### Eclipse Workspace Patch 1.0
#P org.eclipse.jdt.core.tests.model
Index: src/org/eclipse/jdt/core/tests/model/ClasspathTests.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core.tests.model/src/org/eclipse/jdt/core/tests/model/ClasspathTests.java,v
retrieving revision 1.150
diff -u -r1.150 ClasspathTests.java
--- src/org/eclipse/jdt/core/tests/model/ClasspathTests.java	6 Apr 2006 02:17:29 -0000	1.150
+++ src/org/eclipse/jdt/core/tests/model/ClasspathTests.java	6 Apr 2006 14:34:42 -0000
@@ -128,12 +128,6 @@
 		entry,
 		decoded);
 }
-protected void assertMarkers(String message, String expectedMarkers, IJavaProject project) throws CoreException {
-	waitForAutoBuild();
-	IMarker[] markers = project.getProject().findMarkers(IJavaModelMarker.BUILDPATH_PROBLEM_MARKER, false, IResource.DEPTH_ZERO);
-	this.sortMarkers(markers);
-	assertMarkers(message, expectedMarkers, markers);
-}
 protected void assertStatus(String expected, IStatus status) {
 	String actual = status.getMessage();
 	if (!expected.equals(actual)) {
@@ -179,16 +173,6 @@
 	return result;
 }
 
-protected void sortMarkers(IMarker[] markers) {
-	org.eclipse.jdt.internal.core.util.Util.Comparer comparer = new org.eclipse.jdt.internal.core.util.Util.Comparer() {
-		public int compare(Object a, Object b) {
-			IMarker markerA = (IMarker)a;
-			IMarker markerB = (IMarker)b;
-			return markerA.getAttribute(IMarker.MESSAGE, "").compareTo(markerB.getAttribute(IMarker.MESSAGE, "")); //$NON-NLS-1$ //$NON-NLS-2$
-		}
-	};
-	org.eclipse.jdt.internal.core.util.Util.sort(markers, comparer);
-}
 /**
  * Add an entry to the classpath for a non-existent root. Then create
  * the root and ensure that it comes alive.
Index: src/org/eclipse/jdt/core/tests/model/OptionTests.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core.tests.model/src/org/eclipse/jdt/core/tests/model/OptionTests.java,v
retrieving revision 1.21
diff -u -r1.21 OptionTests.java
--- src/org/eclipse/jdt/core/tests/model/OptionTests.java	5 Apr 2006 14:03:00 -0000	1.21
+++ src/org/eclipse/jdt/core/tests/model/OptionTests.java	6 Apr 2006 14:34:42 -0000
@@ -506,6 +506,23 @@
 			preferences.get(JavaModelManager.CP_VARIABLE_PREFERENCES_PREFIX+"TEST", "null"));
 	}
 
+	/*
+	 * Ensures that classpath problems are removed when missing classpath variable is added through the preferences
+	 * (regression test for bug 109691 Importing preferences does not update classpath variables)
+	 */
+	public void test12() throws CoreException {
+		IEclipsePreferences preferences = JavaModelManager.getJavaModelManager().getInstancePreferences();
+		try {
+			IJavaProject project = createJavaProject("P", new String[0], new String[] {"TEST"}, "");
+			waitForAutoBuild();
+			preferences.put(JavaModelManager.CP_VARIABLE_PREFERENCES_PREFIX+"TEST", getExternalJCLPathString());
+			assertMarkers("Unexpected markers", "", project);
+		} finally {
+			deleteProject("P");
+			preferences.remove(JavaModelManager.CP_VARIABLE_PREFERENCES_PREFIX+"TEST");
+		}
+	}
+
 	/**
 	 * Bug 68993: [Preferences] IAE when opening project preferences
 	 * @see "http://bugs.eclipse.org/bugs/show_bug.cgi?id=68993"
Index: src/org/eclipse/jdt/core/tests/model/AbstractJavaModelTests.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core.tests.model/src/org/eclipse/jdt/core/tests/model/AbstractJavaModelTests.java,v
retrieving revision 1.163
diff -u -r1.163 AbstractJavaModelTests.java
--- src/org/eclipse/jdt/core/tests/model/AbstractJavaModelTests.java	29 Mar 2006 04:03:08 -0000	1.163
+++ src/org/eclipse/jdt/core/tests/model/AbstractJavaModelTests.java	6 Apr 2006 14:34:40 -0000
@@ -370,6 +370,22 @@
 		}
 		assertEquals("Unexpected type hierarchy", expected, actual);
 	}
+	protected void assertMarkers(String message, String expectedMarkers, IJavaProject project) throws CoreException {
+		waitForAutoBuild();
+		IMarker[] markers = project.getProject().findMarkers(IJavaModelMarker.BUILDPATH_PROBLEM_MARKER, false, IResource.DEPTH_ZERO);
+		sortMarkers(markers);
+		assertMarkers(message, expectedMarkers, markers);
+	}
+	protected void sortMarkers(IMarker[] markers) {
+		org.eclipse.jdt.internal.core.util.Util.Comparer comparer = new org.eclipse.jdt.internal.core.util.Util.Comparer() {
+			public int compare(Object a, Object b) {
+				IMarker markerA = (IMarker)a;
+				IMarker markerB = (IMarker)b;
+				return markerA.getAttribute(IMarker.MESSAGE, "").compareTo(markerB.getAttribute(IMarker.MESSAGE, "")); //$NON-NLS-1$ //$NON-NLS-2$
+			}
+		};
+		org.eclipse.jdt.internal.core.util.Util.sort(markers, comparer);
+	}
 	protected void assertMarkers(String message, String expectedMarkers, IMarker[] markers) throws CoreException {
 		StringBuffer buffer = new StringBuffer();
 		if (markers != null) {
#P org.eclipse.jdt.core
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 1.538
diff -u -r1.538 JavaCore.java
--- model/org/eclipse/jdt/core/JavaCore.java	6 Apr 2006 01:47:52 -0000	1.538
+++ model/org/eclipse/jdt/core/JavaCore.java	6 Apr 2006 14:34:46 -0000
@@ -3896,7 +3896,7 @@
 		IProgressMonitor monitor) {
 
 		try {
-			JavaModelManager.getJavaModelManager().updateVariableValues(new String[]{ variableName}, new IPath[]{ null }, monitor);
+			JavaModelManager.getJavaModelManager().updateVariableValues(new String[]{ variableName}, new IPath[]{ null }, true/*update preferences*/, monitor);
 		} catch (JavaModelException e) {
 			// cannot happen: ignore
 		}
@@ -4320,7 +4320,7 @@
 		throws JavaModelException {
 
 		if (variableNames.length != paths.length)	Assert.isTrue(false, "Variable names and paths collections should have the same size"); //$NON-NLS-1$
-		JavaModelManager.getJavaModelManager().updateVariableValues(variableNames, paths, monitor);
+		JavaModelManager.getJavaModelManager().updateVariableValues(variableNames, paths, true/*update preferences*/, monitor);
 	}
 
 	/**
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 1.334
diff -u -r1.334 JavaModelManager.java
--- model/org/eclipse/jdt/internal/core/JavaModelManager.java	5 Apr 2006 14:02:49 -0000	1.334
+++ model/org/eclipse/jdt/internal/core/JavaModelManager.java	6 Apr 2006 14:34:48 -0000
@@ -1043,10 +1043,16 @@
 					}
 				} else {
 					String newValue = (String)event.getNewValue();
+					IPath newPath;
 					if (newValue != null && !(newValue = newValue.trim()).equals(CP_ENTRY_IGNORE)) {
-						manager.variables.put(varName, new Path(newValue));
+						newPath = new Path(newValue);
 					} else {
-						manager.variables.remove(varName);
+						newPath = null;
+					}
+					try {
+						manager.updateVariableValues(new String[] {varName}, new IPath[] {newPath}, false/*don't update preferences*/, null/*no progress available*/);
+					} catch (JavaModelException e) {
+						Util.log(e, "Could not set classpath variable " + varName + " to " + newPath); //$NON-NLS-1$ //$NON-NLS-2$
 					}
 				}
 			}
@@ -2940,13 +2946,16 @@
 		void save() throws IOException, JavaModelException {
 			saveProjects(JavaModelManager.this.getJavaModel().getJavaProjects());
 			
-			// don't save classpath variables from the default preferences as there is no delta if they are removed
+			// remove variables that should not be saved
 			HashMap varsToSave = null;
-			Iterator iterator = JavaModelManager.this.variables.keySet().iterator();
+			Iterator iterator = JavaModelManager.this.variables.entrySet().iterator();
 			IEclipsePreferences defaultPreferences = getDefaultPreferences();
 			while (iterator.hasNext()) {
-				String varName = (String) iterator.next();
-				if (defaultPreferences.get(CP_VARIABLE_PREFERENCES_PREFIX + varName, null) != null) {
+				Map.Entry entry = (Map.Entry) iterator.next();
+				String varName = (String) entry.getKey();
+				if (defaultPreferences.get(CP_VARIABLE_PREFERENCES_PREFIX + varName, null) != null // don't save classpath variables from the default preferences as there is no delta if they are removed
+					|| CP_ENTRY_IGNORE_PATH.equals(entry.getValue())) {
+					
 					if (varsToSave == null)
 						varsToSave = new HashMap(JavaModelManager.this.variables);
 					varsToSave.remove(varName);
@@ -3826,6 +3835,7 @@
 	public void updateVariableValues(
 		String[] variableNames,
 		IPath[] variablePaths,
+		boolean updatePreferences,
 		IProgressMonitor monitor) throws JavaModelException {
 	
 		if (monitor != null && monitor.isCanceled()) return;
@@ -3921,7 +3931,9 @@
 		}
 		// update variables
 		for (int i = 0; i < varLength; i++){
-			this.variablePut(variableNames[i], variablePaths[i]);
+			variablePut(variableNames[i], variablePaths[i]);
+			if (updatePreferences)
+				variablePreferencesPut(variableNames[i], variablePaths[i]);
 		}
 		final String[] dbgVariableNames = variableNames;
 				
@@ -4024,7 +4036,9 @@
 			// discard obsoleted information about previous session
 			this.previousSessionVariables.remove(variableName);
 		}
-	
+	}
+
+	private void variablePreferencesPut(String variableName, IPath variablePath) {
 		String variableKey = CP_VARIABLE_PREFERENCES_PREFIX+variableName;
 		if (variablePath == null) {
 			this.variablesWithInitializer.remove(variableName);