[422957] Remove some of the deprecated methods Sirius's APIs

See the release notes for the details of what methods and types have
been removed and what to replace them with.

Signed-off-by: Pierre-Charles David <pierre-charles.david@obeo.fr>
Change-Id: I42517793707ddf1ca9839069abb1680328e0c778

42 files changed, 258 insertions, 1014 deletions

diff --git a/plugins/org.eclipse.sirius.common.ui/src/org/eclipse/sirius/common/ui/tools/api/dialog/FeatureEditorDialog.java b/plugins/org.eclipse.sirius.common.ui/src/org/eclipse/sirius/common/ui/tools/api/dialog/FeatureEditorDialog.java
index 2622878bfd..c6497c9ed0 100644
--- a/plugins/org.eclipse.sirius.common.ui/src/org/eclipse/sirius/common/ui/tools/api/dialog/FeatureEditorDialog.java
+++ b/plugins/org.eclipse.sirius.common.ui/src/org/eclipse/sirius/common/ui/tools/api/dialog/FeatureEditorDialog.java
@@ -107,31 +107,6 @@ public class FeatureEditorDialog extends Dialog {
         }
     }
 
-    /**
-     * @deprecated Use
-     *             {@link #FeatureEditorDialog(Shell, ILabelProvider, Object, EClassifier, List, String, List, boolean, boolean, boolean)}
-     *             , which provides proper behaviour for unique and non-unique
-     *             features. This form retains the old behaviour, where
-     *             specifying a list of choices enforces uniqueness.
-     */
-    @Deprecated
-    public FeatureEditorDialog(Shell parent, ILabelProvider labelProvider, Object object, EClassifier eClassifier, List<?> currentValues, String displayName, List<?> choiceOfValues,
-            boolean multiLine, boolean sortChoices) {
-        this(parent, labelProvider, object, eClassifier, currentValues, displayName, choiceOfValues, multiLine, sortChoices, choiceOfValues != null);
-    }
-
-    /**
-     * @deprecated Use
-     *             {@link #FeatureEditorDialog(Shell, ILabelProvider, Object, EClassifier, List, String, List, boolean, boolean, boolean)}
-     *             , which provides proper behaviour for unique and non-unique
-     *             features. This form retains the old behaviour, where
-     *             specifying a list of choices enforces uniqueness.
-     */
-    @Deprecated
-    public FeatureEditorDialog(Shell parent, ILabelProvider labelProvider, Object object, EClassifier eClassifier, List<?> currentValues, String displayName, List<?> choiceOfValues) {
-        this(parent, labelProvider, object, eClassifier, currentValues, displayName, choiceOfValues, false, false, choiceOfValues != null);
-    }
-
     public FeatureEditorDialog(Shell parent, ILabelProvider labelProvider, EObject eObject, EStructuralFeature eStructuralFeature, String displayName, List<?> choiceOfValues) {
         this(parent, labelProvider, eObject, eStructuralFeature.getEType(), (List<?>) eObject.eGet(eStructuralFeature), displayName, choiceOfValues, false, false, eStructuralFeature.isUnique());
     }
diff --git a/plugins/org.eclipse.sirius.common/src/org/eclipse/sirius/common/tools/api/editing/IEditingDomainFactory.java b/plugins/org.eclipse.sirius.common/src/org/eclipse/sirius/common/tools/api/editing/IEditingDomainFactory.java
index 4c5aa4fc48..7f6103f602 100644
--- a/plugins/org.eclipse.sirius.common/src/org/eclipse/sirius/common/tools/api/editing/IEditingDomainFactory.java
+++ b/plugins/org.eclipse.sirius.common/src/org/eclipse/sirius/common/tools/api/editing/IEditingDomainFactory.java
@@ -10,9 +10,7 @@
  *******************************************************************************/
 package org.eclipse.sirius.common.tools.api.editing;
 
-import org.eclipse.emf.transaction.TransactionalEditingDomain;
 import org.eclipse.emf.transaction.TransactionalEditingDomain.Factory;
-
 import org.eclipse.sirius.common.tools.DslCommonPlugin;
 
 /**
@@ -32,15 +30,4 @@ public interface IEditingDomainFactory extends Factory {
 
     /** . */
     String EXTENSION_POINT_CLASS_ATTRIBUTE = "class";
-
-    /**
-     * Create a new the EditingDomain.
-     * 
-     * @return a newly created EditingDomain
-     * @deprecated to make sure you'll support any kind of models (Xtext one for
-     *             instances) you should use createEditingDomain(ResourceSet)
-     *             with the resourceSet returned by the ResourceSetFatory.
-     */
-    TransactionalEditingDomain createEditingDomain();
-
 }
diff --git a/plugins/org.eclipse.sirius.common/src/org/eclipse/sirius/common/tools/api/listener/Notification.java b/plugins/org.eclipse.sirius.common/src/org/eclipse/sirius/common/tools/api/listener/Notification.java
index 276d7f201a..a036c51ef9 100644
--- a/plugins/org.eclipse.sirius.common/src/org/eclipse/sirius/common/tools/api/listener/Notification.java
+++ b/plugins/org.eclipse.sirius.common/src/org/eclipse/sirius/common/tools/api/listener/Notification.java
@@ -51,13 +51,4 @@ public interface Notification {
      * @since 0.9.0
      */
     int REFRESH_VISIBILITY_ON_DIAGRAM = 3;
-
-    /**
-     * Activate the visibility propagator for edge folding.
-     * 
-     * @since 0.9.0
-     */
-    @Deprecated
-    int FOLD = 4;
-
 }
diff --git a/plugins/org.eclipse.sirius.common/src/org/eclipse/sirius/common/tools/api/util/EclipseUtil.java b/plugins/org.eclipse.sirius.common/src/org/eclipse/sirius/common/tools/api/util/EclipseUtil.java
index 75a4d4d52c..44d081e860 100644
--- a/plugins/org.eclipse.sirius.common/src/org/eclipse/sirius/common/tools/api/util/EclipseUtil.java
+++ b/plugins/org.eclipse.sirius.common/src/org/eclipse/sirius/common/tools/api/util/EclipseUtil.java
@@ -11,10 +11,7 @@
 package org.eclipse.sirius.common.tools.api.util;
 
 import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.Iterator;
 import java.util.List;
-import java.util.Set;
 
 import org.eclipse.core.resources.IFile;
 import org.eclipse.core.resources.IResource;
@@ -28,13 +25,12 @@ 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.sirius.common.tools.DslCommonPlugin;
 
 import com.google.common.base.Predicate;
 import com.google.common.base.Predicates;
 import com.google.common.collect.Lists;
 
-import org.eclipse.sirius.common.tools.DslCommonPlugin;
-
 /**
  * This class is should contains useful static functions related to Eclipse
  * platform.
@@ -171,70 +167,6 @@ public final class EclipseUtil {
     }
 
     /**
-     * Get the list of plug-ins which contribute to an extension ID.
-     * 
-     * @param extensionId
-     *            the extension point id
-     * @param attribute
-     *            the attribute of the configuration element
-     * @param pattern
-     *            pattern to match.
-     * 
-     * @return a Set of {@link IExtension} instances
-     */
-    @Deprecated
-    public static Set<?> getExtensionPlugins(final String extensionId, final String attribute, final String pattern) {
-        return EclipseUtil.retrieveInPlugins(extensionId, attribute, pattern, null);
-    }
-
-    /**
-     * return a set of table object containing for each an IExtension instance
-     * and the attribute value of elementAttribute.
-     * 
-     * @param extensionId
-     *            the extension point id
-     * @param attribute
-     *            the attribute of the configuration element
-     * @param pattern
-     *            pattern to match
-     * 
-     * @param elementAttributes
-     *            the attributes to get the value for (must be {@link String}
-     * @return a set of table object containing for each an IExtension instance
-     *         and the attribute value of elementAttribute
-     */
-    @Deprecated
-    public static Set<?> getElementsProvidedByPlugin(final String extensionId, final String attribute, final String pattern, final List<String> elementAttributes) {
-        return EclipseUtil.retrieveInPlugins(extensionId, attribute, pattern, elementAttributes);
-    }
-
-    @Deprecated
-    private static Set<?> retrieveInPlugins(final String extensionId, final String attribute, final String pattern, final List<String> elementAttributes) {
-        final IExtension[] extensions = EclipseUtil.getExtensions(extensionId);
-        final Set<Object> contributors = new HashSet<Object>(extensions.length);
-
-        for (final IExtension ext : extensions) {
-            final IConfigurationElement[] ce = ext.getConfigurationElements();
-            for (IConfigurationElement element : ce) {
-                if (element.getAttribute(attribute).matches(pattern)) {
-                    if (elementAttributes == null) {
-                        contributors.add(ext);
-                    } else {
-                        final List<String> values = new ArrayList<String>(elementAttributes.size());
-                        final Iterator<String> it = elementAttributes.iterator();
-                        while (it.hasNext()) {
-                            final String elementAttribute = it.next();
-                            values.add(element.getAttribute(elementAttribute));
-                        }
-                        contributors.add(new Object[] { ext.getContributor().getName(), values });
-                    }
-                }
-            }
-        }
-        return contributors;
-    }
-
-    /**
      * Get the files in the workspace. You may filter the returned files with
      * start and end prefixes.
      * 
diff --git a/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/tools/internal/editor/DDiagramEditorImpl.java b/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/tools/internal/editor/DDiagramEditorImpl.java
index 131fa585d2..e136801d81 100644
--- a/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/tools/internal/editor/DDiagramEditorImpl.java
+++ b/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/tools/internal/editor/DDiagramEditorImpl.java
@@ -25,6 +25,7 @@ import org.eclipse.core.resources.IFile;
 import org.eclipse.core.resources.IMarker;
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.eclipse.core.runtime.IStatus;
+import org.eclipse.core.runtime.NullProgressMonitor;
 import org.eclipse.core.runtime.Platform;
 import org.eclipse.core.runtime.Status;
 import org.eclipse.core.runtime.jobs.Job;
@@ -77,6 +78,7 @@ import org.eclipse.gmf.runtime.notation.Diagram;
 import org.eclipse.gmf.runtime.notation.View;
 import org.eclipse.jface.action.IAction;
 import org.eclipse.jface.action.IToolBarManager;
+import org.eclipse.jface.dialogs.ProgressMonitorDialog;
 import org.eclipse.jface.resource.ImageDescriptor;
 import org.eclipse.jface.text.AbstractInformationControlManager;
 import org.eclipse.jface.text.IDocument;
@@ -1258,7 +1260,7 @@ public class DDiagramEditorImpl extends SiriusDiagramEditor implements DDiagramE
 
                     command = compoundCommand;
                 } else {
-                    command = new RefreshRepresentationsCommand(getEditingDomain(), dDiagram);
+                    command = new RefreshRepresentationsCommand(getEditingDomain(), new NullProgressMonitor(), dDiagram);
                 }
                 getEditingDomain().getCommandStack().execute(command);
             }
diff --git a/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/tools/internal/graphical/edit/policies/MyNiceCustomBarPolicy.java b/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/tools/internal/graphical/edit/policies/MyNiceCustomBarPolicy.java
index 214349ff43..c8a599c688 100644
--- a/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/tools/internal/graphical/edit/policies/MyNiceCustomBarPolicy.java
+++ b/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/tools/internal/graphical/edit/policies/MyNiceCustomBarPolicy.java
@@ -14,6 +14,7 @@ import java.util.ArrayList;
 import java.util.List;
 
 import org.eclipse.core.runtime.IAdaptable;
+import org.eclipse.core.runtime.NullProgressMonitor;
 import org.eclipse.draw2d.FreeformLayer;
 import org.eclipse.draw2d.IFigure;
 import org.eclipse.draw2d.ImageFigure;
@@ -211,7 +212,7 @@ public class MyNiceCustomBarPolicy extends DiagramAssistantEditPolicy implements
                         hideDiagramAssistant();
 
                         TransactionalEditingDomain domain = TransactionUtil.getEditingDomain(dDiagram);
-                        Command changeActivatedLayersCmd = new ChangeLayerActivationCommand(domain, dDiagram, additionalLayer);
+                        Command changeActivatedLayersCmd = new ChangeLayerActivationCommand(domain, dDiagram, additionalLayer, new NullProgressMonitor());
                         domain.getCommandStack().execute(changeActivatedLayersCmd);
                     }
                 });
diff --git a/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/ui/tools/internal/commands/ChangeLayerActivationCommand.java b/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/ui/tools/internal/commands/ChangeLayerActivationCommand.java
index 0f0d275ff9..dea7f2408d 100644
--- a/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/ui/tools/internal/commands/ChangeLayerActivationCommand.java
+++ b/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/ui/tools/internal/commands/ChangeLayerActivationCommand.java
@@ -11,16 +11,15 @@
 package org.eclipse.sirius.diagram.ui.tools.internal.commands;
 
 import org.eclipse.core.runtime.IProgressMonitor;
-import org.eclipse.core.runtime.NullProgressMonitor;
 import org.eclipse.core.runtime.SubProgressMonitor;
 import org.eclipse.emf.transaction.RecordingCommand;
 import org.eclipse.emf.transaction.TransactionalEditingDomain;
 import org.eclipse.emf.transaction.util.TransactionUtil;
-import org.eclipse.sirius.common.tools.api.listener.Notification;
-import org.eclipse.sirius.common.tools.api.listener.NotificationUtil;
 import org.eclipse.sirius.business.api.dialect.command.RefreshRepresentationsCommand;
 import org.eclipse.sirius.business.api.query.IdentifiedElementQuery;
 import org.eclipse.sirius.business.internal.metamodel.helper.LayerHelper;
+import org.eclipse.sirius.common.tools.api.listener.Notification;
+import org.eclipse.sirius.common.tools.api.listener.NotificationUtil;
 import org.eclipse.sirius.viewpoint.DDiagram;
 import org.eclipse.sirius.viewpoint.description.Layer;
 
@@ -46,23 +45,6 @@ public final class ChangeLayerActivationCommand extends RecordingCommand {
      *            the {@link DDiagram} for which change the activated layers
      * @param layer
      *            the {@link Layer} concerned by this change
-     * @deprecated use
-     *             {@link ChangeLayerActivationCommand#ChangeLayerActivationCommand(TransactionalEditingDomain, DDiagram, Layer, IProgressMonitor)}
-     *             instead
-     */
-    public ChangeLayerActivationCommand(TransactionalEditingDomain domain, DDiagram dDiagram, Layer layer) {
-        this(domain, dDiagram, layer, new NullProgressMonitor());
-    }
-
-    /**
-     * Default Constructor.
-     * 
-     * @param domain
-     *            the editing domain.
-     * @param dDiagram
-     *            the {@link DDiagram} for which change the activated layers
-     * @param layer
-     *            the {@link Layer} concerned by this change
      * @param monitor
      *            a {@link IProgressMonitor} to show progression of layer
      *            activation changes
diff --git a/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/ui/tools/internal/dialogs/ColorPalettePopup.java b/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/ui/tools/internal/dialogs/ColorPalettePopup.java
index 742a37126d..68700b8fee 100644
--- a/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/ui/tools/internal/dialogs/ColorPalettePopup.java
+++ b/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/ui/tools/internal/dialogs/ColorPalettePopup.java
@@ -198,24 +198,6 @@ public class ColorPalettePopup {
     private boolean useDefaultColor;
 
     /**
-     * Creates a color palette popup above the specified shell.
-     * 
-     * @param parent
-     *            a Shell control which will be the parent of the new instance
-     *            (cannot be null)
-     * @param preferenceId
-     *            the preference id
-     * @param rowHeight
-     *            the row height
-     * @deprecated Use the other constructor. This one does not retrieve the
-     *             default value from the correct preference store.
-     */
-    @Deprecated
-    public ColorPalettePopup(Shell parent, String preferenceId, int rowHeight) {
-        this(parent, rowHeight);
-    }
-
-    /**
      * Creates a PopupList above the specified shell.
      * 
      * @param parent
diff --git a/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/ui/tools/internal/layout/provider/AbstractCompositeLayoutProvider.java b/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/ui/tools/internal/layout/provider/AbstractCompositeLayoutProvider.java
index d9ada91b9f..2a316be321 100644
--- a/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/ui/tools/internal/layout/provider/AbstractCompositeLayoutProvider.java
+++ b/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/ui/tools/internal/layout/provider/AbstractCompositeLayoutProvider.java
@@ -291,18 +291,6 @@ public abstract class AbstractCompositeLayoutProvider extends CompositeLayoutPro
      * 
      * @see org.eclipse.gmf.runtime.diagram.ui.providers.internal.DefaultProvider#build_edges(java.util.List,
      *      java.util.Map)
-     * @deprecated
-     */
-    @Override
-    protected EdgeList build_edges(final List selectedObjects, final Map editPartToNodeDict) {
-        return buildEdges(selectedObjects, editPartToNodeDict);
-    }
-
-    /**
-     * {@inheritDoc}
-     * 
-     * @see org.eclipse.gmf.runtime.diagram.ui.providers.internal.DefaultProvider#build_edges(java.util.List,
-     *      java.util.Map)
      */
     @Override
     protected EdgeList buildEdges(final List selectedObjects, final Map editPartToNodeDict) {
diff --git a/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/ui/tools/internal/views/providers/layers/LayersCellModifier.java b/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/ui/tools/internal/views/providers/layers/LayersCellModifier.java
index 17c7a59b25..9db4fe6038 100644
--- a/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/ui/tools/internal/views/providers/layers/LayersCellModifier.java
+++ b/plugins/org.eclipse.sirius.diagram/src/org/eclipse/sirius/diagram/ui/tools/internal/views/providers/layers/LayersCellModifier.java
@@ -151,7 +151,7 @@ public class LayersCellModifier implements ICellModifier {
                             public void run(final IProgressMonitor monitor) throws InvocationTargetException, InterruptedException {
                                 monitor.beginTask("Apply layer modifications...", 1);
                                 TransactionalEditingDomain domain = TransactionUtil.getEditingDomain(dDiagram);
-                                Command changeActivatedLayersCmd = new ChangeLayerActivationCommand(domain, dDiagram, layer);
+                                Command changeActivatedLayersCmd = new ChangeLayerActivationCommand(domain, dDiagram, layer, monitor);
                                 domain.getCommandStack().execute(changeActivatedLayersCmd);
                                 monitor.done();
                             }
diff --git a/plugins/org.eclipse.sirius.doc/doc/Release Notes.html b/plugins/org.eclipse.sirius.doc/doc/Release Notes.html
index 511d7e193b..a477b0ed59 100644
--- a/plugins/org.eclipse.sirius.doc/doc/Release Notes.html
+++ b/plugins/org.eclipse.sirius.doc/doc/Release Notes.html
@@ -13,12 +13,159 @@
 				<a href="#ReleaseNotesforSirius">Release Notes for Sirius</a>
 				<ol style="list-style: disc;">
 					<li>
+						<a href="#ChangesinSirius1.0.0M4fromSirius0.9">Changes in Sirius 1.0.0M4 (from Sirius 0.9)</a>
+					</li>
+					<li>
 						<a href="#ChangesfromViewpoint6.9toSirius0.9">Changes from Viewpoint 6.9 to Sirius 0.9</a>
 					</li>
 				</ol>
 			</li>
 		</ol>
 		<p>This document contains the release notes for all major releases of Sirius.</p>
+		<h2 id="ChangesinSirius1.0.0M4fromSirius0.9">Changes in Sirius 1.0.0M4 (from Sirius 0.9)</h2>
+		<h3 id="UserVisibleChanges">User-Visible Changes</h3>
+		<h3 id="APIChanges">API Changes</h3>
+		<p>Sirius 1.0.0M4 includes a lots of API-breaking changes, as part of a global effort to improve the quality of the Sirius internals. In this milestone in particular, most of the APIs which were marked as deprecated in previous versions of Sirius (and before that of Viewpoint) have been either removed (if a replacement exists) or marked as non-deprecated (if no replacement exists yet).</p>
+		<h4 id="Changesinorg.eclipse.sirius.common">Changes in  
+			<code>org.eclipse.sirius.common</code>
+		</h4>
+		<ul>
+			<li>Two deprecated constructors have been removed in 
+				<code>FeatureEditorDialog</code>. Use the remaining constructor instead, which provides proper behaviour for both unique and non-unique features.
+			</li>
+			<li>The deprecated method 
+				<code>IEditingDomainFactory.createEditingDomain()</code> has been removed. Use the (inherited) 
+				<code>createEditingDomain(ResourceSet)</code> instead, which ensures correct behavior for all kinds of models (Xtext for example).
+			</li>
+			<li>The deprecated field 
+				<code>org.eclipse.sirius.common.tools.api.listener.Notification.FOLD</code> has been removed. It was never used by Sirius itself, so if your code tried to listen to this kind of notification it was never actually called and can be safely removed.
+			</li>
+			<li>The deprecated methods 
+				<code>getExtensionPlugins()</code> and 
+				<code>getElementsProvidedByPlugin</code> from 
+				<code>EcliseUtil</code> have been removed. If you need this kind of functionality, use the Eclipse APIs directly instead.
+			</li>
+		</ul>
+		<h4 id="Changesinorg.eclipse.sirius">Changes in 
+			<code>org.eclipse.sirius</code>
+		</h4>
+		<ul>
+			<li>The deprecated method 
+				<code>DialectServices.initRepresentations(Viewpoint, EObject)</code> has been removed. Use the version which takes an additional 
+				<code>IProgressMonitor</code> instead. 
+			</li>
+			<li>The deprecated constructor in 
+				<code>CreateRepresentationCommand</code> has been removed. Use the alternative constructor which takes an additional 
+				<code>IProgressMonitor</code> instead.
+			</li>
+			<li>The two deprecated constructors in 
+				<code>RefreshRepresentationCommand</code> have been removed. Use the alternative constructors which take an additional 
+				<code>IProgressMonitor</code> instead.
+			</li>
+			<li>The deprecated method 
+				<code>DisplayService.computeVisibility(Session, DDiagram, DDiagramElement)</code> has been removed. Use the variant 
+				<code>computeVisibility()</code> which takes a 
+				<code>DiagramMappingsManager</code> instead of a 
+				<code>Session</code>.
+			</li>
+			<li>The following deprecated methods in 
+				<code>FilterService</code> have been removed:
+				<ul>
+					<li>
+						<code>activateCache()</code>: use 
+						<code>DisplayService.activateCache()</code> instead.
+					</li>
+					<li>
+						<code>deactivateCache()</code>: use 
+						<code>DisplayService.deactivateCache()</code> instead.
+					</li>
+					<li>
+						<code>activate()</code>: use 
+						<code>DisplayService.activate()</code> instead.
+					</li>
+					<li>
+						<code>deactivate()</code>: use 
+						<code>DisplayService.deactivate()</code> instead.
+					</li>
+					<li>
+						<code>isActivated()</code>: use 
+						<code>DisplayServiceManager.INSTANCE.getMode() == DisplayMode.NORMAL</code> instead.
+					</li>
+					<li>
+						<code>isCollapse()</code>: use 
+						<code>isCollapsed()</code> instead.
+					</li>
+					<li>
+						<code>isVisibleForFilters()</code>: use 
+						<code>getAppliedFilters()</code> instead.
+					</li>
+					<li>
+						<code>isVisible()</code>: use 
+						<code>DisplayService.isDisplayed()</code> instead.
+					</li>
+					<li>
+						<code>isFiltered()</code>, 
+						<code>isNotFiltered()</code>, 
+						<code>isVisibleForActivatedFilters(), @checkFilters()</code>: use 
+						<code>getAppliedFilters()</code> and 
+						<code>DDiagram.getActivatedFilters()</code> instead.
+					</li>
+				</ul>
+			</li>
+			<li>The deprecated methods 
+				<code>isDirectlyHidden()</code> and 
+				<code>isIndirectlyHidden()</code> in 
+				<code>HideFilterHelper</code> have been removed. Use the corresponding methods in 
+				<code>DDiagramElementQuery</code> instead.
+			</li>
+			<li>The deprecated method 
+				<code>SavingPolicy.save(Iterable, Map)</code> has been removed. Use the variant which takes an additional 
+				<code>IProgressMonitor</code> instead.
+			</li>
+			<li>The deprecated constructor 
+				<code>AbstractCommandFactory(TransactionalEditingDomain, ModelAccessor)</code> has been removed. Use the variant without the 
+				<code>ModelAccessor</code> argument instead.
+			</li>
+			<li>The deprecated constructor 
+				<code>CommandContext(EObject)</code> has been removed. Use the variant which takes an additional 
+				<code>DRepresentation</code> instead.
+			</li>
+			<li>The deprecated methods 
+				<code>activate(TransactionalEditingDomain)</code> and 
+				<code>deactivate(TransactionalEditingDomain)</code> in 
+				<code>IChangeListener</code> have been removed. Use the variants with no argument instead.
+			</li>
+			<li>The deprecated constructor 
+				<code>AddSemanticResourceCommand(Session, URI)</code> has been removed. Use the variant which takes an additional 
+				<code>IProgressMonitor</code> instead.
+			</li>
+			<li>The deprecated constructors of 
+				<code>RemoveSemanticResourceCommand</code> have been removed. Use the variants which takes an additional 
+				<code>IProgressMonitor</code> instead.
+			</li>
+			<li>The deprecated constructor in 
+				<code>CreateDiagramWithInitialOperation</code> has been removed. Use the variant which takes an additional 
+				<code>IProgressMonitor</code> instead.
+			</li>
+		</ul>
+		<h4 id="Changesinorg.eclipse.sirius.ui">Changes in  
+			<code>org.eclipse.sirius.ui</code>
+		</h4>
+		<ul>
+			<li>All deprecated methods in 
+				<code>ModelingProjectManager</code> have been removed. Use the corresponding versions which take an additional 
+				<code>IProgressMonitor</code> parameter instead.
+			</li>
+		</ul>
+		<h4 id="Changesinorg.eclipse.sirius.tree">Changes in 
+			<code>org.eclipse.sirius.tree</code>
+		</h4>
+		<ul>
+			<li>The deprecated method 
+				<code>DTreeUserInteraction.refreshContent()</code> has been removed. Use the variant which take an additional 
+				<code>IProgressMonitor</code> parameter instead.
+			</li>
+		</ul>
 		<h2 id="ChangesfromViewpoint6.9toSirius0.9">Changes from Viewpoint 6.9 to Sirius 0.9</h2>
 		<h3 id="Pluginsversionnumbers.">Plug-ins version numbers.</h3>
 		<p>As of Sirius 0.9, and probably at least until Sirius 1.0 when the APIs will be more stable, all the bundles share the same version, which is also the version for the feature. If you used versioned dependencies to the old Viewpoint code (e.g. dependencies towards Viewpoint 6.8), you need to adjust the versions in your 
@@ -243,7 +390,7 @@ void addSelectedView(DView view) throws IllegalArgumentException;
 void removeSelectedView(DView view);
 
 </pre>
-		<h3 id="UserVisibleChanges">User-Visible Changes</h3>
+		<h3 id="UserVisibleChanges2">User-Visible Changes</h3>
 		<ul>
 			<li>The ability to print table representations has been disabled for the 0.9 release due to an external dependency issue (see 
 				<a href="https://bugs.eclipse.org/bugs/show_bug.cgi?id=422223">bug #422223</a> for the details). It should be re-introduced in 1.0.
diff --git a/plugins/org.eclipse.sirius.doc/doc/Release Notes.textile b/plugins/org.eclipse.sirius.doc/doc/Release Notes.textile
index d525f58510..882b8640c4 100644
--- a/plugins/org.eclipse.sirius.doc/doc/Release Notes.textile
+++ b/plugins/org.eclipse.sirius.doc/doc/Release Notes.textile
@@ -4,6 +4,54 @@ h1. Release Notes for Sirius
 
 This document contains the release notes for all major releases of Sirius.
 
+h2. Changes in Sirius 1.0.0M4 (from Sirius 0.9)
+
+h3. User-Visible Changes
+
+h3. API Changes
+
+Sirius 1.0.0M4 includes a lots of API-breaking changes, as part of a global effort to improve the quality of the Sirius internals. In this milestone in particular, most of the APIs which were marked as deprecated in previous versions of Sirius (and before that of Viewpoint) have been either removed (if a replacement exists) or marked as non-deprecated (if no replacement exists yet).
+
+h4. Changes in  @org.eclipse.sirius.common@
+
+* Two deprecated constructors have been removed in @FeatureEditorDialog@. Use the remaining constructor instead, which provides proper behaviour for both unique and non-unique features.
+* The deprecated method @IEditingDomainFactory.createEditingDomain()@ has been removed. Use the (inherited) @createEditingDomain(ResourceSet)@ instead, which ensures correct behavior for all kinds of models (Xtext for example).
+* The deprecated field @org.eclipse.sirius.common.tools.api.listener.Notification.FOLD@ has been removed. It was never used by Sirius itself, so if your code tried to listen to this kind of notification it was never actually called and can be safely removed.
+* The deprecated methods @getExtensionPlugins()@ and @getElementsProvidedByPlugin@ from @EcliseUtil@ have been removed. If you need this kind of functionality, use the Eclipse APIs directly instead.
+
+h4. Changes in @org.eclipse.sirius@
+
+* The deprecated method @DialectServices.initRepresentations(Viewpoint, EObject)@ has been removed. Use the version which takes an additional @IProgressMonitor@ instead. 
+* The deprecated constructor in @CreateRepresentationCommand@ has been removed. Use the alternative constructor which takes an additional @IProgressMonitor@ instead.
+* The two deprecated constructors in @RefreshRepresentationCommand@ have been removed. Use the alternative constructors which take an additional @IProgressMonitor@ instead.
+* The deprecated method @DisplayService.computeVisibility(Session, DDiagram, DDiagramElement)@ has been removed. Use the variant @computeVisibility()@ which takes a @DiagramMappingsManager@ instead of a @Session@.
+* The following deprecated methods in @FilterService@ have been removed:
+** @activateCache()@: use @DisplayService.activateCache()@ instead.
+** @deactivateCache()@: use @DisplayService.deactivateCache()@ instead.
+** @activate()@: use @DisplayService.activate()@ instead.
+** @deactivate()@: use @DisplayService.deactivate()@ instead.
+** @isActivated()@: use @DisplayServiceManager.INSTANCE.getMode() == DisplayMode.NORMAL@ instead.
+** @isCollapse()@: use @isCollapsed()@ instead.
+** @isVisibleForFilters()@: use @getAppliedFilters()@ instead.
+** @isVisible()@: use @DisplayService.isDisplayed()@ instead.
+** @isFiltered()@, @isNotFiltered()@, @isVisibleForActivatedFilters(), @checkFilters()@: use @getAppliedFilters()@ and @DDiagram.getActivatedFilters()@ instead.
+* The deprecated methods @isDirectlyHidden()@ and @isIndirectlyHidden()@ in @HideFilterHelper@ have been removed. Use the corresponding methods in @DDiagramElementQuery@ instead.
+* The deprecated method @SavingPolicy.save(Iterable, Map)@ has been removed. Use the variant which takes an additional @IProgressMonitor@ instead.
+* The deprecated constructor @AbstractCommandFactory(TransactionalEditingDomain, ModelAccessor)@ has been removed. Use the variant without the @ModelAccessor@ argument instead.
+* The deprecated constructor @CommandContext(EObject)@ has been removed. Use the variant which takes an additional @DRepresentation@ instead.
+* The deprecated methods @activate(TransactionalEditingDomain)@ and @deactivate(TransactionalEditingDomain)@ in @IChangeListener@ have been removed. Use the variants with no argument instead.
+* The deprecated constructor @AddSemanticResourceCommand(Session, URI)@ has been removed. Use the variant which takes an additional @IProgressMonitor@ instead.
+* The deprecated constructors of @RemoveSemanticResourceCommand@ have been removed. Use the variants which takes an additional @IProgressMonitor@ instead.
+* The deprecated constructor in @CreateDiagramWithInitialOperation@ has been removed. Use the variant which takes an additional @IProgressMonitor@ instead.
+
+h4. Changes in  @org.eclipse.sirius.ui@
+
+* All deprecated methods in @ModelingProjectManager@ have been removed. Use the corresponding versions which take an additional @IProgressMonitor@ parameter instead.
+
+h4. Changes in @org.eclipse.sirius.tree@
+
+* The deprecated method @DTreeUserInteraction.refreshContent()@ has been removed. Use the variant which take an additional @IProgressMonitor@ parameter instead.
+
 h2. Changes from Viewpoint 6.9 to Sirius 0.9
 
 h3. Plug-ins version numbers.
diff --git a/plugins/org.eclipse.sirius.tree.ui/src/org/eclipse/sirius/tree/ui/tools/internal/editor/DTreeEditor.java b/plugins/org.eclipse.sirius.tree.ui/src/org/eclipse/sirius/tree/ui/tools/internal/editor/DTreeEditor.java
index 0275b6cc0f..a69750d56d 100644
--- a/plugins/org.eclipse.sirius.tree.ui/src/org/eclipse/sirius/tree/ui/tools/internal/editor/DTreeEditor.java
+++ b/plugins/org.eclipse.sirius.tree.ui/src/org/eclipse/sirius/tree/ui/tools/internal/editor/DTreeEditor.java
@@ -356,7 +356,7 @@ public class DTreeEditor extends AbstractDTreeEditor implements org.eclipse.siri
      * {@inheritDoc}
      * */
     protected void launchRefresh(boolean loading) {
-        getEditingDomain().getCommandStack().execute(new RefreshRepresentationsCommand(getEditingDomain(), getTreeModel()));
+        getEditingDomain().getCommandStack().execute(new RefreshRepresentationsCommand(getEditingDomain(), new NullProgressMonitor(), getTreeModel()));
         if (!loading) {
             getViewer().refresh();
         }
diff --git a/plugins/org.eclipse.sirius.tree/src/org/eclipse/sirius/tree/business/api/interaction/DTreeUserInteraction.java b/plugins/org.eclipse.sirius.tree/src/org/eclipse/sirius/tree/business/api/interaction/DTreeUserInteraction.java
index 553b32550b..4e591028d8 100644
--- a/plugins/org.eclipse.sirius.tree/src/org/eclipse/sirius/tree/business/api/interaction/DTreeUserInteraction.java
+++ b/plugins/org.eclipse.sirius.tree/src/org/eclipse/sirius/tree/business/api/interaction/DTreeUserInteraction.java
@@ -13,14 +13,9 @@ package org.eclipse.sirius.tree.business.api.interaction;
 import java.util.Iterator;
 
 import org.eclipse.core.runtime.IProgressMonitor;
-import org.eclipse.core.runtime.NullProgressMonitor;
 import org.eclipse.core.runtime.SubProgressMonitor;
-import org.eclipse.sirius.synchronizer.SemanticPartitionInvalidator;
-
-import com.google.common.base.Predicate;
-import com.google.common.collect.Iterators;
-
 import org.eclipse.sirius.common.tools.DslCommonPlugin;
+import org.eclipse.sirius.synchronizer.SemanticPartitionInvalidator;
 import org.eclipse.sirius.tools.api.profiler.SiriusTasksKey;
 import org.eclipse.sirius.tree.DTree;
 import org.eclipse.sirius.tree.DTreeItem;
@@ -28,6 +23,9 @@ import org.eclipse.sirius.tree.business.api.query.TreeDescriptionQuery;
 import org.eclipse.sirius.tree.business.internal.dialect.common.tree.DTreeRefresh;
 import org.eclipse.sirius.tree.business.internal.dialect.common.viewpoint.GlobalContext;
 
+import com.google.common.base.Predicate;
+import com.google.common.collect.Iterators;
+
 /**
  * This class is responsible for providing an entry point to all the user
  * interactions available on an opened DTree instance.
@@ -57,19 +55,6 @@ public class DTreeUserInteraction {
     /**
      * Refreshes the content of the DTree.
      * 
-     * @return this user interaction
-     * 
-     * @deprecated use
-     *             {@link DTreeUserInteraction#refreshContent(IProgressMonitor)}
-     *             instead
-     */
-    public DTreeUserInteraction refreshContent() {
-        return refreshContent(new NullProgressMonitor());
-    }
-
-    /**
-     * Refreshes the content of the DTree.
-     * 
      * @param monitor
      *            a {@link IProgressMonitor} to use
      * 
diff --git a/plugins/org.eclipse.sirius.tree/src/org/eclipse/sirius/tree/business/internal/helper/RefreshTreeElementTask.java b/plugins/org.eclipse.sirius.tree/src/org/eclipse/sirius/tree/business/internal/helper/RefreshTreeElementTask.java
index 50ccf53d4c..844139f491 100644
--- a/plugins/org.eclipse.sirius.tree/src/org/eclipse/sirius/tree/business/internal/helper/RefreshTreeElementTask.java
+++ b/plugins/org.eclipse.sirius.tree/src/org/eclipse/sirius/tree/business/internal/helper/RefreshTreeElementTask.java
@@ -115,7 +115,7 @@ public class RefreshTreeElementTask extends AbstractCommandTask {
             while (it.hasNext()) {
                 final Object obj = it.next();
                 if (obj instanceof DTree) {
-                    editingDomain.getCommandStack().execute(new RefreshRepresentationsCommand(editingDomain, (DTree) obj));
+                    editingDomain.getCommandStack().execute(new RefreshRepresentationsCommand(editingDomain, monitor, (DTree) obj));
                 } else if (obj instanceof DTreeElement) {
                     editingDomain.getCommandStack().execute(new RefreshTreeElementCommand(editingDomain, (DTreeItem) obj, monitor));
                 }
diff --git a/plugins/org.eclipse.sirius.tree/src/org/eclipse/sirius/tree/business/internal/refresh/CreateTreeTask.java b/plugins/org.eclipse.sirius.tree/src/org/eclipse/sirius/tree/business/internal/refresh/CreateTreeTask.java
index 7c07d0710d..a3ea062f63 100644
--- a/plugins/org.eclipse.sirius.tree/src/org/eclipse/sirius/tree/business/internal/refresh/CreateTreeTask.java
+++ b/plugins/org.eclipse.sirius.tree/src/org/eclipse/sirius/tree/business/internal/refresh/CreateTreeTask.java
@@ -46,23 +46,6 @@ public class CreateTreeTask extends AbstractCommandTask {
      *            the tree description.
      * @param semanticElement
      *            semantic element on which the user requested the creation of
-     *            the {@link org.eclipse.sirius.tree.metamodel.tree.DTree} .
-     * @deprecated use
-     *             {@link CreateTreeTask#CreateTreeTask(TreeDescription, EObject, IProgressMonitor)}
-     *             instead
-     */
-    public CreateTreeTask(final TreeDescription desc, final EObject semanticElement) {
-        this.semanticElement = semanticElement;
-        this.description = desc;
-    }
-
-    /**
-     * Creates the command.
-     * 
-     * @param desc
-     *            the tree description.
-     * @param semanticElement
-     *            semantic element on which the user requested the creation of
      *            the {@link org.eclipse.sirius.tree.metamodel.tree.DTree}
      * @param monitor
      *            a {@link IProgressMonitor} to show progression of
diff --git a/plugins/org.eclipse.sirius.tree/src/org/eclipse/sirius/tree/tools/internal/command/TreeCommandFactory.java b/plugins/org.eclipse.sirius.tree/src/org/eclipse/sirius/tree/tools/internal/command/TreeCommandFactory.java
index cfa91cb728..d25e1933d6 100644
--- a/plugins/org.eclipse.sirius.tree/src/org/eclipse/sirius/tree/tools/internal/command/TreeCommandFactory.java
+++ b/plugins/org.eclipse.sirius.tree/src/org/eclipse/sirius/tree/tools/internal/command/TreeCommandFactory.java
@@ -19,7 +19,6 @@ import java.util.Map;
 import java.util.Set;
 
 import org.eclipse.core.runtime.IProgressMonitor;
-import org.eclipse.core.runtime.NullProgressMonitor;
 import org.eclipse.core.runtime.Platform;
 import org.eclipse.emf.common.command.AbstractCommand;
 import org.eclipse.emf.common.command.Command;
@@ -29,13 +28,6 @@ import org.eclipse.emf.ecore.EObject;
 import org.eclipse.emf.ecore.util.EcoreUtil;
 import org.eclipse.emf.transaction.RecordingCommand;
 import org.eclipse.emf.transaction.TransactionalEditingDomain;
-
-import com.google.common.collect.Sets;
-
-import org.eclipse.sirius.common.tools.api.interpreter.EvaluationException;
-import org.eclipse.sirius.common.tools.api.interpreter.IInterpreter;
-import org.eclipse.sirius.common.tools.api.interpreter.IInterpreterSiriusVariables;
-import org.eclipse.sirius.common.tools.api.util.StringUtil;
 import org.eclipse.sirius.business.api.helper.task.ICommandTask;
 import org.eclipse.sirius.business.api.helper.task.InitInterpreterVariablesTask;
 import org.eclipse.sirius.business.api.helper.task.RemoveDanglingReferencesTask;
@@ -45,6 +37,12 @@ import org.eclipse.sirius.business.api.helper.task.UnexecutableTask;
 import org.eclipse.sirius.business.api.helper.task.label.InitInterpreterFromParsedVariableTask2;
 import org.eclipse.sirius.business.api.logger.RuntimeLoggerManager;
 import org.eclipse.sirius.business.api.preferences.SiriusPreferencesKeys;
+import org.eclipse.sirius.common.tools.api.interpreter.EvaluationException;
+import org.eclipse.sirius.common.tools.api.interpreter.IInterpreter;
+import org.eclipse.sirius.common.tools.api.interpreter.IInterpreterSiriusVariables;
+import org.eclipse.sirius.common.tools.api.util.StringUtil;
+import org.eclipse.sirius.ecore.extender.business.api.accessor.ModelAccessor;
+import org.eclipse.sirius.ecore.extender.business.api.permission.IPermissionAuthority;
 import org.eclipse.sirius.tools.api.command.AbstractCommandFactory;
 import org.eclipse.sirius.tools.api.command.DCommand;
 import org.eclipse.sirius.tools.api.command.InvalidPermissionCommand;
@@ -78,8 +76,8 @@ import org.eclipse.sirius.viewpoint.description.tool.ExternalJavaAction;
 import org.eclipse.sirius.viewpoint.description.tool.OperationAction;
 import org.eclipse.sirius.viewpoint.description.tool.RepresentationCreationDescription;
 import org.eclipse.sirius.viewpoint.description.tool.ToolPackage;
-import org.eclipse.sirius.ecore.extender.business.api.accessor.ModelAccessor;
-import org.eclipse.sirius.ecore.extender.business.api.permission.IPermissionAuthority;
+
+import com.google.common.collect.Sets;
 
 /**
  * A command factory that creates commands that can be undone.
@@ -395,22 +393,6 @@ public class TreeCommandFactory extends AbstractCommandFactory implements ITreeC
      *            the tool that describes how to create the table.
      * @param semanticElement
      *            the element from which the table will be created.
-     * @return a command that is able to create a table.
-     * @deprecated use
-     *             {@link TreeCommandFactory#buildCreateTreeFromDescription(TreeDescription, EObject, IProgressMonitor)}
-     *             instead
-     */
-    public DCommand buildCreateTreeFromDescription(final TreeDescription description, final EObject semanticElement) {
-        return buildCreateTreeFromDescription(description, semanticElement, new NullProgressMonitor());
-    }
-
-    /**
-     * Create a command that is able to create a table.
-     * 
-     * @param description
-     *            the tool that describes how to create the table.
-     * @param semanticElement
-     *            the element from which the table will be created.
      * @param monitor
      *            a {@link IProgressMonitor} to show progression of
      *            {@link DTree} creation
diff --git a/plugins/org.eclipse.sirius.ui/src/org/eclipse/sirius/ui/business/internal/commands/ChangeViewpointSelectionCommand.java b/plugins/org.eclipse.sirius.ui/src/org/eclipse/sirius/ui/business/internal/commands/ChangeViewpointSelectionCommand.java
index b170a44fb3..dc32dfdc1f 100644
--- a/plugins/org.eclipse.sirius.ui/src/org/eclipse/sirius/ui/business/internal/commands/ChangeViewpointSelectionCommand.java
+++ b/plugins/org.eclipse.sirius.ui/src/org/eclipse/sirius/ui/business/internal/commands/ChangeViewpointSelectionCommand.java
@@ -17,7 +17,6 @@ import java.util.List;
 import java.util.Set;
 
 import org.eclipse.core.runtime.IProgressMonitor;
-import org.eclipse.core.runtime.NullProgressMonitor;
 import org.eclipse.core.runtime.SubProgressMonitor;
 import org.eclipse.emf.transaction.RecordingCommand;
 import org.eclipse.sirius.business.api.query.IdentifiedElementQuery;
@@ -46,23 +45,6 @@ public class ChangeViewpointSelectionCommand extends RecordingCommand {
     private IProgressMonitor monitor;
 
     /**
-     * Specific command to change viewpoints selection.
-     * 
-     * @param session
-     *            the current session.
-     * @param callback
-     *            the current ViewpointSelection.Callback
-     * @param newSelectedViewpoints
-     *            the new selected viewpoints.
-     * @param newDeselectedViewpoints
-     *            the new deselected viewpoints.
-     * @deprecated use the constructor with a {@link IProgressMonitor}
-     */
-    public ChangeViewpointSelectionCommand(Session session, Callback callback, Set<Viewpoint> newSelectedViewpoints, Set<Viewpoint> newDeselectedViewpoints) {
-        this(session, callback, newSelectedViewpoints, newDeselectedViewpoints, new NullProgressMonitor());
-    }
-
-    /**
      * Specific command to change viewpoint selection.
      * 
      * @param session
diff --git a/plugins/org.eclipse.sirius.ui/src/org/eclipse/sirius/ui/tools/api/project/ModelingProjectManager.java b/plugins/org.eclipse.sirius.ui/src/org/eclipse/sirius/ui/tools/api/project/ModelingProjectManager.java
index 2a1b12012b..e64de7f765 100644
--- a/plugins/org.eclipse.sirius.ui/src/org/eclipse/sirius/ui/tools/api/project/ModelingProjectManager.java
+++ b/plugins/org.eclipse.sirius.ui/src/org/eclipse/sirius/ui/tools/api/project/ModelingProjectManager.java
@@ -46,7 +46,7 @@ public interface ModelingProjectManager {
      * @param representationsFileURI
      *            The URI of the representations file to open.
      */
-    void loadAndOpenRepresentationsFile(final URI representationsFileURI);
+    void loadAndOpenRepresentationsFile(URI representationsFileURI);
 
     /**
      * Load and open representations files.
@@ -54,7 +54,7 @@ public interface ModelingProjectManager {
      * @param representationsFilesURIs
      *            The URIs of the representations files to open.
      */
-    void loadAndOpenRepresentationsFiles(final List<URI> representationsFilesURIs);
+    void loadAndOpenRepresentationsFiles(List<URI> representationsFilesURIs);
 
     /**
      * Clear the cache for this representations file.
@@ -72,23 +72,6 @@ public interface ModelingProjectManager {
      * @param createAndOpenBlankRepresentationsFile
      *            true if a blank representations file must be created and open,
      *            false otherwise
-     * @return The new project
-     * @throws CoreException
-     *             in case of problem
-     * @deprecated use
-     *             {@link ModelingProjectManager#createNewModelingProject(String, boolean, IProgressMonitor)}
-     *             instead
-     */
-    IProject createNewModelingProject(final String projectName, boolean createAndOpenBlankRepresentationsFile) throws CoreException;
-
-    /**
-     * Create a new modeling project.
-     * 
-     * @param projectName
-     *            The project name
-     * @param createAndOpenBlankRepresentationsFile
-     *            true if a blank representations file must be created and open,
-     *            false otherwise
      * @param monitor
      *            a {@link IProgressMonitor} to show progression of Modeling
      *            Project creation
@@ -96,26 +79,7 @@ public interface ModelingProjectManager {
      * @throws CoreException
      *             in case of problem
      */
-    IProject createNewModelingProject(final String projectName, boolean createAndOpenBlankRepresentationsFile, IProgressMonitor monitor) throws CoreException;
-
-    /**
-     * Create a new modeling project.
-     * 
-     * @param projectName
-     *            The project name
-     * @param projectLocationPath
-     *            The project location path
-     * @param createAndOpenBlankRepresentationsFile
-     *            true if a blank representations file must be created and open,
-     *            false otherwise
-     * @return The new project
-     * @throws CoreException
-     *             in case of problem
-     * @deprecated use
-     *             {@link ModelingProjectManager#createNewModelingProject(String, IPath, boolean, IProgressMonitor)}
-     *             instead
-     */
-    IProject createNewModelingProject(final String projectName, final IPath projectLocationPath, final boolean createAndOpenBlankRepresentationsFile) throws CoreException;
+    IProject createNewModelingProject(String projectName, boolean createAndOpenBlankRepresentationsFile, IProgressMonitor monitor) throws CoreException;
 
     /**
      * Create a new modeling project.
@@ -134,20 +98,7 @@ public interface ModelingProjectManager {
      * @throws CoreException
      *             in case of problem
      */
-    IProject createNewModelingProject(final String projectName, final IPath projectLocationPath, final boolean createAndOpenBlankRepresentationsFile, IProgressMonitor monitor) throws CoreException;
-
-    /**
-     * Create a local representation.
-     * 
-     * @param project
-     *            the {@link IProject} to convert.
-     * @throws CoreException
-     *             in case of problem (2 aird and no main one for example).
-     * @deprecated use
-     *             {@link ModelingProjectManager#createLocalRepresentationsFile(IProject, IProgressMonitor)}
-     *             instead
-     */
-    void createLocalRepresentationsFile(IProject project) throws CoreException;
+    IProject createNewModelingProject(String projectName, IPath projectLocationPath, boolean createAndOpenBlankRepresentationsFile, IProgressMonitor monitor) throws CoreException;
 
     /**
      * Create a local representation.
@@ -163,22 +114,6 @@ public interface ModelingProjectManager {
     void createLocalRepresentationsFile(IProject project, IProgressMonitor monitor) throws CoreException;
 
     /**
-     * Convert an existing project to a modeling project : add a the modeling
-     * project nature, look for an existing main aird file or create it and then
-     * populate the semantic resources with existing models contained in the
-     * project.
-     * 
-     * @param project
-     *            IProject
-     * @throws CoreException
-     *             in case of problem
-     * @deprecated use
-     *             {@link ModelingProjectManager#convertToModelingProject(IProject, IProgressMonitor)}
-     *             instead
-     */
-    void convertToModelingProject(IProject project) throws CoreException;
-
-    /**
      * Convert an existing project to a modeling project : add the modeling
      * project nature, look for an existing main aird file or create it and then
      * populate the semantic resources with existing models contained in the
@@ -198,19 +133,6 @@ public interface ModelingProjectManager {
      * 
      * @param project
      *            IProject
-     * @throws CoreException
-     *             in case of problem
-     * @deprecated use
-     *             {@link ModelingProjectManager#removeModelingNature(IProject, IProgressMonitor)}
-     *             instead
-     */
-    void removeModelingNature(IProject project) throws CoreException;
-
-    /**
-     * Convert an existing project to a modeling project.
-     * 
-     * @param project
-     *            IProject
      * @param monitor
      *            a {@link IProgressMonitor} to show progression of Modeling
      *            Project nature removal
diff --git a/plugins/org.eclipse.sirius.ui/src/org/eclipse/sirius/ui/tools/internal/actions/analysis/RemoveSemanticResourceAction.java b/plugins/org.eclipse.sirius.ui/src/org/eclipse/sirius/ui/tools/internal/actions/analysis/RemoveSemanticResourceAction.java
index 0cbcca9f18..761858dcd2 100644
--- a/plugins/org.eclipse.sirius.ui/src/org/eclipse/sirius/ui/tools/internal/actions/analysis/RemoveSemanticResourceAction.java
+++ b/plugins/org.eclipse.sirius.ui/src/org/eclipse/sirius/ui/tools/internal/actions/analysis/RemoveSemanticResourceAction.java
@@ -13,6 +13,7 @@ package org.eclipse.sirius.ui.tools.internal.actions.analysis;
 import java.util.ArrayList;
 import java.util.Collection;
 
+import org.eclipse.core.runtime.NullProgressMonitor;
 import org.eclipse.emf.common.command.CompoundCommand;
 import org.eclipse.emf.ecore.resource.Resource;
 import org.eclipse.emf.transaction.TransactionalEditingDomain;
@@ -81,7 +82,7 @@ public class RemoveSemanticResourceAction extends Action {
         final TransactionalEditingDomain transDomain = session.getTransactionalEditingDomain();
         CompoundCommand compoundCommand = new CompoundCommand();
         for (Resource semanticResourceToRemove : toRemove) {
-            compoundCommand.append(new RemoveSemanticResourceCommand(session, semanticResourceToRemove, true, false));
+            compoundCommand.append(new RemoveSemanticResourceCommand(session, semanticResourceToRemove, false, new NullProgressMonitor()));
         }
         transDomain.getCommandStack().execute(compoundCommand);
     }
diff --git a/plugins/org.eclipse.sirius.ui/src/org/eclipse/sirius/ui/tools/internal/views/common/modelingproject/manager/ModelingProjectManagerImpl.java b/plugins/org.eclipse.sirius.ui/src/org/eclipse/sirius/ui/tools/internal/views/common/modelingproject/manager/ModelingProjectManagerImpl.java
index 0c2ef0a95c..e532b6aa5a 100644
--- a/plugins/org.eclipse.sirius.ui/src/org/eclipse/sirius/ui/tools/internal/views/common/modelingproject/manager/ModelingProjectManagerImpl.java
+++ b/plugins/org.eclipse.sirius.ui/src/org/eclipse/sirius/ui/tools/internal/views/common/modelingproject/manager/ModelingProjectManagerImpl.java
@@ -25,7 +25,6 @@ import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.IPath;
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.eclipse.core.runtime.IStatus;
-import org.eclipse.core.runtime.NullProgressMonitor;
 import org.eclipse.core.runtime.Status;
 import org.eclipse.core.runtime.SubProgressMonitor;
 import org.eclipse.core.runtime.jobs.Job;
@@ -191,20 +190,6 @@ public class ModelingProjectManagerImpl implements ModelingProjectManager {
     /**
      * {@inheritDoc}
      */
-    public IProject createNewModelingProject(final String projectName, boolean createAndOpenBlankRepresentationsFile) throws CoreException {
-        return createNewModelingProject(projectName, null, createAndOpenBlankRepresentationsFile, new NullProgressMonitor());
-    }
-
-    /**
-     * {@inheritDoc}
-     */
-    public IProject createNewModelingProject(final String projectName, final IPath projectLocationPath, final boolean createAndOpenBlankRepresentationsFile) throws CoreException {
-        return createNewModelingProject(projectName, null, createAndOpenBlankRepresentationsFile, new NullProgressMonitor());
-    }
-
-    /**
-     * {@inheritDoc}
-     */
     public IProject createNewModelingProject(String projectName, boolean createAndOpenBlankRepresentationsFile, IProgressMonitor monitor) throws CoreException {
         return createNewModelingProject(projectName, null, createAndOpenBlankRepresentationsFile, monitor);
     }
@@ -254,13 +239,6 @@ public class ModelingProjectManagerImpl implements ModelingProjectManager {
     /**
      * {@inheritDoc}
      */
-    public void convertToModelingProject(final IProject project) throws CoreException {
-        convertToModelingProject(project, new NullProgressMonitor());
-    }
-
-    /**
-     * {@inheritDoc}
-     */
     public void convertToModelingProject(final IProject project, IProgressMonitor monitor) throws CoreException {
         final IWorkspaceRunnable create = new IWorkspaceRunnable() {
             public void run(final IProgressMonitor monitor) throws CoreException {
@@ -288,13 +266,6 @@ public class ModelingProjectManagerImpl implements ModelingProjectManager {
     /**
      * {@inheritDoc}
      */
-    public void removeModelingNature(final IProject project) throws CoreException {
-        removeModelingNature(project, new NullProgressMonitor());
-    }
-
-    /**
-     * {@inheritDoc}
-     */
     public void removeModelingNature(final IProject project, IProgressMonitor monitor) throws CoreException {
         final IWorkspaceRunnable create = new IWorkspaceRunnable() {
             public void run(final IProgressMonitor monitor) throws CoreException {
@@ -307,13 +278,6 @@ public class ModelingProjectManagerImpl implements ModelingProjectManager {
     /**
      * {@inheritDoc}
      */
-    public void createLocalRepresentationsFile(IProject project) throws CoreException {
-        createLocalRepresentationsFile(project, new NullProgressMonitor());
-    }
-
-    /**
-     * {@inheritDoc}
-     */
     public void createLocalRepresentationsFile(IProject project, IProgressMonitor monitor) throws CoreException {
         URI representationsURI = URI.createPlatformResourceURI(project.getFullPath().append(ModelingProject.DEFAULT_REPRESENTATIONS_FILE_NAME).toString(), true);
 
diff --git a/plugins/org.eclipse.sirius.ui/src/org/eclipse/sirius/ui/tools/internal/views/sessionview/DesignerSessionView.java b/plugins/org.eclipse.sirius.ui/src/org/eclipse/sirius/ui/tools/internal/views/sessionview/DesignerSessionView.java
index 4fa7f41ae9..bab8927d1e 100644
--- a/plugins/org.eclipse.sirius.ui/src/org/eclipse/sirius/ui/tools/internal/views/sessionview/DesignerSessionView.java
+++ b/plugins/org.eclipse.sirius.ui/src/org/eclipse/sirius/ui/tools/internal/views/sessionview/DesignerSessionView.java
@@ -353,6 +353,7 @@ public class DesignerSessionView extends ViewPart implements SessionManagerListe
      * 
      * @see org.eclipse.sirius.business.api.session.SessionManagerListener#notifyUpdatedSession(org.eclipse.sirius.business.api.session.Session)
      */
+    @Deprecated
     public void notifyUpdatedSession(final Session updated) {
         // do nothing as this method is deprecated
     }
diff --git a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/dialect/DialectServices.java b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/dialect/DialectServices.java
index 8ddd9902b9..682b540db1 100644
--- a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/dialect/DialectServices.java
+++ b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/dialect/DialectServices.java
@@ -190,19 +190,6 @@ public interface DialectServices {
      *            the viewpoint
      * @param semantic
      *            the semantic element
-     * @deprecated use
-     *             {@link DialectServices#initRepresentations(Viewpoint, EObject, IProgressMonitor)}
-     *             instead
-     */
-    void initRepresentations(Viewpoint vp, EObject semantic);
-
-    /**
-     * Init all the representations of a the viewpoint.
-     * 
-     * @param vp
-     *            the viewpoint
-     * @param semantic
-     *            the semantic element
      * @param monitor
      *            a {@link IProgressMonitor} to show progression of
      *            representations initialization
diff --git a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/dialect/command/CreateRepresentationCommand.java b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/dialect/command/CreateRepresentationCommand.java
index a291182ab8..22dab89a74 100644
--- a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/dialect/command/CreateRepresentationCommand.java
+++ b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/dialect/command/CreateRepresentationCommand.java
@@ -14,23 +14,21 @@ import java.util.Collection;
 import java.util.Set;
 
 import org.eclipse.core.runtime.IProgressMonitor;
-import org.eclipse.core.runtime.NullProgressMonitor;
 import org.eclipse.emf.ecore.EObject;
 import org.eclipse.emf.transaction.RecordingCommand;
-
-import com.google.common.collect.Sets;
-
-import org.eclipse.sirius.common.tools.api.interpreter.EvaluationException;
-import org.eclipse.sirius.common.tools.api.interpreter.IInterpreter;
-import org.eclipse.sirius.common.tools.api.util.StringUtil;
 import org.eclipse.sirius.business.api.dialect.DialectManager;
 import org.eclipse.sirius.business.api.logger.RuntimeLoggerManager;
 import org.eclipse.sirius.business.api.session.Session;
+import org.eclipse.sirius.common.tools.api.interpreter.EvaluationException;
+import org.eclipse.sirius.common.tools.api.interpreter.IInterpreter;
+import org.eclipse.sirius.common.tools.api.util.StringUtil;
 import org.eclipse.sirius.viewpoint.DRepresentation;
 import org.eclipse.sirius.viewpoint.description.RepresentationDescription;
 import org.eclipse.sirius.viewpoint.description.tool.RepresentationCreationDescription;
 import org.eclipse.sirius.viewpoint.description.tool.ToolPackage;
 
+import com.google.common.collect.Sets;
+
 /**
  * Create representation command.
  * 
@@ -56,23 +54,6 @@ public class CreateRepresentationCommand extends RecordingCommand {
     private IProgressMonitor monitor;
 
     /**
-     * Construct a new instance.
-     * 
-     * @param session
-     *            the session
-     * @param description
-     *            the representation description
-     * @param eObject
-     *            the semantic element on which to create the representation
-     * @param name
-     *            the representation name
-     * @deprecated use the constructor with a {@link IProgressMonitor}
-     */
-    public CreateRepresentationCommand(Session session, RepresentationDescription description, EObject eObject, String name) {
-        this(session, description, eObject, name, new NullProgressMonitor());
-    }
-
-    /**
      * Construct a new instance with {@link IProgressMonitor}.
      * 
      * @param session
diff --git a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/dialect/command/RefreshRepresentationsCommand.java b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/dialect/command/RefreshRepresentationsCommand.java
index bc747b160b..84b150a6e5 100644
--- a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/dialect/command/RefreshRepresentationsCommand.java
+++ b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/dialect/command/RefreshRepresentationsCommand.java
@@ -41,36 +41,6 @@ public class RefreshRepresentationsCommand extends RecordingCommand {
      * 
      * @param domain
      *            the editing domain.
-     * @param representationsToRefresh
-     *            the representations to refresh.
-     * @deprecated use
-     *             {@link RefreshRepresentationsCommand#RefreshRepresentationsCommand(TransactionalEditingDomain, IProgressMonitor, DRepresentation...)}
-     *             instead instead
-     */
-    public RefreshRepresentationsCommand(TransactionalEditingDomain domain, DRepresentation... representationsToRefresh) {
-        this(domain, null, representationsToRefresh);
-    }
-
-    /**
-     * Construct a new instance.
-     * 
-     * @param domain
-     *            the editing domain.
-     * @param representationsToRefresh
-     *            the representations to refresh.
-     * @deprecated use
-     *             {@link RefreshRepresentationsCommand#RefreshRepresentationsCommand(TransactionalEditingDomain, IProgressMonitor, Collection)}
-     *             instead
-     */
-    public RefreshRepresentationsCommand(TransactionalEditingDomain domain, Collection<DRepresentation> representationsToRefresh) {
-        this(domain, null, representationsToRefresh);
-    }
-
-    /**
-     * Construct a new instance.
-     * 
-     * @param domain
-     *            the editing domain.
      * @param monitor
      *            a progress monitor.
      * @param representationsToRefresh
diff --git a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/helper/display/DisplayService.java b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/helper/display/DisplayService.java
index 73a04f5076..a788026bb2 100644
--- a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/helper/display/DisplayService.java
+++ b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/helper/display/DisplayService.java
@@ -11,7 +11,6 @@
 package org.eclipse.sirius.business.api.helper.display;
 
 import org.eclipse.sirius.business.api.componentization.DiagramMappingsManager;
-import org.eclipse.sirius.business.api.session.Session;
 import org.eclipse.sirius.viewpoint.DDiagram;
 import org.eclipse.sirius.viewpoint.DDiagramElement;
 
@@ -55,22 +54,6 @@ public interface DisplayService {
      * @return true if the element is visible, false otherwise
      */
     boolean computeVisibility(DiagramMappingsManager session, final DDiagram diagram, final DDiagramElement element);
-    
-    /**
-     * Check if an element has to be displayed in the diagram.
-     * 
-     * This method is deprecated, instead of passing the session you should use the other method taking the DiagramMappingsManager as a parameter.
-     * @param session
-     *            the current session.
-     * @param diagram
-     *            the diagram
-     * @param element
-     *            the element
-     * @return true if the element is visible, false otherwise
-     * @since 0.9.0
-     */
-    @Deprecated
-    boolean computeVisibility(Session session, final DDiagram diagram, final DDiagramElement element);
 
     /**
 
diff --git a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/helper/filter/FilterService.java b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/helper/filter/FilterService.java
index 3bbc016a73..5cee23c9aa 100644
--- a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/helper/filter/FilterService.java
+++ b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/helper/filter/FilterService.java
@@ -17,11 +17,10 @@ import java.util.Comparator;
 import java.util.Iterator;
 import java.util.List;
 
-import org.eclipse.emf.ecore.EObject;
-import org.eclipse.sirius.common.tools.DslCommonPlugin;
 import org.eclipse.sirius.business.api.helper.display.DisplayMode;
 import org.eclipse.sirius.business.api.helper.display.DisplayServiceManager;
 import org.eclipse.sirius.business.api.query.CompositeFilterDescriptionQuery;
+import org.eclipse.sirius.common.tools.DslCommonPlugin;
 import org.eclipse.sirius.tools.api.profiler.SiriusTasksKey;
 import org.eclipse.sirius.viewpoint.DDiagram;
 import org.eclipse.sirius.viewpoint.DDiagramElement;
@@ -44,159 +43,6 @@ public final class FilterService {
     }
 
     /**
-     * Activate the global filter cache.
-     * 
-     * @deprecated use {@link DisplayServiceManager#getDisplayService()} and
-     *             {@link org.eclipse.sirius.business.api.helper.display.DisplayService#activateCache()}
-     *             instead
-     */
-    @Deprecated
-    public static void activateCache() {
-        DisplayServiceManager.INSTANCE.getDisplayService().activateCache();
-    }
-
-    /**
-     * De-activate the global filter cache.
-     * 
-     * @deprecated use {@link DisplayServiceManager#getDisplayService()} and
-     *             {@link org.eclipse.sirius.business.api.helper.display.DisplayService#deactivateCache()}
-     *             instead
-     */
-    @Deprecated
-    public static void deactivateCache() {
-        DisplayServiceManager.INSTANCE.getDisplayService().deactivateCache();
-    }
-
-    /**
-     * Return if an element is visible in the diagram.
-     * 
-     * @param diagram
-     *            the diagram
-     * @param element
-     *            the element
-     * @return true if the element is visible, false otherwise
-     * @deprecated use {@link DisplayServiceManager#getDisplayService()} and
-     *             {@link import
-     *             org.eclipse.sirius.business.api.helper.display
-     *             .DisplayService#isDisplayed(DDiagram, DDiagramElement)}
-     *             instead
-     */
-    @Deprecated
-    public static boolean isVisible(final DDiagram diagram, final DDiagramElement element) {
-        return DisplayServiceManager.INSTANCE.getDisplayService().isDisplayed(diagram, element);
-    }
-
-    /**
-     * Check if an element or one of its parent is filtered in the diagram.
-     * 
-     * 
-     * @deprecated Use
-     *             {@link FilterService#getAppliedFilters(DDiagram, DDiagramElement)}
-     *             to compute filter application,
-     *             {@link org.eclipse.sirius.business.api.query.DDiagramElementQuery#isFiltered()}
-     *             to know the result of this application,
-     *             {@link org.eclipse.sirius.business.api.query.DDiagramElementQuery#getAppliedCompositeFilters()}
-     *             to applied composite filters.
-     * @param diagram
-     *            the diagram
-     * @param element
-     *            the element
-     * @return <code>true</code> if the element is filtered, <code>false</code>
-     *         otherwise
-     */
-    @Deprecated
-    public static boolean isFiltered(final DDiagram diagram, final DDiagramElement element) {
-        return !FilterService.isVisibleForActivatedFiltersAndParentIsVisible(diagram, element);
-    }
-
-    /**
-     * Check if an element is not filtered in the diagram.
-     * 
-     * @param diagram
-     *            the diagram
-     * @param element
-     *            the element
-     * @return <code>true</code> if the element is visible for filters (not
-     *         filtered), <code>false</code> otherwise
-     * @deprecated
-     */
-    @Deprecated
-    public static boolean isNotFiltered(final DDiagram diagram, final DDiagramElement element) {
-        return FilterService.isVisibleForActivatedFiltersAndParentIsVisible(diagram, element);
-    }
-
-    /**
-     * @deprecated
-     * @param diagram
-     * @param element
-     * @return
-     */
-    @Deprecated
-    private static boolean isVisibleForActivatedFiltersAndParentIsVisible(final DDiagram diagram, final DDiagramElement element) {
-
-        boolean isVisible = FilterService.isVisibleForActivatedFilters(diagram, element);
-
-        if (isVisible) {
-            final EObject eContainer = element.eContainer();
-            if (eContainer instanceof DDiagramElement) {
-                isVisible = FilterService.isVisibleForActivatedFiltersAndParentIsVisible(diagram, (DDiagramElement) eContainer);
-            }
-        }
-        return isVisible;
-    }
-
-    /**
-     * Check that element is visible for the activated filters. If no filter is
-     * activated, all the elements is consider to be visible.
-     * 
-     * @deprecated Use
-     *             {@link FilterService#getAppliedFilters(DDiagram, DDiagramElement)}
-     *             to compute filter application,
-     *             {@link org.eclipse.sirius.business.api.query.DDiagramElementQuery#isFiltered()}
-     *             to know the result of this application,
-     *             {@link org.eclipse.sirius.business.api.query.DDiagramElementQuery#getAppliedCompositeFilters()}
-     *             to applied composite filters.
-     * @param diagram
-     *            the diagram
-     * @param element
-     *            the element
-     * @return <code>true</code> if the element is visible for the activated
-     *         filtered, <code>false</code> otherwise
-     */
-    @Deprecated
-    public static boolean isVisibleForActivatedFilters(final DDiagram diagram, final DDiagramElement element) {
-        final List<FilterDescription> filters = FilterService.sortFilters(diagram.getActivatedFilters());
-        if (filters.isEmpty()) {
-            return true;
-        }
-        return FilterService.isVisibleForFilters(filters, element);
-    }
-
-    /**
-     * Check that element is filtered or not. In other words, check that the
-     * element is visible for the activated filters). If no filter is activated,
-     * all the elements is consider to be visible.
-     * 
-     * @param diagram
-     *            the diagram
-     * @param element
-     *            the element
-     * @return <code>true</code> if the element is filtered, <code>false</code>
-     *         otherwise
-     * @deprecated Use
-     *             {@link FilterService#getAppliedFilters(DDiagram, DDiagramElement)}
-     *             to compute filter application,
-     *             {@link org.eclipse.sirius.business.api.query.DDiagramElementQuery#isFiltered()}
-     *             to know the result of this application,
-     *             {@link org.eclipse.sirius.business.api.query.DDiagramElementQuery#getAppliedCompositeFilters()}
-     *             to applied composite filters.
-     */
-    @Deprecated
-    public static boolean checkFilters(final DDiagram diagram, final DDiagramElement element) {
-        return FilterService.isVisibleForActivatedFilters(diagram, element);
-    }
-
-    /**
      * Get the list of the activated filters applied to the element.
      * 
      * @param diagram
@@ -232,28 +78,6 @@ public final class FilterService {
     }
 
     /**
-     * @deprecated Use
-     *             {@link FilterService#getAppliedFilters(DDiagram, DDiagramElement)}
-     * @param filters
-     *            The filters to apply
-     * @param element
-     *            The element to check
-     * @return true is the element is visible for the filters.
-     */
-    @Deprecated
-    private static boolean isVisibleForFilters(final List<FilterDescription> filters, final DDiagramElement element) {
-        boolean result = true;
-        final Iterator<FilterDescription> it = filters.iterator();
-        while (it.hasNext() && result) {
-            final FilterDescription filter = it.next();
-            if (!filter.isVisible(element)) {
-                result = false;
-            }
-        }
-        return result;
-    }
-
-    /**
      * Tell whether an element is collapsed or not.
      * 
      * @param diagram
@@ -272,21 +96,6 @@ public final class FilterService {
         return isCollapsed;
     }
 
-    /**
-     * Tell whether an element is collapsed or not.
-     * 
-     * @param diagram
-     *            the viewpoint.
-     * @param element
-     *            the element.
-     * @return true if it collapsed.
-     * @deprecated Replaced by {@link #isCollapsed(DDiagram, DDiagramElement)}
-     */
-    @Deprecated
-    public static boolean isCollapse(final DDiagram diagram, final DDiagramElement element) {
-        return FilterService.isCollapsed(diagram, element);
-    }
-
     private static boolean isCollapsed(final Collection<FilterDescription> sortedFilters, final DDiagramElement element) {
         boolean isCollapsed = false;
         final Iterator<FilterDescription> it = sortedFilters.iterator();
@@ -349,35 +158,4 @@ public final class FilterService {
         });
         return result;
     }
-
-    /**
-     * Activate filters.
-     * 
-     * @deprecated
-     */
-    @Deprecated
-    public static void activate() {
-        DisplayServiceManager.INSTANCE.activateMode(DisplayMode.NORMAL);
-    }
-
-    /**
-     * deactivate filters.
-     * 
-     * @deprecated
-     */
-    @Deprecated
-    public static void deactivate() {
-        DisplayServiceManager.INSTANCE.activateMode(DisplayMode.ALL_IS_DISPLAYED);
-    }
-
-    /**
-     * Returns <code>true</code> if the service is active.
-     * 
-     * @return <code>true</code> if the service is active.
-     * @deprecated
-     */
-    @Deprecated
-    public static boolean isActivated() {
-        return DisplayServiceManager.INSTANCE.getMode() == DisplayMode.NORMAL;
-    }
 }
diff --git a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/helper/graphicalfilters/HideFilterHelper.java b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/helper/graphicalfilters/HideFilterHelper.java
index aa721b34aa..5807529215 100644
--- a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/helper/graphicalfilters/HideFilterHelper.java
+++ b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/helper/graphicalfilters/HideFilterHelper.java
@@ -27,34 +27,6 @@ public interface HideFilterHelper {
     HideFilterHelper INSTANCE = HideFilterHelperImpl.init();
 
     /**
-     * Check if an element has been hidden by an hide action.
-     * 
-     * @deprecated Use
-     *             {@link org.eclipse.sirius.business.api.query.DDiagramElementQuery#isHidden()}
-     * @param element
-     *            the element
-     * @return <code>true</code> if the element is hidden by a HideFilter,
-     *         <code>false</code> otherwise
-     */
-    @Deprecated
-    boolean isDirectlyHidden(final DDiagramElement element);
-
-    /**
-     * Check if an element has been hidden or is hidden thanks to another
-     * element (container in case of {@link org.eclipse.sirius.viewpoint.AbstractDNode}
-     * , source or target in case of {@link org.eclipse.sirius.viewpoint.DEdge}.
-     * 
-     * @deprecated Use
-     *             {@link org.eclipse.sirius.business.api.query.DDiagramElementQuery#isIndirectlyHidden()}
-     * @param element
-     *            the element
-     * @return <code>true</code> if the element is hidden by a HideFilter,
-     *         <code>false</code> otherwise
-     */
-    @Deprecated
-    boolean isIndirectlyHidden(final DDiagramElement element);
-
-    /**
      * Hide the current element.
      * 
      * @param element
diff --git a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/session/SavingPolicy.java b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/session/SavingPolicy.java
index eb355bcd61..e5f1f830af 100644
--- a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/session/SavingPolicy.java
+++ b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/session/SavingPolicy.java
@@ -23,21 +23,6 @@ import org.eclipse.emf.ecore.resource.Resource;
  * @since 0.9.0
  */
 public interface SavingPolicy {
-
-    /**
-     * Save the given resources with the provided options.
-     * 
-     * @param resourcesToSave
-     *            the resources to save
-     * @param options
-     *            the options to use for saving
-     * @return the list of saved resource
-     * @deprecated use
-     *             {@link SavingPolicy#save(Iterable, Map, IProgressMonitor)}
-     *             instead
-     */
-    Collection<Resource> save(final Iterable<Resource> resourcesToSave, final Map<?, ?> options);
-
     /**
      * Save the given resources with the provided options.
      * 
@@ -49,6 +34,5 @@ public interface SavingPolicy {
      *            a {@link IProgressMonitor} to show progression of the saving
      * @return the list of saved resource
      */
-    Collection<Resource> save(final Iterable<Resource> resourcesToSave, final Map<?, ?> options, IProgressMonitor monitor);
-
+    Collection<Resource> save(Iterable<Resource> resourcesToSave, Map<?, ?> options, IProgressMonitor monitor);
 }
diff --git a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/session/SavingPolicyImpl.java b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/session/SavingPolicyImpl.java
index 597ca498d3..caf9210ec7 100644
--- a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/session/SavingPolicyImpl.java
+++ b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/api/session/SavingPolicyImpl.java
@@ -21,22 +21,20 @@ import org.eclipse.core.resources.IWorkspaceRunnable;
 import org.eclipse.core.resources.ResourcesPlugin;
 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.IProgressMonitor;
-import org.eclipse.core.runtime.NullProgressMonitor;
 import org.eclipse.core.runtime.SubProgressMonitor;
 import org.eclipse.core.runtime.jobs.Job;
 import org.eclipse.emf.ecore.resource.Resource;
 import org.eclipse.emf.ecore.xmi.XMLResource;
 import org.eclipse.emf.transaction.TransactionalEditingDomain;
+import org.eclipse.sirius.business.internal.session.danalysis.ResourceSaveDiagnose;
+import org.eclipse.sirius.common.tools.api.resource.ResourceSetSync;
+import org.eclipse.sirius.common.tools.api.resource.ResourceSetSync.ResourceStatus;
+import org.eclipse.sirius.viewpoint.SiriusPlugin;
 
 import com.google.common.base.Predicate;
 import com.google.common.collect.Iterables;
 import com.google.common.collect.Lists;
 
-import org.eclipse.sirius.common.tools.api.resource.ResourceSetSync;
-import org.eclipse.sirius.common.tools.api.resource.ResourceSetSync.ResourceStatus;
-import org.eclipse.sirius.viewpoint.SiriusPlugin;
-import org.eclipse.sirius.business.internal.session.danalysis.ResourceSaveDiagnose;
-
 /**
  * A policy implementing save operation.
  * 
@@ -95,21 +93,6 @@ public class SavingPolicyImpl implements SavingPolicy {
     }
 
     /**
-     * The specified options to save are merged with
-     * {@link Resource#OPTION_SAVE_ONLY_IF_CHANGED} having
-     * {@link Resource#OPTION_SAVE_ONLY_IF_CHANGED_FILE_BUFFER} as value to do a
-     * save only if serialization is different.
-     * 
-     * {@inheritDoc}
-     * 
-     * @see org.eclipse.sirius.business.api.session.SavingPolicy#save(java.lang.Iterable,
-     *      java.util.Map)
-     */
-    public Collection<Resource> save(final Iterable<Resource> allResources, final Map<?, ?> options) {
-        return save(allResources, options, new NullProgressMonitor());
-    }
-
-    /**
      * {@inheritDoc}
      */
     public Collection<Resource> save(final Iterable<Resource> allResources, final Map<?, ?> options, IProgressMonitor monitor) {
diff --git a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/internal/helper/display/CreationDisplayServiceImpl.java b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/internal/helper/display/CreationDisplayServiceImpl.java
index 8e5d59930c..ba39d57656 100644
--- a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/internal/helper/display/CreationDisplayServiceImpl.java
+++ b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/internal/helper/display/CreationDisplayServiceImpl.java
@@ -13,13 +13,11 @@ package org.eclipse.sirius.business.internal.helper.display;
 import java.util.HashMap;
 import java.util.Map;
 
-import org.eclipse.sirius.common.tools.DslCommonPlugin;
 import org.eclipse.sirius.business.api.componentization.DiagramMappingsManager;
-import org.eclipse.sirius.business.api.componentization.DiagramMappingsManagerRegistry;
 import org.eclipse.sirius.business.api.helper.display.DisplayService;
 import org.eclipse.sirius.business.api.query.DDiagramElementQuery;
-import org.eclipse.sirius.business.api.session.Session;
 import org.eclipse.sirius.business.internal.metamodel.helper.LayerHelper;
+import org.eclipse.sirius.common.tools.DslCommonPlugin;
 import org.eclipse.sirius.tools.api.profiler.SiriusTasksKey;
 import org.eclipse.sirius.viewpoint.DDiagram;
 import org.eclipse.sirius.viewpoint.DDiagramElement;
@@ -95,15 +93,6 @@ public final class CreationDisplayServiceImpl implements DisplayService {
 
     /**
      * {@inheritDoc}
-     */
-    public boolean computeVisibility(Session session, final DDiagram diagram, final DDiagramElement element) {
-        DiagramMappingsManager manager = DiagramMappingsManagerRegistry.INSTANCE.getDiagramMappingsManager(session, diagram);
-        final boolean result = doIsVisible(manager, diagram, element);
-        return result;
-    }
-
-    /**
-     * {@inheritDoc}
      * 
      * @see org.eclipse.sirius.business.api.helper.display.DisplayService#computeVisibility(org.eclipse.sirius.business.api.session.Session,
      *      org.eclipse.sirius.viewpoint.DDiagram,
diff --git a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/internal/metamodel/helper/HideFilterHelperImpl.java b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/internal/metamodel/helper/HideFilterHelperImpl.java
index 81c77019ff..0cb54efa00 100644
--- a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/internal/metamodel/helper/HideFilterHelperImpl.java
+++ b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/business/internal/metamodel/helper/HideFilterHelperImpl.java
@@ -42,30 +42,6 @@ public final class HideFilterHelperImpl implements HideFilterHelper {
     /**
      * {@inheritDoc}
      * 
-     * @deprecated Use
-     *             {@link org.eclipse.sirius.business.api.query.DDiagramElementQuery#isHidden()}
-     */
-    @Deprecated
-    public boolean isDirectlyHidden(final DDiagramElement element) {
-        DDiagramElementQuery query = new DDiagramElementQuery(element);
-        return element != null && query.isHidden();
-    }
-
-    /**
-     * {@inheritDoc}
-     * 
-     * @deprecated Use
-     *             {@link org.eclipse.sirius.business.api.query.DDiagramElementQuery#isIndirectlyHidden()}
-     */
-    @Deprecated
-    public boolean isIndirectlyHidden(final DDiagramElement element) {
-        DDiagramElementQuery query = new DDiagramElementQuery(element);
-        return element != null && query.isIndirectlyHidden();
-    }
-
-    /**
-     * {@inheritDoc}
-     * 
      * @see HideFilterHelper#hide(DDiagramElement, boolean)
      */
     public void hide(final DDiagramElement element) {
@@ -93,6 +69,11 @@ public final class HideFilterHelperImpl implements HideFilterHelper {
         }
     }
 
+    private boolean isDirectlyHidden(final DDiagramElement element) {
+        DDiagramElementQuery query = new DDiagramElementQuery(element);
+        return element != null && query.isHidden();
+    }
+
     /**
      * {@inheritDoc}
      * 
diff --git a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/AbstractCommandFactory.java b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/AbstractCommandFactory.java
index 2707f4cc51..3df02f70be 100644
--- a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/AbstractCommandFactory.java
+++ b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/AbstractCommandFactory.java
@@ -22,6 +22,9 @@ import org.eclipse.sirius.business.api.helper.task.RemoveDanglingReferencesTask;
 import org.eclipse.sirius.business.api.query.DRepresentationElementQuery;
 import org.eclipse.sirius.business.api.session.Session;
 import org.eclipse.sirius.business.api.session.SessionManager;
+import org.eclipse.sirius.ecore.extender.business.api.accessor.ModelAccessor;
+import org.eclipse.sirius.ecore.extender.business.api.accessor.exception.FeatureNotFoundException;
+import org.eclipse.sirius.ecore.extender.business.api.accessor.exception.MetaClassNotFoundException;
 import org.eclipse.sirius.tools.api.command.ui.UICallBack;
 import org.eclipse.sirius.viewpoint.DRepresentation;
 import org.eclipse.sirius.viewpoint.DRepresentationElement;
@@ -30,9 +33,6 @@ import org.eclipse.sirius.viewpoint.SiriusPlugin;
 import org.eclipse.sirius.viewpoint.description.tool.AbstractToolDescription;
 import org.eclipse.sirius.viewpoint.description.tool.RepresentationCreationDescription;
 import org.eclipse.sirius.viewpoint.description.tool.ToolPackage;
-import org.eclipse.sirius.ecore.extender.business.api.accessor.ModelAccessor;
-import org.eclipse.sirius.ecore.extender.business.api.accessor.exception.FeatureNotFoundException;
-import org.eclipse.sirius.ecore.extender.business.api.accessor.exception.MetaClassNotFoundException;
 
 /**
  * .
@@ -63,27 +63,6 @@ public abstract class AbstractCommandFactory implements ICommandFactory {
     }
 
     /**
-     * Construct a new instance.
-     * 
-     * @param domain
-     *            the editing domain
-     * @param accessor
-     *            the model accessor
-     * 
-     * @deprecated since 4.0.0 : because
-     *             {@link org.eclipse.sirius.ecore.extender.business.api.accessor.ModelAccessorsRegistry}
-     *             allows to retrieve a ModelAccessor from its
-     *             TransactionalEditingDomain, then use
-     *             AbstractCommandFactory(final TransactionalEditingDomain)
-     *             constructor instead.
-     */
-    @Deprecated
-    public AbstractCommandFactory(final TransactionalEditingDomain domain, final ModelAccessor accessor) {
-        this.domain = domain;
-        this.modelAccessor = accessor;
-    }
-
-    /**
      * {@inheritDoc}
      * 
      * @see org.eclipse.sirius.tools.api.command.ICommandFactory#buildCreateRepresentationFromDescription(org.eclipse.sirius.viewpoint.description.tool.RepresentationCreationDescription,
diff --git a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/CommandContext.java b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/CommandContext.java
index a9fe721da0..907c1729f4 100644
--- a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/CommandContext.java
+++ b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/CommandContext.java
@@ -15,17 +15,16 @@ import java.util.List;
 import java.util.Stack;
 
 import org.eclipse.emf.ecore.EObject;
-
-import com.google.common.collect.Lists;
-
-import org.eclipse.sirius.common.tools.api.interpreter.IInterpreter;
 import org.eclipse.sirius.business.api.logger.RuntimeLoggerInterpreter;
 import org.eclipse.sirius.business.api.logger.RuntimeLoggerManager;
+import org.eclipse.sirius.common.tools.api.interpreter.IInterpreter;
 import org.eclipse.sirius.tools.api.interpreter.InterpreterUtil;
 import org.eclipse.sirius.viewpoint.DRepresentation;
 import org.eclipse.sirius.viewpoint.description.tool.For;
 import org.eclipse.sirius.viewpoint.description.tool.ToolPackage;
 
+import com.google.common.collect.Lists;
+
 /**
  * This class keeps the trace of all contexts.
  * 
@@ -46,18 +45,6 @@ public class CommandContext {
      * 
      * @param target
      *            the first context.
-     * @deprecated
-     */
-    @Deprecated
-    public CommandContext(final EObject target) {
-        this(target, null);
-    }
-
-    /**
-     * Create a new {@link CommandContext}.
-     * 
-     * @param target
-     *            the first context.
      * @param representation
      *            the current representation
      * @since 0.9.0
diff --git a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/listener/IChangeListener.java b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/listener/IChangeListener.java
index 37bee5eb9e..c13c173c2b 100644
--- a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/listener/IChangeListener.java
+++ b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/listener/IChangeListener.java
@@ -11,7 +11,6 @@
 package org.eclipse.sirius.tools.api.command.listener;
 
 import org.eclipse.emf.common.notify.Adapter;
-import org.eclipse.emf.transaction.TransactionalEditingDomain;
 
 /**
  * A listener which record created, modified and deleted elements and which is
@@ -23,26 +22,6 @@ import org.eclipse.emf.transaction.TransactionalEditingDomain;
 public interface IChangeListener extends Adapter {
     /**
      * Activate this listener.
-     * 
-     * @deprecated
-     * 
-     * @param domain
-     *            the domain on which to listen
-     */
-    void activate(TransactionalEditingDomain domain);
-
-    /**
-     * Deactivate this listener.
-     * 
-     * @deprecated
-     * 
-     * @param domain
-     *            the domain on which we were listening
-     */
-    void deactivate(TransactionalEditingDomain domain);
-
-    /**
-     * Activate this listener.
      */
     void activate();
 
diff --git a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/semantic/AddSemanticResourceCommand.java b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/semantic/AddSemanticResourceCommand.java
index b960b1259a..63e0f42c6d 100644
--- a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/semantic/AddSemanticResourceCommand.java
+++ b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/semantic/AddSemanticResourceCommand.java
@@ -51,22 +51,6 @@ public class AddSemanticResourceCommand extends RecordingCommand {
     private Collection<Session> result = Sets.newLinkedHashSet();
 
     /**
-     * Specific command to add semantic resources to the given session.
-     * 
-     * @param session
-     *            the session to update.
-     * @param semanticResourceURI
-     *            the {@link URI} of semantic model resource to add to the given
-     *            session.
-     * @deprecated use
-     *             {@link AddSemanticResourceCommand#AddSemanticResourceCommand(Session, URI, IProgressMonitor)}
-     *             instead
-     */
-    public AddSemanticResourceCommand(Session session, URI semanticResourceURI) {
-        this(session, semanticResourceURI, new NullProgressMonitor());
-    }
-
-    /**
      * Specific command to add semantic resources to the given sessions.
      * 
      * @param session
diff --git a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/semantic/RemoveSemanticResourceCommand.java b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/semantic/RemoveSemanticResourceCommand.java
index 2615a78044..6264c7bc8a 100644
--- a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/semantic/RemoveSemanticResourceCommand.java
+++ b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/semantic/RemoveSemanticResourceCommand.java
@@ -54,21 +54,6 @@ public class RemoveSemanticResourceCommand extends RecordingCommand {
     private IProgressMonitor monitor;
 
     /**
-     * Constructor.
-     * 
-     * @param session
-     *            contextual {@link Session}
-     * @param semanticResource
-     *            Resource
-     * @deprecated use {@link
-     *             RemoveSemanticResourceCommand(Session,Resource,boolean,
-     *             IProgressMonitor)} instead
-     */
-    public RemoveSemanticResourceCommand(Session session, Resource semanticResource) {
-        this(session, semanticResource, true, true);
-    }
-
-    /**
      * Default Constructor.
      * 
      * @param session
@@ -91,51 +76,6 @@ public class RemoveSemanticResourceCommand extends RecordingCommand {
     }
 
     /**
-     * Constructor.
-     * 
-     * @param session
-     *            contextual {@link Session}
-     * @param semanticResource
-     *            Resource
-     * @param removeCrossReferencedResources
-     *            true if any cross referenced resource should be removed to,
-     *            false otherwise.
-     * @param removeFromControlledResources
-     *            true if the given resource will removed from controlled
-     *            resources
-     * @deprecated use {@link
-     *             RemoveSemanticResourceCommand(Session,Resource,boolean)}
-     *             instead as the <code>removeCrossReferencedResources</code>
-     *             parameter is useless now, see
-     *             {@link Session#removeSemanticResource(Resource, boolean, IProgressMonitor)}
-     */
-    public RemoveSemanticResourceCommand(Session session, Resource semanticResource, boolean removeCrossReferencedResources, boolean removeFromControlledResources) {
-        super(session.getTransactionalEditingDomain(), "Remove model");
-        this.semanticResource = semanticResource;
-        this.session = session;
-        this.removeCrossReferencedResources = removeCrossReferencedResources;
-        this.removeFromControlledResources = removeFromControlledResources;
-    }
-
-    /**
-     * Constructor.
-     * 
-     * @param session
-     *            contextual {@link Session}
-     * @param semanticResource
-     *            Resource
-     * @param removeFromControlledResources
-     *            true if the given resource will removed from controlled
-     *            resources
-     * @deprecated use {@link
-     *             RemoveSemanticResourceCommand(Session,Resource,boolean,
-     *             IProgressMonitor)} instead
-     */
-    public RemoveSemanticResourceCommand(Session session, Resource semanticResource, boolean removeFromControlledResources) {
-        this(session, semanticResource, true, removeFromControlledResources);
-    }
-
-    /**
      * Execute the command.
      */
     @Override
diff --git a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/view/CreateDiagramWithInitialOperation.java b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/view/CreateDiagramWithInitialOperation.java
index 78904a55d8..0f5588dc9e 100644
--- a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/view/CreateDiagramWithInitialOperation.java
+++ b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/command/view/CreateDiagramWithInitialOperation.java
@@ -53,24 +53,6 @@ public class CreateDiagramWithInitialOperation extends AbstractCommandTask {
      *            the {@link org.eclipse.sirius.viewpoint.DDiagram}.
      * @param uiCallBack
      *            the ui callback used to ask for the detail name.
-     * @deprecated use
-     *             {@link CreateDiagramWithInitialOperation#CreateDiagramWithInitialOperation(DiagramDescription, EObject, UICallBack, IProgressMonitor)}
-     *             instead
-     */
-    public CreateDiagramWithInitialOperation(final DiagramDescription desc, final EObject semanticElement, final UICallBack uiCallBack) {
-        this(desc, semanticElement, uiCallBack, new NullProgressMonitor());
-    }
-
-    /**
-     * Creates the command.
-     * 
-     * @param desc
-     *            the diagram description.
-     * @param semanticElement
-     *            semantic element on which the user requested the creation of
-     *            the {@link org.eclipse.sirius.viewpoint.DDiagram}.
-     * @param uiCallBack
-     *            the ui callback used to ask for the detail name.
      * @param monitor
      *            a {@link IProgressMonitor} to show progression of
      *            representation initialization
diff --git a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/ui/RefreshEditorsPrecommitListener.java b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/ui/RefreshEditorsPrecommitListener.java
index 7f77b5319f..122d1b6623 100644
--- a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/ui/RefreshEditorsPrecommitListener.java
+++ b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/api/ui/RefreshEditorsPrecommitListener.java
@@ -14,6 +14,7 @@ import java.util.ArrayList;
 import java.util.Collection;
 import java.util.LinkedHashSet;
 
+import org.eclipse.core.runtime.NullProgressMonitor;
 import org.eclipse.core.runtime.Platform;
 import org.eclipse.emf.common.command.Command;
 import org.eclipse.emf.common.command.CompoundCommand;
@@ -175,7 +176,7 @@ public class RefreshEditorsPrecommitListener extends ResourceSetListenerImpl imp
 
         if (!representationsToRefresh.isEmpty()) {
             CompoundCommand cc = new CompoundCommand();
-            cc.append(new RefreshRepresentationsCommand(transactionalEditingDomain, representationsToRefresh));
+            cc.append(new RefreshRepresentationsCommand(transactionalEditingDomain, new NullProgressMonitor(), representationsToRefresh));
 
             // Additionnal commands ?
             for (PostRefreshCommandFactory listener : postRefreshCommandFactories) {
diff --git a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/internal/command/EMFCommandFactoryProvider.java b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/internal/command/EMFCommandFactoryProvider.java
index a4f5bbf14e..62a4849b64 100644
--- a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/internal/command/EMFCommandFactoryProvider.java
+++ b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/internal/command/EMFCommandFactoryProvider.java
@@ -11,10 +11,8 @@
 package org.eclipse.sirius.tools.internal.command;
 
 import org.eclipse.emf.transaction.TransactionalEditingDomain;
-
 import org.eclipse.sirius.tools.api.command.IDiagramCommandFactory;
 import org.eclipse.sirius.tools.api.command.IDiagramCommandFactoryProvider;
-import org.eclipse.sirius.ecore.extender.business.api.accessor.ModelAccessor;
 
 /**
  * This class is the default provider for a EMFCommandFactory instance.
@@ -37,21 +35,4 @@ public class EMFCommandFactoryProvider implements IDiagramCommandFactoryProvider
         }
         return commandFactory;
     }
-
-    /**
-     * {@inheritDoc}
-     * 
-     * @see org.eclipse.sirius.tools.api.command.IDiagramCommandFactoryProvider#getCommandFactory(org.eclipse.emf.transaction.TransactionalEditingDomain)
-     * 
-     * @deprecated since 4.0.0 use getCommandFactory(TransactionalEditingDomain)
-     *             instead
-     */
-    @Deprecated
-    public IDiagramCommandFactory getCommandFactory(final ModelAccessor modelAccessor, final TransactionalEditingDomain editingDomain) {
-        if (commandFactory == null) {
-            commandFactory = new UndoRedoCapableEMFCommandFactory(modelAccessor, editingDomain);
-        }
-        return commandFactory;
-    }
-
 }
diff --git a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/internal/command/UndoRedoCapableEMFCommandFactory.java b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/internal/command/UndoRedoCapableEMFCommandFactory.java
index b5ba209346..66145223c2 100644
--- a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/internal/command/UndoRedoCapableEMFCommandFactory.java
+++ b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/internal/command/UndoRedoCapableEMFCommandFactory.java
@@ -26,10 +26,6 @@ import org.eclipse.emf.common.command.UnexecutableCommand;
 import org.eclipse.emf.ecore.EObject;
 import org.eclipse.emf.ecore.util.EcoreUtil;
 import org.eclipse.emf.transaction.TransactionalEditingDomain;
-import org.eclipse.sirius.common.tools.api.interpreter.IInterpreter;
-import org.eclipse.sirius.common.tools.api.interpreter.IInterpreterSiriusVariables;
-import org.eclipse.sirius.common.tools.api.util.Option;
-import org.eclipse.sirius.common.tools.api.util.StringUtil;
 import org.eclipse.sirius.business.api.helper.SiriusUtil;
 import org.eclipse.sirius.business.api.helper.task.AbstractCommandTask;
 import org.eclipse.sirius.business.api.helper.task.ICommandTask;
@@ -37,6 +33,11 @@ import org.eclipse.sirius.business.api.helper.task.InitInterpreterVariablesTask;
 import org.eclipse.sirius.business.api.helper.task.TaskHelper;
 import org.eclipse.sirius.business.api.query.DDiagramElementQuery;
 import org.eclipse.sirius.business.api.query.EObjectQuery;
+import org.eclipse.sirius.common.tools.api.interpreter.IInterpreter;
+import org.eclipse.sirius.common.tools.api.interpreter.IInterpreterSiriusVariables;
+import org.eclipse.sirius.common.tools.api.util.Option;
+import org.eclipse.sirius.common.tools.api.util.StringUtil;
+import org.eclipse.sirius.ecore.extender.business.api.permission.IPermissionAuthority;
 import org.eclipse.sirius.tools.api.command.AbstractCommandFactory;
 import org.eclipse.sirius.tools.api.command.DCommand;
 import org.eclipse.sirius.tools.api.command.IDiagramCommandFactory;
@@ -94,8 +95,6 @@ import org.eclipse.sirius.viewpoint.description.tool.RepresentationCreationDescr
 import org.eclipse.sirius.viewpoint.description.tool.SelectionWizardDescription;
 import org.eclipse.sirius.viewpoint.description.tool.ToolDescription;
 import org.eclipse.sirius.viewpoint.description.validation.ValidationFix;
-import org.eclipse.sirius.ecore.extender.business.api.accessor.ModelAccessor;
-import org.eclipse.sirius.ecore.extender.business.api.permission.IPermissionAuthority;
 
 /**
  * A command factory that creates commands that can be undone.
@@ -117,24 +116,6 @@ public class UndoRedoCapableEMFCommandFactory extends AbstractCommandFactory imp
         commandTaskHelper = new TaskHelper(modelAccessor, uiCallBack);
     }
 
-    /**
-     * Create a new Factory. the autoRefresh is by default deactivated
-     * 
-     * @param modelAccesor
-     *            used for metamodel extensions.
-     * @param domain
-     *            current editing domain.
-     * 
-     * @deprecated since 4.0.0 use
-     *             UndoRedoCapableEMFCommandFactory(TransactionalEditingDomain)
-     *             instead
-     */
-    @Deprecated
-    public UndoRedoCapableEMFCommandFactory(final ModelAccessor modelAccesor, final TransactionalEditingDomain domain) {
-        super(domain, modelAccesor);
-        commandTaskHelper = new TaskHelper(modelAccessor, uiCallBack);
-    }
-
     private IPermissionAuthority getPermissionAuthority() {
         return modelAccessor.getPermissionAuthority();
     }
diff --git a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/internal/command/listener/ChangeListener.java b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/internal/command/listener/ChangeListener.java
index 1582087bc4..8f3157a780 100644
--- a/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/internal/command/listener/ChangeListener.java
+++ b/plugins/org.eclipse.sirius/src/org/eclipse/sirius/tools/internal/command/listener/ChangeListener.java
@@ -14,14 +14,12 @@ import java.util.Collection;
 
 import org.eclipse.emf.common.notify.Notification;
 import org.eclipse.emf.ecore.EReference;
-import org.eclipse.emf.transaction.TransactionalEditingDomain;
-
-import com.google.common.collect.Sets;
-
 import org.eclipse.sirius.common.tools.api.util.SmartAdapter;
 import org.eclipse.sirius.tools.api.command.listener.IChangeListener;
 import org.eclipse.sirius.tools.api.command.listener.TriggerOperation;
 
+import com.google.common.collect.Sets;
+
 /**
  * A listener which record created, modified and deleted elements and which is
  * able to launch a trigger operation with these elements as parameters.
@@ -43,37 +41,6 @@ public final class ChangeListener extends SmartAdapter implements IChangeListene
     private int activateRecursiveCount;
 
     /**
-     * Create a new instance.
-     */
-    public ChangeListener() {
-        super();
-    }
-
-    /**
-     * Activate this listener.
-     * 
-     * @deprecated
-     * 
-     * @param domain
-     *            the domain on which to listen
-     */
-    public void activate(TransactionalEditingDomain domain) {
-        activate();
-    }
-
-    /**
-     * Deactivate this listener.
-     * 
-     * @deprecated
-     * 
-     * @param domain
-     *            the domain on which we were listening
-     */
-    public void deactivate(TransactionalEditingDomain domain) {
-        deactivate();
-    }
-
-    /**
      * Activate this listener.
      */
     public void activate() {