### Eclipse Workspace Patch 1.0
#P org.eclipse.jdt.core.tests.performance
Index: src/org/eclipse/jdt/core/tests/performance/FullSourceWorkspaceTests.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core.tests.performance/src/org/eclipse/jdt/core/tests/performance/FullSourceWorkspaceTests.java,v
retrieving revision 1.45
diff -u -r1.45 FullSourceWorkspaceTests.java
--- src/org/eclipse/jdt/core/tests/performance/FullSourceWorkspaceTests.java	29 May 2007 15:43:10 -0000	1.45
+++ src/org/eclipse/jdt/core/tests/performance/FullSourceWorkspaceTests.java	28 Aug 2007 08:59:20 -0000
@@ -128,7 +128,7 @@
 
 
 	// Index variables
-	protected static IndexManager INDEX_MANAGER = JavaModelManager.getJavaModelManager().getIndexManager();
+	protected static IndexManager INDEX_MANAGER = JavaModelManager.getIndexManager();
 	
 	// Tests infos
 	protected static int ALL_TESTS_COUNT = 0;
#P org.eclipse.jdt.core.tests.model
Index: src/org/eclipse/jdt/core/tests/model/SearchTests.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core.tests.model/src/org/eclipse/jdt/core/tests/model/SearchTests.java,v
retrieving revision 1.42
diff -u -r1.42 SearchTests.java
--- src/org/eclipse/jdt/core/tests/model/SearchTests.java	24 Aug 2007 05:58:27 -0000	1.42
+++ src/org/eclipse/jdt/core/tests/model/SearchTests.java	28 Aug 2007 08:59:26 -0000
@@ -233,7 +233,7 @@
  * a project causes another request to reindex.
  */
 public void testChangeClasspath() throws CoreException, TimeOutException {
-	IndexManager indexManager = JavaModelManager.getJavaModelManager().getIndexManager();
+	IndexManager indexManager = JavaModelManager.getIndexManager();
 	WaitingJob job = new WaitingJob();
 	try {
 		// setup: suspend indexing and create a project (prj=src) with one cu
@@ -335,7 +335,7 @@
  * (regression test for bug 35306 Index update request can be incorrectly handled)
  */
 public void testConcurrentJob() throws CoreException, InterruptedException, IOException, TimeOutException {
-	IndexManager indexManager = JavaModelManager.getJavaModelManager().getIndexManager();
+	IndexManager indexManager = JavaModelManager.getIndexManager();
 	WaitingJob job = new WaitingJob();
 	try {
 		// setup: suspend indexing and create a project with one empty jar on its classpath
@@ -413,7 +413,7 @@
  * (regression test for bug 33571 SearchEngine.searchAllTypeNames: NPE when passing null as progress monitor)
  */
  public void testNullProgressMonitor() throws CoreException, TimeOutException {
-	IndexManager indexManager = JavaModelManager.getJavaModelManager().getIndexManager();
+	IndexManager indexManager = JavaModelManager.getIndexManager();
 	WaitingJob job = new WaitingJob();
  	try {
  		// add waiting job and wait for it to be executed
Index: src/org/eclipse/jdt/core/tests/model/JavaSearchBugsTests.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core.tests.model/src/org/eclipse/jdt/core/tests/model/JavaSearchBugsTests.java,v
retrieving revision 1.120
diff -u -r1.120 JavaSearchBugsTests.java
--- src/org/eclipse/jdt/core/tests/model/JavaSearchBugsTests.java	24 Aug 2007 13:52:11 -0000	1.120
+++ src/org/eclipse/jdt/core/tests/model/JavaSearchBugsTests.java	28 Aug 2007 08:59:25 -0000
@@ -8404,7 +8404,7 @@
  */
 public void testBug181488a() throws CoreException {
 	waitUntilIndexesReady();
-	IndexManager manager = JavaModelManager.getJavaModelManager().getIndexManager();
+	IndexManager manager = JavaModelManager.getIndexManager();
 	Index index = manager.getIndex(JAVA_PROJECT.getPath(), true, false);
 	long lastModified = index.getIndexFile().lastModified();
 	simulateExitRestart();
@@ -8416,7 +8416,7 @@
 	IJavaProject project = createJavaProject("Bug181488");
 	try {
 		waitUntilIndexesReady();
-		IndexManager manager = JavaModelManager.getJavaModelManager().getIndexManager();
+		IndexManager manager = JavaModelManager.getIndexManager();
 		Index index = manager.getIndex(project.getPath(), true, false);
 		assertEquals("Index file should at least contains the signature!!!", DiskIndex.SIGNATURE.length()+6, index.getIndexFile().length());
 	}
Index: src/org/eclipse/jdt/core/tests/model/JavaSearchScopeTests.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core.tests.model/src/org/eclipse/jdt/core/tests/model/JavaSearchScopeTests.java,v
retrieving revision 1.10
diff -u -r1.10 JavaSearchScopeTests.java
--- src/org/eclipse/jdt/core/tests/model/JavaSearchScopeTests.java	8 Aug 2007 15:28:12 -0000	1.10
+++ src/org/eclipse/jdt/core/tests/model/JavaSearchScopeTests.java	28 Aug 2007 08:59:25 -0000
@@ -997,7 +997,7 @@
 		deleteFile("/P1/src/Test.java");
 
 		// Index the output location as it is a library for the project
-		IndexManager indexManager = JavaModelManager.getJavaModelManager().getIndexManager();
+		IndexManager indexManager = JavaModelManager.getIndexManager();
 		indexManager.indexLibrary(new Path("/P1/bin"), project.getProject());
 		waitUntilIndexesReady();
 		
Index: src/org/eclipse/jdt/core/tests/model/ClasspathInitializerTests.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core.tests.model/src/org/eclipse/jdt/core/tests/model/ClasspathInitializerTests.java,v
retrieving revision 1.52
diff -u -r1.52 ClasspathInitializerTests.java
--- src/org/eclipse/jdt/core/tests/model/ClasspathInitializerTests.java	18 Aug 2007 18:03:17 -0000	1.52
+++ src/org/eclipse/jdt/core/tests/model/ClasspathInitializerTests.java	28 Aug 2007 08:59:23 -0000
@@ -20,7 +20,6 @@
 import org.eclipse.jdt.internal.core.JavaModelManager;
 import org.eclipse.jdt.internal.core.JavaModelStatus;
 import org.eclipse.jdt.internal.core.UserLibraryClasspathContainer;
-import org.eclipse.jdt.internal.core.UserLibraryManager;
 
 import junit.framework.Test;
 
@@ -1379,7 +1378,7 @@
 
 		// Modify user library
 		Preferences preferences = JavaCore.getPlugin().getPluginPreferences();
-		String propertyName = UserLibraryManager.CP_USERLIBRARY_PREFERENCES_PREFIX+"SWT";
+		String propertyName = JavaModelManager.CP_USERLIBRARY_PREFERENCES_PREFIX+"SWT";
 		StringBuffer propertyValue = new StringBuffer("<?xml version=\"1.0\" encoding=\"UTF-8\"?>\r\n<userlibrary systemlibrary=\"false\" version=\"1\">\r\n<archive");
 		String jarFullPath = getWorkspaceRoot().getLocation().append(jarFile.getFullPath()).toString();
 		propertyValue.append(" path=\""+jarFullPath);
Index: src/org/eclipse/jdt/core/tests/model/ReconcilerTests.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core.tests.model/src/org/eclipse/jdt/core/tests/model/ReconcilerTests.java,v
retrieving revision 1.118
diff -u -r1.118 ReconcilerTests.java
--- src/org/eclipse/jdt/core/tests/model/ReconcilerTests.java	8 Aug 2007 15:28:12 -0000	1.118
+++ src/org/eclipse/jdt/core/tests/model/ReconcilerTests.java	28 Aug 2007 08:59:26 -0000
@@ -107,7 +107,7 @@
 }
 // Expect no error as soon as indexing is finished
 protected void assertNoProblem(char[] source, ICompilationUnit unit) throws InterruptedException, JavaModelException {
-	IndexManager indexManager = JavaModelManager.getJavaModelManager().getIndexManager();
+	IndexManager indexManager = JavaModelManager.getIndexManager();
 	if (this.problemRequestor.problemCount > 0) {
 		// If errors then wait for indexes to finish
 		while (indexManager.awaitingJobsCount() > 0) {
Index: src/org/eclipse/jdt/core/tests/model/ReconcilerStatementsRecoveryTests.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core.tests.model/src/org/eclipse/jdt/core/tests/model/ReconcilerStatementsRecoveryTests.java,v
retrieving revision 1.6
diff -u -r1.6 ReconcilerStatementsRecoveryTests.java
--- src/org/eclipse/jdt/core/tests/model/ReconcilerStatementsRecoveryTests.java	16 Mar 2007 18:35:31 -0000	1.6
+++ src/org/eclipse/jdt/core/tests/model/ReconcilerStatementsRecoveryTests.java	28 Aug 2007 08:59:25 -0000
@@ -74,7 +74,7 @@
 }
 // Expect no error as soon as indexing is finished
 protected void assertNoProblem(char[] source, ICompilationUnit unit) throws InterruptedException, JavaModelException {
-	IndexManager indexManager = JavaModelManager.getJavaModelManager().getIndexManager();
+	IndexManager indexManager = JavaModelManager.getIndexManager();
 	if (this.problemRequestor.problemCount > 0) {
 		// If errors then wait for indexes to finish
 		while (indexManager.awaitingJobsCount() > 0) {
Index: src/org/eclipse/jdt/core/tests/model/JavaProjectTests.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core.tests.model/src/org/eclipse/jdt/core/tests/model/JavaProjectTests.java,v
retrieving revision 1.87
diff -u -r1.87 JavaProjectTests.java
--- src/org/eclipse/jdt/core/tests/model/JavaProjectTests.java	24 Aug 2007 13:02:27 -0000	1.87
+++ src/org/eclipse/jdt/core/tests/model/JavaProjectTests.java	28 Aug 2007 08:59:23 -0000
@@ -26,7 +26,6 @@
 import org.eclipse.jdt.internal.compiler.classfmt.ClassFileConstants;
 import org.eclipse.jdt.internal.core.JavaModelManager;
 import org.eclipse.jdt.internal.core.PackageFragmentRoot;
-import org.eclipse.jdt.internal.core.UserLibraryManager;
 import org.eclipse.jdt.internal.core.util.Util;
 
 public class JavaProjectTests extends ModifyingResourceTests {
@@ -1526,7 +1525,7 @@
 	
 	// Verify it has been written in preferences
 	IEclipsePreferences instancePreferences = JavaModelManager.getJavaModelManager().getInstancePreferences();
-	String containerKey = UserLibraryManager.CP_USERLIBRARY_PREFERENCES_PREFIX+"TEST";
+	String containerKey = JavaModelManager.CP_USERLIBRARY_PREFERENCES_PREFIX+"TEST";
 	String libraryPreference = instancePreferences.get(containerKey, null);
 	assertNotNull("Should get a preference for TEST user library", libraryPreference);
 
#P org.eclipse.jdt.core.tests
Index: Eclipse Java Tests Model/src/org/eclipse/jdt/tests/core/OldSearchTests.java
===================================================================
RCS file: /home/cvs/numbat/org.eclipse.jdt.core.tests/Eclipse Java Tests Model/src/org/eclipse/jdt/tests/core/OldSearchTests.java,v
retrieving revision 1.29
diff -u -r1.29 OldSearchTests.java
--- Eclipse Java Tests Model/src/org/eclipse/jdt/tests/core/OldSearchTests.java	6 Mar 2007 04:29:56 -0000	1.29
+++ Eclipse Java Tests Model/src/org/eclipse/jdt/tests/core/OldSearchTests.java	28 Aug 2007 08:57:00 -0000
@@ -4790,7 +4790,7 @@
 	};
 	
 	IJavaSearchScope scope = SearchEngine.createJavaSearchScope(new IJavaElement[] {project});
-	IndexManager indexManager = JavaModelManager.getJavaModelManager().getIndexManager();
+	IndexManager indexManager = JavaModelManager.getIndexManager();
 
 	IProgressMonitor progressMonitor = new SearchProgress("<querying constructor decl Compiler>", new StringBuffer(100));
 	indexManager.performConcurrentJob(
@@ -4833,7 +4833,7 @@
 	};
 	
 	IJavaSearchScope scope = SearchEngine.createJavaSearchScope(new IJavaElement[] {project});
-	IndexManager indexManager = JavaModelManager.getJavaModelManager().getIndexManager();
+	IndexManager indexManager = JavaModelManager.getIndexManager();
 
 	IProgressMonitor progressMonitor = new SearchProgress("<querying constructor ref BlockScope>", new StringBuffer(100));
 	indexManager.performConcurrentJob(
@@ -4881,7 +4881,7 @@
 	};
 	
 	IJavaSearchScope scope = SearchEngine.createJavaSearchScope(new IJavaElement[] {project});
-	IndexManager indexManager = JavaModelManager.getJavaModelManager().getIndexManager();
+	IndexManager indexManager = JavaModelManager.getIndexManager();
 
 	IProgressMonitor progressMonitor = new SearchProgress("<querying constructor ref Object>", new StringBuffer(100));
 	indexManager.performConcurrentJob(
@@ -5365,7 +5365,7 @@
 	};
 	
 	IJavaSearchScope scope = SearchEngine.createJavaSearchScope(new IJavaElement[] {project});
-	IndexManager indexManager = JavaModelManager.getJavaModelManager().getIndexManager();
+	IndexManager indexManager = JavaModelManager.getIndexManager();
 
 	IProgressMonitor progressMonitor = new SearchProgress("<querying method computeConstantOperation*>", new StringBuffer(100));
 	indexManager.performConcurrentJob(
@@ -5424,7 +5424,7 @@
 	};
 	
 	IJavaSearchScope scope = SearchEngine.createJavaSearchScope(new IJavaElement[] {project});
-	IndexManager indexManager = JavaModelManager.getJavaModelManager().getIndexManager();
+	IndexManager indexManager = JavaModelManager.getIndexManager();
 
 	IProgressMonitor progressMonitor = new SearchProgress("<querying method computeConstantOperation* ref>", new StringBuffer(100));
 	indexManager.performConcurrentJob(
@@ -5483,7 +5483,7 @@
 	};
 	
 	IJavaSearchScope scope = SearchEngine.createJavaSearchScope(new IJavaElement[] {project});
-	IndexManager indexManager = JavaModelManager.getJavaModelManager().getIndexManager();
+	IndexManager indexManager = JavaModelManager.getIndexManager();
 
 	IProgressMonitor progressMonitor = new SearchProgress("<querying method ana*Code ref>", new StringBuffer(100));
 	indexManager.performConcurrentJob(
#P org.eclipse.jdt.core
Index: model/org/eclipse/jdt/internal/core/JavaModelManager.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/model/org/eclipse/jdt/internal/core/JavaModelManager.java,v
retrieving revision 1.375
diff -u -r1.375 JavaModelManager.java
--- model/org/eclipse/jdt/internal/core/JavaModelManager.java	24 Aug 2007 13:02:31 -0000	1.375
+++ model/org/eclipse/jdt/internal/core/JavaModelManager.java	28 Aug 2007 08:59:34 -0000
@@ -133,6 +133,7 @@
 
 	public final static String CP_VARIABLE_PREFERENCES_PREFIX = JavaCore.PLUGIN_ID+".classpathVariable."; //$NON-NLS-1$
 	public final static String CP_CONTAINER_PREFERENCES_PREFIX = JavaCore.PLUGIN_ID+".classpathContainer."; //$NON-NLS-1$
+	public final static String CP_USERLIBRARY_PREFERENCES_PREFIX = JavaCore.PLUGIN_ID+".userLibrary."; //$NON-NLS-1$
 	public final static String CP_ENTRY_IGNORE = "##<cp entry ignore>##"; //$NON-NLS-1$
 	public final static IPath CP_ENTRY_IGNORE_PATH = new Path(CP_ENTRY_IGNORE);
 	public final static String TRUE = "true"; //$NON-NLS-1$
@@ -1213,7 +1214,7 @@
 	 */
 	private ThreadLocal zipFiles = new ThreadLocal();
 	
-	private UserLibraryManager userLibraryManager;
+	UserLibraryManager userLibraryManager;
 	
 	/**
 	 * Update the classpath variable cache
@@ -1281,9 +1282,49 @@
 				} catch (JavaModelException e) {
 					// skip
 				}
+        	} else if (propertyName.startsWith(CP_USERLIBRARY_PREFERENCES_PREFIX)) {
+				String libName = propertyName.substring(CP_USERLIBRARY_PREFERENCES_PREFIX.length());
+				UserLibraryManager manager = JavaModelManager.getUserLibraryManager();
+        		manager.updateUserLibrary(libName, (String)event.getNewValue());
         	}
         }
 	}
+	/**
+	 * Listener on eclipse preferences changes.
+	 */
+	EclipsePreferencesListener instancePreferencesListener = new EclipsePreferencesListener();
+	/**
+	 * Listener on eclipse preferences default/instance node changes.
+	 */
+	IEclipsePreferences.INodeChangeListener instanceNodeListener = new IEclipsePreferences.INodeChangeListener() {
+		public void added(IEclipsePreferences.NodeChangeEvent event) {
+			// do nothing
+		}
+		public void removed(IEclipsePreferences.NodeChangeEvent event) {
+			if (event.getChild() == preferencesLookup[PREF_INSTANCE]) {
+				preferencesLookup[PREF_INSTANCE] = ((IScopeContext) new InstanceScope()).getNode(JavaCore.PLUGIN_ID);
+				preferencesLookup[PREF_INSTANCE].addPreferenceChangeListener(new EclipsePreferencesListener());
+			}
+		}
+	};
+	IEclipsePreferences.INodeChangeListener defaultNodeListener = new IEclipsePreferences.INodeChangeListener() {
+		public void added(IEclipsePreferences.NodeChangeEvent event) {
+			// do nothing
+		}
+		public void removed(IEclipsePreferences.NodeChangeEvent event) {
+			if (event.getChild() == preferencesLookup[PREF_DEFAULT]) {
+				preferencesLookup[PREF_DEFAULT] = ((IScopeContext) new DefaultScope()).getNode(JavaCore.PLUGIN_ID);
+			}
+		}
+	};
+	/**
+	 * Listener on properties changes.
+	 */
+	Preferences.IPropertyChangeListener propertyListener = new Preferences.IPropertyChangeListener() {
+		public void propertyChange(Preferences.PropertyChangeEvent event) {
+			JavaModelManager.this.optionsCache = null;
+		}
+	};
 
 	/**
 	 * Constructs a new JavaModelManager
@@ -1552,6 +1593,10 @@
 	public DeltaProcessor getDeltaProcessor() {
 		return this.deltaState.getDeltaProcessor();
 	}
+
+	public static DeltaProcessingState getDeltaState() {
+		return MANAGER.deltaState;
+	}
 	
 	/** 
 	 * Returns the set of elements which are out of synch with their buffers.
@@ -1560,8 +1605,8 @@
 		return this.elementsOutOfSynchWithBuffers;
 	}
 
-	public IndexManager getIndexManager() {
-		return this.indexManager;
+	public static IndexManager getIndexManager() {
+		return MANAGER.indexManager;
 	}
 
 	/**
@@ -1579,7 +1624,7 @@
 	}
 
 	/**
-	 * Get workpsace eclipse preference for JavaCore plugin.
+	 * Get workspace eclipse preference for JavaCore plug-in.
 	 */
 	public IEclipsePreferences getInstancePreferences() {
 		return preferencesLookup[PREF_INSTANCE];
@@ -1954,17 +1999,15 @@
 	}
 	
 	public static UserLibraryManager getUserLibraryManager() {
-		JavaModelManager modelManager = getJavaModelManager();
-		if (modelManager.userLibraryManager == null) {
+		if (MANAGER.userLibraryManager == null) {
 			UserLibraryManager libraryManager = new UserLibraryManager();
-			synchronized(modelManager) {
-				if (modelManager.userLibraryManager == null) { // ensure another library manager was not set while creating the instance above
-					modelManager.userLibraryManager = libraryManager;
-					modelManager.getInstancePreferences().addPreferenceChangeListener(libraryManager);
+			synchronized(MANAGER) {
+				if (MANAGER.userLibraryManager == null) { // ensure another library manager was not set while creating the instance above
+					MANAGER.userLibraryManager = libraryManager;
 				}
 			}
 		}
-		return modelManager.userLibraryManager;
+		return MANAGER.userLibraryManager;
 	}
 	
 	/*
@@ -2352,16 +2395,16 @@
 	}
 
 	/**
-	 * Initialize preferences lookups for JavaCore plugin.
+	 * Initialize preferences lookups for JavaCore plug-in.
 	 */
 	public void initializePreferences() {
-		
+
 		// Create lookups
 		preferencesLookup[PREF_INSTANCE] = ((IScopeContext) new InstanceScope()).getNode(JavaCore.PLUGIN_ID);
 		preferencesLookup[PREF_DEFAULT] = ((IScopeContext) new DefaultScope()).getNode(JavaCore.PLUGIN_ID);
 
 		// Listen to instance preferences node removal from parent in order to refresh stored one
-		IEclipsePreferences.INodeChangeListener listener = new IEclipsePreferences.INodeChangeListener() {
+		this.instanceNodeListener = new IEclipsePreferences.INodeChangeListener() {
 			public void added(IEclipsePreferences.NodeChangeEvent event) {
 				// do nothing
 			}
@@ -2372,11 +2415,11 @@
 				}
 			}
 		};
-		((IEclipsePreferences) preferencesLookup[PREF_INSTANCE].parent()).addNodeChangeListener(listener);
-		preferencesLookup[PREF_INSTANCE].addPreferenceChangeListener(new EclipsePreferencesListener());
+		((IEclipsePreferences) preferencesLookup[PREF_INSTANCE].parent()).addNodeChangeListener(this.instanceNodeListener);
+		preferencesLookup[PREF_INSTANCE].addPreferenceChangeListener(this.instancePreferencesListener = new EclipsePreferencesListener());
 
 		// Listen to default preferences node removal from parent in order to refresh stored one
-		listener = new IEclipsePreferences.INodeChangeListener() {
+		this.defaultNodeListener = new IEclipsePreferences.INodeChangeListener() {
 			public void added(IEclipsePreferences.NodeChangeEvent event) {
 				// do nothing
 			}
@@ -2386,7 +2429,7 @@
 				}
 			}
 		};
-		((IEclipsePreferences) preferencesLookup[PREF_DEFAULT].parent()).addNodeChangeListener(listener);
+		((IEclipsePreferences) preferencesLookup[PREF_DEFAULT].parent()).addNodeChangeListener(this.defaultNodeListener);
 	}
 
 	public synchronized char[] intern(char[] array) {
@@ -3893,55 +3936,55 @@
 	}
 
 	/**
-	 * Remove from secondary types cache all types belonging to a given file.
-	 * Clean secondary types cache built while indexing if requested.
-	 * 
-	 * Project's secondary types cache is found using file location.
-	 * 
-	 * @param file File to remove
-	 */
-	public void secondaryTypesRemoving(IFile file, boolean cleanIndexCache) {
-		if (VERBOSE) {
-			StringBuffer buffer = new StringBuffer("JavaModelManager.removeFromSecondaryTypesCache("); //$NON-NLS-1$
-			buffer.append(file.getName());
-			buffer.append(')');
-			Util.verbose(buffer.toString());
-		}
-		if (file != null) {
-			PerProjectInfo projectInfo = getPerProjectInfo(file.getProject(), false);
-			if (projectInfo != null && projectInfo.secondaryTypes != null) {
-				if (VERBOSE) {
-					Util.verbose("-> remove file from cache of project: "+file.getProject().getName()); //$NON-NLS-1$
-				}
-
-				// Clean current cache
-				secondaryTypesRemoving(projectInfo.secondaryTypes, file);
-				
-				// Clean indexing cache if necessary
-				if (!cleanIndexCache) return;
-				HashMap indexingCache = (HashMap) projectInfo.secondaryTypes.get(INDEXED_SECONDARY_TYPES);
-				if (indexingCache != null) {
-					Set keys = indexingCache.keySet();
-					int filesSize = keys.size(), filesCount = 0;
-					IFile[] removed = null;
-					Iterator cachedFiles = keys.iterator();
-					while (cachedFiles.hasNext()) {
-						IFile cachedFile = (IFile) cachedFiles.next();
-						if (file.equals(cachedFile)) {
-							if (removed == null) removed = new IFile[filesSize];
-							filesSize--;
-							removed[filesCount++] = cachedFile;
-						}
-					}
-					if (removed != null) {
-						for (int i=0; i<filesCount; i++) {
-							indexingCache.remove(removed[i]);
-						}
-					}
-				}
-			}
-		}
-	}
+     * Remove from secondary types cache all types belonging to a given file.
+     * Clean secondary types cache built while indexing if requested.
+     * 
+     * Project's secondary types cache is found using file location.
+     * 
+     * @param file File to remove
+     */
+    public void secondaryTypesRemoving(IFile file, boolean cleanIndexCache) {
+    	if (VERBOSE) {
+    		StringBuffer buffer = new StringBuffer("JavaModelManager.removeFromSecondaryTypesCache("); //$NON-NLS-1$
+    		buffer.append(file.getName());
+    		buffer.append(')');
+    		Util.verbose(buffer.toString());
+    	}
+    	if (file != null) {
+    		PerProjectInfo projectInfo = getPerProjectInfo(file.getProject(), false);
+    		if (projectInfo != null && projectInfo.secondaryTypes != null) {
+    			if (VERBOSE) {
+    				Util.verbose("-> remove file from cache of project: "+file.getProject().getName()); //$NON-NLS-1$
+    			}
+    
+    			// Clean current cache
+    			secondaryTypesRemoving(projectInfo.secondaryTypes, file);
+    			
+    			// Clean indexing cache if necessary
+    			if (!cleanIndexCache) return;
+    			HashMap indexingCache = (HashMap) projectInfo.secondaryTypes.get(INDEXED_SECONDARY_TYPES);
+    			if (indexingCache != null) {
+    				Set keys = indexingCache.keySet();
+    				int filesSize = keys.size(), filesCount = 0;
+    				IFile[] removed = null;
+    				Iterator cachedFiles = keys.iterator();
+    				while (cachedFiles.hasNext()) {
+    					IFile cachedFile = (IFile) cachedFiles.next();
+    					if (file.equals(cachedFile)) {
+    						if (removed == null) removed = new IFile[filesSize];
+    						filesSize--;
+    						removed[filesCount++] = cachedFile;
+    					}
+    				}
+    				if (removed != null) {
+    					for (int i=0; i<filesCount; i++) {
+    						indexingCache.remove(removed[i]);
+    					}
+    				}
+    			}
+    		}
+    	}
+    }
 
 	/*
 	 * Remove from a given cache map all secondary types belonging to a given file.
@@ -4136,12 +4179,12 @@
 			initializePreferences();
 
 			// Listen to preference changes
-			Preferences.IPropertyChangeListener propertyListener = new Preferences.IPropertyChangeListener() {
+			this.propertyListener = new Preferences.IPropertyChangeListener() {
 				public void propertyChange(Preferences.PropertyChangeEvent event) {
 					JavaModelManager.this.optionsCache = null;
 				}
 			};
-			JavaCore.getPlugin().getPluginPreferences().addPropertyChangeListener(propertyListener);
+			JavaCore.getPlugin().getPluginPreferences().addPropertyChangeListener(this.propertyListener);
 			
 			// Listen to content-type changes
 			 Platform.getContentTypeManager().addContentTypeChangeListener(this);
@@ -4203,10 +4246,10 @@
 
 	/**
 	 * Initiate the background indexing process.
-	 * This should be deferred after the plugin activation.
+	 * This should be deferred after the plug-in activation.
 	 */
 	private void startIndexing() {
-		getIndexManager().reset();
+		if (this.indexManager != null) this.indexManager.reset();
 	}
 
 	public void shutdown () {
@@ -4218,15 +4261,20 @@
 		
 		// Stop listening to content-type changes
 		Platform.getContentTypeManager().removeContentTypeChangeListener(this);
-		
-		// Stop listening to user library changes
-		if (this.userLibraryManager != null)
-			getInstancePreferences().removePreferenceChangeListener(this.userLibraryManager);
-	
-		if (this.indexManager != null){ // no more indexing
+
+		// Stop indexing
+		if (this.indexManager != null) {
 			this.indexManager.shutdown();
 		}
 		
+		// Stop listening to preferences changes
+		JavaCore.getPlugin().getPluginPreferences().removePropertyChangeListener(this.propertyListener);
+		((IEclipsePreferences) preferencesLookup[PREF_DEFAULT].parent()).removeNodeChangeListener(this.defaultNodeListener);
+		preferencesLookup[PREF_DEFAULT] = null;
+		((IEclipsePreferences) preferencesLookup[PREF_INSTANCE].parent()).removeNodeChangeListener(this.instanceNodeListener);
+		preferencesLookup[PREF_INSTANCE].removePreferenceChangeListener(this.instancePreferencesListener);
+		preferencesLookup[PREF_INSTANCE] = null;
+		
 		// wait for the initialization job to finish
 		try {
 			Job.getJobManager().join(JavaCore.PLUGIN_ID, null);
Index: model/org/eclipse/jdt/internal/core/ChangeClasspathOperation.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/model/org/eclipse/jdt/internal/core/ChangeClasspathOperation.java,v
retrieving revision 1.4
diff -u -r1.4 ChangeClasspathOperation.java
--- model/org/eclipse/jdt/internal/core/ChangeClasspathOperation.java	24 May 2007 13:15:25 -0000	1.4
+++ model/org/eclipse/jdt/internal/core/ChangeClasspathOperation.java	28 Aug 2007 08:59:33 -0000
@@ -40,7 +40,7 @@
 	 * - create resolved classpath markers
 	 */
 	protected void classpathChanged(JavaProject project) throws JavaModelException {
-		DeltaProcessingState state = JavaModelManager.getJavaModelManager().deltaState;
+		DeltaProcessingState state = JavaModelManager.getDeltaState();
 		DeltaProcessor deltaProcessor = state.getDeltaProcessor();
 		ClasspathChange change = (ClasspathChange) deltaProcessor.classpathChanges.get(project.getProject());
 		if (this.canChangeResources) {
Index: model/org/eclipse/jdt/internal/core/UserLibraryManager.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/model/org/eclipse/jdt/internal/core/UserLibraryManager.java,v
retrieving revision 1.13
diff -u -r1.13 UserLibraryManager.java
--- model/org/eclipse/jdt/internal/core/UserLibraryManager.java	24 Aug 2007 13:02:31 -0000	1.13
+++ model/org/eclipse/jdt/internal/core/UserLibraryManager.java	28 Aug 2007 08:59:34 -0000
@@ -31,7 +31,7 @@
 /**
  *
  */
-public class UserLibraryManager implements IEclipsePreferences.IPreferenceChangeListener {
+public class UserLibraryManager {
 	
 	public final static String CP_USERLIBRARY_PREFERENCES_PREFIX = JavaCore.PLUGIN_ID+".userLibrary."; //$NON-NLS-1$
 
@@ -98,59 +98,54 @@
 		}
 	}
 
-	public void preferenceChange(IEclipsePreferences.PreferenceChangeEvent event) {
-		String key = event.getKey();
-		if (key.startsWith(CP_USERLIBRARY_PREFERENCES_PREFIX)) {
-			String libName = key.substring(CP_USERLIBRARY_PREFERENCES_PREFIX.length());
-			try {
-				// find affected projects
-				IPath containerPath = new Path(JavaCore.USER_LIBRARY_CONTAINER_ID).append(libName);
-				IJavaProject[] allJavaProjects = JavaCore.create(ResourcesPlugin.getWorkspace().getRoot()).getJavaProjects();
-				ArrayList affectedProjects = new ArrayList();
-				for (int i= 0; i < allJavaProjects.length; i++) {
-					IJavaProject javaProject = allJavaProjects[i];
-					IClasspathEntry[] entries= javaProject.getRawClasspath();
-					for (int j= 0; j < entries.length; j++) {
-						IClasspathEntry entry = entries[j];
-						if (entry.getEntryKind() == IClasspathEntry.CPE_CONTAINER) {
-							if (containerPath.equals(entry.getPath())) {
-								affectedProjects.add(javaProject);
-								break;
-							}				
-						}
+	public void updateUserLibrary(String libName, String encodedUserLibrary) {
+		try {
+			// find affected projects
+			IPath containerPath = new Path(JavaCore.USER_LIBRARY_CONTAINER_ID).append(libName);
+			IJavaProject[] allJavaProjects = JavaCore.create(ResourcesPlugin.getWorkspace().getRoot()).getJavaProjects();
+			ArrayList affectedProjects = new ArrayList();
+			for (int i= 0; i < allJavaProjects.length; i++) {
+				IJavaProject javaProject = allJavaProjects[i];
+				IClasspathEntry[] entries= javaProject.getRawClasspath();
+				for (int j= 0; j < entries.length; j++) {
+					IClasspathEntry entry = entries[j];
+					if (entry.getEntryKind() == IClasspathEntry.CPE_CONTAINER) {
+						if (containerPath.equals(entry.getPath())) {
+							affectedProjects.add(javaProject);
+							break;
+						}				
 					}
 				}
-				
-				// decode user library
-				String encodedUserLibrary = (String) event.getNewValue();
-				UserLibrary userLibrary = encodedUserLibrary == null ? null : UserLibrary.createFromString(new StringReader(encodedUserLibrary));
-				
-				// update user libraries map
-				if (userLibrary != null) {
-					this.userLibraries.put(libName, userLibrary);
-				} else {
-					this.userLibraries.remove(libName);
-				}
-				
-				// update affected projects
-				int length = affectedProjects.size();
-				if (length == 0)
-					return;
-				IJavaProject[] projects = new IJavaProject[length];
-				affectedProjects.toArray(projects);
-				IClasspathContainer[] containers = new IClasspathContainer[length];
-				if (userLibrary != null) {
-					UserLibraryClasspathContainer container = new UserLibraryClasspathContainer(libName);
-					for (int i = 0; i < length; i++) {
-						containers[i] = container;
-					}
+			}
+			
+			// decode user library
+			UserLibrary userLibrary = encodedUserLibrary == null ? null : UserLibrary.createFromString(new StringReader(encodedUserLibrary));
+			
+			// update user libraries map
+			if (userLibrary != null) {
+				this.userLibraries.put(libName, userLibrary);
+			} else {
+				this.userLibraries.remove(libName);
+			}
+			
+			// update affected projects
+			int length = affectedProjects.size();
+			if (length == 0)
+				return;
+			IJavaProject[] projects = new IJavaProject[length];
+			affectedProjects.toArray(projects);
+			IClasspathContainer[] containers = new IClasspathContainer[length];
+			if (userLibrary != null) {
+				UserLibraryClasspathContainer container = new UserLibraryClasspathContainer(libName);
+				for (int i = 0; i < length; i++) {
+					containers[i] = container;
 				}
-				JavaCore.setClasspathContainer(containerPath, projects, containers, null);
-			} catch (IOException e) {
-				Util.log(e, "Exception while decoding user library '"+ libName +"'."); //$NON-NLS-1$ //$NON-NLS-2$
-			} catch (JavaModelException e) {
-				Util.log(e, "Exception while setting user library '"+ libName +"'."); //$NON-NLS-1$ //$NON-NLS-2$
 			}
+			JavaCore.setClasspathContainer(containerPath, projects, containers, null);
+		} catch (IOException e) {
+			Util.log(e, "Exception while decoding user library '"+ libName +"'."); //$NON-NLS-1$ //$NON-NLS-2$
+		} catch (JavaModelException e) {
+			Util.log(e, "Exception while setting user library '"+ libName +"'."); //$NON-NLS-1$ //$NON-NLS-2$
 		}
 	}
 	
Index: model/org/eclipse/jdt/internal/core/ModelUpdater.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/model/org/eclipse/jdt/internal/core/ModelUpdater.java,v
retrieving revision 1.17
diff -u -r1.17 ModelUpdater.java
--- model/org/eclipse/jdt/internal/core/ModelUpdater.java	29 Mar 2006 03:08:47 -0000	1.17
+++ model/org/eclipse/jdt/internal/core/ModelUpdater.java	28 Aug 2007 08:59:34 -0000
@@ -125,7 +125,7 @@
 
 		switch (elementType) {
 			case IJavaElement.JAVA_MODEL :
-				JavaModelManager.getJavaModelManager().getIndexManager().reset();
+				JavaModelManager.getIndexManager().reset();
 				break;
 			case IJavaElement.JAVA_PROJECT :
 				JavaModelManager manager = JavaModelManager.getJavaModelManager();
Index: model/org/eclipse/jdt/internal/core/JavaModelOperation.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/model/org/eclipse/jdt/internal/core/JavaModelOperation.java,v
retrieving revision 1.67
diff -u -r1.67 JavaModelOperation.java
--- model/org/eclipse/jdt/internal/core/JavaModelOperation.java	26 Apr 2007 15:05:51 -0000	1.67
+++ model/org/eclipse/jdt/internal/core/JavaModelOperation.java	28 Aug 2007 08:59:34 -0000
@@ -714,7 +714,7 @@
 				if (canModifyRoots()) {
 					// computes the root infos before executing the operation
 					// noop if aready initialized
-					JavaModelManager.getJavaModelManager().deltaState.initializeRoots();
+					JavaModelManager.getDeltaState().initializeRoots();
 				}
 				
 				executeOperation();
Index: search/org/eclipse/jdt/internal/core/search/matching/SuperTypeNamesCollector.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/search/org/eclipse/jdt/internal/core/search/matching/SuperTypeNamesCollector.java,v
retrieving revision 1.56
diff -u -r1.56 SuperTypeNamesCollector.java
--- search/org/eclipse/jdt/internal/core/search/matching/SuperTypeNamesCollector.java	29 Mar 2006 03:13:59 -0000	1.56
+++ search/org/eclipse/jdt/internal/core/search/matching/SuperTypeNamesCollector.java	28 Aug 2007 08:59:34 -0000
@@ -226,7 +226,7 @@
 
 	final PathCollector pathCollector = new PathCollector();
 	IJavaSearchScope scope = SearchEngine.createWorkspaceScope();
-	IndexManager indexManager = JavaModelManager.getJavaModelManager().getIndexManager();
+	IndexManager indexManager = JavaModelManager.getIndexManager();
 	SearchPattern searchPattern = new TypeDeclarationPattern(
 		this.typeSimpleName != null ? null : this.typeQualification, // use the qualification only if no simple name
 		null, // do find member types
Index: search/org/eclipse/jdt/internal/core/search/BasicSearchEngine.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/search/org/eclipse/jdt/internal/core/search/BasicSearchEngine.java,v
retrieving revision 1.48
diff -u -r1.48 BasicSearchEngine.java
--- search/org/eclipse/jdt/internal/core/search/BasicSearchEngine.java	24 Aug 2007 05:59:05 -0000	1.48
+++ search/org/eclipse/jdt/internal/core/search/BasicSearchEngine.java	28 Aug 2007 08:59:34 -0000
@@ -186,7 +186,7 @@
 			int length = participants.length;
 			if (monitor != null)
 				monitor.beginTask(Messages.engine_searching, 100 * length); 
-			IndexManager indexManager = JavaModelManager.getJavaModelManager().getIndexManager();
+			IndexManager indexManager = JavaModelManager.getIndexManager();
 			requestor.beginReporting();
 			for (int i = 0; i < length; i++) {
 				if (monitor != null && monitor.isCanceled()) throw new OperationCanceledException();
@@ -528,7 +528,7 @@
 			Util.verbose(buffer.toString());
 		}
 
-		IndexManager indexManager = JavaModelManager.getJavaModelManager().getIndexManager();
+		IndexManager indexManager = JavaModelManager.getIndexManager();
 		final TypeDeclarationPattern pattern = new SecondaryTypeDeclarationPattern();
 
 		// Get working copy path(s). Store in a single string in case of only one to optimize comparison in requestor
@@ -656,7 +656,7 @@
 		}
 
 		// Create pattern
-		IndexManager indexManager = JavaModelManager.getJavaModelManager().getIndexManager();
+		IndexManager indexManager = JavaModelManager.getIndexManager();
 		final char typeSuffix;
 		switch(searchFor){
 			case IJavaSearchConstants.CLASS :
@@ -907,7 +907,7 @@
 			Util.verbose("	- search for: "+searchFor); //$NON-NLS-1$
 			Util.verbose("	- scope: "+scope); //$NON-NLS-1$
 		}
-		IndexManager indexManager = JavaModelManager.getJavaModelManager().getIndexManager();
+		IndexManager indexManager = JavaModelManager.getIndexManager();
 
 		final char typeSuffix;
 		switch(searchFor){
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 1.37
diff -u -r1.37 IndexSelector.java
--- search/org/eclipse/jdt/internal/core/search/IndexSelector.java	13 Apr 2007 16:02:15 -0000	1.37
+++ search/org/eclipse/jdt/internal/core/search/IndexSelector.java	28 Aug 2007 08:59:34 -0000
@@ -118,7 +118,7 @@
  */
 private void initializeIndexLocations() {
 	IPath[] projectsAndJars = this.searchScope.enclosingProjectsAndJars();
-	IndexManager manager = JavaModelManager.getJavaModelManager().getIndexManager();
+	IndexManager manager = JavaModelManager.getIndexManager();
 	SimpleSet locations = new SimpleSet();
 	IJavaElement focus = MatchLocator.projectOrJarFocus(this.pattern);
 	if (focus == null) {
Index: search/org/eclipse/jdt/internal/core/search/PatternSearchJob.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/search/org/eclipse/jdt/internal/core/search/PatternSearchJob.java,v
retrieving revision 1.47
diff -u -r1.47 PatternSearchJob.java
--- search/org/eclipse/jdt/internal/core/search/PatternSearchJob.java	25 Jan 2007 16:05:55 -0000	1.47
+++ search/org/eclipse/jdt/internal/core/search/PatternSearchJob.java	28 Aug 2007 08:59:34 -0000
@@ -81,7 +81,7 @@
 	int length = indexLocations.length;
 	Index[] indexes = new Index[length];
 	int count = 0;
-	IndexManager indexManager = JavaModelManager.getJavaModelManager().getIndexManager();
+	IndexManager indexManager = JavaModelManager.getIndexManager();
 	for (int i = 0; i < length; i++) {
 		if (progressMonitor != null && progressMonitor.isCanceled()) throw new OperationCanceledException();
 		// may trigger some index recreation work
Index: model/org/eclipse/jdt/internal/core/hierarchy/IndexBasedHierarchyBuilder.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/model/org/eclipse/jdt/internal/core/hierarchy/IndexBasedHierarchyBuilder.java,v
retrieving revision 1.103
diff -u -r1.103 IndexBasedHierarchyBuilder.java
--- model/org/eclipse/jdt/internal/core/hierarchy/IndexBasedHierarchyBuilder.java	28 Mar 2007 13:17:39 -0000	1.103
+++ model/org/eclipse/jdt/internal/core/hierarchy/IndexBasedHierarchyBuilder.java	28 Aug 2007 08:59:34 -0000
@@ -451,7 +451,7 @@
 	final Queue queue = new Queue();
 	final HashtableOfObject foundSuperNames = new HashtableOfObject(5);
 
-	IndexManager indexManager = JavaModelManager.getJavaModelManager().getIndexManager();
+	IndexManager indexManager = JavaModelManager.getIndexManager();
 
 	/* use a special collector to collect paths and queue new subtype names */
 	IndexQueryRequestor searchRequestor = new IndexQueryRequestor() {
Index: model/org/eclipse/jdt/core/JavaCore.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/model/org/eclipse/jdt/core/JavaCore.java,v
retrieving revision 1.579
diff -u -r1.579 JavaCore.java
--- model/org/eclipse/jdt/core/JavaCore.java	24 Aug 2007 13:02:31 -0000	1.579
+++ model/org/eclipse/jdt/core/JavaCore.java	28 Aug 2007 08:59:33 -0000
@@ -1224,7 +1224,7 @@
 	 * @since 2.0
 	 */
 	public static void addElementChangedListener(IElementChangedListener listener, int eventMask) {
-		JavaModelManager.getJavaModelManager().deltaState.addElementChangedListener(listener, eventMask);
+		JavaModelManager.getDeltaState().addElementChangedListener(listener, eventMask);
 	}
 
 	/**
@@ -1317,7 +1317,7 @@
 	 * @since 3.2
 	 */
 	public static void addPreProcessingResourceChangedListener(IResourceChangeListener listener, int eventMask) {
-		JavaModelManager.getJavaModelManager().deltaState.addPreResourceChangedListener(listener, eventMask);
+		JavaModelManager.getDeltaState().addPreResourceChangedListener(listener, eventMask);
 	}
 
 	/**
@@ -4396,7 +4396,7 @@
 	 * @param listener the listener
 	 */
 	public static void removeElementChangedListener(IElementChangedListener listener) {
-		JavaModelManager.getJavaModelManager().deltaState.removeElementChangedListener(listener);
+		JavaModelManager.getDeltaState().removeElementChangedListener(listener);
 	}
 
 	/**
@@ -4421,7 +4421,7 @@
 	 * @since 3.0
 	 */
 	public static void removePreProcessingResourceChangedListener(IResourceChangeListener listener) {
-		JavaModelManager.getJavaModelManager().deltaState.removePreResourceChangedListener(listener);
+		JavaModelManager.getDeltaState().removePreResourceChangedListener(listener);
 	}
 
 
Index: search/org/eclipse/jdt/core/search/SearchParticipant.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/search/org/eclipse/jdt/core/search/SearchParticipant.java,v
retrieving revision 1.23
diff -u -r1.23 SearchParticipant.java
--- search/org/eclipse/jdt/core/search/SearchParticipant.java	25 Jan 2007 16:05:56 -0000	1.23
+++ search/org/eclipse/jdt/core/search/SearchParticipant.java	28 Aug 2007 08:59:34 -0000
@@ -173,7 +173,7 @@
 	 * @since 3.2
 	 */
 	public void removeIndex(IPath indexLocation){
-		IndexManager manager = JavaModelManager.getJavaModelManager().getIndexManager();
+		IndexManager manager = JavaModelManager.getIndexManager();
 		manager.removeIndexPath(indexLocation);
 	}
 
@@ -204,7 +204,7 @@
 		} else if (file == null) {
 			containerPath = documentPath.removeLastSegments(documentPath.segmentCount()-1);
 		}
-		IndexManager manager = JavaModelManager.getJavaModelManager().getIndexManager();
+		IndexManager manager = JavaModelManager.getIndexManager();
 		// TODO (frederic) should not have to create index manually, should expose API that recreates index instead
 		manager.ensureIndexExists(indexLocation, containerPath);
 		manager.scheduleDocumentIndexing(document, containerPath, indexLocation, this);