### Eclipse Workspace Patch 1.0
#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 1.468
diff -u -r1.468 JavaModelManager.java
--- model/org/eclipse/jdt/internal/core/JavaModelManager.java	28 Jul 2011 17:07:05 -0000	1.468
+++ model/org/eclipse/jdt/internal/core/JavaModelManager.java	14 Aug 2011 15:27:04 -0000
@@ -4788,10 +4788,11 @@
 	 * @param optionValue The value of the option. If <code>null</code>, then
 	 * 	the option will be removed from the preferences instead.
 	 * @param eclipsePreferences The eclipse preferences to be updated
+	 * @param otherOptions more options being stored, used to avoid conflict between deprecated option and its compatible
 	 * @return <code>true</code> if the preferences have been changed,
 	 * 	<code>false</code> otherwise.
 	 */
-	public boolean storePreference(String optionName, String optionValue, IEclipsePreferences eclipsePreferences) {
+	public boolean storePreference(String optionName, String optionValue, IEclipsePreferences eclipsePreferences, Map otherOptions) {
 		int optionLevel = this.getOptionLevel(optionName);
 		if (optionLevel == UNKNOWN_OPTION) return false; // unrecognized option
 		
@@ -4809,6 +4810,8 @@
 				eclipsePreferences.remove(optionName); // get rid off old preference
 				String[] compatibleOptions = (String[]) this.deprecatedOptions.get(optionName);
 				for (int co=0, length=compatibleOptions.length; co < length; co++) {
+					if (otherOptions != null && otherOptions.containsKey(compatibleOptions[co]))
+						continue; // don't overwrite explicit value of otherOptions at compatibleOptions[co]
 					if (optionValue == null) {
 						eclipsePreferences.remove(compatibleOptions[co]);
 					} else {
@@ -4862,7 +4865,7 @@
 					if (defaultValue != null && defaultValue.equals(value)) {
 						value = null;
 					}
-					storePreference(key, value, instancePreferences);
+					storePreference(key, value, instancePreferences, newOptions);
 				}
 				try {
 					// persist options
Index: model/org/eclipse/jdt/internal/core/JavaProject.java
===================================================================
RCS file: /cvsroot/eclipse/org.eclipse.jdt.core/model/org/eclipse/jdt/internal/core/JavaProject.java,v
retrieving revision 1.447
diff -u -r1.447 JavaProject.java
--- model/org/eclipse/jdt/internal/core/JavaProject.java	10 May 2011 19:29:43 -0000	1.447
+++ model/org/eclipse/jdt/internal/core/JavaProject.java	14 Aug 2011 15:27:07 -0000
@@ -2928,7 +2928,7 @@
 	public void setOption(String optionName, String optionValue) {
 		// Store option value
 		IEclipsePreferences projectPreferences = getEclipsePreferences();
-		boolean modified = JavaModelManager.getJavaModelManager().storePreference(optionName, optionValue, projectPreferences);
+		boolean modified = JavaModelManager.getJavaModelManager().storePreference(optionName, optionValue, projectPreferences, null);
 
 		// Write changes
 		if (modified) {
@@ -2957,7 +2957,7 @@
 					Map.Entry entry = (Map.Entry) entries.next();
 					String key = (String) entry.getKey();
 					String value = (String) entry.getValue();
-					javaModelManager.storePreference(key, value, projectPreferences);
+					javaModelManager.storePreference(key, value, projectPreferences, newOptions);
 				}
 
 				// reset to default all options not in new map