAVIOR,
-				MessageDialogWithToggle.PROMPT);
+		String sync = preferences.getString(FiltersPreferencePage.SYNCHRONIZATION_BEHAVIOR);
+		if ("".equals(sync)) { //$NON-NLS-1$
+			sync = MessageDialogWithToggle.PROMPT;
+		}
 		final Shell shell = event.display.getActiveShell();
 		if (MessageDialogWithToggle.PROMPT.equals(sync) && shell != null) {
 			shell.getDisplay().asyncExec(new SynchronizationBehaviorRunnable(shell));
@@ -145,9 +145,8 @@ public class FilterAction extends Action {
 		}
 
 		/**
-		 * {@inheritDoc} Does not use InstanceScope#Instance for compatibility issues with Helios.
+		 * {@inheritDoc}
 		 */
-		@SuppressWarnings("deprecation")
 		public void run() {
 			MessageDialogWithToggle dialog = new SynchronizerDialog(shell,
 					EMFCompareRCPUIMessages.getString("FilterAction.synchronization.dialog.title"), //$NON-NLS-1$
@@ -155,8 +154,7 @@ public class FilterAction extends Action {
 					FiltersPreferencePage.PAGE_ID);
 
 			dialog.setPrefKey(FiltersPreferencePage.SYNCHRONIZATION_BEHAVIOR);
-			dialog.setPrefStore(
-					new ScopedPreferenceStore(new InstanceScope(), EMFCompareRCPUIPlugin.PLUGIN_ID));
+			dialog.setPrefStore(EMFCompareRCPUIPlugin.getDefault().getPreferenceStore());
 			if (dialog.open() == IDialogConstants.YES_ID) {
 				synchonizeFilters();
 			}
diff --git a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/structuremergeviewer/actions/GroupAction.java b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/structuremergeviewer/actions/GroupAction.java
index 08e7d0bef..f0929d7f9 100644
--- a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/structuremergeviewer/actions/GroupAction.java
+++ b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/structuremergeviewer/actions/GroupAction.java
@@ -14,7 +14,6 @@ import java.util.Iterator;
 import java.util.List;
 
 import org.eclipse.core.runtime.IStatus;
-import org.eclipse.core.runtime.preferences.InstanceScope;
 import org.eclipse.emf.compare.rcp.internal.extension.IItemDescriptor;
 import org.eclipse.emf.compare.rcp.ui.EMFCompareRCPUIPlugin;
 import org.eclipse.emf.compare.rcp.ui.internal.EMFCompareRCPUIMessages;
@@ -28,10 +27,9 @@ import org.eclipse.jface.action.Action;
 import org.eclipse.jface.action.IAction;
 import org.eclipse.jface.dialogs.IDialogConstants;
 import org.eclipse.jface.dialogs.MessageDialogWithToggle;
+import org.eclipse.jface.preference.IPreferenceStore;
 import org.eclipse.swt.widgets.Event;
 import org.eclipse.swt.widgets.Shell;
-import org.eclipse.ui.preferences.ScopedPreferenceStore;
-import org.osgi.service.prefs.Preferences;
 
 /**
  * This action will allow us to group differences by their kind.
@@ -56,7 +54,7 @@ public class GroupAction extends Action {
 	private final DifferenceGroupManager groupManager;
 
 	/** Preferences holding synchronization behavior value. */
-	private final Preferences preferences;
+	private final IPreferenceStore preferences;
 
 	/**
 	 * Instantiates our action given its target grouper.
@@ -80,7 +78,7 @@ public class GroupAction extends Action {
 		this.groupManager = groupManager;
 		this.isThreeWay = isThreeWay;
 		this.provider = gp;
-		this.preferences = EMFCompareRCPUIPlugin.getDefault().getEMFCompareUIPreferences();
+		this.preferences = EMFCompareRCPUIPlugin.getDefault().getPreferenceStore();
 	}
 
 	@Override
@@ -108,9 +106,11 @@ public class GroupAction extends Action {
 	 */
 	private void handleSynchronization(Event event) {
 		final Shell shell = event.display.getActiveShell();
-		String preferenceValue = preferences.get(
-				GroupsPreferencePage.getGroupSynchronizationPreferenceKey(isThreeWay),
-				MessageDialogWithToggle.PROMPT);
+		String preferenceValue = preferences
+				.getString(GroupsPreferencePage.getGroupSynchronizationPreferenceKey(isThreeWay));
+		if ("".equals(preferenceValue)) { //$NON-NLS-1$
+			preferenceValue = MessageDialogWithToggle.PROMPT;
+		}
 		if (MessageDialogWithToggle.PROMPT.equals(preferenceValue)) {
 			shell.getDisplay().asyncExec(new SynchronizationRunnable(shell));
 		} else if (MessageDialogWithToggle.ALWAYS.equals(preferenceValue)) {
@@ -173,8 +173,7 @@ public class GroupAction extends Action {
 					GroupsPreferencePage.PAGE_ID);
 
 			dialog.setPrefKey(GroupsPreferencePage.getGroupSynchronizationPreferenceKey(isThreeWay));
-			dialog.setPrefStore(
-					new ScopedPreferenceStore(new InstanceScope(), EMFCompareRCPUIPlugin.PLUGIN_ID));
+			dialog.setPrefStore(EMFCompareRCPUIPlugin.getDefault().getPreferenceStore());
 			if (dialog.open() == IDialogConstants.YES_ID) {
 				setSelectedGroupAsDefault();
 			}
diff --git a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/structuremergeviewer/actions/GroupActionMenu.java b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/structuremergeviewer/actions/GroupActionMenu.java
index 34111ac24..edc26e015 100644
--- a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/structuremergeviewer/actions/GroupActionMenu.java
+++ b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/structuremergeviewer/actions/GroupActionMenu.java
@@ -72,8 +72,8 @@ public class GroupActionMenu extends Action implements IMenuCreator {
 	public void updateMenu(IComparisonScope scope, Comparison comparison) {
 		menuManager.removeAll();
 		DifferenceGroupManager groupManager = new DifferenceGroupManager(
-				EMFCompareRCPUIPlugin.getDefault().getEMFCompareUIPreferences(),
-				EMFCompareRCPUIPlugin.getDefault().getItemDifferenceGroupProviderRegistry());
+				EMFCompareRCPUIPlugin.getDefault().getItemDifferenceGroupProviderRegistry(),
+				EMFCompareRCPUIPlugin.getDefault().getPreferenceStore());
 		for (IDifferenceGroupProvider.Descriptor dgp : registry.getGroupProviders(scope, comparison)) {
 			IDifferenceGroupProvider gp = dgp.createGroupProvider();
 			if (gp != null) {
diff --git a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/structuremergeviewer/filters/impl/DifferenceFilterManager.java b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/structuremergeviewer/filters/impl/DifferenceFilterManager.java
index 77b104a7c..17aac3e36 100644
--- a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/structuremergeviewer/filters/impl/DifferenceFilterManager.java
+++ b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/structuremergeviewer/filters/impl/DifferenceFilterManager.java
@@ -33,7 +33,7 @@ import org.eclipse.emf.compare.rcp.internal.tracer.TracingConstant;
 import org.eclipse.emf.compare.rcp.ui.EMFCompareRCPUIPlugin;
 import org.eclipse.emf.compare.rcp.ui.structuremergeviewer.filters.IDeactivableDiffFilter;
 import org.eclipse.emf.compare.rcp.ui.structuremergeviewer.filters.IDifferenceFilter;
-import org.osgi.service.prefs.Preferences;
+import org.eclipse.jface.preference.IPreferenceStore;
 
 /**
  * Manager of filters.
@@ -57,8 +57,8 @@ public class DifferenceFilterManager {
 	/** A map that associates the class name to their {@link IDifferenceFilter}s. */
 	private final Map<String, DifferenceFilterDefaultConfiguration> map;
 
-	/** The {@link Preferences} holding the value for filter preferences. */
-	private final Preferences preferenceStore;
+	/** The {@link IPreferenceStore} holding the value for filter preferences. */
+	private final IPreferenceStore preferenceStore;
 
 	/**
 	 * Predicate use to transform {@link DifferenceFilterDefaultConfiguration} to {@link IDifferenceFilter}.
@@ -77,9 +77,9 @@ public class DifferenceFilterManager {
 	 * Constructor.
 	 * 
 	 * @param preferenceStore
-	 *            The {@link Preferences} holding the value for filter preferences.
+	 *            The {@link IPreferenceStore} holding the value for filter preferences.
 	 */
-	public DifferenceFilterManager(Preferences preferenceStore) {
+	public DifferenceFilterManager(IPreferenceStore preferenceStore) {
 		map = Collections.synchronizedMap(new LinkedHashMap<String, DifferenceFilterDefaultConfiguration>());
 		this.preferenceStore = preferenceStore;
 	}
@@ -183,7 +183,7 @@ public class DifferenceFilterManager {
 			StringBuilder builder = new StringBuilder();
 			// Print each preferences
 			builder.append("Preference ").append(BY_DEFAULT_DISABLED_FILTER).append(":\n"); //$NON-NLS-1$ //$NON-NLS-2$
-			String preferenceValue = preferenceStore.get(BY_DEFAULT_DISABLED_FILTER, ""); //$NON-NLS-1$
+			String preferenceValue = preferenceStore.getString(BY_DEFAULT_DISABLED_FILTER);
 			String[] groups = preferenceValue.split(ItemUtil.PREFERENCE_DELIMITER);
 			for (int rank = 0; rank < groups.length; rank++) {
 				builder.append(rank).append(". ").append(groups[rank]).append("\n"); //$NON-NLS-1$ //$NON-NLS-2$
@@ -215,7 +215,7 @@ public class DifferenceFilterManager {
 			StringBuilder builder = new StringBuilder();
 			// Print each preferences
 			builder.append("Preference ").append(INACTIVE_FILTERS_PREF_KEY).append(":\n"); //$NON-NLS-1$ //$NON-NLS-2$
-			String preferenceValue = preferenceStore.get(INACTIVE_FILTERS_PREF_KEY, ""); //$NON-NLS-1$
+			String preferenceValue = preferenceStore.getString(INACTIVE_FILTERS_PREF_KEY);
 			String[] groups = preferenceValue.split(ItemUtil.PREFERENCE_DELIMITER);
 			for (int rank = 0; rank < groups.length; rank++) {
 				builder.append(rank).append(". ").append(groups[rank]).append("\n"); //$NON-NLS-1$ //$NON-NLS-2$
@@ -243,9 +243,9 @@ public class DifferenceFilterManager {
 	 * @return A {@link Set} of disabled by default {@link IDifferenceFilter} from preferences.
 	 */
 	private Set<IDifferenceFilter> getDisabledFilters() {
-		String diffEngineKey = preferenceStore.get(BY_DEFAULT_DISABLED_FILTER, null);
+		String diffEngineKey = preferenceStore.getString(BY_DEFAULT_DISABLED_FILTER);
 		Set<IDifferenceFilter> result = null;
-		if (diffEngineKey != null) {
+		if (diffEngineKey != null && !diffEngineKey.isEmpty()) {
 			String[] diffEngineKeys = diffEngineKey.split(ItemUtil.PREFERENCE_DELIMITER);
 			for (String nonTrimedKey : diffEngineKeys) {
 				String key = nonTrimedKey.trim();
@@ -271,9 +271,9 @@ public class DifferenceFilterManager {
 	 *         not implement {@link IDeactivableDiffFilter} cannot be deactivated).
 	 */
 	private Set<IDeactivableDiffFilter> getInactiveFilters() {
-		String diffEngineKey = preferenceStore.get(INACTIVE_FILTERS_PREF_KEY, null);
+		String diffEngineKey = preferenceStore.getString(INACTIVE_FILTERS_PREF_KEY);
 		Set<IDeactivableDiffFilter> result = null;
-		if (diffEngineKey != null) {
+		if (diffEngineKey != null && !diffEngineKey.isEmpty()) {
 			String[] diffEngineKeys = diffEngineKey.split(ItemUtil.PREFERENCE_DELIMITER);
 			for (String nonTrimedKey : diffEngineKeys) {
 				String key = nonTrimedKey.trim();
@@ -306,9 +306,9 @@ public class DifferenceFilterManager {
 			Map<String, IDifferenceFilter> toStore = Maps.filterValues(Maps.transformValues(map, TO_FILTER),
 					Predicates.in(currentValue));
 			String preferenceValue = Joiner.on(ItemUtil.PREFERENCE_DELIMITER).join(toStore.keySet());
-			preferenceStore.put(prefKey, preferenceValue);
+			preferenceStore.putValue(prefKey, preferenceValue);
 		} else {
-			preferenceStore.remove(prefKey);
+			preferenceStore.setToDefault(prefKey);
 		}
 	}
 
diff --git a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/structuremergeviewer/groups/impl/DifferenceGroupManager.java b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/structuremergeviewer/groups/impl/DifferenceGroupManager.java
index 45d936a6c..f3a321dd8 100644
--- a/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/structuremergeviewer/groups/impl/DifferenceGroupManager.java
+++ b/plugins/org.eclipse.emf.compare.rcp.ui/src/org/eclipse/emf/compare/rcp/ui/internal/structuremergeviewer/groups/impl/DifferenceGroupManager.java
@@ -31,7 +31,7 @@ import org.eclipse.emf.compare.rcp.ui.EMFCompareRCPUIPlugin;
 import org.eclipse.emf.compare.rcp.ui.structuremergeviewer.groups.IDifferenceGroupProvider;
 import org.eclipse.emf.compare.rcp.ui.structuremergeviewer.groups.IDifferenceGroupProvider.ComparisonType;
 import org.eclipse.emf.compare.rcp.ui.structuremergeviewer.groups.IDifferenceGroupProvider.Descriptor;
-import org.osgi.service.prefs.Preferences;
+import org.eclipse.jface.preference.IPreferenceStore;
 
 /**
  * This manager can be used to modify EMF Compare UI behavior regarding groups.
@@ -78,25 +78,24 @@ public class DifferenceGroupManager {
 	/** Ordered list of groups for three way comparison. */
 	private static final String THREE_WAY_GROUP_RANKING = "org.eclipse.emf.compare.rcp.ui.groups.3way.ranking"; //$NON-NLS-1$
 
-	/** Preferences holding preference values. */
-	private final Preferences preferences;
-
 	/** Registry of {@link IDifferenceGroupProvider.Descriptor}. */
 	private final IItemRegistry<IDifferenceGroupProvider.Descriptor> registry;
 
+	/** The {@link IPreferenceStore} holding the value for group preferences. */
+	private final IPreferenceStore preferenceStore;
+
 	/**
 	 * Constructor.
 	 * 
-	 * @param preferences
-	 *            Preferences holding preference values.
 	 * @param registry
 	 *            Registry of {@link IDifferenceGroupProvider.Descriptor}.
+	 * @param preferenceStore
+	 *            The {@link IPreferenceStore} holding the value for group preferences.
 	 */
-	public DifferenceGroupManager(Preferences preferences,
-			IItemRegistry<IDifferenceGroupProvider.Descriptor> registry) {
-		super();
-		this.preferences = preferences;
+	public DifferenceGroupManager(IItemRegistry<IDifferenceGroupProvider.Descriptor> registry,
+			IPreferenceStore preferenceStore) {
 		this.registry = registry;
+		this.preferenceStore = preferenceStore;
 	}
 
 	/**
@@ -178,7 +177,7 @@ public class DifferenceGroupManager {
 	private <T> List<IItemDescriptor<T>> getOrderedItems(List<IItemDescriptor<T>> orderedDefaultDescriptor,
 			IItemRegistry<T> descriptorRegistry, String orderedItemPreferenceKey) {
 		List<IItemDescriptor<T>> itemsDescriptor = ItemUtil.getItemsDescriptor(descriptorRegistry,
-				orderedItemPreferenceKey, preferences);
+				EMFCompareRCPUIPlugin.PLUGIN_ID, orderedItemPreferenceKey);
 
 		if (itemsDescriptor == null) {
 			itemsDescriptor = orderedDefaultDescriptor;
@@ -218,7 +217,7 @@ public class DifferenceGroupManager {
 			StringBuilder builder = new StringBuilder();
 			// Print each preferences
 			builder.append("Preference ").append(getGroupPreferenceKey(isThreeWay)).append(":\n"); //$NON-NLS-1$ //$NON-NLS-2$
-			String preferenceValue = preferences.get(getGroupPreferenceKey(isThreeWay), ""); //$NON-NLS-1$
+			String preferenceValue = preferenceStore.getString(getGroupPreferenceKey(isThreeWay));
 			String[] groups = preferenceValue.split(ItemUtil.PREFERENCE_DELIMITER);
 			for (int rank = 0; rank < groups.length; rank++) {
 				builder.append(rank).append(". ").append(groups[rank]).append("\n"); //$NON-NLS-1$ //$NON-NLS-2$
@@ -250,9 +249,9 @@ public class DifferenceGroupManager {
 						}
 					});
 			String preferenceValue = Joiner.on(ItemUtil.PREFERENCE_DELIMITER).join(currentIDs);
-			preferences.put(preferenceKey, preferenceValue);
+			preferenceStore.putValue(preferenceKey, preferenceValue);
 		} else {
-			preferences.remove(preferenceKey);
+			preferenceStore.setToDefault(preferenceKey);
 		}
 	}
 
diff --git a/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/EMFCompareRCPPlugin.java b/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/EMFCompareRCPPlugin.java
index f59a25914..38b7da5e2 100644
--- a/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/EMFCompareRCPPlugin.java
+++ b/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/EMFCompareRCPPlugin.java
@@ -8,6 +8,7 @@
  * Contributors:
  *     Obeo - initial API and implementation
  *     Martin Fleck - bug 483798
+ *     Mathias Schaefer - preferences refactoring
  *******************************************************************************/
 package org.eclipse.emf.compare.rcp;
 
@@ -17,6 +18,7 @@ import static org.eclipse.emf.compare.rcp.internal.preferences.EMFComparePrefere
 import static org.eclipse.emf.compare.rcp.internal.preferences.EMFComparePreferences.LOG_FILENAME_KEY;
 import static org.eclipse.emf.compare.rcp.internal.preferences.EMFComparePreferences.LOG_FILE_MAX_SIZE_KEY;
 import static org.eclipse.emf.compare.rcp.internal.preferences.EMFComparePreferences.LOG_FILE_SIZE_DEFAULT;
+import static org.eclipse.emf.compare.rcp.internal.preferences.EMFComparePreferences.LOG_LEVEL_DEFAULT;
 import static org.eclipse.emf.compare.rcp.internal.preferences.EMFComparePreferences.LOG_LEVEL_KEY;
 import static org.eclipse.emf.compare.rcp.internal.preferences.EMFComparePreferences.LOG_PATTERN;
 
@@ -42,9 +44,9 @@ import org.eclipse.core.runtime.IStatus;
 import org.eclipse.core.runtime.Platform;
 import org.eclipse.core.runtime.Plugin;
 import org.eclipse.core.runtime.Status;
-import org.eclipse.core.runtime.preferences.IEclipsePreferences;
 import org.eclipse.core.runtime.preferences.IEclipsePreferences.IPreferenceChangeListener;
 import org.eclipse.core.runtime.preferences.IEclipsePreferences.PreferenceChangeEvent;
+import org.eclipse.core.runtime.preferences.IPreferencesService;
 import org.eclipse.core.runtime.preferences.InstanceScope;
 import org.eclipse.emf.common.util.URI;
 import org.eclipse.emf.compare.conflict.IConflictDetector;
@@ -202,24 +204,13 @@ public class EMFCompareRCPPlugin extends Plugin {
 	private WeightProviderDescriptorRegistryListener weightProviderListener;
 
 	/** Will listen to preference changes and update log4j configuration accordingly. */
-	private IPreferenceChangeListener preferenceChangeListener;
+	private LoggingPreferenceChangeListener preferenceChangeListener;
 
 	/**
 	 * Keep all resources graphs identified by their id.
 	 */
 	private Map<String, IGraphView<URI>> graphsById = new HashMap<String, IGraphView<URI>>();
 
-	/**
-	 * Instance scope for preferences.
-	 * <p>
-	 * Do not use singleton to respect Helios compatibility
-	 * </p>
-	 * 
-	 * @see org.eclipse.core.runtime.preferences.InstanceScope#INSTANCE
-	 */
-	@SuppressWarnings("deprecation")
-	private InstanceScope instanceScope = new InstanceScope();
-
 	/*
 	 * (non-Javadoc)
 	 * @see org.osgi.framework.BundleActivator#start(org.osgi.framework.BundleContext)
@@ -285,8 +276,7 @@ public class EMFCompareRCPPlugin extends Plugin {
 		matchEngineFactoryRegistryListener = new MatchEngineFactoryRegistryListener(PLUGIN_ID,
 				MATCH_ENGINE_PPID, getLog(), matchEngineFactoryRegistry);
 		matchEngineFactoryRegistryListener.readRegistry(registry);
-		matchEngineFactoryRegistryWrapped = new MatchEngineFactoryRegistryWrapper(matchEngineFactoryRegistry,
-				EMFCompareRCPPlugin.getDefault().getEMFComparePreferences());
+		matchEngineFactoryRegistryWrapped = new MatchEngineFactoryRegistryWrapper(matchEngineFactoryRegistry);
 	}
 
 	/**
@@ -411,11 +401,10 @@ public class EMFCompareRCPPlugin extends Plugin {
 	@Override
 	public void stop(BundleContext bundleContext) throws Exception {
 		if (preferenceChangeListener != null) {
-			getEMFComparePreferences().removePreferenceChangeListener(preferenceChangeListener);
+			InstanceScope.INSTANCE.getNode(EMFCompareRCPPlugin.PLUGIN_ID)
+					.removePreferenceChangeListener(preferenceChangeListener);
 		}
 
-		EMFCompareRCPPlugin.plugin = null;
-
 		final IExtensionRegistry registry = Platform.getExtensionRegistry();
 
 		discardConflictDetectorRegistry(registry);
@@ -602,7 +591,7 @@ public class EMFCompareRCPPlugin extends Plugin {
 	public RankedAdapterFactoryDescriptor.Registry createFilteredAdapterFactoryRegistry(
 			Map<Object, Object> context) {
 		final List<String> disabledAdapterFactories = EMFComparePreferences
-				.getDisabledAdapterFacotryDescriptorIds(getEMFComparePreferences());
+				.getDisabledAdapterFactoryDescriptorIds();
 		// Filters disabled adapter factories
 		Multimap<Collection<?>, RankedAdapterFactoryDescriptor> filteredBackingMultimap = ImmutableMultimap
 				.copyOf(Multimaps.filterValues(adapterFactoryRegistryBackingMultimap,
@@ -741,39 +730,36 @@ public class EMFCompareRCPPlugin extends Plugin {
 	}
 
 	/**
-	 * Get the {@link IEclipsePreferences} for this plugin.
-	 * 
-	 * @return {@link IEclipsePreferences}
-	 */
-	public IEclipsePreferences getEMFComparePreferences() {
-		return instanceScope.getNode(EMFCompareRCPPlugin.PLUGIN_ID);
-	}
-
-	/**
 	 * Initializes log4j by reading the preferences.
 	 */
 	private void initLogging() {
-		IEclipsePreferences prefs = getEMFComparePreferences();
-		LOGGER.setLevel(Level.toLevel(prefs.get(LOG_LEVEL_KEY, "OFF"))); //$NON-NLS-1$
+		LOGGER.setLevel(Level.toLevel(Platform.getPreferencesService()
+				.getString(EMFCompareRCPPlugin.PLUGIN_ID, LOG_LEVEL_KEY, LOG_LEVEL_DEFAULT, null)));
 		if (!Level.OFF.equals(LOGGER.getLevel())) {
 			RollingFileAppender appender = (RollingFileAppender)LOGGER.getAppender(EMFC_APPENDER_NAME);
-			String logFileName = prefs.get(LOG_FILENAME_KEY, ""); //$NON-NLS-1$
+			String logFileName = Platform.getPreferencesService().getString(EMFCompareRCPPlugin.PLUGIN_ID,
+					LOG_FILENAME_KEY, "", null); //$NON-NLS-1$
 			if (logFileName.length() > 0) {
 				if (appender == null) {
 					try {
 						createLogAppender(logFileName);
 					} catch (IOException e) {
 						// Invalidate file name
-						prefs.put(LOG_FILENAME_KEY, ""); //$NON-NLS-1$
+						Platform.getPreferencesService().getString(EMFCompareRCPPlugin.PLUGIN_ID,
+								LOG_FILENAME_KEY, "", null); //$NON-NLS-1$
 					}
 				} else {
-					appender.setMaxBackupIndex(prefs.getInt(LOG_BACKUP_COUNT_KEY, 10));
-					appender.setMaximumFileSize((prefs.getInt(LOG_FILE_MAX_SIZE_KEY, 100)) * MEGABYTE);
+					appender.setMaxBackupIndex(Platform.getPreferencesService().getInt(
+							EMFCompareRCPPlugin.PLUGIN_ID, LOG_BACKUP_COUNT_KEY, LOG_BACKUP_DEFAULT, null));
+					appender.setMaximumFileSize(
+							(Platform.getPreferencesService().getInt(EMFCompareRCPPlugin.PLUGIN_ID,
+									LOG_FILE_MAX_SIZE_KEY, LOG_FILE_SIZE_DEFAULT, null)) * MEGABYTE);
 				}
 			}
 		}
 		preferenceChangeListener = new LoggingPreferenceChangeListener();
-		prefs.addPreferenceChangeListener(preferenceChangeListener);
+		InstanceScope.INSTANCE.getNode(EMFCompareRCPPlugin.PLUGIN_ID)
+				.addPreferenceChangeListener(preferenceChangeListener);
 	}
 
 	/**
@@ -790,10 +776,10 @@ public class EMFCompareRCPPlugin extends Plugin {
 		appender = new RollingFileAppender(new PatternLayout(LOG_PATTERN), newFileName, true);
 		LOGGER.removeAllAppenders(); // We don't want to log elsewhere
 		LOGGER.addAppender(appender);
-		appender.setMaxBackupIndex(
-				getEMFComparePreferences().getInt(LOG_BACKUP_COUNT_KEY, LOG_BACKUP_DEFAULT));
-		appender.setMaximumFileSize(
-				(getEMFComparePreferences().getInt(LOG_FILE_MAX_SIZE_KEY, LOG_FILE_SIZE_DEFAULT)) * MEGABYTE);
+		appender.setMaxBackupIndex(Platform.getPreferencesService().getInt(EMFCompareRCPPlugin.PLUGIN_ID,
+				LOG_BACKUP_COUNT_KEY, LOG_BACKUP_DEFAULT, null));
+		appender.setMaximumFileSize((Platform.getPreferencesService().getInt(EMFCompareRCPPlugin.PLUGIN_ID,
+				LOG_FILE_MAX_SIZE_KEY, LOG_FILE_SIZE_DEFAULT, null)) * MEGABYTE);
 	}
 
 	/**
@@ -804,16 +790,6 @@ public class EMFCompareRCPPlugin extends Plugin {
 	private static class LoggingPreferenceChangeListener implements IPreferenceChangeListener {
 
 		/**
-		 * Instance scope for preferences.
-		 * <p>
-		 * Do not use singleton to respect Helios compatibility
-		 * </p>
-		 * 
-		 * @see org.eclipse.core.runtime.preferences.InstanceScope#INSTANCE
-		 */
-		private InstanceScope instanceScope = new InstanceScope();
-
-		/**
 		 * The path of the logging file.
 		 */
 		private String path;
@@ -830,8 +806,9 @@ public class EMFCompareRCPPlugin extends Plugin {
 		 *            the preference change event.
 		 */
 		public void preferenceChange(PreferenceChangeEvent event) {
-			IEclipsePreferences prefs = instanceScope.getNode(EMFCompareRCPPlugin.PLUGIN_ID);
-			path = prefs.get(LOG_FILENAME_KEY, ""); //$NON-NLS-1$
+			final IPreferencesService prefs = Platform.getPreferencesService();
+
+			path = prefs.getString(EMFCompareRCPPlugin.PLUGIN_ID, LOG_FILENAME_KEY, "", null); //$NON-NLS-1$
 			if (LOG_LEVEL_KEY.equals(event.getKey())) {
 				loggingLevel = Level.toLevel((String)event.getNewValue());
 				LOGGER.setLevel(loggingLevel);
@@ -863,7 +840,8 @@ public class EMFCompareRCPPlugin extends Plugin {
 				try {
 					EMFCompareRCPPlugin.getDefault().createLogAppender(path);
 				} catch (IOException e) {
-					EMFCompareRCPPlugin.getDefault().getEMFComparePreferences().put(LOG_FILENAME_KEY, ""); //$NON-NLS-1$
+					// Force the value to be harmless
+					InstanceScope.INSTANCE.getNode(EMFCompareRCPPlugin.PLUGIN_ID).put(LOG_FILENAME_KEY, ""); //$NON-NLS-1$
 					getDefault().log(IStatus.ERROR,
 							EMFCompareRCPMessages.getString("logging.appender.error", path, e.getMessage())); //$NON-NLS-1$
 				}
diff --git a/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/extension/IConfigurableItem.java b/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/extension/IConfigurableItem.java
deleted file mode 100644
index 381c5aeb7..000000000
--- a/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/extension/IConfigurableItem.java
+++ /dev/null
@@ -1,37 +0,0 @@
-/*******************************************************************************
- * Copyright (c) 2014 Obeo.
- * 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:
- *     Obeo - initial API and implementation
- *******************************************************************************/
-package org.eclipse.emf.compare.rcp.internal.extension;
-
-import org.osgi.service.prefs.Preferences;
-
-/**
- * Represente an item that can be configured from preferences.
- * 
- * @author <a href="mailto:arthur.daussy@obeo.fr">Arthur Daussy</a>
- */
-public interface IConfigurableItem {
-
-	/**
-	 * Get the configuration of the Item.
-	 * 
-	 * @return the configuration.
-	 */
-	Preferences getConfiguration();
-
-	/**
-	 * Set the configuration of an Item.
-	 * 
-	 * @param config
-	 *            Configuration to set.
-	 */
-	void setConfiguration(Preferences config);
-
-}
diff --git a/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/extension/impl/EMFCompareBuilderConfigurator.java b/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/extension/impl/EMFCompareBuilderConfigurator.java
index 44bc7dbcb..01f11bcc5 100644
--- a/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/extension/impl/EMFCompareBuilderConfigurator.java
+++ b/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/extension/impl/EMFCompareBuilderConfigurator.java
@@ -10,9 +10,6 @@
  *******************************************************************************/
 package org.eclipse.emf.compare.rcp.internal.extension.impl;
 
-import com.google.common.base.Preconditions;
-
-import org.eclipse.core.runtime.preferences.IEclipsePreferences;
 import org.eclipse.emf.compare.EMFCompare.Builder;
 import org.eclipse.emf.compare.conflict.IConflictDetector;
 import org.eclipse.emf.compare.diff.IDiffEngine;
@@ -31,9 +28,6 @@ import org.eclipse.emf.compare.req.IReqEngine;
  */
 public class EMFCompareBuilderConfigurator implements IEMFCompareBuilderConfigurator {
 
-	/** {@link IEclipsePreferences} holding engines information. */
-	private final IEclipsePreferences enginePreferences;
-
 	/** Match engine factory registry. */
 	private final IMatchEngine.Factory.Registry matchEngineFactoryRegistry;
 
@@ -43,18 +37,13 @@ public class EMFCompareBuilderConfigurator implements IEMFCompareBuilderConfigur
 	/**
 	 * Constructor.
 	 * 
-	 * @param enginePreferences
-	 *            {@link EMFCompareBuilderConfigurator#enginePreferences}
 	 * @param matchEngineFactoryRegistry
 	 *            {@link IMatchEngine.Factory.Registry} that holds Match Engine factories.
 	 * @param postProcessorRegistry
 	 *            {@link IPostProcessor.Descriptor.Registry} that holds post processors.
 	 */
-	public EMFCompareBuilderConfigurator(IEclipsePreferences enginePreferences,
-			IMatchEngine.Factory.Registry matchEngineFactoryRegistry,
+	protected EMFCompareBuilderConfigurator(IMatchEngine.Factory.Registry matchEngineFactoryRegistry,
 			IPostProcessor.Descriptor.Registry<String> postProcessorRegistry) {
-		Preconditions.checkNotNull(enginePreferences);
-		this.enginePreferences = enginePreferences;
 		this.matchEngineFactoryRegistry = matchEngineFactoryRegistry;
 		this.postProcessorRegistry = postProcessorRegistry;
 	}
@@ -67,7 +56,7 @@ public class EMFCompareBuilderConfigurator implements IEMFCompareBuilderConfigur
 	 * @return Default EMFCompareBuilderConfigurator;
 	 */
 	public static EMFCompareBuilderConfigurator createDefault() {
-		return new EMFCompareBuilderConfigurator(EMFCompareRCPPlugin.getDefault().getEMFComparePreferences(),
+		return new EMFCompareBuilderConfigurator(
 				EMFCompareRCPPlugin.getDefault().getMatchEngineFactoryRegistry(),
 				EMFCompareRCPPlugin.getDefault().getPostProcessorRegistry());
 	}
@@ -80,7 +69,7 @@ public class EMFCompareBuilderConfigurator implements IEMFCompareBuilderConfigur
 	 */
 	private IDiffEngine getDiffEngine() {
 		return ItemUtil.getItem(EMFCompareRCPPlugin.getDefault().getDiffEngineDescriptorRegistry(),
-				EMFComparePreferences.DIFF_ENGINES, enginePreferences);
+				EMFComparePreferences.DIFF_ENGINES);
 	}
 
 	/**
@@ -91,7 +80,7 @@ public class EMFCompareBuilderConfigurator implements IEMFCompareBuilderConfigur
 	 */
 	private IEquiEngine getEquiEngine() {
 		return ItemUtil.getItem(EMFCompareRCPPlugin.getDefault().getEquiEngineDescriptorRegistry(),
-				EMFComparePreferences.EQUI_ENGINES, enginePreferences);
+				EMFComparePreferences.EQUI_ENGINES);
 	}
 
 	/**
@@ -102,7 +91,7 @@ public class EMFCompareBuilderConfigurator implements IEMFCompareBuilderConfigur
 	 */
 	private IReqEngine getReqEngine() {
 		return ItemUtil.getItem(EMFCompareRCPPlugin.getDefault().getReqEngineDescriptorRegistry(),
-				EMFComparePreferences.REQ_ENGINES, enginePreferences);
+				EMFComparePreferences.REQ_ENGINES);
 	}
 
 	/**
@@ -113,7 +102,7 @@ public class EMFCompareBuilderConfigurator implements IEMFCompareBuilderConfigur
 	 */
 	private IConflictDetector getConflictDetector() {
 		return ItemUtil.getItem(EMFCompareRCPPlugin.getDefault().getConflictDetectorDescriptorRegistry(),
-				EMFComparePreferences.CONFLICTS_DETECTOR, enginePreferences);
+				EMFComparePreferences.CONFLICTS_DETECTOR);
 	}
 
 	/**
diff --git a/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/extension/impl/ItemUtil.java b/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/extension/impl/ItemUtil.java
index 4a1e425f6..a65777f24 100644
--- a/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/extension/impl/ItemUtil.java
+++ b/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/extension/impl/ItemUtil.java
@@ -16,11 +16,10 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.Set;
 
-import org.eclipse.core.runtime.preferences.IEclipsePreferences;
+import org.eclipse.core.runtime.Platform;
 import org.eclipse.emf.compare.rcp.EMFCompareRCPPlugin;
 import org.eclipse.emf.compare.rcp.internal.extension.IItemDescriptor;
 import org.eclipse.emf.compare.rcp.internal.extension.IItemRegistry;
-import org.osgi.service.prefs.Preferences;
 
 /**
  * Util class for item.
@@ -46,15 +45,12 @@ public final class ItemUtil {
 	 *            The item registry
 	 * @param preferenceKey
 	 *            The preference to retrieve the key.
-	 * @param itemPreferences
-	 *            Eclipse preference where are stored the items to use
 	 * @param <T>
 	 *            Type of item
 	 * @return an item or null if nothing has been found.
 	 */
-	public static <T> T getItem(IItemRegistry<T> registry, String preferenceKey,
-			IEclipsePreferences itemPreferences) {
-		IItemDescriptor<T> desc = getDefaultItemDescriptor(registry, preferenceKey, itemPreferences);
+	public static <T> T getItem(IItemRegistry<T> registry, String preferenceKey) {
+		IItemDescriptor<T> desc = getDefaultItemDescriptor(registry, preferenceKey);
 		if (desc != null) {
 			return desc.getItem();
 		}
@@ -69,15 +65,13 @@ public final class ItemUtil {
 	 *            {@link IItemRegistry} of the item type
 	 * @param preferenceKey
 	 *            Preference key use to retrieve the item
-	 * @param itemPreferences
-	 *            {@link IEclipsePreferences} where are stored the item preferences.
 	 * @param <T>
 	 *            Type of item
 	 * @return {@link IItemDescriptor}
 	 */
 	public static <T> IItemDescriptor<T> getDefaultItemDescriptor(IItemRegistry<T> registry,
-			String preferenceKey, IEclipsePreferences itemPreferences) {
-		IItemDescriptor<T> result = getItemDescriptorFromPref(registry, itemPreferences, preferenceKey);
+			String preferenceKey) {
+		IItemDescriptor<T> result = getItemDescriptorFromPref(registry, preferenceKey);
 		if (result == null) {
 			IItemDescriptor<T> descriptor = registry.getHighestRankingDescriptor();
 			if (descriptor != null) {
@@ -94,20 +88,19 @@ public final class ItemUtil {
 	 *            Registry for the {@link IItemDescriptor}
 	 * @param preferenceKey
 	 *            Key for this {@link IItemDescriptor} in preferences
-	 * @param itemPreferences
-	 *            {@link IEclipsePreferences} where are stored {@link IItemDescriptor} values
 	 * @param <T>
 	 *            Type of {@link IItemDescriptor}
 	 * @return {@link IItemDescriptor} or null if nothing in preferences
 	 */
 	private static <T> IItemDescriptor<T> getItemDescriptorFromPref(IItemRegistry<T> registry,
-			IEclipsePreferences itemPreferences, String preferenceKey) {
-		String itemKey = itemPreferences.get(preferenceKey, null);
+			String preferenceKey) {
+		String itemKey = Platform.getPreferencesService().getString(EMFCompareRCPPlugin.PLUGIN_ID,
+				preferenceKey, null, null);
 		IItemDescriptor<T> result = null;
 		if (itemKey != null) {
-			IItemDescriptor<T> descritpor = registry.getItemDescriptor(itemKey);
-			if (descritpor != null) {
-				result = descritpor;
+			IItemDescriptor<T> descriptor = registry.getItemDescriptor(itemKey);
+			if (descriptor != null) {
+				result = descriptor;
 			}
 		}
 		return result;
@@ -118,28 +111,29 @@ public final class ItemUtil {
 	 * 
 	 * @param registry
 	 *            Registry for the {@link IItemDescriptor}
+	 * @param qualifier
+	 *            the preference qualifier (plug-in ID)
 	 * @param preferenceKey
 	 *            Key for this {@link IItemDescriptor} in preferences
-	 * @param itemPreferences
-	 *            {@link Preferences} where are stored {@link IItemDescriptor} values
 	 * @param <T>
 	 *            Type of {@link IItemDescriptor}
 	 * @return List of {@link IItemDescriptor} or null if nothing in preferences
 	 */
-	public static <T> List<IItemDescriptor<T>> getItemsDescriptor(IItemRegistry<T> registry,
-			String preferenceKey, Preferences itemPreferences) {
-		String diffEngineKey = itemPreferences.get(preferenceKey, null);
+	public static <T> List<IItemDescriptor<T>> getItemsDescriptor(IItemRegistry<T> registry, String qualifier,
+			String preferenceKey) {
+		String diffEngineKey = Platform.getPreferencesService().getString(qualifier, preferenceKey, null,
+				null);
 		List<IItemDescriptor<T>> result = null;
 		if (diffEngineKey != null) {
 			String[] diffEngineKeys = diffEngineKey.split(PREFERENCE_DELIMITER);
 			for (String nonTrimedKey : diffEngineKeys) {
 				String key = nonTrimedKey.trim();
-				IItemDescriptor<T> descritpor = registry.getItemDescriptor(key);
-				if (descritpor != null) {
+				IItemDescriptor<T> descriptor = registry.getItemDescriptor(key);
+				if (descriptor != null) {
 					if (result == null) {
 						result = new ArrayList<IItemDescriptor<T>>();
 					}
-					result.add(descritpor);
+					result.add(descriptor);
 				}
 			}
 		}
@@ -148,19 +142,6 @@ public final class ItemUtil {
 	}
 
 	/**
-	 * Return the node holding the configuration for an item.
-	 * 
-	 * @param type
-	 *            Type of item.
-	 * @param itemId
-	 *            Id of the item we want to retrieve the configuration for.
-	 * @return The {@link Preferences} holding the configuration.
-	 */
-	public static Preferences getConfigurationPreferenceNode(String type, String itemId) {
-		return EMFCompareRCPPlugin.getDefault().getEMFComparePreferences().node(type).node(itemId);
-	}
-
-	/**
 	 * Get all active item from a registry.
 	 * <p>
 	 * (Filter out all disable element stored in preferences)
@@ -168,16 +149,18 @@ public final class ItemUtil {
 	 * 
 	 * @param registry
 	 *            Registry holding all items of this kind
+	 * @param qualifier
+	 *            The preference qualifier (plug-in ID)
 	 * @param disabledItemPreferenceKey
 	 *            Preference key where are stored disabled items.
 	 * @return {@link Set} of active items
 	 * @param <T>
 	 *            Item type
 	 */
-	public static <T> Set<IItemDescriptor<T>> getActiveItems(IItemRegistry<T> registry,
+	public static <T> Set<IItemDescriptor<T>> getActiveItems(IItemRegistry<T> registry, String qualifier,
 			String disabledItemPreferenceKey) {
-		List<IItemDescriptor<T>> itemsDescriptor = ItemUtil.getItemsDescriptor(registry,
-				disabledItemPreferenceKey, EMFCompareRCPPlugin.getDefault().getEMFComparePreferences());
+		List<IItemDescriptor<T>> itemsDescriptor = getItemsDescriptor(registry, qualifier,
+				disabledItemPreferenceKey);
 
 		if (itemsDescriptor == null) {
 			return Sets.newLinkedHashSet(registry.getItemDescriptors());
diff --git a/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/match/DefaultRCPMatchEngineFactory.java b/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/match/DefaultRCPMatchEngineFactory.java
index bec9117ea..f94fc982a 100644
--- a/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/match/DefaultRCPMatchEngineFactory.java
+++ b/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/match/DefaultRCPMatchEngineFactory.java
@@ -11,21 +11,20 @@
 package org.eclipse.emf.compare.rcp.internal.match;
 
 import org.eclipse.core.runtime.IStatus;
+import org.eclipse.core.runtime.Platform;
 import org.eclipse.emf.compare.EMFCompareMessages;
 import org.eclipse.emf.compare.match.DefaultMatchEngine;
 import org.eclipse.emf.compare.match.IMatchEngine;
 import org.eclipse.emf.compare.rcp.EMFCompareRCPPlugin;
-import org.eclipse.emf.compare.rcp.internal.extension.IConfigurableItem;
 import org.eclipse.emf.compare.scope.IComparisonScope;
 import org.eclipse.emf.compare.utils.UseIdentifiers;
-import org.osgi.service.prefs.Preferences;
 
 /**
  * Implementation of {@link IMatchEngine.Factory} for the {@link DefaultMatchEngine} that can be configured.
  * 
  * @author <a href="mailto:arthur.daussy@obeo.fr">Arthur Daussy</a>
  */
-public class DefaultRCPMatchEngineFactory implements IMatchEngine.Factory, IConfigurableItem {
+public class DefaultRCPMatchEngineFactory implements IMatchEngine.Factory {
 
 	/** Attribute used to retrieve UseIdentifier attribute from preferences. */
 	public static final String USE_IDENTIFIER_ATTR = "UseIdentifier"; //$NON-NLS-1$
@@ -36,9 +35,6 @@ public class DefaultRCPMatchEngineFactory implements IMatchEngine.Factory, IConf
 	/** Rank of the factory. */
 	private int rank;
 
-	/** Configuration used to instance the match engine. */
-	private Preferences config;
-
 	/**
 	 * Constructor.
 	 */
@@ -50,22 +46,17 @@ public class DefaultRCPMatchEngineFactory implements IMatchEngine.Factory, IConf
 	 * Parse the input preference to retrieve the value of
 	 * {@link DefaultRCPMatchEngineFactory#USE_IDENTIFIER_ATTR}.
 	 * 
-	 * @param pref
-	 *            {@link Preferences} holding configuration for this {@link IMatchEngine.Factory}.
 	 * @return The value of {@link DefaultRCPMatchEngineFactory#USE_IDENTIFIER_ATTR}.
 	 */
-	public static UseIdentifiers getUseIdentifierValue(Preferences pref) {
+	public static UseIdentifiers getUseIdentifierValue() {
 		UseIdentifiers result;
-		if (pref != null) {
-			String storedPref = pref.get(USE_IDENTIFIER_ATTR, DEFAULT_USE_IDENTIFIER_ATRIBUTE.toString());
-			try {
-				result = UseIdentifiers.valueOf(storedPref);
-			} catch (IllegalArgumentException e) {
-				EMFCompareRCPPlugin.getDefault().log(IStatus.ERROR, EMFCompareMessages
-						.getString("RCPMatchEngineFactory.INCORECT_USE_IDENTIFIER_ATTRIBUTE")); //$NON-NLS-1$
-				result = DEFAULT_USE_IDENTIFIER_ATRIBUTE;
-			}
-		} else {
+		String storedPref = Platform.getPreferencesService().getString(EMFCompareRCPPlugin.PLUGIN_ID,
+				USE_IDENTIFIER_ATTR, DEFAULT_USE_IDENTIFIER_ATRIBUTE.toString(), null);
+		try {
+			result = UseIdentifiers.valueOf(storedPref);
+		} catch (IllegalArgumentException e) {
+			EMFCompareRCPPlugin.getDefault().log(IStatus.ERROR,
+					EMFCompareMessages.getString("RCPMatchEngineFactory.INCORECT_USE_IDENTIFIER_ATTRIBUTE")); //$NON-NLS-1$
 			result = DEFAULT_USE_IDENTIFIER_ATRIBUTE;
 		}
 		return result;
@@ -75,7 +66,7 @@ public class DefaultRCPMatchEngineFactory implements IMatchEngine.Factory, IConf
 	 * {@inheritDoc}
 	 */
 	public IMatchEngine getMatchEngine() {
-		final UseIdentifiers useUdentifier = getUseIdentifierValue(config);
+		final UseIdentifiers useUdentifier = getUseIdentifierValue();
 		return DefaultMatchEngine.create(useUdentifier,
 				EMFCompareRCPPlugin.getDefault().getWeightProviderRegistry());
 	}
@@ -102,19 +93,4 @@ public class DefaultRCPMatchEngineFactory implements IMatchEngine.Factory, IConf
 		return true;
 	}
 
-	/**
-	 * {@inheritDoc}
-	 */
-	public Preferences getConfiguration() {
-		return config;
-	}
-
-	/**
-	 * {@inheritDoc}
-	 */
-	public void setConfiguration(Preferences inputConfig) {
-		this.config = inputConfig;
-
-	}
-
 }
diff --git a/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/match/MatchEngineFactoryDescriptor.java b/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/match/MatchEngineFactoryDescriptor.java
index e224438d7..3b0cb4561 100644
--- a/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/match/MatchEngineFactoryDescriptor.java
+++ b/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/match/MatchEngineFactoryDescriptor.java
@@ -16,11 +16,7 @@ import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.IConfigurationElement;
 import org.eclipse.emf.compare.match.IMatchEngine;
 import org.eclipse.emf.compare.match.IMatchEngine.Factory;
-import org.eclipse.emf.compare.rcp.internal.extension.IConfigurableItem;
-import org.eclipse.emf.compare.rcp.internal.extension.impl.ItemUtil;
 import org.eclipse.emf.compare.rcp.internal.extension.impl.LazyItemDescriptor;
-import org.eclipse.emf.compare.rcp.internal.preferences.EMFComparePreferences;
-import org.osgi.service.prefs.Preferences;
 
 /**
  * Descriptor for {@link IMatchEngine.Factory}.
@@ -39,7 +35,7 @@ public class MatchEngineFactoryDescriptor extends LazyItemDescriptor<IMatchEngin
 	 * @param rank
 	 *            {@link LazyItemDescriptor#getRank()}
 	 * @param config
-	 *            {@link IConfigurableItem} element used to create this item.
+	 *            {@link IConfigurationElement} element used to create this item.
 	 * @param id
 	 *            {@link LazyItemDescriptor#getID()}
 	 */
@@ -58,11 +54,6 @@ public class MatchEngineFactoryDescriptor extends LazyItemDescriptor<IMatchEngin
 			factory = (Factory)getConfig()
 					.createExecutableExtension(MatchEngineFactoryRegistryListener.ATT_CLASS);
 			factory.setRanking(getRank());
-			if (factory instanceof IConfigurableItem) {
-				Preferences configuration = ItemUtil.getConfigurationPreferenceNode(
-						EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES, getID());
-				((IConfigurableItem)factory).setConfiguration(configuration);
-			}
 		} catch (CoreException e) {
 			Throwables.propagate(e);
 		}
diff --git a/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/match/MatchEngineFactoryRegistryWrapper.java b/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/match/MatchEngineFactoryRegistryWrapper.java
index 0b09cbb69..ab05a0f35 100644
--- a/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/match/MatchEngineFactoryRegistryWrapper.java
+++ b/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/match/MatchEngineFactoryRegistryWrapper.java
@@ -24,9 +24,9 @@ import java.util.Collections;
 import java.util.Iterator;
 import java.util.List;
 
-import org.eclipse.core.runtime.preferences.IEclipsePreferences;
 import org.eclipse.emf.compare.match.IMatchEngine;
 import org.eclipse.emf.compare.match.IMatchEngine.Factory;
+import org.eclipse.emf.compare.rcp.EMFCompareRCPPlugin;
 import org.eclipse.emf.compare.rcp.internal.extension.IItemDescriptor;
 import org.eclipse.emf.compare.rcp.internal.extension.IItemRegistry;
 import org.eclipse.emf.compare.rcp.internal.extension.impl.AbstractItemDescriptor;
@@ -48,22 +48,14 @@ public class MatchEngineFactoryRegistryWrapper implements IMatchEngine.Factory.R
 	/** Instance of the registry that need to be wrapped. */
 	private IItemRegistry<IMatchEngine.Factory> registry;
 
-	/** Preferences holding disabled match engines. */
-	private final IEclipsePreferences preferences;
-
 	/**
 	 * Constructor.
 	 * 
-	 * @param registy
+	 * @param registry
 	 *            {@link MatchEngineFactoryRegistryWrapper#registry}
-	 * @param preferences
-	 *            Preferences holding disabled match engines.
 	 */
-	public MatchEngineFactoryRegistryWrapper(IItemRegistry<Factory> registy,
-			IEclipsePreferences preferences) {
-		super();
-		this.registry = registy;
-		this.preferences = preferences;
+	public MatchEngineFactoryRegistryWrapper(IItemRegistry<Factory> registry) {
+		this.registry = registry;
 	}
 
 	/**
@@ -176,7 +168,7 @@ public class MatchEngineFactoryRegistryWrapper implements IMatchEngine.Factory.R
 	 */
 	private Collection<IItemDescriptor<IMatchEngine.Factory>> getDisabledEngines() {
 		Collection<IItemDescriptor<Factory>> result = ItemUtil.getItemsDescriptor(registry,
-				EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES, preferences);
+				EMFCompareRCPPlugin.PLUGIN_ID, EMFComparePreferences.MATCH_ENGINE_DISABLE_ENGINES);
 		if (result == null) {
 			result = Collections.emptyList();
 		}
diff --git a/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/postprocessor/PostProcessorRegistryImpl.java b/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/postprocessor/PostProcessorRegistryImpl.java
index 927128c88..ac6a6af01 100644
--- a/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/postprocessor/PostProcessorRegistryImpl.java
+++ b/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/postprocessor/PostProcessorRegistryImpl.java
@@ -103,8 +103,7 @@ public class PostProcessorRegistryImpl implements IPostProcessor.Descriptor.Regi
 	 */
 	private Collection<IItemDescriptor<IPostProcessor.Descriptor>> getDisabledEngines() {
 		List<IItemDescriptor<IPostProcessor.Descriptor>> result = ItemUtil.getItemsDescriptor(baseRegisty,
-				EMFComparePreferences.DISABLED_POST_PROCESSOR,
-				EMFCompareRCPPlugin.getDefault().getEMFComparePreferences());
+				EMFCompareRCPPlugin.PLUGIN_ID, EMFComparePreferences.DISABLED_POST_PROCESSOR);
 		if (result == null) {
 			result = Collections.emptyList();
 		}
diff --git a/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/preferences/EMFComparePreferences.java b/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/preferences/EMFComparePreferences.java
index 53cf6052a..f3340866f 100644
--- a/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/preferences/EMFComparePreferences.java
+++ b/plugins/org.eclipse.emf.compare.rcp/src/org/eclipse/emf/compare/rcp/internal/preferences/EMFComparePreferences.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2014, 2015 Obeo.
+ * Copyright (c) 2014, 2016 Obeo.
  * 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
@@ -15,10 +15,11 @@ import com.google.common.collect.Lists;
 
 import java.util.List;
 
-import org.eclipse.core.runtime.preferences.IEclipsePreferences;
+import org.eclipse.core.runtime.Platform;
+import org.eclipse.emf.compare.rcp.EMFCompareRCPPlugin;
 
-/**
- * All preferences constant for EMF Compare.
+/***
+ * Preferences constants and utilities for the EMF Compare RCP plug-in.
  * 
  * @author <a href="mailto:arthur.daussy@obeo.fr">Arthur Daussy</a>
  */
@@ -91,13 +92,11 @@ public final class EMFComparePreferences {
 	/**
 	 * Gets the ids of all disabled EMF Compare adapter factory descriptors.
 	 * 
-	 * @param preferenceStore
-	 *            {@link IEclipsePreferences} where are stored the preferences.
 	 * @return List of ids;
 	 */
-	public static List<String> getDisabledAdapterFacotryDescriptorIds(IEclipsePreferences preferenceStore) {
-		String disabledAdapterFactoriesString = preferenceStore
-				.get(EMFComparePreferences.DISABLED_ADAPTER_FACTORY, ""); //$NON-NLS-1$
+	public static List<String> getDisabledAdapterFactoryDescriptorIds() {
+		String disabledAdapterFactoriesString = Platform.getPreferencesService()
+				.getString(EMFCompareRCPPlugin.PLUGIN_ID, DISABLED_ADAPTER_FACTORY, "", null); //$NON-NLS-1$
 
 		final List<String> disabledAdapterFactories = Lists.newArrayList(
 				Splitter.on(';').omitEmptyStrings().trimResults().split(disabledAdapterFactoriesString));