Index: search/org/eclipse/jdt/internal/core/search/IndexSelector.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/search/org/eclipse/jdt/internal/core/search/IndexSelector.java,v
retrieving revision 1.48.2.1
diff -u -r1.48.2.1 IndexSelector.java
--- search/org/eclipse/jdt/internal/core/search/IndexSelector.java	28 Jun 2010 06:57:23 -0000	1.48.2.1
+++ search/org/eclipse/jdt/internal/core/search/IndexSelector.java	21 Jun 2011 05:57:57 -0000
@@ -7,9 +7,12 @@
  *
  * Contributors:
  *     IBM Corporation - initial API and implementation
+ *     Nikolay Botev - Bug 348507
  *******************************************************************************/
 package org.eclipse.jdt.internal.core.search;
 
+import java.util.LinkedHashSet;
+
 import org.eclipse.core.resources.IFolder;
 import org.eclipse.core.resources.ResourcesPlugin;
 import org.eclipse.core.runtime.IPath;
@@ -180,7 +183,8 @@
 private void initializeIndexLocations() {
 	IPath[] projectsAndJars = this.searchScope.enclosingProjectsAndJars();
 	IndexManager manager = JavaModelManager.getIndexManager();
-	SimpleSet locations = new SimpleSet();
+	// use a linked set to preserve the order during search: see bug 348507
+	LinkedHashSet locations = new LinkedHashSet();
 	IJavaElement focus = MatchLocator.projectOrJarFocus(this.pattern);
 	if (focus == null) {
 		for (int i = 0; i < projectsAndJars.length; i++) {
@@ -263,12 +267,8 @@
 		}
 	}
 
-	this.indexLocations = new IPath[locations.elementSize];
-	Object[] values = locations.values;
-	int count = 0;
-	for (int i = values.length; --i >= 0;)
-		if (values[i] != null)
-			this.indexLocations[count++] = (IPath) values[i];
+	locations.remove(null); // Ensure no nulls
+	this.indexLocations = (IPath[]) locations.toArray(new IPath[locations.size()]);
 }
 
 public IPath[] getIndexLocations() {
Index: search/org/eclipse/jdt/internal/core/search/JavaWorkspaceScope.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/search/org/eclipse/jdt/internal/core/search/JavaWorkspaceScope.java,v
retrieving revision 1.36
diff -u -r1.36 JavaWorkspaceScope.java
--- search/org/eclipse/jdt/internal/core/search/JavaWorkspaceScope.java	27 Jun 2008 16:04:09 -0000	1.36
+++ search/org/eclipse/jdt/internal/core/search/JavaWorkspaceScope.java	21 Jun 2011 05:57:57 -0000
@@ -7,11 +7,12 @@
  *
  * Contributors:
  *     IBM Corporation - initial API and implementation
+ *     Nikolay Botev - Bug 348507
  *******************************************************************************/
 package org.eclipse.jdt.internal.core.search;
 
 import java.util.HashMap;
-import java.util.HashSet;
+import java.util.LinkedHashSet;
 import java.util.Set;
 
 import org.eclipse.core.resources.IFolder;
@@ -72,13 +73,22 @@
 	long start = BasicSearchEngine.VERBOSE ? System.currentTimeMillis() : -1;
 	try {
 		IJavaProject[] projects = JavaModelManager.getJavaModelManager().getJavaModel().getJavaProjects();
-		Set paths = new HashSet(projects.length * 2);
+		// use a linked set to preserve the order during search: see bug 348507
+		Set paths = new LinkedHashSet(projects.length * 2);
 		for (int i = 0, length = projects.length; i < length; i++) {
 			JavaProject javaProject = (JavaProject) projects[i];
 
 			// Add project full path
 			IPath projectPath = javaProject.getProject().getFullPath();
 			paths.add(projectPath);
+		}
+
+		// add the project source paths first in a separate loop above
+		// to ensure source files always get higher precedence during search.
+		// see bug 348507
+
+		for (int i = 0, length = projects.length; i < length; i++) {
+			JavaProject javaProject = (JavaProject) projects[i];
 
 			// Add project libraries paths
 			IClasspathEntry[] entries = javaProject.getResolvedClasspath();