diff -r b5a20bd41f6a parsing.api/src/org/netbeans/modules/parsing/impl/indexing/FileObjectCrawler.java
--- a/parsing.api/src/org/netbeans/modules/parsing/impl/indexing/FileObjectCrawler.java	Fri Jan 11 12:49:06 2013 +0100
+++ b/parsing.api/src/org/netbeans/modules/parsing/impl/indexing/FileObjectCrawler.java	Mon Jan 14 17:46:41 2013 +0100
@@ -53,6 +53,7 @@
 import java.util.HashSet;
 import java.util.Iterator;
 import java.util.Map;
+import java.util.Map.Entry;
 import java.util.Set;
 import java.util.TreeMap;
 import java.util.TreeSet;
@@ -114,18 +115,35 @@
         if (files != null) {
             if (files.length > 1) {
                 Map<FileObject, Set<FileObject>> clusters = new HashMap<FileObject, Set<FileObject>>();
-                for(FileObject f : files) {
+                Map<FileObject, StringBuilder> relPaths = new HashMap<FileObject, StringBuilder>();
+                OUTER: for(FileObject f : files) {
                     FileObject parent = f.getParent();
                     Set<FileObject> cluster = clusters.get(parent);
                     if (cluster == null) {
+                        StringBuilder currentRelPath = getRelativePath(root, parent);
+                        
+                        for (Iterator<Entry<FileObject, StringBuilder>> it = relPaths.entrySet().iterator(); it.hasNext();) {
+                            Entry<FileObject, StringBuilder> e = it.next();
+                            switch (computeStartsRelation(e.getValue(), currentRelPath)) {
+                                case FIRST_STARTS_WITH_SECOND:
+                                    //we are currently processing a parent folder of something that was already added, skip the old value:
+                                    clusters.remove(e.getKey());
+                                    it.remove();
+                                    break;
+                                case SECOND_STARTS_WITH_FIRST:
+                                    //something existing is a parent folder of what we are processing now - ignore the current request
+                                    continue OUTER;
+                            }
+                        }
                         cluster = new HashSet<FileObject>();
                         clusters.put(parent, cluster);
+                        relPaths.put(parent, currentRelPath);
                     }
                     cluster.add(f);
                 }
                 for(FileObject parent : clusters.keySet()) {
                     Set<FileObject> cluster = clusters.get(parent);
-                    StringBuilder relativePath = getRelativePath(root, parent);
+                    StringBuilder relativePath = relPaths.get(parent);
                     if (relativePath != null) {
                         finished = collect(
                                 cluster.toArray(new FileObject[cluster.size()]),
@@ -274,6 +292,21 @@
             return null;
         }
     }
+    
+    private static enum SubstringKind {
+        FIRST_STARTS_WITH_SECOND,
+        SECOND_STARTS_WITH_FIRST,
+        UNRELATED;
+    }
+    private SubstringKind computeStartsRelation(StringBuilder first, StringBuilder second) {
+        int end = Math.min(first.length(), second.length());
+        
+        for (int i = 0; i < end; i++) {
+            if (first.charAt(i) != second.charAt(i)) return SubstringKind.UNRELATED;
+        }
+        
+        return first.length() > second.length() ? SubstringKind.FIRST_STARTS_WITH_SECOND : SubstringKind.SECOND_STARTS_WITH_FIRST;
+    } 
 
     private boolean isVisible (final @NonNull FileObject fo) {
         try {
diff -r b5a20bd41f6a parsing.api/test/unit/src/org/netbeans/modules/parsing/impl/indexing/FileObjectCrawlerTest.java
--- a/parsing.api/test/unit/src/org/netbeans/modules/parsing/impl/indexing/FileObjectCrawlerTest.java	Fri Jan 11 12:49:06 2013 +0100
+++ b/parsing.api/test/unit/src/org/netbeans/modules/parsing/impl/indexing/FileObjectCrawlerTest.java	Mon Jan 14 17:46:41 2013 +0100
@@ -46,14 +46,16 @@
 import java.io.File;
 import java.io.IOException;
 import java.net.URL;
+import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
+import java.util.Collections;
 import java.util.EnumSet;
 import java.util.HashMap;
-import java.util.HashSet;
+import java.util.List;
 import java.util.Map;
-import java.util.Set;
 import java.util.regex.Pattern;
+import static junit.framework.Assert.assertNull;
 import org.netbeans.api.java.classpath.ClassPath;
 import org.netbeans.junit.NbTestCase;
 import org.netbeans.modules.parsing.spi.indexing.Indexable;
@@ -303,17 +305,49 @@
                 "folder2/data3.txt");
     }
 
+    public void testDuplicateResults1() throws IOException {
+        File root = new File(getWorkDir(), "src");
+        String [] paths = new String [] {
+                "org/pckg1/file1.txt",
+                "org/pckg1/pckg2/file1.txt",
+                "org/pckg1/pckg2/file2.txt",
+        };
+        
+        populateFolderStructure(root, paths);
+        
+        FileObject rootFO = FileUtil.toFileObject(root);
+        FileObjectCrawler crawler = new FileObjectCrawler(rootFO, new FileObject[] {rootFO.getFileObject("org/pckg1/pckg2/file1.txt"), rootFO.getFileObject("org/pckg1/pckg2")}, EnumSet.<Crawler.TimeStampAction>of(Crawler.TimeStampAction.UPDATE), null, CR, SuspendSupport.NOP);
+        assertCollectedFiles("Wrong files collected", crawler.getResources(), new String[] {"org/pckg1/pckg2/file1.txt", "org/pckg1/pckg2/file2.txt"});
+    }
+    
+    public void testDuplicateResults2() throws IOException {
+        File root = new File(getWorkDir(), "src");
+        String [] paths = new String [] {
+                "org/pckg1/file1.txt",
+                "org/pckg1/pckg2/file1.txt",
+                "org/pckg1/pckg2/file2.txt",
+        };
+        
+        populateFolderStructure(root, paths);
+        
+        FileObject rootFO = FileUtil.toFileObject(root);
+        FileObjectCrawler crawler = new FileObjectCrawler(rootFO, new FileObject[] {rootFO.getFileObject("org/pckg1/pckg2/file1.txt"), rootFO.getFileObject("org/pckg1/pckg2/file2.txt")}, EnumSet.<Crawler.TimeStampAction>of(Crawler.TimeStampAction.UPDATE), null, CR, SuspendSupport.NOP);
+        assertCollectedFiles("Wrong files collected", crawler.getResources(), new String[] {"org/pckg1/pckg2/file1.txt", "org/pckg1/pckg2/file2.txt"});
+    }
+    
     protected void assertCollectedFiles(String message, Collection<Indexable> resources, String... expectedPaths) throws IOException {
-        Set<String> collectedPaths = new HashSet<String>();
+        List<String> collectedPaths = new ArrayList<String>();
         for(Indexable ii : resources) {
             collectedPaths.add(ii.getRelativePath());
         }
-        Set<String> expectedPathsFiltered = new HashSet<String>();
+        List<String> expectedPathsFiltered = new ArrayList<String>();
         for(String path : expectedPaths) {
             if (!path.endsWith("/")) { // crawler only collects files
                 expectedPathsFiltered.add(path);
             }
         }
+        Collections.sort(collectedPaths);
+        Collections.sort(expectedPathsFiltered);
         assertEquals(message, expectedPathsFiltered, collectedPaths);
     }