diff --git a/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/internal/ui/ToolsSettingsBlock.java b/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/internal/ui/ToolsSettingsBlock.java
index 4b4c1b0735f..e8a64d763ca 100644
--- a/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/internal/ui/ToolsSettingsBlock.java
+++ b/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/internal/ui/ToolsSettingsBlock.java
@@ -18,7 +18,6 @@ import java.util.ListIterator;
 import java.util.Map;
 
 import org.eclipse.cdt.managedbuilder.core.BuildException;
-import org.eclipse.cdt.managedbuilder.core.IBuildObject;
 import org.eclipse.cdt.managedbuilder.core.IConfiguration;
 import org.eclipse.cdt.managedbuilder.core.IHoldsOptions;
 import org.eclipse.cdt.managedbuilder.core.IOption;
@@ -38,6 +37,7 @@ import org.eclipse.cdt.managedbuilder.ui.properties.BuildToolSettingsPreferenceS
 import org.eclipse.cdt.managedbuilder.ui.properties.ResourceBuildPropertyPage;
 import org.eclipse.cdt.managedbuilder.ui.properties.ToolListContentProvider;
 import org.eclipse.cdt.managedbuilder.ui.properties.ToolListLabelProvider;
+import org.eclipse.cdt.managedbuilder.ui.properties.ToolListElement;
 import org.eclipse.cdt.ui.dialogs.AbstractCOptionPage;
 import org.eclipse.cdt.ui.dialogs.ICOptionContainer;
 import org.eclipse.cdt.utils.ui.controls.ControlFactory;
@@ -75,8 +75,6 @@ public class ToolsSettingsBlock extends AbstractCOptionPage {
 	//private static final String TREE_LABEL = LABEL + ".ToolTree";	//$NON-NLS-1$
 	//private static final String OPTIONS_LABEL = LABEL + ".ToolOptions";	//$NON-NLS-1$
 	private static final int[] DEFAULT_SASH_WEIGHTS = new int[] { 20, 30 };
-
-	private static final String EMPTY_STRING = new String();
 	
 	/*
 	 * Dialog widgets
@@ -94,10 +92,9 @@ public class ToolsSettingsBlock extends AbstractCOptionPage {
 	private BuildPropertyPage parent;
 	private ResourceBuildPropertyPage resParent;
 	private BuildSettingsPage currentSettingsPage;
-	private IOptionCategory selectedCategory;
+	private ToolListElement selectedElement;
 	private ToolListContentProvider provider;
-	private ITool selectedTool;
-	private Object element;
+	private Object propertyObject;
 	
 	private boolean defaultNeeded;
 
@@ -152,7 +149,7 @@ public class ToolsSettingsBlock extends AbstractCOptionPage {
 		super.setContainer(parent);
 		this.parent = parent;
 		configToPageListMap = new HashMap();
-		this.element = element;
+		this.propertyObject = element;
 		settingsStore = new BuildToolSettingsPreferenceStore(this);
 	}
 
@@ -162,7 +159,7 @@ public class ToolsSettingsBlock extends AbstractCOptionPage {
 		super.setContainer((ICOptionContainer) resParent);
 		this.resParent = resParent;
 		configToPageListMap = new HashMap();
-		this.element = element;
+		this.propertyObject = element;
 		settingsStore = new BuildToolSettingsPreferenceStore(this);
 	}
 	
@@ -214,9 +211,10 @@ public class ToolsSettingsBlock extends AbstractCOptionPage {
 	 * Method displayOptionsForCategory
 	 * @param category
 	 */
-	private void displayOptionsForCategory(IOptionCategory category) {
-		selectedTool = null;
-		selectedCategory = category;
+	private void displayOptionsForCategory(ToolListElement toolListElement) {
+		selectedElement = toolListElement;
+		IOptionCategory category = toolListElement.getOptionCategory();
+		IHoldsOptions optionHolder = toolListElement.getHoldOptions();
 		
 		// Cache the current build setting page
 		BuildSettingsPage oldPage = currentSettingsPage;
@@ -228,18 +226,18 @@ public class ToolsSettingsBlock extends AbstractCOptionPage {
 		while (iter.hasNext()) {
 			BuildSettingsPage page = (BuildSettingsPage) iter.next();
 			if (page instanceof BuildOptionSettingsPage && 
-					((BuildOptionSettingsPage)page).isForCategory(category)) {
+					((BuildOptionSettingsPage)page).isForCategory(optionHolder, category)) {
 				currentSettingsPage = page;
 				break;
 			}
 		}
 		if (currentSettingsPage == null) {
-			if ( this.element instanceof IProject) {
-				currentSettingsPage = new BuildOptionSettingsPage(parent,parent.getSelectedConfigurationClone(), category);
+			if ( this.propertyObject instanceof IProject) {
+				currentSettingsPage = new BuildOptionSettingsPage(parent,parent.getSelectedConfigurationClone(), optionHolder, category);
 				pages.add(currentSettingsPage);
 				currentSettingsPage.setContainer(parent);
-			} else if ( this.element instanceof IFile) {
-				currentSettingsPage = new BuildOptionSettingsPage(resParent,resParent.getCurrentResourceConfigClone(), category);
+			} else if ( this.propertyObject instanceof IFile) {
+				currentSettingsPage = new BuildOptionSettingsPage(resParent,resParent.getCurrentResourceConfigClone(), optionHolder, category);
 				pages.add(currentSettingsPage);
 				currentSettingsPage.setContainer(resParent);
 			}
@@ -273,11 +271,9 @@ public class ToolsSettingsBlock extends AbstractCOptionPage {
 	 * Method displayOptionsForTool
 	 * @param tool
 	 */
-	private void displayOptionsForTool(ITool tool) {
-		// Unselect the category
-		selectedCategory = null;
-		// record that the tool selection has changed
-		selectedTool = tool;
+	private void displayOptionsForTool(ToolListElement toolListElement) {
+		selectedElement = toolListElement;
+		ITool tool = toolListElement.getTool();
 		
 		// Cache the current build setting page
 		BuildSettingsPage oldPage = currentSettingsPage;
@@ -295,12 +291,12 @@ public class ToolsSettingsBlock extends AbstractCOptionPage {
 			}
 		}
 		if (currentSettingsPage == null) {
-			if ( this.element instanceof IProject) {
+			if ( this.propertyObject instanceof IProject) {
 				currentSettingsPage = new BuildToolSettingsPage(parent, 
 						parent.getSelectedConfigurationClone(), tool);
 				pages.add(currentSettingsPage);
 				currentSettingsPage.setContainer(parent);
-			} else if(this.element instanceof IFile) {
+			} else if(this.propertyObject instanceof IFile) {
 				currentSettingsPage = new BuildToolSettingsPage(resParent,
 						resParent.getCurrentResourceConfigClone(), tool);
 				pages.add(currentSettingsPage);
@@ -378,101 +374,112 @@ public class ToolsSettingsBlock extends AbstractCOptionPage {
 
 	public void setVisible(boolean visible){
 		if(visible){
-			selectedCategory = null;
-			selectedTool = null;
+			selectedElement = null;
 			handleOptionSelection();
 		}
 		super.setVisible(visible);
 	}
 
 	protected void setValues() {
-		
-		IConfiguration config = null;	
-		IResourceConfiguration resConfig = null;
-		
+		/*
+		 *  This method updates the context of the build property pages
+		 *   - Which configuration/resource configuration is selected
+		 *   - Which tool/option category is selected
+		 *    
+		 *  It is called:
+		 *   - When a property page becomes visible
+		 *   - When the user changes the configuration selection
+		 *   - When the user changes the "exclude" setting for a resource
+		 */
+
+		//  Create the Tree Viewer content provider if first time
 		if (provider == null) {
-//			IResource element = parent.getProject(); 
-			IResource resource = (IResource) element;
+			IResource resource = (IResource) propertyObject;
 			provider = new ToolListContentProvider(resource.getType());
 			optionList.setContentProvider(provider);
 		}
-		if ( element instanceof IProject ) {
+
+		//  Update the selected configuration and the Tree Viewer
+		IConfiguration config = null;	
+		IResourceConfiguration resConfig = null;
+		ToolListElement[] newElements;
+		
+		if ( propertyObject instanceof IProject ) {
 			config = parent.getSelectedConfigurationClone();	
 			optionList.setInput(config);	
-		} else if ( element instanceof IFile){
+			newElements = (ToolListElement[])provider.getElements(config);
+		} else if ( propertyObject instanceof IFile){
 			resConfig = resParent.getCurrentResourceConfigClone();
 			optionList.setInput(resConfig);
-		}
+			newElements = (ToolListElement[])provider.getElements(resConfig);
+		} else
+			return;		// This should not happen
 		
 		optionList.expandAll();
 		
-		// Determine what the selection in the tree should be
-		Object primary = null;
-		if (selectedTool != null) {
-			// There is a selected tool defined.  See if it matches any current tool (by name)
-			ITool[] tools = null;
-			if ( element instanceof IProject ) {
-				tools = config.getFilteredTools();
-			} else if ( element instanceof IFile){
-				tools = resConfig.getTools();
-			}			
-			String matchName = selectedTool.getName();
-			for (int i=0; i<tools.length; i++) {
-				ITool tool = tools[i];
-				if (tool.getName().equals(matchName)) {
-					primary = tool;
-					break;
-				}
-			}
-		} else if (selectedCategory != null) {
-			// There is a selected option or category.  
-			// See if it matches any category in the current config (by name)
-			ITool[] tools = null;
-			IToolChain toolChain = null;
-			
-			if ( element instanceof IProject ) {
-				tools = config.getFilteredTools();
-				toolChain = config.getToolChain();
-			} else if ( element instanceof IFile){
-				tools = resConfig.getTools();
-			}
-			IBuildObject catOrTool = selectedCategory;
-			// Make the match name
-			String matchName = makeMatchName(catOrTool);
-			// Search for selected category/tool in toolChain
-			if ( toolChain != null ) {
-				primary = findOptionCategoryByMatchName(matchName, toolChain.getChildCategories());
-			}			
-			// Search for selected category/tool in tools
-			if ( primary == null ) {
-				for (int i=0; i<tools.length && primary == null; i++) {
-					primary = findOptionCategoryByMatchName(matchName, tools[i].getChildCategories());
-				}
-			}
-		} 
-		
-		if (primary == null) {
-			// Select the first tool in the list
-			Object[] elements = null;
-			if( element instanceof IProject){
-				elements = provider.getElements(parent.getSelectedConfigurationClone());
-			} else if ( element instanceof IFile) {
-				elements = provider.getElements(resParent.getCurrentResourceConfigClone());
-			}
-			primary = elements.length > 0 ? elements[0] : null;			
+		//  Determine what the selection in the tree should be
+		//  If the saved selection is not null, try to match the saved selection
+		//  with an object in the new element list.
+		//  Otherwise, select the first tool in the tree
+		Object primaryObject = null;
+		if (selectedElement != null) {
+			selectedElement = matchSelectionElement(selectedElement, newElements);
 		}
-		
-		if (primary != null) {
-			if(primary instanceof IOptionCategory){
-				if(resConfig != null)
-					settingsStore.setSelection(resConfig,(IOptionCategory)primary);
-				else
-					settingsStore.setSelection(config,(IOptionCategory)primary);
+			
+		if (selectedElement == null) {
+			selectedElement = (ToolListElement)(newElements.length > 0 ? newElements[0] : null);
+		}
+			
+		if (selectedElement != null) {
+			primaryObject = selectedElement.getTool();
+			if (primaryObject == null) {
+				primaryObject = selectedElement.getOptionCategory();
+			}
+			if (primaryObject != null) {
+				if (primaryObject instanceof IOptionCategory) {
+					if(resConfig != null)
+						settingsStore.setSelection(resConfig, selectedElement, (IOptionCategory)primaryObject);
+					else
+						settingsStore.setSelection(config, selectedElement, (IOptionCategory)primaryObject);
+				}
+				optionList.setSelection(new StructuredSelection(selectedElement), true);
 			}
-			optionList.setSelection(new StructuredSelection(primary), true);
 		}
 	}
+						
+	private ToolListElement matchSelectionElement(ToolListElement currentElement, ToolListElement[] elements) {
+		//  First, look for an exact match
+		ToolListElement match = exactMatchSelectionElement(currentElement, elements);
+		if (match == null)
+			//  Else, look for the same tool/category in the new set of elements
+			match = equivalentMatchSelectionElement(currentElement, elements);
+		return match;
+	}
 
+	private ToolListElement exactMatchSelectionElement(ToolListElement currentElement, ToolListElement[] elements) {
+		for (int i=0; i<elements.length; i++) {
+			ToolListElement e = elements[i];
+			if (e == currentElement) {
+				return currentElement;
+			}
+			e = exactMatchSelectionElement(currentElement, e.getChildElements());
+			if (e != null) return e;
+		}
+		return null;
+	}
+
+	private ToolListElement equivalentMatchSelectionElement(ToolListElement currentElement, ToolListElement[] elements) {
+		for (int i=0; i<elements.length; i++) {
+			ToolListElement e = elements[i];
+			if (e.isEquivalentTo(currentElement)) {
+				return e;
+			}
+			e = equivalentMatchSelectionElement(currentElement, e.getChildElements());
+			if (e != null) return e;
+		}
+		return null;
+	}
+	
 	public void removeValues(String id) {
 	}
 
@@ -481,17 +488,24 @@ public class ToolsSettingsBlock extends AbstractCOptionPage {
 		IStructuredSelection selection = (IStructuredSelection) optionList.getSelection();
 	
 		// Set the option page based on the selection
-		Object element = selection.getFirstElement();
-		if(element instanceof IOptionCategory){
-			if(resParent != null)
-				settingsStore.setSelection(resParent.getCurrentResourceConfigClone(),(IOptionCategory)element);
-			else
-				settingsStore.setSelection(parent.getSelectedConfigurationClone(),(IOptionCategory)element);
-		}
-		if (element instanceof ITool) {
-			displayOptionsForTool((ITool)element);
-		} else if (element instanceof IOptionCategory) {
-			displayOptionsForCategory((IOptionCategory)element);
+		ToolListElement toolListElement = (ToolListElement)selection.getFirstElement();
+		if (toolListElement != null) {
+			IOptionCategory cat = toolListElement.getOptionCategory();
+			if (cat == null)
+				cat = (IOptionCategory)toolListElement.getTool();
+			if (cat != null) {
+				if(resParent != null)
+					settingsStore.setSelection(resParent.getCurrentResourceConfigClone(), toolListElement, cat);
+				else
+					settingsStore.setSelection(parent.getSelectedConfigurationClone(), toolListElement, cat);
+			}
+
+			cat = toolListElement.getOptionCategory();
+			if (cat != null) {
+				displayOptionsForCategory(toolListElement);
+			} else {
+				displayOptionsForTool(toolListElement);
+			}
 		}
 	}
 
@@ -519,10 +533,10 @@ public class ToolsSettingsBlock extends AbstractCOptionPage {
 	 * @see org.eclipse.cdt.ui.dialogs.ICOptionPage#performDefaults()
 	 */
 	public void performDefaults() {
-		if ( element instanceof IProject) {
-			performDefaults( (IProject)element);
-		} else if ( element instanceof IFile) {
-			performDefaults( (IFile)element);
+		if ( propertyObject instanceof IProject) {
+			performDefaults( (IProject)propertyObject);
+		} else if ( propertyObject instanceof IFile) {
+			performDefaults( (IFile)propertyObject);
 		}
 		defaultNeeded = true;
 		return;
@@ -544,8 +558,7 @@ public class ToolsSettingsBlock extends AbstractCOptionPage {
 		}
 		
 		// Reset the category or tool selection and run selection event handler
-		selectedCategory = null;
-		selectedTool = null;
+		selectedElement = null;
 		handleOptionSelection();
 		
 		setDirty(true);
@@ -566,8 +579,7 @@ public class ToolsSettingsBlock extends AbstractCOptionPage {
 		}
 
 		// Reset the category or tool selection and run selection event handler
-		selectedCategory = null;
-		selectedTool = null;
+		selectedElement = null;
 		handleOptionSelection();
 		
 		setDirty(true);
@@ -579,11 +591,11 @@ public class ToolsSettingsBlock extends AbstractCOptionPage {
 	 */
 	public void performApply(IProgressMonitor monitor) throws CoreException {
 		
-		if(element instanceof IFile)
+		if(propertyObject instanceof IFile)
 			resParent.getCurrentResourceConfig(true);
 		
 		if(defaultNeeded){
-			if(element instanceof IFile)
+			if(propertyObject instanceof IFile)
 				ManagedBuildManager.resetResourceConfiguration(resParent.getProject(), resParent.getCurrentResourceConfig(true));
 			else
 				ManagedBuildManager.resetConfiguration(parent.getProject(), parent.getSelectedConfiguration());
@@ -846,13 +858,13 @@ public class ToolsSettingsBlock extends AbstractCOptionPage {
 	 */
 	private List getPagesForConfig() {
 		List pages = null;
-		if ( element instanceof IProject) {
+		if ( propertyObject instanceof IProject) {
 //			 Make sure that something was selected
 			if (parent.getSelectedConfigurationClone() == null) {
 				return null;
 			}
 			pages = (List) configToPageListMap.get(parent.getSelectedConfigurationClone().getId());	
-		} else if (element instanceof IFile) {
+		} else if (propertyObject instanceof IFile) {
 			if ( resParent.getCurrentResourceConfigClone() == null ) {
 				return null;
 			}
@@ -861,9 +873,9 @@ public class ToolsSettingsBlock extends AbstractCOptionPage {
 		
 		if (pages == null) {
 			pages = new ArrayList();
-			if ( element instanceof IProject) {
+			if ( propertyObject instanceof IProject) {
 				configToPageListMap.put(parent.getSelectedConfigurationClone().getId(), pages);	
-			} else if ( element instanceof IFile) {
+			} else if ( propertyObject instanceof IFile) {
 				configToPageListMap.put(resParent.getCurrentResourceConfigClone().getId(), pages);
 			}
 		}
@@ -938,59 +950,5 @@ public class ToolsSettingsBlock extends AbstractCOptionPage {
 		}
 		return (BuildMacroProvider)ManagedBuildManager.getBuildMacroProvider();
 	}
-	
-	/**
-	 * Creates a name that uniquely identifies a category. The match name is 
-	 * a concatenation of the tool and categories, e.g. Tool->Cat1->Cat2 
-	 * maps onto the string "Tool|Cat1|Cat2|"
-	 * 
-	 * @param category or tool for which to build the match name 
-	 * @return match name
-	 */
-	private String makeMatchName(IBuildObject catOrTool) {
-		String catName = EMPTY_STRING;
-		
-		// Build the match name.
-		do {
-			catName = catOrTool.getName() + "|" + catName; //$NON-NLS-1$
-			if (catOrTool instanceof ITool) break;
-			else if (catOrTool instanceof IOptionCategory) {
-				catOrTool = ((IOptionCategory)catOrTool).getOwner();					
-			} else 
-				break;
-		} while (catOrTool != null);
-		
-		return catName;
-	}
-	
-	/**
-	 * Finds an option category from an array of categories by comparing against
-	 * a match name. The match name is a concatenation of the tool and categories, 
-	 * e.g. Tool->Cat1->Cat2 maps onto the string "Tool|Cat1|Cat2|"
-	 * 
-	 * @param matchName an identifier to search 
-	 * @param categories as returned by getChildCategories(), i.e. non-flattened 
-	 * @return category or tool, if found and null otherwise
-	 */
-	private Object findOptionCategoryByMatchName(String matchName, IOptionCategory[] cats) {
-		Object primary = null;
-		
-		for (int j=0; j<cats.length; j++) {
-			IBuildObject catOrTool = cats[j]; 
-			// Build the match name
-			String catName = makeMatchName(catOrTool);
-			// Check whether the name matches
-			if (catName.equals(matchName)) {
-				primary = cats[j];
-				break;
-			} else if (matchName.startsWith(catName)) {
-				// If there is a common root then check for any further children
-				primary = findOptionCategoryByMatchName(matchName, cats[j].getChildCategories());
-				if (primary != null)
-					break;
-			}
-		}
-		return primary;
-	}	
 }
 
diff --git a/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/BuildOptionSettingsPage.java b/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/BuildOptionSettingsPage.java
index 1131c7612c5..6cee5546b1e 100644
--- a/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/BuildOptionSettingsPage.java
+++ b/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/BuildOptionSettingsPage.java
@@ -40,24 +40,27 @@ import org.eclipse.swt.widgets.Composite;
 public class BuildOptionSettingsPage extends BuildSettingsPage {
 	private Map fieldsMap = new HashMap();
 	private IOptionCategory clonedCategory;
+	private IHoldsOptions optionHolder;
 	private boolean isItResourceConfigPage;
 	private Map fieldEditorsToParentMap = new HashMap();
 	private AbstractBuildPropertyPage buildPropPage;
 
 	public BuildOptionSettingsPage(AbstractBuildPropertyPage page,
-			IConfiguration clonedConfig, IOptionCategory clonedCategory) {
+			IConfiguration clonedConfig, IHoldsOptions optionHolder, IOptionCategory clonedCategory) {
 		// Cache the configuration and option category this page is created for
 		super(clonedConfig);
 		this.clonedCategory = clonedCategory;
+		this.optionHolder = optionHolder;
 		isItResourceConfigPage = false;
 		buildPropPage = page;
 	}
 	
 	public BuildOptionSettingsPage(AbstractBuildPropertyPage page,
-			IResourceConfiguration clonedResConfig, IOptionCategory clonedCategory) {
+			IResourceConfiguration clonedResConfig, IHoldsOptions optionHolder, IOptionCategory clonedCategory) {
 		// Cache the configuration and option category this page is created for
 		super(clonedResConfig);
 		this.clonedCategory = clonedCategory;
+		this.optionHolder = optionHolder;
 		isItResourceConfigPage = true;
 		buildPropPage = page;
 	}
@@ -78,9 +81,9 @@ public class BuildOptionSettingsPage extends BuildSettingsPage {
 		// for each
 		Object[][] options;
 		if ( isItResourceConfigPage ) {
-			options = clonedCategory.getOptions(clonedResConfig);
+			options = clonedCategory.getOptions(clonedResConfig, optionHolder);
 		} else {
-			options = clonedCategory.getOptions(clonedConfig);
+			options = clonedCategory.getOptions(clonedConfig, optionHolder);
 		}
 		
 		for (int index = 0; index < options.length; ++index) {
@@ -204,9 +207,10 @@ public class BuildOptionSettingsPage extends BuildSettingsPage {
 	 * @param category
 	 * @return
 	 */
-	public boolean isForCategory(IOptionCategory category) {
+	public boolean isForCategory(IHoldsOptions optionHolder, IOptionCategory category) {
 		if (category != null) {
-			return category.equals(this.clonedCategory);
+			if (this.optionHolder == optionHolder && category.equals(this.clonedCategory))
+				return true;
 		}
 		return false;
 	}
@@ -229,13 +233,13 @@ public class BuildOptionSettingsPage extends BuildSettingsPage {
 			if(realRcCfg == null)
 				return false;
 			handler = realRcCfg;
-			clonedOptions = clonedCategory.getOptions(clonedResConfig);
+			clonedOptions = clonedCategory.getOptions(clonedResConfig, optionHolder);
 		} else {
 			realCfg = buildPropPage.getRealConfig(clonedConfig);
 			if(realCfg == null)
 				return false;
 			handler = realCfg;
-			clonedOptions = clonedCategory.getOptions(clonedConfig);
+			clonedOptions = clonedCategory.getOptions(clonedConfig, optionHolder);
 		}
 		
 		for (int i = 0; i < clonedOptions.length; i++) {
@@ -353,9 +357,9 @@ public class BuildOptionSettingsPage extends BuildSettingsPage {
 	public void updateFields() {
 		Object[][] options;
 		if (isItResourceConfigPage) {
-			options = clonedCategory.getOptions(clonedResConfig);
+			options = clonedCategory.getOptions(clonedResConfig, optionHolder);
 		} else {
-			options = clonedCategory.getOptions(clonedConfig);
+			options = clonedCategory.getOptions(clonedConfig, optionHolder);
 		}
 
 		// some option has changed on this page... update enabled/disabled state for all options
@@ -518,9 +522,9 @@ public class BuildOptionSettingsPage extends BuildSettingsPage {
 
 		Object[][] options;
 		if (isItResourceConfigPage) {
-			options = clonedCategory.getOptions(clonedResConfig);
+			options = clonedCategory.getOptions(clonedResConfig, optionHolder);
 		} else {
-			options = clonedCategory.getOptions(clonedConfig);
+			options = clonedCategory.getOptions(clonedConfig, optionHolder);
 		}
 
 		// some option has changed on this page... update enabled/disabled state for all options
diff --git a/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/BuildToolSettingsPage.java b/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/BuildToolSettingsPage.java
index 865f1a10b1a..11fed1d23b5 100644
--- a/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/BuildToolSettingsPage.java
+++ b/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/BuildToolSettingsPage.java
@@ -543,13 +543,13 @@ public class BuildToolSettingsPage extends BuildSettingsPage {
 			if(realRcCfg == null)
 				return false;
 //			handler = realRcCfg;
-			clonedOptions = clonedCategory.getOptions(clonedResConfig);
+			clonedOptions = clonedCategory.getOptions(clonedResConfig, clonedTool);
 		} else {
 			realCfg = buildPropPage.getRealConfig(clonedConfig);
 			if(realCfg == null)
 				return false;
 //			handler = realCfg;
-			clonedOptions = clonedCategory.getOptions(clonedConfig);
+			clonedOptions = clonedCategory.getOptions(clonedConfig, clonedTool);
 		}
 
 		if ( clonedOptions == null)
diff --git a/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/BuildToolSettingsPreferenceStore.java b/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/BuildToolSettingsPreferenceStore.java
index 26cc2dd0de9..e11cb2141be 100644
--- a/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/BuildToolSettingsPreferenceStore.java
+++ b/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/BuildToolSettingsPreferenceStore.java
@@ -43,6 +43,7 @@ public class BuildToolSettingsPreferenceStore implements IPreferenceStore {
 	private IConfiguration config;
 	private IResourceConfiguration rcConfig;
 	private IOptionCategory optCategory;
+	private ToolListElement selectedElement;
 	private ListenerList listenerList;
 	private boolean dirtyFlag;
 	
@@ -90,26 +91,20 @@ public class BuildToolSettingsPreferenceStore implements IPreferenceStore {
 		this.block = block;
 	}
 	
-	public void setSelection(IConfiguration cfg, IOptionCategory category){
+	public void setSelection(IConfiguration cfg, ToolListElement element, IOptionCategory category){
+		selectedElement = element;
 		optCategory = category;
 		rcConfig = null;
 		config = cfg;
 	}
 
-	public void setSelection(IResourceConfiguration cfg, IOptionCategory category){
+	public void setSelection(IResourceConfiguration cfg, ToolListElement element, IOptionCategory category){
+		selectedElement = element;
 		optCategory = category;
 		rcConfig = cfg;
 		config = cfg.getParent();
 	}
 	
-	public IOptionCategory getSelecedCategory(){
-		return optCategory;
-	}
-	
-	public IResourceConfiguration getSelectedRcConfig(){
-		return rcConfig;
-	}
-	
 	public IConfiguration getSelectedConfig(){
 		return config;
 	}
@@ -264,10 +259,12 @@ public class BuildToolSettingsPreferenceStore implements IPreferenceStore {
 	public Object[] getOption(String name){
 		Object options[][];
         
+		IHoldsOptions selectedHolder = selectedElement.getHoldOptions();
+		if (selectedHolder == null) selectedHolder = selectedElement.getTool();
 		if(rcConfig != null)
-			options = optCategory.getOptions(rcConfig);
+			options = optCategory.getOptions(rcConfig, selectedHolder);
 		else
-			options = optCategory.getOptions(config);
+			options = optCategory.getOptions(config, selectedHolder);
 
 		for(int i = 0; i < options.length; i++){
 			IHoldsOptions ho = (IHoldsOptions)options[i][0];
diff --git a/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/ToolListContentProvider.java b/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/ToolListContentProvider.java
index 5586d07f73c..0d04accfa0f 100644
--- a/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/ToolListContentProvider.java
+++ b/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/ToolListContentProvider.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2002, 2005 IBM Corporation and others.
+ * Copyright (c) 2002, 2006 IBM Corporation and others.
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
  * which accompanies this distribution, and is available at
@@ -11,21 +11,19 @@
  *******************************************************************************/
 package org.eclipse.cdt.managedbuilder.ui.properties;
 
-import org.eclipse.cdt.managedbuilder.core.IConfiguration;
-import org.eclipse.cdt.managedbuilder.core.IResourceConfiguration;
-import org.eclipse.cdt.managedbuilder.core.IOptionCategory;
-import org.eclipse.cdt.managedbuilder.core.ITool;
-import org.eclipse.cdt.managedbuilder.core.IToolChain;
+import org.eclipse.cdt.managedbuilder.core.*;
 import org.eclipse.jface.viewers.ITreeContentProvider;
 import org.eclipse.jface.viewers.Viewer;
+import java.util.ArrayList;
+import java.util.List;
 
 public class ToolListContentProvider implements ITreeContentProvider{
 	public static final int FILE = 0x1;
 	public static final int PROJECT = 0x4;
-	private static Object[] EMPTY_ARRAY = new Object[0];
 	private IConfiguration configRoot;
 	private IResourceConfiguration resConfigRoot;
 	private int elementType;
+	private ToolListElement[] elements;
 
 	/**
 	 * @see org.eclipse.jface.viewers.IContentProvider#dispose()
@@ -36,88 +34,87 @@ public class ToolListContentProvider implements ITreeContentProvider{
 	public ToolListContentProvider(int elementType) {
 		this.elementType = elementType;
 	}
-	
-	/**
-	 *  Gets the top level contents to be displayed in the tool list.
-	 *  If defined, first display the toolChain's option categories (unfiltered).
-	 *  Then display the the tools which are relevant for the project's nature.
-	 */
-	private Object[] getToplevelContent(IConfiguration config) {
-		Object toolChainsCategories[]; 
-		Object filteredTools[];
-		Object all[];
-		// Get the the option categories of the toolChain  
-		IToolChain toolChain = config.getToolChain();
-		toolChainsCategories = toolChain.getChildCategories();
-		// Get the tools to be displayed
-		filteredTools = config.getFilteredTools();
-		// Add up both arrays and return
-		int i;
-		int len = toolChainsCategories.length+filteredTools.length;
-		all = new Object[len];
-		for (i=0; i < toolChainsCategories.length; i++) 
-			all[i] = toolChainsCategories[i];
-		for (; i < len; i++) 
-			all[i] = filteredTools[i-toolChainsCategories.length];
-		
-		return all;
+
+	private ToolListElement[] createElements(IConfiguration config) {
+		IOptionCategory toolChainCategories[]; 
+		ITool filteredTools[];
+		List elementList = new ArrayList();
+		if (config != null) {
+			// Get the the option categories of the toolChain  
+			IToolChain toolChain = config.getToolChain();
+			toolChainCategories = toolChain.getChildCategories();
+			//  Create an element for each one
+			for (int i=0; i<toolChainCategories.length; i++) {
+				ToolListElement e = new ToolListElement(null, toolChain, toolChainCategories[i]);
+				elementList.add(e);
+				createChildElements(e);
+			}
+			//  Get the tools to be displayed
+			filteredTools = config.getFilteredTools();
+			//  Create an element for each one
+			for (int i=0; i<filteredTools.length; i++) {
+				ToolListElement e = new ToolListElement(filteredTools[i]);
+				elementList.add(e);
+				createChildElements(e);
+			}
+		}
+		return (ToolListElement[])elementList.toArray(new ToolListElement[elementList.size()]);		
+	}
+
+	private ToolListElement[] createElements(IResourceConfiguration resConfig) {
+		List elementList = new ArrayList();
+		if (resConfig != null) {
+			ITool[] tools = resConfig.getTools();
+			//  Create an element for each one
+			for (int i=0; i<tools.length; i++) {
+				ToolListElement e = new ToolListElement(tools[i]);
+				elementList.add(e);
+				createChildElements(e);
+			}
+		}
+		return (ToolListElement[])elementList.toArray(new ToolListElement[elementList.size()]);		
+	}
+
+	private void createChildElements(ToolListElement parentElement) {
+
+		IOptionCategory parent = parentElement.getOptionCategory();
+		IHoldsOptions optHolder = parentElement.getHoldOptions();
+		if (parent == null) {
+			parent = parentElement.getTool().getTopOptionCategory();	//  Must be an ITool
+			optHolder = parentElement.getTool();
+		}
+		IOptionCategory[] cats = parent.getChildCategories();
+		//  Create an element for each one
+		for (int i=0; i<cats.length; i++) {
+			ToolListElement e = new ToolListElement(parentElement, optHolder, cats[i]);
+			parentElement.addChildElement(e);
+			createChildElements(e);
+		}
 	}
 	
 	/**
 	 * @see org.eclipse.jface.viewers.ITreeContentProvider#getChildren(java.lang.Object)
 	 */
 	public Object[] getChildren(Object parentElement) {
-		// If parent is configuration, return a list of its option categories
-		if (parentElement instanceof IConfiguration) {
-			IConfiguration config = (IConfiguration)parentElement;
-			// Get the contents to be displayed for the configuration
-			return getToplevelContent(config);
-		} else if( parentElement instanceof IResourceConfiguration) {
-			// If parent is a resource configuration, return a list of its tools.
-			// Resource configurations do not support categories that are children 
-			// of toolchains. The reason for this is that options in such categories 
-			// are intended to be global.
-			// TODO: Remove this restriction in future? Requires getToplevelContent() variant
-			IResourceConfiguration resConfig = (IResourceConfiguration)parentElement;
-			return resConfig.getTools();
-		} else if (parentElement instanceof ITool) {
-			// If this is a tool, return the categories it contains
-			ITool tool = (ITool)parentElement;
-			return tool.getTopOptionCategory().getChildCategories();
-		} else if (parentElement instanceof IOptionCategory) {
-			// Categories can have child categories
-			IOptionCategory cat = (IOptionCategory)parentElement;
-			return cat.getChildCategories();
-		} else {
-			return EMPTY_ARRAY;
+		if (parentElement instanceof IConfiguration ||
+			parentElement instanceof IResourceConfiguration	) {
+			return elements;
 		}
+		return ((ToolListElement)parentElement).getChildElements();
 	}
-
+	
 	/**
 	 * @see org.eclipse.jface.viewers.IStructuredContentProvider#getElements(java.lang.Object)
 	 */
 	public Object[] getElements(Object inputElement) {
-		return getChildren(inputElement);
+		return elements;
 	}
 
 	/**
 	 * @see org.eclipse.jface.viewers.ITreeContentProvider#getParent(java.lang.Object)
 	 */
 	public Object getParent(Object element) {
-		if (element instanceof IOptionCategory) {
-			// Find the parent category
-			IOptionCategory cat = (IOptionCategory)element; 
-			IOptionCategory parent = cat.getOwner();
-			// Then we need to get the configuration we belong to
-			if (parent == null) {
-				if(elementType == FILE)
-					return resConfigRoot;
-				else
-					return configRoot;
-			}
-			return parent;
-		}
-		return null;
+		return ((ToolListElement)element).getParent();
 	}
 
 	/**
@@ -131,13 +128,22 @@ public class ToolListContentProvider implements ITreeContentProvider{
 	 * @see org.eclipse.jface.viewers.IContentProvider#inputChanged(org.eclipse.jface.viewers.Viewer, java.lang.Object, java.lang.Object)
 	 */
 	public void inputChanged(Viewer viewer, Object oldInput, Object newInput) {
+		//  If the input hasn't changed, there is no reason to re-create the content
+		if (oldInput == newInput) return;
+		
 		if(elementType == FILE) {
 			resConfigRoot = (IResourceConfiguration)newInput;
 			configRoot = null;
+			//  Create a ToolListElement to represent each item that will appear
+			//  in the TreeViewer.
+			elements = createElements(resConfigRoot);
 		}
 		else if(elementType == PROJECT) {
 			configRoot = (IConfiguration) newInput;
 			resConfigRoot = null;
+			//  Create a ToolListElement to represent each item that will appear
+			//  in the TreeViewer.
+			elements = createElements(configRoot);
 		}
 	}
 }
diff --git a/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/ToolListElement.java b/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/ToolListElement.java
new file mode 100644
index 00000000000..b49cf4c2b90
--- /dev/null
+++ b/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/ToolListElement.java
@@ -0,0 +1,120 @@
+/*******************************************************************************
+ * Copyright (c) 2006 Intel Corporation and others.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
+ *
+ * Contributors:
+ * Intel Corporation - Initial API and implementation
+ *******************************************************************************/
+
+package org.eclipse.cdt.managedbuilder.ui.properties;
+
+import org.eclipse.cdt.managedbuilder.core.*;
+import org.eclipse.cdt.managedbuilder.internal.core.OptionCategory;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/*******************************************************************************
+ * This class represent the elements in the TreeViewer that displays the tools
+ * and categories in the tool options property pages.  The reason for these
+ * elements is illustrated by bugzilla #123461.  We used to use the ToolChain, 
+ * Tool and OptionCategory objects themselves as the elements in the TreeViewer,
+ * but the same OptionCategory can appear more than once in the list of Tree
+ * Viewer items, and this caused problems.
+ *******************************************************************************/
+public class ToolListElement {
+	
+	/*
+	 * Bookeeping variables
+	 */
+	private ToolListElement parent = null;
+	private List childElements = null;
+
+	private IHoldsOptions optionHolder = null;
+	private IOptionCategory optionCategory = null;
+	private ITool tool = null;
+
+	/*
+	 * Constructor for an element tha represents an option category
+	 */
+	public ToolListElement(ToolListElement parent, IHoldsOptions optionHolder, IOptionCategory optionCategory) {
+		this.parent = parent;
+		this.optionHolder = optionHolder;
+		this.optionCategory = optionCategory;
+	}
+
+	/*
+	 * Constructor for an element tha represents a tool
+	 */
+	public ToolListElement(ITool tool) {
+		this.tool = tool;
+	}
+	
+	public boolean isEquivalentTo(ToolListElement e) {
+	
+		if (tool != null) {
+			//  Look for a matching tool
+			ITool matchTool = e.getTool();
+			if (matchTool == tool) return true;
+			if (matchTool == null) return false;
+			if (matchTool.getName().equals(tool.getName())) return true;
+			return false;
+		}
+	
+		if (optionCategory != null) {
+			IOptionCategory matchCategory = e.getOptionCategory();
+			IHoldsOptions matchHolder = e.getHoldOptions();
+			if (matchCategory == optionCategory &&
+				matchHolder == optionHolder) return true;
+			if (matchCategory == null) return false;
+			
+			//String matchCategoryName = matchCategory.getName();
+			//String optionCategoryName = optionCategory.getName();
+			String matchCategoryName = OptionCategory.makeMatchName(matchCategory);
+			String optionCategoryName = OptionCategory.makeMatchName(optionCategory);
+			if (matchHolder.getName().equals(optionHolder.getName()) &&
+				matchCategoryName.equals(optionCategoryName)) return true;
+
+			return false;
+		}
+		return false;
+	}
+
+	/*
+	 * Field accessors
+	 */
+	public ToolListElement getParent() {
+		return parent;
+	}
+	
+	public IHoldsOptions getHoldOptions() {
+		return optionHolder;
+	}
+	
+	public IOptionCategory getOptionCategory() {
+		return optionCategory;
+	}
+	
+	public ITool getTool() {
+		return tool;
+	}
+	
+	/*
+	 * Children handling
+	 */
+	public ToolListElement[] getChildElements() {
+		if (childElements != null)
+			return (ToolListElement[])childElements.toArray(new ToolListElement[childElements.size()]);
+		else
+			return new ToolListElement[0];
+	}
+	
+	public void addChildElement(ToolListElement element) {
+		if (childElements == null)
+			childElements = new ArrayList();
+		childElements.add(element);
+	}
+}
diff --git a/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/ToolListLabelProvider.java b/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/ToolListLabelProvider.java
index 15a8dd337e1..ddb9c1d0587 100644
--- a/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/ToolListLabelProvider.java
+++ b/build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/properties/ToolListLabelProvider.java
@@ -1,5 +1,5 @@
 /*******************************************************************************
- * Copyright (c) 2002, 2005 IBM Corporation and others.
+ * Copyright (c) 2002, 2006 IBM Corporation and others.
  * All rights reserved. This program and the accompanying materials
  * are made available under the terms of the Eclipse Public License v1.0
  * which accompanies this distribution, and is available at
@@ -13,6 +13,7 @@ package org.eclipse.cdt.managedbuilder.ui.properties;
 import java.net.URL;
 
 import org.eclipse.cdt.managedbuilder.core.IOptionCategory;
+import org.eclipse.cdt.managedbuilder.core.IHoldsOptions;
 import org.eclipse.cdt.managedbuilder.core.ITool;
 import org.eclipse.cdt.managedbuilder.internal.ui.ManagedBuilderUIImages;
 import org.eclipse.cdt.managedbuilder.internal.ui.ManagedBuilderUIMessages;
@@ -56,50 +57,46 @@ public class ToolListLabelProvider extends LabelProvider {
 	}
 
 	public Image getImage(Object element) {
-		// Return a tool image for a tool or tool reference
-		if (element instanceof ITool) {
-			if (element instanceof IOptionCategory) {
-				// Retrieve the Image from Icon information included 
-				IOptionCategory cat = (IOptionCategory)element;
-				Image img = getIconFromOptionCategory(cat);
-				
-				if (img != null) {
-					return img;
-				}
-			}
-			// Use default icon for display 
-			return IMG_TOOL;
-
-		} else if (element instanceof IOptionCategory) { 
+		if (!(element instanceof ToolListElement)) {
+			throw unknownElement(element);
+		}
+		Image defaultImage = IMG_CAT;
+		ToolListElement toolListElement = (ToolListElement)element;
+		IOptionCategory cat = toolListElement.getOptionCategory();
+	
+		if (cat == null) {
+			defaultImage = IMG_TOOL;
+			cat = (IOptionCategory)toolListElement.getTool();
+		}
+		
+		if (cat != null) {
 			// Return a OptionCategory image for an OptionCategory reference
-			IOptionCategory cat = (IOptionCategory)element;
 			Image img = getIconFromOptionCategory(cat);
 			
 			if (img != null) {
 				return img;
 			}
-			// Use default icon for display 
-			return IMG_CAT;
-		} else {
-			throw unknownElement(element);
 		}
+		// Use default icon for display 
+		return defaultImage;
 	}
 
 	/* (non-Javadoc)
 	 * @see org.eclipse.jface.viewers.ILabelProvider#getText(Object)
 	 */
 	public String getText(Object element) {
-		if (element instanceof ITool) {
-			// Handles tool references as well
-			ITool tool = (ITool)element;
+		if (!(element instanceof ToolListElement)) {
+			throw unknownElement(element);
+		}
+		ToolListElement toolListElement = (ToolListElement)element;
+		IOptionCategory cat = toolListElement.getOptionCategory();
+	
+		if (cat == null) {
+			ITool tool = toolListElement.getTool();
 			return tool.getName();
 		}
-		else if (element instanceof IOptionCategory) {
-			IOptionCategory cat = (IOptionCategory)element;
-			return cat.getName();
-		}
 		else {
-			throw unknownElement(element);
+			return cat.getName();
 		}
 	}