1. fix to [bug 175662] [Build] Include directory from workspace shows up invalid

2. fix to [Bug 175508] [New project model] Invalid warnings about includes in problems view
3. fix to [Bug 175198] Internal Builder does nothing after a clean.
4. fix to [Bug 175087] [New project model] PathEntry not converted

build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/core/CommonBuilder.java

@@ -636,7 +636,7 @@ public class CommonBuilder extends ACBuilder {
 		
 		IConfiguration cfg = builder.getParent().getParent();
 		boolean isParallel = builder.getParallelizationNum() != 0;
-		boolean buildIncrementaly = true;
+//		boolean buildIncrementaly = true;
 		boolean resumeOnErr = !builder.isStopOnError();
 		
 		// Get the project and make sure there's a monitor to cancel the build
@@ -654,13 +654,15 @@ public class CommonBuilder extends ACBuilder {
 		OutputStream epmOutputStream = null;
 		try {
 			int flags = 0;
-			IResourceDelta delta = null;
+			IResourceDelta delta = getDelta(currentProject);
 			
-			if(buildIncrementaly){
+			if(delta != null){
 				flags = BuildDescriptionManager.REBUILD | BuildDescriptionManager.REMOVED | BuildDescriptionManager.DEPS;
-				delta = getDelta(currentProject);
+//				delta = getDelta(currentProject);
 			}
 			
+			boolean buildIncrementaly = delta != null;
+			
 			IBuildDescription des = BuildDescriptionManager.createBuildDescription(cfg, delta, flags);
 	
 			DescriptionBuilder dBuilder = null;

build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/dataprovider/ConfigurationDataProvider.java

@@ -84,7 +84,9 @@ public class ConfigurationDataProvider extends CConfigurationDataProvider implem
 	}
 
 	public CConfigurationData applyConfiguration(
-			ICConfigurationDescription des, CConfigurationData base)
+			ICConfigurationDescription des, 
+			ICConfigurationDescription baseDescription,
+			CConfigurationData base)
 			throws CoreException {
 		if(des.isPreferenceConfiguration())
 			return applyPreferences(des, base);
@@ -115,7 +117,9 @@ public class ConfigurationDataProvider extends CConfigurationDataProvider implem
 			
 
 	public CConfigurationData createConfiguration(
-			ICConfigurationDescription des, CConfigurationData base, boolean clone)
+			ICConfigurationDescription des, 
+			ICConfigurationDescription baseDescription,
+			CConfigurationData base, boolean clone)
 			throws CoreException {
 		if(des.isPreferenceConfiguration())
 			return createPreferences(des, base);

build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/dataprovider/EntryStorage.java

@@ -189,6 +189,9 @@ public class EntryStorage {
 				if(size > 0){
 					for(int j = 0; j < size; j++){
 						String value = (String)list.get(j);
+						if(value.indexOf('"') == 0 && value.lastIndexOf('"') == value.length() - 1 && value.length() != 1){
+							value = value.substring(1, value.length() - 1);
+						}
 						ICLanguageSettingEntry entry = createEntry(discoveredEntryFromString(value), false, false);
 						EntryInfo discoveredInfo = fDiscoveredEntries.getEntryInfo(entry);
 						if(discoveredInfo != null){

build/org.eclipse.cdt.managedbuilder.core/src/org/eclipse/cdt/managedbuilder/internal/dataprovider/ExternalExtensionMacroSupplier.java

@@ -149,7 +149,7 @@ public class ExternalExtensionMacroSupplier implements ICdtVariableSupplier{
 		case IBuildMacroProvider.CONTEXT_PROJECT:
 			if (contextData instanceof IManagedProject) {
 				IManagedProject project = (IManagedProject)contextData; 
-				IProjectBuildMacroSupplier supplier = project.getProjectType().getBuildMacroSupplier();
+				IProjectBuildMacroSupplier supplier = project.getProjectType() != null ? project.getProjectType().getBuildMacroSupplier() : null;
 				if(supplier == null)
 					return null;
 				return supplier.getMacro(macroName,project,new ExtensionMacroProvider(contextType, contextData));
@@ -187,7 +187,7 @@ public class ExternalExtensionMacroSupplier implements ICdtVariableSupplier{
 		case IBuildMacroProvider.CONTEXT_PROJECT:
 			if (contextData instanceof IManagedProject) {
 				IManagedProject project = (IManagedProject)contextData; 
-				IProjectBuildMacroSupplier supplier = project.getProjectType().getBuildMacroSupplier();
+				IProjectBuildMacroSupplier supplier = project.getProjectType() != null ? project.getProjectType().getBuildMacroSupplier() : null;
 				if(supplier != null)
 					macros = supplier.getMacros(project,new ExtensionMacroProvider(contextType, contextData));
 			}

build/org.eclipse.cdt.managedbuilder.ui/src/org/eclipse/cdt/managedbuilder/ui/newui/CPropertyVarsTab.java

@@ -452,7 +452,7 @@ public class CPropertyVarsTab extends AbstractCPropertyTab {
 	}
 	
 	private boolean isUserVar(ICdtVariable v) {
-		return mgr.isUserVariable(v, cfgd);
+		return cfgd != null ? mgr.isUserVariable(v, cfgd) : vars.contains(v);
 	}
 	
 	/* check whether variable is dynamic */

core/org.eclipse.cdt.core/model/org/eclipse/cdt/core/settings/model/extension/CConfigurationDataProvider.java

@@ -40,7 +40,9 @@ public abstract class CConfigurationDataProvider {
 	 * @return
 	 * @throws CoreException
 	 */
-	public abstract CConfigurationData createConfiguration(ICConfigurationDescription des, CConfigurationData base, boolean clone) throws CoreException;
+	public abstract CConfigurationData createConfiguration(ICConfigurationDescription des, 
+			ICConfigurationDescription baseDescription,
+			CConfigurationData baseData, boolean clone) throws CoreException;
 	
 	/**
 	 * called to notify the provider that the configuration is removed
@@ -60,5 +62,7 @@ public abstract class CConfigurationDataProvider {
 	 * @return
 	 * @throws CoreException
 	 */
-	public abstract CConfigurationData applyConfiguration(ICConfigurationDescription des, CConfigurationData base) throws CoreException;
+	public abstract CConfigurationData applyConfiguration(ICConfigurationDescription des, 
+			ICConfigurationDescription baseDescription,
+			CConfigurationData baseData) throws CoreException;
 }

core/org.eclipse.cdt.core/model/org/eclipse/cdt/core/settings/model/util/PathEntryTranslator.java

@@ -21,6 +21,9 @@ import java.util.Map;
 import java.util.Set;
 
 import org.eclipse.cdt.core.CCorePlugin;
+import org.eclipse.cdt.core.cdtvariables.CdtVariableException;
+import org.eclipse.cdt.core.cdtvariables.ICdtVariable;
+import org.eclipse.cdt.core.cdtvariables.ICdtVariableManager;
 import org.eclipse.cdt.core.model.CModelException;
 import org.eclipse.cdt.core.model.CoreModel;
 import org.eclipse.cdt.core.model.CoreModelUtil;
@@ -54,7 +57,11 @@ import org.eclipse.cdt.core.settings.model.extension.CFileData;
 import org.eclipse.cdt.core.settings.model.extension.CFolderData;
 import org.eclipse.cdt.core.settings.model.extension.CLanguageData;
 import org.eclipse.cdt.core.settings.model.extension.CResourceData;
+import org.eclipse.cdt.internal.core.CdtVarPathEntryVariableManager;
 import org.eclipse.cdt.internal.core.CharOperation;
+import org.eclipse.cdt.internal.core.cdtvariables.CoreVariableSubstitutor;
+import org.eclipse.cdt.internal.core.cdtvariables.DefaultVariableContextInfo;
+import org.eclipse.cdt.internal.core.cdtvariables.ICoreVariableContextInfo;
 import org.eclipse.cdt.internal.core.model.APathEntry;
 import org.eclipse.cdt.internal.core.model.CModelStatus;
 import org.eclipse.cdt.internal.core.model.PathEntry;
@@ -62,6 +69,7 @@ import org.eclipse.cdt.internal.core.settings.model.CConfigurationDescriptionCac
 import org.eclipse.cdt.internal.core.settings.model.CExternalSetting;
 import org.eclipse.cdt.internal.core.settings.model.CProjectDescriptionManager;
 import org.eclipse.cdt.internal.core.settings.model.IInternalCCfgInfo;
+import org.eclipse.cdt.utils.cdtvariables.CdtVariableResolver;
 import org.eclipse.core.resources.IContainer;
 import org.eclipse.core.resources.IFolder;
 import org.eclipse.core.resources.IProject;
@@ -112,6 +120,24 @@ public class PathEntryTranslator {
 	private Map fResourceMap = new HashMap();
 	private IWorkspaceRoot fRoot = ResourcesPlugin.getWorkspace().getRoot();
 	
+	
+	private static class VarSubstitutor extends CoreVariableSubstitutor {
+		ICConfigurationDescription fCfg;
+		ICdtVariableManager fMngr = CCorePlugin.getDefault().getCdtVariableManager();
+		
+		public VarSubstitutor(ICConfigurationDescription cfg) {
+			super(new DefaultVariableContextInfo(ICoreVariableContextInfo.CONTEXT_CONFIGURATION, cfg), "", " ");  //$NON-NLS-1$  //$NON-NLS-2$
+			fCfg = cfg;
+		}
+
+		protected ResolvedMacro resolveMacro(ICdtVariable macro)
+				throws CdtVariableException {
+			if(!CdtVarPathEntryVariableManager.isPathEntryVariable(macro, fCfg, fMngr))
+				return super.resolveMacro(macro);
+			return new ResolvedMacro(macro.getName(), CdtVariableResolver.createVariableReference(macro.getName()));
+		}
+	}
+
 	public static final class ReferenceSettingsInfo{
 		private IPath[] fRefProjPaths;
 		private ICExternalSetting[] fExtSettings;
@@ -390,7 +416,7 @@ public class PathEntryTranslator {
 				}
 				
 				if(path != null){
-					return new CLibraryFileEntry(path, flags);
+					return new CLibraryFileEntry(value.getName(), flags);
 				}
 				break;
 			}
@@ -407,7 +433,7 @@ public class PathEntryTranslator {
 				}
 				
 				if(path != null){
-					return new CIncludePathEntry(path, flags);
+					return new CIncludePathEntry(value.getName(), flags);
 				}
 				break;
 			}
@@ -431,7 +457,7 @@ public class PathEntryTranslator {
 				}
 				
 				if(path != null){
-					return new CIncludeFileEntry(path, flags);
+					return new CIncludeFileEntry(value.getName(), flags);
 				}
 				break;
 			}
@@ -444,7 +470,7 @@ public class PathEntryTranslator {
 				}
 				
 				if(path != null){
-					return new CMacroFileEntry(path, flags);
+					return new CMacroFileEntry(value.getName(), flags);
 				}
 				break;
 			}
@@ -563,6 +589,9 @@ public class PathEntryTranslator {
 					
 					basePath = mngr.resolvePath(basePath);
 					valuePath = mngr.resolvePath(valuePath);
+
+					fName = unresolvedBase.append(unresolvedValue).toString();
+					fValue = fName;
 					
 					if (!basePath.isEmpty()) {
 						IPath loc = basePath;
@@ -580,8 +609,6 @@ public class PathEntryTranslator {
 							}
 						}
 						fLocation = loc.append(valuePath);
-						fName = unresolvedBase.append(unresolvedValue).toString();
-						fValue = fName;
 //						fName = fValuePath.toString();
 //						fValue = fValuePath.toString();
 						break;
@@ -604,11 +631,12 @@ public class PathEntryTranslator {
 								fResourceInfo = rcInfo;
 //								fFullPath = fResourceInfo.fRc.getFullPath();
 //								fLocation = fResourceInfo.fRc.getLocation();
+								break;
 							}
 						}
-					} else {
-						fLocation = valuePath;
 					}
+					
+					fLocation = valuePath;
 				}while(false);
 			}
 		}
@@ -722,27 +750,30 @@ public class PathEntryTranslator {
 		private Set fFiltersSet;
 		private boolean fIsExported;
 		private IProject fProject;
+		private ICConfigurationDescription fCfg;
 
-		PathEntryComposer(String projName, IProject project){
+		PathEntryComposer(String projName, IProject project, ICConfigurationDescription cfg){
-			this(new Path(projName).makeAbsolute(), project);
+			this(new Path(projName).makeAbsolute(), project, cfg);
 		}
 
-		PathEntryComposer(IPath path, IProject project){
+		PathEntryComposer(IPath path, IProject project, ICConfigurationDescription cfg){
 			fPath = toProjectPath(path);
 			fProject = project;
+			fCfg = cfg;
 		}
 
 		private static IPath toProjectPath(IPath path){
 			if(path.segmentCount() > 1)
 				path = new Path(path.segment(0));
-			
+
 			return path.makeAbsolute();
 		}
 
-		PathEntryComposer(ICExclusionPatternPathEntry entry, IProject project){
+		PathEntryComposer(ICExclusionPatternPathEntry entry, IProject project, ICConfigurationDescription cfg){
 			fPath = new Path(entry.getValue());
 			fLangEntry = entry;
 			fProject = project;
+			fCfg = cfg;
 			IPath[] exclusions = entry.getExclusionPatterns();
 			if(exclusions.length != 0){
 				fFiltersSet = new HashSet(exclusions.length);
@@ -750,11 +781,12 @@ public class PathEntryTranslator {
 			}
 		}
 
-		PathEntryComposer(IPath path, ICLanguageSettingEntry entry, boolean exported, IProject project){
+		PathEntryComposer(IPath path, ICLanguageSettingEntry entry, boolean exported, IProject project, ICConfigurationDescription cfg){
 			fPath = path;
 			fLangEntry = entry;
 			fIsExported = exported;
 			fProject = project;
+			fCfg = cfg;
 		}
 		
 		public void addFilter(IPath path){
@@ -778,32 +810,48 @@ public class PathEntryTranslator {
 			return new IPath[0];
 		}
 
-		private IPath[] getEntryPath(ICSettingEntry entry){
+		private IPath[] getEntryPath(ICSettingEntry entry, ICConfigurationDescription cfg){
-			return valueToEntryPath(entry.getName(), (entry.getFlags() & ICSettingEntry.VALUE_WORKSPACE_PATH) != 0);
+			return valueToEntryPath(entry.getName(), (entry.getFlags() & ICSettingEntry.VALUE_WORKSPACE_PATH) != 0, cfg);
 		}
 
-		private IPath[] valueToEntryPath(String value, boolean isWsp){
+		private IPath[] valueToEntryPath(String value, boolean isWsp, ICConfigurationDescription cfg){
-			IPath path = new Path(value);
+			String pathVarValue = resolveKeepingPathEntryFars(value, cfg);
+			String resolvedValue = resolveAll(value, cfg);
+			IPath resolvedPath = new Path(resolvedValue);
+			IPath pathVarPath = new Path(pathVarValue);
 			IPath result[] = new IPath[2];
 			if(isWsp){
-				if(!path.isAbsolute()){
+				if(!resolvedPath.isAbsolute()){
 					result[0] = fProject.getFullPath().makeRelative();
-					result[1] = path;
+					result[1] = pathVarPath;
-					path = fProject.getFullPath().append(path);
+//					path = fProject.getFullPath().append(path);
 				} else {
-					if(path.segmentCount() != 0){
+					if(resolvedPath.segmentCount() != 0){
-						result[0] = new Path(path.segment(0));
+						String projName = resolvedPath.segment(0);
-						result[1] = path.removeFirstSegments(1).makeRelative();
+						IPath valuePath = resolvedPath.removeFirstSegments(1).makeRelative();
+						if(pathVarPath.segmentCount() != 0){
+							String resolvedProjName = projName;
+							String varProjName = pathVarPath.segment(0);
+							IPath resolvedProjPath = CCorePlugin.getDefault().getPathEntryVariableManager().resolvePath(new Path(varProjName));
+							if(resolvedProjPath.segmentCount() == 1 && resolvedProjName.equals(resolvedProjPath.segment(0))){
+								projName = varProjName;
+								valuePath = pathVarPath.removeFirstSegments(1).makeRelative();
+							}
+						}
+						
+						
+						result[0] = new Path(projName);
+						result[1] = valuePath;
 					}
 				}
 //				path = path.makeRelative();
 			} else {
-				if(!path.isAbsolute()){
+				if(!resolvedPath.isAbsolute()){
 					IPath location = fProject.getLocation();
 					if(location != null)
-						path = location.append(path);
+						pathVarPath = location.append(pathVarPath);
 				}
-				result[1] = path;
+				result[1] = pathVarPath;
 			}
 			
 			return result;
@@ -813,24 +861,24 @@ public class PathEntryTranslator {
 			if(fLangEntry != null){
 				switch(fLangEntry.getKind()){
 				case ICLanguageSettingEntry.INCLUDE_FILE:{
-						IPath paths[] = getEntryPath(fLangEntry);
+						IPath paths[] = getEntryPath(fLangEntry, fCfg);
 						return CoreModel.newIncludeFileEntry(fPath, null, paths[0], paths[1], getExclusionPatterns(), fIsExported);
 					}
 				case ICLanguageSettingEntry.INCLUDE_PATH:{
-						IPath paths[] = getEntryPath(fLangEntry);
+						IPath paths[] = getEntryPath(fLangEntry, fCfg);
 						ICIncludePathEntry ipe = (ICIncludePathEntry)fLangEntry;
 						return CoreModel.newIncludeEntry(fPath, paths[0], paths[1], !ipe.isLocal(), getExclusionPatterns(), fIsExported);
 					}
 				case ICLanguageSettingEntry.MACRO:
 					return CoreModel.newMacroEntry(fPath, fLangEntry.getName(), fLangEntry.getValue(), getExclusionPatterns(), fIsExported);
 				case ICLanguageSettingEntry.MACRO_FILE:{
-						IPath paths[] = getEntryPath(fLangEntry);
+						IPath paths[] = getEntryPath(fLangEntry, fCfg);
 						return CoreModel.newMacroFileEntry(fPath, paths[0], null, paths[1], getExclusionPatterns(), fIsExported);
 					}
 				case ICLanguageSettingEntry.LIBRARY_PATH:
 					return null;
 				case ICLanguageSettingEntry.LIBRARY_FILE:{
-						IPath paths[] = getEntryPath(fLangEntry);
+						IPath paths[] = getEntryPath(fLangEntry, fCfg);
 						return CoreModel.newLibraryEntry(fPath, paths[0], paths[1], null, null, null, fIsExported);
 					}
 				case ICLanguageSettingEntry.OUTPUT_PATH:
@@ -847,29 +895,52 @@ public class PathEntryTranslator {
 		}
 	}
 	
+	private static String resolveAll(String value, ICConfigurationDescription cfg){
+		try {
+			return CCorePlugin.getDefault().getCdtVariableManager().resolveValue(value, "", " ", cfg);
+		} catch (CdtVariableException e) {
+			CCorePlugin.log(e);
+		}
+		return value;
+	}
+
+	private static String resolveKeepingPathEntryFars(String value, ICConfigurationDescription cfg){
+		try {
+			VarSubstitutor substitutor = new VarSubstitutor(cfg);
+			
+			return CdtVariableResolver.resolveToString(value, substitutor);
+		} catch (CdtVariableException e) {
+			CCorePlugin.log(e);
+		}
+		return value;
+	}
+
 	public static class PathEntryCollector {
 		private PathSettingsContainer fStorage;
 		private KindBasedStore fStore;
 		private LinkedHashMap fRefProjMap;
 		private IProject fProject;
+		private ICConfigurationDescription fCfg;
 		
-		private PathEntryCollector(IProject project){
+		private PathEntryCollector(IProject project, ICConfigurationDescription cfg){
 			fStorage = PathSettingsContainer.createRootContainer();
 			fStorage.setValue(this);
 			fStore = new KindBasedStore(false);
+			fCfg = cfg;
 			fProject = project;
 		}
 
-		private PathEntryCollector(PathSettingsContainer container, KindBasedStore store, IProject project){
+		private PathEntryCollector(PathSettingsContainer container, KindBasedStore store, IProject project, ICConfigurationDescription cfg){
 			fStorage = container;
 			fStore = store;
+			fCfg = cfg;
 			fProject = project;
 		}
 
 		public void setSourceOutputEntries(int kind, ICExclusionPatternPathEntry entries[]){
 			Map map = getEntriesMap(kind, true);
 			for(int i = 0; i < entries.length; i++){
-				map.put(entries[i], new PathEntryComposer(entries[i], fProject));
+				map.put(entries[i], new PathEntryComposer(entries[i], fProject, fCfg));
 			}
 		}
 		
@@ -879,7 +950,7 @@ public class PathEntryTranslator {
 			else {
 				fRefProjMap = new LinkedHashMap();
 				for(int i = 0; i < paths.length; i++){
-					PathEntryComposer cs = new PathEntryComposer(paths[i], fProject);
+					PathEntryComposer cs = new PathEntryComposer(paths[i], fProject, fCfg);
 					IPath path = cs.getPath();
 					fRefProjMap.put(path, cs);
 				}
@@ -906,7 +977,7 @@ public class PathEntryTranslator {
 					info[i].setInfo((LinkedHashMap)map.clone());
 				}
 			}
-			PathEntryCollector newCr = new PathEntryCollector(newContainer, cloneStore, fProject);
+			PathEntryCollector newCr = new PathEntryCollector(newContainer, cloneStore, fProject, fCfg);
 			newContainer.setValue(newCr);
 			return newCr;
 		}
@@ -944,7 +1015,7 @@ public class PathEntryTranslator {
 						continue;
 
 					ICLanguageSettingEntry entry = entries[i];
-					map.put(entry, new PathEntryComposer(fullPath, entry, exportedEntries.contains(entry), fProject));
+					map.put(entry, new PathEntryComposer(fullPath, entry, exportedEntries.contains(entry), fProject, fCfg));
 				}
 			}
 		}
@@ -2157,13 +2228,13 @@ public class PathEntryTranslator {
 		CConfigurationData data = des instanceof CConfigurationDescriptionCache ? 
 				(CConfigurationData)des : ((IInternalCCfgInfo)des).getConfigurationData(false);
 				
-		ReferenceSettingsInfo info = new ReferenceSettingsInfo(des);
+		ReferenceSettingsInfo refInfo = new ReferenceSettingsInfo(des);
 		
-		return collectEntries(project, data, info);
+//		return collectEntries(project, data, info);
-	}
+//	}
-
+//
-	public static PathEntryCollector collectEntries(IProject project, CConfigurationData data, ReferenceSettingsInfo refInfo){
+//	public static PathEntryCollector collectEntries(IProject project, CConfigurationData data, ReferenceSettingsInfo refInfo){
-		final PathEntryCollector cr = new PathEntryCollector(project);
+		final PathEntryCollector cr = new PathEntryCollector(project, des);
 		PathSettingsContainer rcDatas = createRcDataHolder(data);
 		IPath srcPaths[] = data.getSourcePaths();
 		ICSourceEntry sEntries[] = calculateSourceEntriesFromPaths(project, rcDatas, srcPaths);
@@ -2250,8 +2321,9 @@ public class PathEntryTranslator {
 		return false;
 	}
 
-	public static IPathEntry[] getPathEntries(IProject project, CConfigurationData data, ReferenceSettingsInfo refInfo, int flags){
+//	public static IPathEntry[] getPathEntries(IProject project, CConfigurationData data, ReferenceSettingsInfo refInfo, int flags){
-		PathEntryCollector cr = collectEntries(project, data, refInfo);
+	public static IPathEntry[] getPathEntries(IProject project, ICConfigurationDescription cfg, int flags){
+		PathEntryCollector cr = collectEntries(project, cfg);
 		return cr.getEntries(flags);
 	}
 //	

core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CConfigurationDescription.java

@@ -41,7 +41,6 @@ import org.eclipse.cdt.core.settings.model.extension.CFolderData;
 import org.eclipse.cdt.core.settings.model.extension.CLanguageData;
 import org.eclipse.cdt.core.settings.model.extension.CResourceData;
 import org.eclipse.cdt.core.settings.model.extension.CTargetPlatformData;
-import org.eclipse.cdt.core.settings.model.extension.impl.CDefaultConfigurationData;
 import org.eclipse.cdt.core.settings.model.util.PathSettingsContainer;
 import org.eclipse.core.resources.IProject;
 import org.eclipse.core.resources.IResource;
@@ -99,7 +98,7 @@ public class CConfigurationDescription extends CDataProxyContainer implements IC
 		if(baseData instanceof CConfigurationDescriptionCache){
 			baseData = ((CConfigurationDescriptionCache)baseData).getConfigurationData();
 		}
-		setData(CProjectDescriptionManager.getInstance().createData(this, baseData, false));
+		setData(CProjectDescriptionManager.getInstance().createData(this, base, baseData, false));
 	}
 
 	/*
@@ -138,8 +137,9 @@ public class CConfigurationDescription extends CDataProxyContainer implements IC
 	void doWritable() throws CoreException{
 		CConfigurationData data = getConfigurationData(false);
 		if(data instanceof CConfigurationDescriptionCache){
-			data = ((CConfigurationDescriptionCache)data).getConfigurationData();
+			CConfigurationDescriptionCache cache = (CConfigurationDescriptionCache)data;
-			setData(CProjectDescriptionManager.getInstance().createData(this, data, true));
+			data = cache.getConfigurationData();
+			setData(CProjectDescriptionManager.getInstance().createData(this, cache, data, true));
 		}
 	}
 	

core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CConfigurationDescriptionCache.java

@@ -89,7 +89,7 @@ public class CConfigurationDescriptionCache extends CDefaultConfigurationData
 		fInitializing = false;
 	}
 
-	CConfigurationDescriptionCache(CConfigurationData base, CConfigurationSpecSettings settingsBase, CProjectDescription parent, ICStorageElement rootEl, boolean saving) throws CoreException {
+	CConfigurationDescriptionCache(ICConfigurationDescription baseDescription, CConfigurationData base, CConfigurationSpecSettings settingsBase, CProjectDescription parent, ICStorageElement rootEl, boolean saving) throws CoreException {
 		super(base.getId(), base.getName(), null);
 		fInitializing = true;
 		fParent = parent;
@@ -97,9 +97,10 @@ public class CConfigurationDescriptionCache extends CDefaultConfigurationData
 		
 		if(base instanceof CConfigurationDescriptionCache){
 			fData = ((CConfigurationDescriptionCache)base).getConfigurationData();
-			fData = CProjectDescriptionManager.getInstance().applyData(this, fData);
+			fData = CProjectDescriptionManager.getInstance().applyData(this, baseDescription, fData);
 		} else {
-			base = CProjectDescriptionManager.getInstance().applyData(this, base);
+			fData = base;
+			base = CProjectDescriptionManager.getInstance().applyData(this, baseDescription, base);
 			fData = base;
 		} 
 		fDataLoadded = true;

core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CProjectDescription.java

@@ -108,7 +108,7 @@ public class CProjectDescription implements ICProjectDescription, ICDataProxyCon
 					if(baseData instanceof CConfigurationDescriptionCache){
 						baseData = ((CConfigurationDescriptionCache)baseData).getConfigurationData();
 					}
-					CConfigurationDescriptionCache cache = new CConfigurationDescriptionCache(baseData, cfgDes.getSpecSettings(), this, null, saving);
+					CConfigurationDescriptionCache cache = new CConfigurationDescriptionCache((ICConfigurationDescription)cfgDes, baseData, cfgDes.getSpecSettings(), this, null, saving);
 					configurationCreated(cache);
 				} else {
 					CConfigurationData baseData = cfgDes.getConfigurationData(false);

core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CProjectDescriptionManager.java

@@ -149,6 +149,7 @@ public class CProjectDescriptionManager {
 	private static final String DEFAULT_CFG_NAME = "Configuration"; //$NON-NLS-1$
 	
 	private static final QualifiedName SCANNER_INFO_PROVIDER_PROPERTY = new QualifiedName(CCorePlugin.PLUGIN_ID, "scannerInfoProvider"); //$NON-NLS-1$
+	private static final QualifiedName LOAD_FLAG = new QualifiedName(CCorePlugin.PLUGIN_ID, "descriptionLoadded"); //$NON-NLS-1$
 
 	private class CompositeSafeRunnable implements ISafeRunnable {
 		private List fRunnables = new ArrayList();
@@ -376,7 +377,7 @@ public class CProjectDescriptionManager {
 			}
 	
 			if(des != null){
-				if(setLoaddedDescription(project, des, false)){
+				if(setLoaddedDescriptionOnLoad(project, des)){
 
 					if(eDes != null)
 						saveConversion(project, eDes, (CProjectDescription)des, new NullProgressMonitor());
@@ -414,6 +415,18 @@ public class CProjectDescriptionManager {
 		return des;
 	}
 	
+	private synchronized boolean setLoaddedDescriptionOnLoad(IProject project, ICProjectDescription des){
+		des.setSessionProperty(LOAD_FLAG, Boolean.TRUE);
+		ICProjectDescription oldDes = getLoaddedDescription(project);
+
+		setLoaddedDescription(project, des, true);
+
+		if(oldDes == null)
+			return true;
+
+		return oldDes.getSessionProperty(LOAD_FLAG) == null;
+	}
+
 	private CProjectDescriptionEvent createLoaddedEvent(ICProjectDescription des){
 		return new CProjectDescriptionEvent(CProjectDescriptionEvent.LOADDED,
 				null,
@@ -1304,9 +1317,9 @@ public class CProjectDescriptionManager {
 		return provider.loadConfiguration(des);
 	}
 	
-	CConfigurationData applyData(ICConfigurationDescription des, CConfigurationData base) throws CoreException {
+	CConfigurationData applyData(ICConfigurationDescription des, ICConfigurationDescription baseDescription, CConfigurationData base) throws CoreException {
 		CConfigurationDataProvider provider = getProvider(des);
-		return provider.applyConfiguration(des, base);
+		return provider.applyConfiguration(des, baseDescription, base);
 	}
 	
 	void removeData(ICConfigurationDescription des, CConfigurationData data) throws CoreException{
@@ -1314,9 +1327,9 @@ public class CProjectDescriptionManager {
 		provider.removeConfiguration(des, data);
 	}
 	
-	CConfigurationData createData(ICConfigurationDescription des, CConfigurationData base, boolean clone) throws CoreException{
+	CConfigurationData createData(ICConfigurationDescription des, ICConfigurationDescription baseDescription, CConfigurationData base, boolean clone) throws CoreException{
 		CConfigurationDataProvider provider = getProvider(des);
-		return provider.createConfiguration(des, base, clone);
+		return provider.createConfiguration(des, baseDescription, base, clone);
 	}
 	
 	private CConfigurationDataProvider getProvider(ICConfigurationDescription des) throws CoreException{
@@ -2583,7 +2596,7 @@ public class CProjectDescriptionManager {
 		rootParent.removeChild(rootEl);
 		ICStorageElement baseRootEl = settings.getRootStorageElement();
 		rootEl = rootParent.importChild(baseRootEl);
-		CConfigurationDescriptionCache cache = new CConfigurationDescriptionCache(baseData, cfgDes.getSpecSettings(), null, rootEl, true);
+		CConfigurationDescriptionCache cache = new CConfigurationDescriptionCache(des, baseData, cfgDes.getSpecSettings(), null, rootEl, true);
 		
 		return cache;
 	}

core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/DefaultConfigurationDataProvider.java

@@ -20,14 +20,18 @@ public class DefaultConfigurationDataProvider extends
 		CConfigurationDataProvider {
 
 	public CConfigurationData applyConfiguration(
-			ICConfigurationDescription des, CConfigurationData base)
+			ICConfigurationDescription des, 
+			ICConfigurationDescription baseDescription,
+			CConfigurationData base)
 			throws CoreException {
 		//TODO: implement load/store
 		return base;
 	}
 
 	public CConfigurationData createConfiguration(
-			ICConfigurationDescription des, CConfigurationData base,
+			ICConfigurationDescription des, 
+			ICConfigurationDescription baseDescription,
+			CConfigurationData base,
 			boolean clone) throws CoreException {
 		//TODO: implement load/store
 		CDefaultConfigurationData data = new CDefaultConfigurationData(des.getId(), des.getName(), base, null, clone);

core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/PathEntryConfigurationDataProvider.java

@@ -12,9 +12,7 @@ package org.eclipse.cdt.internal.core.settings.model;
 
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.HashMap;
 import java.util.List;
-import java.util.Map;
 
 import org.eclipse.cdt.core.model.ICProject;
 import org.eclipse.cdt.core.model.IPathEntry;
@@ -220,7 +218,9 @@ public class PathEntryConfigurationDataProvider extends
 	}
 	
 	public CConfigurationData applyConfiguration(
-			ICConfigurationDescription des, CConfigurationData base)
+			ICConfigurationDescription des,
+			ICConfigurationDescription baseDescription,
+			CConfigurationData base)
 			throws CoreException {
 		//TODO: check external/reference info here as well.
 		if(!fFactory.isModified(base))
@@ -229,8 +229,8 @@ public class PathEntryConfigurationDataProvider extends
 		
 		
 		IProject project = des.getProjectDescription().getProject();
-		ReferenceSettingsInfo refInfo = new ReferenceSettingsInfo(des);
+//		ReferenceSettingsInfo refInfo = new ReferenceSettingsInfo(des);
-		IPathEntry entries[] = PathEntryTranslator.getPathEntries(project, base, refInfo, PathEntryTranslator.INCLUDE_USER);
+		IPathEntry entries[] = PathEntryTranslator.getPathEntries(project, baseDescription, PathEntryTranslator.INCLUDE_USER);
 		CModelManager manager = CModelManager.getDefault();
 		ICProject cproject = manager.create(project);
 		IPathEntry[] curRawEntries = PathEntryManager.getDefault().getRawPathEntries(cproject);
@@ -249,7 +249,9 @@ public class PathEntryConfigurationDataProvider extends
 	}
 
 	public CConfigurationData createConfiguration(
-			ICConfigurationDescription des, CConfigurationData base,
+			ICConfigurationDescription des, 
+			ICConfigurationDescription baseDescription,
+			CConfigurationData base,
 			boolean clone) throws CoreException {
 		CfgData copy = new CfgData(des.getId(), des.getName(), base, clone);
 		copy.setModified(false);

core/org.eclipse.cdt.core/src/org/eclipse/cdt/internal/core/CdtVarPathEntryVariableManager.java

@@ -19,9 +19,11 @@ import java.util.Set;
 import org.eclipse.cdt.core.CCorePlugin;
 import org.eclipse.cdt.core.cdtvariables.CdtVariableException;
 import org.eclipse.cdt.core.cdtvariables.ICdtVariable;
+import org.eclipse.cdt.core.cdtvariables.ICdtVariableManager;
 import org.eclipse.cdt.core.resources.IPathEntryVariableChangeListener;
 import org.eclipse.cdt.core.resources.IPathEntryVariableManager;
 import org.eclipse.cdt.core.resources.PathEntryVariableChangeEvent;
+import org.eclipse.cdt.core.settings.model.ICConfigurationDescription;
 import org.eclipse.cdt.internal.core.cdtvariables.ICdtVariableChangeListener;
 import org.eclipse.cdt.internal.core.cdtvariables.ICoreVariableContextInfo;
 import org.eclipse.cdt.internal.core.cdtvariables.UserDefinedVariableSupplier;
@@ -129,6 +131,23 @@ public class CdtVarPathEntryVariableManager implements
 		return null;
 	}
 
+	public static boolean isPathEntryVariable(ICdtVariable var, ICConfigurationDescription cfg){
+		return isPathEntryVariable(var, cfg, CCorePlugin.getDefault().getCdtVariableManager());
+	}
+
+	public static boolean isPathEntryVariable(ICdtVariable var, ICConfigurationDescription cfg, ICdtVariableManager mngr){
+		if(mngr.isUserVariable(var, cfg))
+			return false;
+		
+		if(!mngr.isUserVariable(var, null))
+			return false;
+		
+		if(getVariablePath(var) == null)
+			return false;
+		
+		return true;
+	}
+
 	public String[] getVariableNames() {
 		ICdtVariable[] vars = fUserVarSupplier.getMacros(ICoreVariableContextInfo.CONTEXT_WORKSPACE, null);
 		ArrayList list = new ArrayList();

core/org.eclipse.cdt.core/src/org/eclipse/cdt/internal/core/cdtvariables/BuildSystemVariableSupplier.java

@@ -17,7 +17,16 @@ import org.eclipse.cdt.utils.cdtvariables.IVariableContextInfo;
 import org.eclipse.cdt.utils.cdtvariables.SupplierBasedCdtVariableManager;
 
 public class BuildSystemVariableSupplier extends CoreMacroSupplierBase {
-
+	private static BuildSystemVariableSupplier fInstance;
+	private BuildSystemVariableSupplier(){
+	}
+	
+	public static BuildSystemVariableSupplier getInstance(){
+		if(fInstance == null){
+			fInstance = new BuildSystemVariableSupplier();
+		}
+		return fInstance;
+	}
 	private class ExtensionMacroProvider extends CdtVariableManager{
 		private IVariableContextInfo fStartInfo;
 		private int fContextType;

core/org.eclipse.cdt.core/src/org/eclipse/cdt/internal/core/cdtvariables/CdtVariableManager.java

@@ -31,6 +31,7 @@ public class CdtVariableManager implements ICdtVariableManager {
 	static private CdtVariableManager fDefault;
 	
 	public static UserDefinedVariableSupplier fUserDefinedMacroSupplier = UserDefinedVariableSupplier.getInstance();
+	public static BuildSystemVariableSupplier fBuildSystemVariableSupplier = BuildSystemVariableSupplier.getInstance();
 	public static EnvironmentVariableSupplier fEnvironmentMacroSupplier = EnvironmentVariableSupplier.getInstance();
 	public static CdtMacroSupplier fCdtMacroSupplier = CdtMacroSupplier.getInstance();
 	public static EclipseVariablesVariableSupplier fEclipseVariablesMacroSupplier = EclipseVariablesVariableSupplier.getInstance();
@@ -199,6 +200,12 @@ public class CdtVariableManager implements ICdtVariableManager {
 
 	public boolean isUserVariable(ICdtVariable variable,
 			ICConfigurationDescription cfg) {
-		return variable instanceof StorableCdtVariable;
+		if(!(variable instanceof StorableCdtVariable))
+			return false;
+		
+		if(cfg != null)
+			return UserDefinedVariableSupplier.getInstance().containsVariable(ICoreVariableContextInfo.CONTEXT_CONFIGURATION, cfg, variable);
+		
+		return UserDefinedVariableSupplier.getInstance().containsVariable(ICoreVariableContextInfo.CONTEXT_WORKSPACE, null, variable);
 	}
 }

core/org.eclipse.cdt.core/src/org/eclipse/cdt/internal/core/cdtvariables/DefaultVariableContextInfo.java

@@ -44,6 +44,7 @@ public class DefaultVariableContextInfo implements ICoreVariableContextInfo {
 			if(data instanceof ICConfigurationDescription){
 				return new ICdtVariableSupplier[]{
 						CdtVariableManager.fUserDefinedMacroSupplier,
+						CdtVariableManager.fBuildSystemVariableSupplier,
 						CdtVariableManager.fEnvironmentMacroSupplier,
 						CdtVariableManager.fCdtMacroSupplier
 				};

core/org.eclipse.cdt.core/src/org/eclipse/cdt/internal/core/cdtvariables/StorableCdtVariables.java

@@ -18,6 +18,7 @@ import java.util.Map;
 import org.eclipse.cdt.core.cdtvariables.CdtVariableException;
 import org.eclipse.cdt.core.cdtvariables.ICdtVariable;
 import org.eclipse.cdt.core.settings.model.ICStorageElement;
+import org.eclipse.cdt.internal.core.cdtvariables.UserDefinedVariableSupplier.VarKey;
 import org.eclipse.cdt.internal.core.settings.model.ExceptionFactory;
 import org.eclipse.cdt.utils.cdtvariables.CdtVariableResolver;
 
@@ -375,4 +376,16 @@ public class StorableCdtVariables {
 		}
 		return false;
 	}
+	
+	public boolean contains(ICdtVariable var){
+		ICdtVariable curVar = getMacro(var.getName());
+		if(curVar == null)
+			return false;
+		
+		if(new VarKey(curVar, false).equals(new VarKey(var, false)))
+			return true;
+		
+		return false;
+
+	}
 }

core/org.eclipse.cdt.core/src/org/eclipse/cdt/internal/core/cdtvariables/UserDefinedVariableSupplier.java

@@ -268,7 +268,7 @@ public class UserDefinedVariableSupplier extends CoreMacroSupplierBase {
 		}
 	}
 	
-	private static class VarKey {
+	static class VarKey {
 		private ICdtVariable fVar;
 		private boolean fNameOnly;
 		
@@ -484,7 +484,7 @@ public class UserDefinedVariableSupplier extends CoreMacroSupplierBase {
 		StorableCdtVariables macros = loadNewStileWorkspaceMacros();
 		
 		//now load PathEntry Variables from preferences
-		
+		loadPathEntryVariables(macros);
 		
 		return macros;
 	}
@@ -672,4 +672,15 @@ public class UserDefinedVariableSupplier extends CoreMacroSupplierBase {
 		}
 	}
 	
+	public boolean containsVariable(int context, Object data, ICdtVariable var){
+		ICdtVariable varContained = getMacro(var.getName(), context, data);
+		if(varContained == null)
+			return false;
+		
+		if(new VarKey(varContained, false).equals(new VarKey(var, false)))
+			return true;
+		
+		return false;
+	}
+	
 }