diff -r 4028502c3333 java.source/src/org/netbeans/modules/java/source/usages/RepositoryUpdater.java
--- a/java.source/src/org/netbeans/modules/java/source/usages/RepositoryUpdater.java	Fri Aug 01 12:37:04 2008 +0400
+++ b/java.source/src/org/netbeans/modules/java/source/usages/RepositoryUpdater.java	Fri Aug 01 12:55:50 2008 +0200
@@ -171,6 +171,7 @@
     static final String SOURCE_LEVEL_ROOT = "sourceLevel"; //NOI18N
     static final String EXTRA_COMPILER_OPTIONS = "extraCompilerOptions"; //NOI18N
     static final String CLASSPATH_ATTRIBUTE = "classPath"; //NOI18N
+    static final String DIGEST = "digest"; //NOI18N
     
     //non-final, non-private for tests...
     static int DELAY = Utilities.isWindows() ? 2000 : 1000;
@@ -1788,7 +1789,22 @@
                 Iterable<? extends File> children, Iterable<? extends File> virtualChildren,
                 boolean clean, ProgressHandle handle, JavaFileFilterImplementation filter,
                 Map<String,List<File>> resources, Set<File> compiledFiles, Set<File> toRecompile,
-                Map<URI, List<String>> misplacedSource2FQNs, boolean allowCancel, boolean generateVirtual) throws IOException {
+                Map<URI, List<String>> misplacedSource2FQNs, boolean allowCancel, boolean generateVirtual)
+                throws IOException 
+        {
+            parseFiles(root, classCache, isInitialCompilation, children,
+                    virtualChildren, clean, handle, filter, resources, compiledFiles,
+                    toRecompile, misplacedSource2FQNs, allowCancel, generateVirtual,
+                    true, null);
+        }
+
+        private void parseFiles(URL root, final File classCache, boolean isInitialCompilation,
+                Iterable<? extends File> children, Iterable<? extends File> virtualChildren,
+                boolean clean, ProgressHandle handle, JavaFileFilterImplementation filter,
+                Map<String,List<File>> resources, Set<File> compiledFiles, Set<File> toRecompile,
+                Map<URI, List<String>> misplacedSource2FQNs, boolean allowCancel, boolean generateVirtual,
+                boolean digestChanged, File folderFile) throws IOException {
+        
             assert !allowCancel || compiledFiles != null;
             LOGGER.fine("parseFiles: " + root);            
             final FileObject rootFo = URLMapper.findFileObject(root);
@@ -1876,6 +1892,14 @@
             if (uqImpl == null) {
                 //IDE is exiting, indeces are already closed.
                 return;
+            }
+            if (clean == false && digestChanged == false) {
+                // no need to recompile whole root and no change detected
+                // in source root.
+                return;
+            }
+            if (resources == null && folderFile != null) {
+                resources = getAllClassFiles(classCache, FileObjects.getRelativePath(rootFile, folderFile), true);
             }
             SourceAnalyser sa = uqImpl.getSourceAnalyser();
             assert sa != null;
@@ -2174,15 +2198,10 @@
                 Map<String, List<File>> resources = Collections.<String, List<File>>emptyMap();
                 final FileList children = new FileList(folderFile);
                 Set<File> compiledFiles = new HashSet<File>();
-                children.getJavaFiles();
-                if (children.digestChanged()) {
-                    resources = getAllClassFiles(classCache, FileObjects.getRelativePath(rootFile, folderFile), true);
-                    parseFiles(root, classCache, isInitialCompilation,
-                            children.getJavaFiles(), children.getVirtualJavaFiles(),
-                            clean, handle, filter, resources, compiledFiles, null, misplacedSource2FQNs, false, true);
-                } else {
-                    ClassIndexManager.getDefault().createUsagesQuery(root, true);
-                }
+                parseFiles(root, classCache, isInitialCompilation,
+                        children.getJavaFiles(), children.getVirtualJavaFiles(),
+                        clean, handle, filter, null, compiledFiles, null, misplacedSource2FQNs,
+                        false, true, children.digestChanged(), folderFile);
                 
                 if (!misplacedSource2FQNs.isEmpty()) {
                     if (LOGGER.isLoggable(Level.FINE)) {
@@ -2753,25 +2772,23 @@
 
         private void computeDigest(File root, final List<File> javaFiles) {
             StringBuilder sb = new StringBuilder(200);
-            sb.append(SourceLevelQuery.getSourceLevel(FileUtil.toFileObject(root)));
             for (File f : javaFiles) {
                 sb.append(f.getPath()).append(f.lastModified());
             }
             try {
-                MessageDigest md5 = MessageDigest.getInstance("MD5");
+                MessageDigest md5 = MessageDigest.getInstance("MD5"); // NOI18N
                 byte[] b = sb.toString().getBytes();
                 byte[] digest = md5.digest(b);
                 URL rootUrl = root.toURI().toURL();
-                Properties prop = loadProperties(rootUrl);
-                String data = prop.getProperty("digest");
-                if (data != null) {
+                String data = getAttribute(rootUrl, DIGEST, null);
+                if (data != null && getAttribute(rootUrl, DIRTY_ROOT, null) == null) {
                     String newDigest = printDigest(digest);
                     if (data.equals(newDigest) == true) {
                         digestChanged = false;
+                        return;
                     }
                 }
-                prop.put("digest", printDigest(digest));
-                storeProperties(rootUrl, prop);
+                ensureAttributeValue(rootUrl, DIGEST, printDigest(digest), true);
             } catch (IOException e) {
             } catch (NoSuchAlgorithmException ex) {
                 Exceptions.printStackTrace(ex);