diff --git a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/model/ExternalTranslationUnit.java b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/model/ExternalTranslationUnit.java
index de4af83ea04..7bc00b8ed60 100644
--- a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/model/ExternalTranslationUnit.java
+++ b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/model/ExternalTranslationUnit.java
@@ -17,6 +17,7 @@ import java.net.URI;
 
 import org.eclipse.cdt.core.model.ICElement;
 import org.eclipse.core.filesystem.URIUtil;
+import org.eclipse.core.resources.IFile;
 import org.eclipse.core.runtime.IPath;
 
 /**
@@ -36,4 +37,10 @@ public class ExternalTranslationUnit extends TranslationUnit {
 		super(parent, uri, contentTypeID);
 	}
 
+	/**
+	 * A file included from a different project can still belong to a (non-CDT) project
+	 */
+	public void setResource(IFile file) {
+		resource= file;
+	}
 }
diff --git a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/indexer/PDOMUpdateTask.java b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/indexer/PDOMUpdateTask.java
index fcb459ecc6a..9fd09a5ad4b 100644
--- a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/indexer/PDOMUpdateTask.java
+++ b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/indexer/PDOMUpdateTask.java
@@ -27,7 +27,11 @@ import org.eclipse.cdt.core.model.CoreModel;
 import org.eclipse.cdt.core.model.ICElement;
 import org.eclipse.cdt.core.model.ICProject;
 import org.eclipse.cdt.core.model.ITranslationUnit;
+import org.eclipse.cdt.internal.core.model.ExternalTranslationUnit;
 import org.eclipse.cdt.internal.core.pdom.IndexerProgress;
+import org.eclipse.core.resources.IFile;
+import org.eclipse.core.resources.IResource;
+import org.eclipse.core.resources.ResourcesPlugin;
 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.IPath;
 import org.eclipse.core.runtime.IProgressMonitor;
@@ -98,23 +102,32 @@ public class PDOMUpdateTask implements IPDOMIndexerTask {
 			}
 		}
 		if (haveProject && (fUpdateOptions & IIndexManager.UPDATE_EXTERNAL_FILES_FOR_PROJECT) != 0) {
+			final String projectPrefix= project.getProject().getFullPath().toString() + IPath.SEPARATOR;
 			IIndex index= CCorePlugin.getIndexManager().getIndex(project);
 			index.acquireReadLock();
 			try {
 				IIndexFile[] files= index.getAllFiles();
 				for (IIndexFile indexFile : files) {
 					IIndexFileLocation floc= indexFile.getLocation();
-					if (floc.getFullPath() == null) {
-						IPath path= IndexLocationFactory.getPath(floc);
+					final String fullPath = floc.getFullPath();
+					if (fullPath == null || !fullPath.startsWith(projectPrefix)) {
+						IPath path= IndexLocationFactory.getAbsolutePath(floc);
 						if (path != null) {
 							ITranslationUnit tu= CoreModel.getDefault().createTranslationUnitFrom(project, path);
 							if (tu != null) {
+								if (fullPath != null) {
+									if (tu instanceof ExternalTranslationUnit) {
+										IResource file= ResourcesPlugin.getWorkspace().getRoot().findMember(fullPath);
+										if (file instanceof IFile) {
+											((ExternalTranslationUnit) tu).setResource((IFile) file);
+										}
+									}
+								}
 								set.add(tu);
 							}
 						}
 					}
 				}
-				
 			} finally {
 				index.releaseReadLock();
 			}
diff --git a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/indexer/ProjectIndexerInputAdapter.java b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/indexer/ProjectIndexerInputAdapter.java
index 6ad553c9b70..03fd25491c8 100644
--- a/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/indexer/ProjectIndexerInputAdapter.java
+++ b/core/org.eclipse.cdt.core/parser/org/eclipse/cdt/internal/core/pdom/indexer/ProjectIndexerInputAdapter.java
@@ -42,15 +42,13 @@ import org.eclipse.core.runtime.content.IContentType;
  * @since 5.0
  */
 public class ProjectIndexerInputAdapter extends IndexerInputAdapter {
-	/**
-	 * mstodo
-	 */
 	private static final AbstractLanguage[] NO_LANGUAGE = new AbstractLanguage[0];
 	private final ICProject fCProject;
 	private final HashMap<String, IIndexFileLocation> fIflCache;
 	private final FileExistsCache fExistsCache;
 	private AbstractLanguage fLangC;
 	private AbstractLanguage fLangCpp;
+	private String fProjectPrefix;
 
 	public ProjectIndexerInputAdapter(ICProject cproject) {
 		this(cproject, true);
@@ -58,6 +56,7 @@ public class ProjectIndexerInputAdapter extends IndexerInputAdapter {
 
 	public ProjectIndexerInputAdapter(ICProject cproject, boolean useCache) {
 		fCProject= cproject;
+		fProjectPrefix= cproject.getProject().getFullPath().toString() + IPath.SEPARATOR;
 		if (useCache) {
 			fIflCache= new HashMap<String, IIndexFileLocation>();
 			fExistsCache= new FileExistsCache();
@@ -226,7 +225,8 @@ public class ProjectIndexerInputAdapter extends IndexerInputAdapter {
 	
 	@Override
 	public boolean canBePartOfSDK(IIndexFileLocation ifl) {
-		return ifl.getFullPath() == null;
+		final String fullPath = ifl.getFullPath();
+		return fullPath == null || !fullPath.startsWith(fProjectPrefix);
 	}
 
 	@Override