diff --git a/org.eclipse.debug.ui/ui/org/eclipse/debug/internal/ui/launchConfigurations/LaunchConfigurationTreeContentProvider.java b/org.eclipse.debug.ui/ui/org/eclipse/debug/internal/ui/launchConfigurations/LaunchConfigurationTreeContentProvider.java
index ae4c31c..d8fe82e 100644
--- a/org.eclipse.debug.ui/ui/org/eclipse/debug/internal/ui/launchConfigurations/LaunchConfigurationTreeContentProvider.java
+++ b/org.eclipse.debug.ui/ui/org/eclipse/debug/internal/ui/launchConfigurations/LaunchConfigurationTreeContentProvider.java
@@ -18,12 +18,7 @@
 
 import java.util.ArrayList;
 import java.util.Collections;
-import java.util.HashMap;
-import java.util.HashSet;
 import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
 
 import org.eclipse.core.resources.ResourcesPlugin;
 import org.eclipse.core.runtime.CoreException;
@@ -98,7 +93,6 @@
 						configs.add(launchConfig);
 					}
 				}
-				configs = filterUniqueLaunchConfigurations(configs);
 
 				ILaunchConfiguration[] prototypes = getLaunchManager().getLaunchConfigurations(type, ILaunchConfiguration.PROTOTYPE);
 				Collections.addAll(configs, prototypes);
@@ -230,56 +224,4 @@
 	private Shell getShell() {
 		return fShell;
 	}
-
-	/**
-	 * Returns unique launch configurations from the input list Launch
-	 * configurations are unique if the following criteria are fulfilled:
-	 * <ol>
-	 * <li>The name is unique within the list</li>
-	 * <li>The set of attributes (key and value) for the launch configuration is
-	 * unique within the list</li>
-	 * </ol>
-	 *
-	 * @param launchConfigurations The list of launch configurations to filter
-	 * @return List of unique launch configurations based on criteria above
-	 * @throws CoreException If unable to fetch attributes for launch configuration
-	 */
-	private List<ILaunchConfiguration> filterUniqueLaunchConfigurations(List<ILaunchConfiguration> launchConfigurations) throws CoreException {
-		List<ILaunchConfiguration> configs = new ArrayList<>();
-
-		// Create map between name and list of launch configurations with same
-		// name
-		Map<String, List<ILaunchConfiguration>> configNameMap = new HashMap<>();
-
-		for (ILaunchConfiguration launchConfig : launchConfigurations) {
-			String name = launchConfig.getName();
-			if (!configNameMap.containsKey(name)) {
-				configNameMap.put(name, new ArrayList<>());
-			}
-			configNameMap.get(name).add(launchConfig);
-		}
-
-		// Identify unique configurations
-		for (Entry<String, List<ILaunchConfiguration>> entry : configNameMap.entrySet()) {
-			List<ILaunchConfiguration> configsWithSameName = entry.getValue();
-			if (configsWithSameName.size() == 1) {
-				// Only one configuration, add it
-				configs.add(configsWithSameName.get(0));
-			} else if (configsWithSameName.size() > 1) {
-				// More than one configuration detected with same name,
-				// verify that they are unique
-				Set<Map<String, Object>> seenConfigContent = new HashSet<>();
-				for (ILaunchConfiguration config : configsWithSameName) {
-					Map<String, Object> content = config.getAttributes();
-					if (!seenConfigContent.contains(content)) {
-						// Only add the first one with the same content
-						seenConfigContent.add(content);
-						configs.add(config);
-					}
-				}
-			}
-		}
-
-		return configs;
-	}
 }
diff --git a/org.eclipse.debug.ui/ui/org/eclipse/debug/internal/ui/launchConfigurations/LaunchConfigurationView.java b/org.eclipse.debug.ui/ui/org/eclipse/debug/internal/ui/launchConfigurations/LaunchConfigurationView.java
index 9081204..415a6f7 100644
--- a/org.eclipse.debug.ui/ui/org/eclipse/debug/internal/ui/launchConfigurations/LaunchConfigurationView.java
+++ b/org.eclipse.debug.ui/ui/org/eclipse/debug/internal/ui/launchConfigurations/LaunchConfigurationView.java
@@ -319,11 +319,11 @@
 		if (viewer != null) {
 			try {
 				viewer.getControl().setRedraw(false);
-				if (configuration.getPrototype() != null) {
-					viewer.add(configuration.getPrototype(), configuration);
-				} else {
-					viewer.add(configuration.getType(), configuration);
+				Object parentElement = configuration.getPrototype();
+				if (parentElement == null) {
+					parentElement = configuration.getType();
 				}
+				viewer.add(parentElement, configuration);
 				// if moved, remove original now
 				if (from != null) {
 					viewer.remove(from);
@@ -332,6 +332,10 @@
 					viewer.setSelection(new StructuredSelection(configuration), true);
 				}
 				updateFilterLabel();
+				// Need to refresh here, bug 559758
+				if (!configuration.isLocal()) {
+					viewer.refresh(parentElement);
+				}
 			}
 			catch (CoreException e) {}
 			finally {
diff --git a/org.eclipse.debug.ui/ui/org/eclipse/debug/internal/ui/launchConfigurations/LaunchConfigurationsDialog.java b/org.eclipse.debug.ui/ui/org/eclipse/debug/internal/ui/launchConfigurations/LaunchConfigurationsDialog.java
index c6550db..af6d76e 100644
--- a/org.eclipse.debug.ui/ui/org/eclipse/debug/internal/ui/launchConfigurations/LaunchConfigurationsDialog.java
+++ b/org.eclipse.debug.ui/ui/org/eclipse/debug/internal/ui/launchConfigurations/LaunchConfigurationsDialog.java
@@ -233,6 +233,7 @@
 	private DeletedProjectFilter fDeletedProjectFilter;
 	private LaunchConfigurationTypeFilter fLCTFilter;
 	private WorkingSetsFilter fWorkingSetsFilter;
+	private UniqueLaunchConfigurationFileFilter fUniqueLaunchConfugurationFileFilter;
 
 	/**
 	 * set of reserved names that should not be considered when generating a new name for a launch configuration
@@ -645,6 +646,8 @@
 		if(DebugUIPlugin.getDefault().getPreferenceStore().getBoolean(IInternalDebugUIConstants.PREF_FILTER_WORKING_SETS)) {
 			filters.add(fWorkingSetsFilter);
 		}
+		fUniqueLaunchConfugurationFileFilter = new UniqueLaunchConfigurationFileFilter();
+		filters.add(fUniqueLaunchConfugurationFileFilter);
 		return filters.toArray(new ViewerFilter[filters.size()]);
 	}
 
diff --git a/org.eclipse.debug.ui/ui/org/eclipse/debug/internal/ui/launchConfigurations/UniqueLaunchConfigurationFileFilter.java b/org.eclipse.debug.ui/ui/org/eclipse/debug/internal/ui/launchConfigurations/UniqueLaunchConfigurationFileFilter.java
new file mode 100644
index 0000000..9880db0
--- /dev/null
+++ b/org.eclipse.debug.ui/ui/org/eclipse/debug/internal/ui/launchConfigurations/UniqueLaunchConfigurationFileFilter.java
@@ -0,0 +1,102 @@
+/*******************************************************************************
+ * Copyright (c) 2020 Torbjörn Svensson and others.
+ *
+ * This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License 2.0
+ * which accompanies this distribution, and is available at
+ * https://www.eclipse.org/legal/epl-2.0/
+ *
+ * SPDX-License-Identifier: EPL-2.0
+ *
+ * Contributors:
+ *     Torbjörn Svensson - initial API and implementation
+ *******************************************************************************/
+package org.eclipse.debug.internal.ui.launchConfigurations;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+
+import org.eclipse.core.resources.IFile;
+import org.eclipse.core.runtime.IPath;
+import org.eclipse.debug.core.ILaunchConfiguration;
+import org.eclipse.jface.viewers.Viewer;
+import org.eclipse.jface.viewers.ViewerFilter;
+
+/**
+ * Filters out the instance of ILaunchCOnfiguration where the, possibly nested,
+ * launch configuration files are stored. If the launch configuration is local,
+ * it's simply returned.
+ */
+public class UniqueLaunchConfigurationFileFilter extends ViewerFilter {
+	@Override
+	public Object[] filter(Viewer viewer, Object parent, Object[] elements) {
+		int size = elements.length;
+		if (size == 0) {
+			return elements;
+		}
+
+		List<Object> filteredElements = new ArrayList<>(size);
+
+		Map<String, List<ILaunchConfiguration>> configPathMap = new HashMap<>();
+		for (Object element : elements) {
+			if (element instanceof ILaunchConfiguration) {
+				ILaunchConfiguration config = (ILaunchConfiguration) element;
+
+				String path = toLaunchFileLocation(config);
+				if (!configPathMap.containsKey(path)) {
+					configPathMap.put(path, new ArrayList<>());
+				}
+				configPathMap.get(path).add(config);
+			} else {
+				filteredElements.add(element);
+			}
+		}
+
+		for (Entry<String, List<ILaunchConfiguration>> entry : configPathMap.entrySet()) {
+			List<ILaunchConfiguration> configsWithSamePath = entry.getValue();
+			if (entry.getKey() == null) {
+				// Local configurations ends up here, add them without further filter
+				filteredElements.addAll(configsWithSamePath);
+			} else if (configsWithSamePath.size() == 1) {
+				// Only one configuration, add it
+				filteredElements.add(configsWithSamePath.get(0));
+			} else if (configsWithSamePath.size() > 1) {
+				// More than one config with same path.
+				// Order them with the shortest project relative path first
+				configsWithSamePath.sort((o1, o2) -> {
+					IPath path1 = o1.getFile().getProjectRelativePath();
+					IPath path2 = o2.getFile().getProjectRelativePath();
+					return Integer.compare(path1.segmentCount(), path2.segmentCount());
+				});
+				// Use the configuration with the shortest path.
+				// The other configurations in the list are "identical" but with
+				// the container set to one of the parent project(s) in the
+				// workspace hierarchy.
+				filteredElements.add(configsWithSamePath.get(0));
+			}
+		}
+
+		return filteredElements.toArray();
+	}
+
+	private String toLaunchFileLocation(ILaunchConfiguration config) {
+		if (!config.isLocal()) {
+			IFile file = config.getFile();
+			if (file != null) {
+				IPath path = file.getLocation();
+				if (path != null) {
+					return path.toOSString();
+				}
+			}
+		}
+		return null;
+	}
+
+	@Override
+	public boolean select(Viewer viewer, Object parentElement, Object element) {
+		return true;
+	}
+}