### Eclipse Workspace Patch 1.0
#P org.eclipse.jdt.core.tests.model
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 1.19
diff -u -r1.19 OptionTests.java
--- src/org/eclipse/jdt/core/tests/model/OptionTests.java	3 Mar 2006 09:13:00 -0000	1.19
+++ src/org/eclipse/jdt/core/tests/model/OptionTests.java	20 Mar 2006 16:46:23 -0000
@@ -16,6 +16,7 @@
 import junit.framework.Test;
 import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.Path;
+import org.eclipse.core.runtime.preferences.DefaultScope;
 import org.eclipse.core.runtime.preferences.IEclipsePreferences;
 import org.eclipse.core.runtime.preferences.IEclipsePreferences.PreferenceChangeEvent;
 import org.eclipse.jdt.core.IJavaProject;
@@ -602,4 +603,29 @@
 			deleteProject("P");
 		}
 	}
+	
+	/**
+	 * @bug 131707: Cannot add classpath variables when starting with -pluginCustomization option
+	 * @see "https://bugs.eclipse.org/bugs/show_bug.cgi?id=131707"
+	 */
+	public void testBug131707() throws CoreException {
+		IEclipsePreferences defaultPreferences = new DefaultScope().getNode(JavaCore.PLUGIN_ID);
+		try {
+			defaultPreferences.put("org.eclipse.jdt.core.classpathVariable.MY_DEFAULT_LIB", "c:\\temp\\lib.jar");
+			simulateExitRestart();
+			String[] variableNames = JavaCore.getClasspathVariableNames();
+			for (int i = 0, length = variableNames.length; i < length; i++) {
+				if ("MY_DEFAULT_LIB".equals(variableNames[i])) {
+					assertEquals(
+						"Unexpected value for MY_DEFAULT_LIB", 
+						new Path("c:\\temp\\lib.jar"), 
+						JavaCore.getClasspathVariable("MY_DEFAULT_LIB"));
+					return;
+				}
+			}
+			assertFalse("Variable MY_DEFAULT_LIB not found", true);
+		} finally {
+			defaultPreferences.remove("org.eclipse.jdt.core.classpathVariable.MY_DEFAULT_LIB");
+		}
+	}
 }
#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 1.332
diff -u -r1.332 JavaModelManager.java
--- model/org/eclipse/jdt/internal/core/JavaModelManager.java	14 Mar 2006 01:46:19 -0000	1.332
+++ model/org/eclipse/jdt/internal/core/JavaModelManager.java	20 Mar 2006 16:46:25 -0000
@@ -2106,44 +2106,8 @@
 		}
 
 		// backward compatibility, load variables and containers from preferences into cache
-		IEclipsePreferences preferences = getInstancePreferences();
-		try {
-			// only get variable from preferences not set to their default
-			String[] propertyNames = preferences.keys();
-			int variablePrefixLength = CP_VARIABLE_PREFERENCES_PREFIX.length();
-			for (int i = 0; i < propertyNames.length; i++){
-				String propertyName = propertyNames[i];
-				if (propertyName.startsWith(CP_VARIABLE_PREFERENCES_PREFIX)){
-					String varName = propertyName.substring(variablePrefixLength);
-					String propertyValue = preferences.get(propertyName, null);
-					if (propertyValue != null) {
-						String pathString = propertyValue.trim();
-						
-						if (CP_ENTRY_IGNORE.equals(pathString)) {
-							// cleanup old preferences
-							preferences.remove(propertyName); 
-							continue;
-						}
-						
-						// add variable to table
-						IPath varPath = new Path(pathString);
-						this.variables.put(varName, varPath); 
-						this.previousSessionVariables.put(varName, varPath);
-					}
-				} else if (propertyName.startsWith(CP_CONTAINER_PREFERENCES_PREFIX)){
-					String propertyValue = preferences.get(propertyName, null);
-					if (propertyValue != null) {
-						// cleanup old preferences
-						preferences.remove(propertyName); 
-						
-						// recreate container
-						recreatePersistedContainer(propertyName, propertyValue, true/*add to container values*/);
-					}
-				}
-			}
-		} catch (BackingStoreException e1) {
-			// TODO (frederic) see if it's necessary to report this failure...
-		}
+		loadVariablesAndContainers(getDefaultPreferences());
+		loadVariablesAndContainers(getInstancePreferences());
 
 		// load variables and containers from saved file into cache
 		File file = getVariableAndContainersFile();
@@ -2210,6 +2174,46 @@
 		containersReset(getRegisteredContainerIDs());
 	}
 
+	private void loadVariablesAndContainers(IEclipsePreferences preferences) {
+		try {
+			// only get variable from preferences not set to their default
+			String[] propertyNames = preferences.keys();
+			int variablePrefixLength = CP_VARIABLE_PREFERENCES_PREFIX.length();
+			for (int i = 0; i < propertyNames.length; i++){
+				String propertyName = propertyNames[i];
+				if (propertyName.startsWith(CP_VARIABLE_PREFERENCES_PREFIX)){
+					String varName = propertyName.substring(variablePrefixLength);
+					String propertyValue = preferences.get(propertyName, null);
+					if (propertyValue != null) {
+						String pathString = propertyValue.trim();
+						
+						if (CP_ENTRY_IGNORE.equals(pathString)) {
+							// cleanup old preferences
+							preferences.remove(propertyName); 
+							continue;
+						}
+						
+						// add variable to table
+						IPath varPath = new Path(pathString);
+						this.variables.put(varName, varPath); 
+						this.previousSessionVariables.put(varName, varPath);
+					}
+				} else if (propertyName.startsWith(CP_CONTAINER_PREFERENCES_PREFIX)){
+					String propertyValue = preferences.get(propertyName, null);
+					if (propertyValue != null) {
+						// cleanup old preferences
+						preferences.remove(propertyName); 
+						
+						// recreate container
+						recreatePersistedContainer(propertyName, propertyValue, true/*add to container values*/);
+					}
+				}
+			}
+		} catch (BackingStoreException e1) {
+			// TODO (frederic) see if it's necessary to report this failure...
+		}
+	}
+
 	private static final class PersistedClasspathContainer implements
 			IClasspathContainer {
 
@@ -2935,7 +2939,22 @@
 
 		void save() throws IOException, JavaModelException {
 			saveProjects(JavaModelManager.this.getJavaModel().getJavaProjects());
-			saveVariables(JavaModelManager.this.variables);
+			
+			// don't save classpath variables from the default preferences as there is no delta if they are removed
+			HashMap varsToSave = null;
+			Iterator iterator = JavaModelManager.this.variables.keySet().iterator();
+			IEclipsePreferences defaultPreferences = getDefaultPreferences();
+			while (iterator.hasNext()) {
+				String varName = (String) iterator.next();
+				if (defaultPreferences.get(CP_VARIABLE_PREFERENCES_PREFIX + varName, null) != null) {
+					if (varsToSave == null)
+						varsToSave = new HashMap(JavaModelManager.this.variables);
+					varsToSave.remove(varName);
+				}
+					
+			}
+			
+			saveVariables(varsToSave != null ? varsToSave : JavaModelManager.this.variables);
 		}
 
 		private void saveAccessRule(ClasspathAccessRule rule) throws IOException {