diff --git a/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/ApiAnnotationsClasspathContributor.java b/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/ApiAnnotationsClasspathContributor.java
index 9b21e56aa1..15b354f63c 100644
--- a/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/ApiAnnotationsClasspathContributor.java
+++ b/apitools/org.eclipse.pde.api.tools/src/org/eclipse/pde/api/tools/internal/ApiAnnotationsClasspathContributor.java
@@ -36,9 +36,10 @@ public class ApiAnnotationsClasspathContributor implements IClasspathContributor
 
 	@Override
 	public List<IClasspathEntry> getInitialEntries(BundleDescription project) {
-		IPluginModelBase model = PluginRegistry.findModel(project);
-		if (hasApiNature(model)) {
-			return ClasspathUtilCore.classpathEntries(annotations()).collect(Collectors.toList());
+		IPluginModelBase projectModel = PluginRegistry.findModel(project);
+		if (hasApiNature(projectModel)) {
+			return ClasspathUtilCore.classpathEntries(annotations().filter(model -> !model.equals(projectModel)))
+					.collect(Collectors.toList());
 		}
 		return Collections.emptyList();
 	}
diff --git a/ui/org.eclipse.pde.core/.settings/.api_filters b/ui/org.eclipse.pde.core/.settings/.api_filters
index 5d17ac313d..087f6c65b2 100644
--- a/ui/org.eclipse.pde.core/.settings/.api_filters
+++ b/ui/org.eclipse.pde.core/.settings/.api_filters
@@ -1,5 +1,13 @@
 <?xml version="1.0" encoding="UTF-8" standalone="no"?>
 <component id="org.eclipse.pde.core" version="2">
+    <resource path="src/org/eclipse/pde/core/ModelChangedEvent.java" type="org.eclipse.pde.core.ModelChangedEvent">
+        <filter comment="This is PDEs own implementation" id="576725006">
+            <message_arguments>
+                <message_argument value="IModelChangedEvent"/>
+                <message_argument value="ModelChangedEvent"/>
+            </message_arguments>
+        </filter>
+    </resource>
     <resource path="src/org/eclipse/pde/internal/core/project/BundleProjectService.java" type="org.eclipse.pde.internal.core.project.BundleProjectService">
         <filter comment="Platform Team allows use of bundle importers for PDE import from source repository" id="640712815">
             <message_arguments>
@@ -9,20 +17,4 @@
             </message_arguments>
         </filter>
     </resource>
-    <resource path="src/org/eclipse/pde/internal/core/target/ExportTargetJob.java" type="org.eclipse.pde.internal.core.target.ExportTargetJob">
-        <filter comment="Using IProvidedCapability is the only current available option to export a p2 target correctly" id="640712815">
-            <message_arguments>
-                <message_argument value="IProvidedCapability"/>
-                <message_argument value="ExportTargetJob"/>
-                <message_argument value="getName()"/>
-            </message_arguments>
-        </filter>
-        <filter comment="Using IProvidedCapability is the only current available option to export a p2 target correctly" id="640712815">
-            <message_arguments>
-                <message_argument value="IProvidedCapability"/>
-                <message_argument value="ExportTargetJob"/>
-                <message_argument value="getNamespace()"/>
-            </message_arguments>
-        </filter>
-    </resource>
 </component>
diff --git a/ui/org.eclipse.pde.core/src/org/eclipse/pde/core/plugin/PluginRegistry.java b/ui/org.eclipse.pde.core/src/org/eclipse/pde/core/plugin/PluginRegistry.java
index 0b442f897f..9bad4e0ba5 100644
--- a/ui/org.eclipse.pde.core/src/org/eclipse/pde/core/plugin/PluginRegistry.java
+++ b/ui/org.eclipse.pde.core/src/org/eclipse/pde/core/plugin/PluginRegistry.java
@@ -18,6 +18,7 @@
 
 import org.eclipse.core.resources.IFile;
 import org.eclipse.core.resources.IProject;
+import org.eclipse.core.resources.IResource;
 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.osgi.service.resolver.BundleDescription;
 import org.eclipse.osgi.service.resolver.VersionRange;
@@ -408,13 +409,16 @@ private static IPluginModelBase[] findModels(String id) {
 	 */
 	public static IBuildModel createBuildModel(IPluginModelBase model) throws CoreException {
 		if (model != null) {
-			IProject project = model.getUnderlyingResource().getProject();
-			if (project != null) {
-				IFile buildFile = PDEProject.getBuildProperties(project);
-				if (buildFile.exists()) {
-					IBuildModel buildModel = new WorkspaceBuildModel(buildFile);
-					buildModel.load();
-					return buildModel;
+			IResource resource = model.getUnderlyingResource();
+			if (resource != null) {
+				IProject project = resource.getProject();
+				if (project != null) {
+					IFile buildFile = PDEProject.getBuildProperties(project);
+					if (buildFile.exists()) {
+						IBuildModel buildModel = new WorkspaceBuildModel(buildFile);
+						buildModel.load();
+						return buildModel;
+					}
 				}
 			}
 		}
diff --git a/ui/org.eclipse.pde.core/src/org/eclipse/pde/internal/core/ClasspathUtilCore.java b/ui/org.eclipse.pde.core/src/org/eclipse/pde/internal/core/ClasspathUtilCore.java
index ce616caf81..1e29c4e108 100644
--- a/ui/org.eclipse.pde.core/src/org/eclipse/pde/internal/core/ClasspathUtilCore.java
+++ b/ui/org.eclipse.pde.core/src/org/eclipse/pde/internal/core/ClasspathUtilCore.java
@@ -19,7 +19,10 @@
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
+import java.util.List;
+import java.util.Map;
 import java.util.Objects;
+import java.util.stream.Collectors;
 import java.util.stream.Stream;
 
 import org.eclipse.core.resources.IResource;
@@ -28,6 +31,7 @@
 import org.eclipse.jdt.core.IAccessRule;
 import org.eclipse.jdt.core.IClasspathAttribute;
 import org.eclipse.jdt.core.IClasspathEntry;
+import org.eclipse.jdt.core.IJavaProject;
 import org.eclipse.jdt.core.JavaCore;
 import org.eclipse.osgi.service.resolver.BundleDescription;
 import org.eclipse.pde.core.build.IBuild;
@@ -82,25 +86,40 @@ private static Collection<ClasspathLibrary> collectLibraryEntries(IPluginModelBa
 	}
 
 	public static Stream<IClasspathEntry> classpathEntries(Stream<IPluginModelBase> models) {
-		return models.flatMap(model -> {
-			String location = model.getInstallLocation();
-			if (location == null) {
-				return Stream.empty();
-			}
-			boolean isJarShape = new File(location).isFile();
-			IPluginLibrary[] libraries = model.getPluginBase().getLibraries();
-			if (isJarShape || libraries.length == 0) {
-				return Stream.of(IPath.fromOSString(location));
+		Map<Boolean, List<IPluginModelBase>> collect = models.collect(Collectors.partitioningBy(model -> {
+			IResource resource = model.getUnderlyingResource();
+			if (resource != null) {
+				try {
+					return resource.getProject().hasNature(JavaCore.NATURE_ID);
+				} catch (CoreException e) {
+					// nothing we can do then...
+				}
 			}
-			return Arrays.stream(libraries).filter(library -> !IPluginLibrary.RESOURCE.equals(library.getType()))
-					.map(library -> {
-						String name = library.getName();
-						String expandedName = ClasspathUtilCore.expandLibraryName(name);
-						IPath path = ClasspathUtilCore.getPath(model, expandedName, isJarShape);
-						return path;
-					}).filter(Objects::nonNull);
-		}).map(path -> JavaCore.newLibraryEntry(path, path, IPath.ROOT, new IAccessRule[0], new IClasspathAttribute[0],
-				false));
+			return false;
+		}));
+		List<IPluginModelBase> javaModels = collect.get(true);
+		List<IPluginModelBase> externalModels = collect.get(false);
+		return Stream.concat(
+				javaModels.stream().map(m -> JavaCore.create(m.getUnderlyingResource().getProject()))
+						.map(IJavaProject::getPath).map(JavaCore::newProjectEntry),
+				externalModels.stream().flatMap(model -> {
+					String location = model.getInstallLocation();
+					if (location == null) {
+						return Stream.empty();
+					}
+					boolean isJarShape = new File(location).isFile();
+					IPluginLibrary[] libraries = model.getPluginBase().getLibraries();
+					if (isJarShape || libraries.length == 0) {
+						return Stream.of(IPath.fromOSString(location));
+					}
+					return Arrays.stream(libraries)
+							.filter(library -> !IPluginLibrary.RESOURCE.equals(library.getType())).map(library -> {
+								String name = library.getName();
+								String expandedName = ClasspathUtilCore.expandLibraryName(name);
+								return ClasspathUtilCore.getPath(model, expandedName, isJarShape);
+							}).filter(Objects::nonNull);
+				}).map(path -> JavaCore.newLibraryEntry(path, path, IPath.ROOT, new IAccessRule[0],
+						new IClasspathAttribute[0], false)));
 	}
 
 	private static void addLibraryEntry(IPluginLibrary library, Collection<ClasspathLibrary> entries) {
diff --git a/ui/org.eclipse.pde.core/src/org/eclipse/pde/internal/core/annotations/OSGiAnnotationsClasspathContributor.java b/ui/org.eclipse.pde.core/src/org/eclipse/pde/internal/core/annotations/OSGiAnnotationsClasspathContributor.java
index b5e4b758a9..aaaed1b3cf 100644
--- a/ui/org.eclipse.pde.core/src/org/eclipse/pde/internal/core/annotations/OSGiAnnotationsClasspathContributor.java
+++ b/ui/org.eclipse.pde.core/src/org/eclipse/pde/internal/core/annotations/OSGiAnnotationsClasspathContributor.java
@@ -43,9 +43,11 @@ public class OSGiAnnotationsClasspathContributor implements IClasspathContributo
 
 	@Override
 	public List<IClasspathEntry> getInitialEntries(BundleDescription project) {
-		IPluginModelBase model = PluginRegistry.findModel(project);
-		if (model != null) {
-			return ClasspathUtilCore.classpathEntries(annotations()).collect(Collectors.toList());
+		IPluginModelBase projectModel = PluginRegistry.findModel(project);
+		if (projectModel != null) {
+			return ClasspathUtilCore
+					.classpathEntries(annotations().filter(model -> !model.equals(projectModel)))
+					.collect(Collectors.toList());
 		}
 		return Collections.emptyList();
 	}