1. fix for [Bug 187822] Problem with setRawPathEntries

2.backward compatibility fixes
3. source/output entries fixes

build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/managedbuilder/core/tests/BuildDescriptionModelTests.java

@@ -1104,7 +1104,10 @@ public class BuildDescriptionModelTests extends TestCase {
 		//in this the build system is initiating the core settings update (ICProjectDescription cache refresh)
 		//the refresh is scheduled as a job, so in case we do not wait here the job may not be completed by the time
 		//the test is run
-
+		try {
+			Thread.sleep(10000);
+		} catch (InterruptedException e) {
+		}
 		
 		CCorePlugin.getIndexManager().joinIndexer(-1, new NullProgressMonitor());
 

build/org.eclipse.cdt.managedbuilder.core.tests/tests/org/eclipse/cdt/projectmodel/tests/ProjectModelTests.java

@@ -336,7 +336,11 @@ public class ProjectModelTests extends TestCase implements IElementChangedListen
 		project.delete(false, true, new NullProgressMonitor());
 		
 		project = root.getProject(projectName);
+		assertFalse(project.exists());
+		assertFalse(project.isOpen());
 		des = coreModel.getProjectDescription(project);
+		assertFalse(project.exists());
+		assertFalse(project.isOpen());
 		assertNull("project description is not null for removed project", des);
 		
 		project = createProject(projectName);
@@ -376,6 +380,8 @@ public class ProjectModelTests extends TestCase implements IElementChangedListen
 		project.delete(false, true, new NullProgressMonitor());
 		
 		project = root.getProject(projectName);
+		assertFalse(project.exists());
+		assertFalse(project.isOpen());
 		des = coreModel.getProjectDescription(project);
 		assertNull("project description is not null for removed project", des);
 		

core/org.eclipse.cdt.core.tests/model/org/eclipse/cdt/core/settings/model/BackwardCompatibilityTests.java

@@ -10,6 +10,12 @@
  *******************************************************************************/
 package org.eclipse.cdt.core.settings.model;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
 import junit.framework.TestSuite;
 
 import org.eclipse.cdt.core.dom.IPDOMManager;
@@ -20,11 +26,12 @@ import org.eclipse.cdt.core.testplugin.CProjectHelper;
 import org.eclipse.cdt.core.testplugin.util.BaseTestCase;
 import org.eclipse.core.resources.IProject;
 import org.eclipse.core.runtime.CoreException;
+import org.eclipse.core.runtime.IPath;
 import org.eclipse.core.runtime.Path;
 
 public class BackwardCompatibilityTests extends BaseTestCase {
 	private static final String PROJ_NAME_PREFIX = "BackwardCompatibilityTests_";
-	ICProject p1;
+	ICProject p1, p2;
 	
 	public static TestSuite suite() {
 		return suite(BackwardCompatibilityTests.class, "_");
@@ -54,7 +61,6 @@ public class BackwardCompatibilityTests extends BaseTestCase {
 			CoreModel.newSourceEntry(project.getFullPath()),
 			CoreModel.newOutputEntry(project.getFullPath()),
 		};
-		assertEquals(expectedRawEntries.length, entries.length);
 		checkEntriesMatch(expectedRawEntries, entries);
 		
 		IPathEntry[] expectedResolvedEntries = new IPathEntry[]{
@@ -67,7 +73,6 @@ public class BackwardCompatibilityTests extends BaseTestCase {
 			CoreModel.newIncludeEntry(project.getFullPath(), project.getFullPath().makeRelative(), new Path("g/h/i")),
 			CoreModel.newIncludeEntry(project.getFullPath(), new Path("j"), new Path("k/l")),
 		};
-		assertEquals(expectedResolvedEntries.length, resolvedentries.length);
 		checkEntriesMatch(expectedResolvedEntries, resolvedentries);
 
 		IPathEntry[] newEntries = new IPathEntry[entries.length + 1];
@@ -81,7 +86,6 @@ public class BackwardCompatibilityTests extends BaseTestCase {
 		CoreModel.setRawPathEntries(p1, newEntries, null);
 		
 		entries = CoreModel.getRawPathEntries(p1);
-		assertEquals(newExpectedRawEntries.length, entries.length);
 		checkEntriesMatch(entries, newExpectedRawEntries);
 		
 		IPathEntry[] newExpectedResolved = new IPathEntry[resolvedentries.length + 1];
@@ -89,9 +93,125 @@ public class BackwardCompatibilityTests extends BaseTestCase {
 		newExpectedResolved[resolvedentries.length] = CoreModel.newIncludeEntry(project.getFullPath().append("d"), null, new Path("/C/d/e"), true, new Path[]{new Path("a"), new Path("b")}, false);
 		resolvedentries = CoreModel.getResolvedPathEntries(p1);
 		checkEntriesMatch(resolvedentries, newExpectedResolved);
+		
+		entries = concatEntries(entries, new IPathEntry[]{
+		       CoreModel.newSourceEntry(project.getFullPath().append("test_src")),
+		       CoreModel.newOutputEntry(project.getFullPath().append("test_out")),});
+		
+		newExpectedRawEntries = concatEntries(newExpectedRawEntries, new IPathEntry[]{
+		       CoreModel.newSourceEntry(project.getFullPath().append("test_src")),
+		       CoreModel.newOutputEntry(project.getFullPath().append("test_out")),});
+		
+		for(int i = 0; i < newExpectedRawEntries.length; i++){
+			IPathEntry entry = newExpectedRawEntries[i];
+			if(entry.getEntryKind() == IPathEntry.CDT_SOURCE && entry.getPath().equals(project.getFullPath())){
+				newExpectedRawEntries[i] = CoreModel.newSourceEntry(project.getFullPath(), new Path[]{new Path("test_src")});
+			}
+//			if(entry.getEntryKind() == IPathEntry.CDT_OUTPUT && entry.getPath().equals(project.getFullPath())){
+//				newExpectedRawEntries[i] = CoreModel.newOutputEntry(project.getFullPath(), new Path[]{new Path("test_out")});
+//			}
 		}
 		
-	private void checkEntriesMatch(IPathEntry[] e1, IPathEntry[] e2){
+		newExpectedResolved = concatEntries(newExpectedResolved, new IPathEntry[]{
+			       CoreModel.newSourceEntry(project.getFullPath().append("test_src")),
+			       CoreModel.newOutputEntry(project.getFullPath().append("test_out")),});
+			
+		for(int i = 0; i < newExpectedResolved.length; i++){
+			IPathEntry entry = newExpectedResolved[i];
+			if(entry.getEntryKind() == IPathEntry.CDT_SOURCE && entry.getPath().equals(project.getFullPath())){
+				newExpectedResolved[i] = CoreModel.newSourceEntry(project.getFullPath(), new Path[]{new Path("test_src")});
+			}
+//			if(entry.getEntryKind() == IPathEntry.CDT_OUTPUT && entry.getPath().equals(project.getFullPath())){
+//				newExpectedResolved[i] = CoreModel.newOutputEntry(project.getFullPath(), new Path[]{new Path("test_out")});
+//			}
+		}
+		
+		CoreModel.setRawPathEntries(p1, entries, null);
+		
+		entries = CoreModel.getRawPathEntries(p1);
+		resolvedentries = CoreModel.getResolvedPathEntries(p1);
+		
+		checkEntriesMatch(newExpectedRawEntries, entries);
+		checkEntriesMatch(newExpectedResolved, resolvedentries);
+		
+		CoreModel.setRawPathEntries(p1, expectedRawEntries, null);
+		entries = CoreModel.getRawPathEntries(p1);
+		resolvedentries = CoreModel.getResolvedPathEntries(p1);
+		
+		checkEntriesMatch(expectedRawEntries, entries);
+		checkEntriesMatch(expectedResolvedEntries, resolvedentries);
+		
+		//check to see that setting the same entries do not give errors
+		CoreModel.setRawPathEntries(p1, expectedRawEntries, null);
+		entries = CoreModel.getRawPathEntries(p1);
+		resolvedentries = CoreModel.getResolvedPathEntries(p1);
+		
+		checkEntriesMatch(expectedRawEntries, entries);
+		checkEntriesMatch(expectedResolvedEntries, resolvedentries);
+	}
+	
+	public void testCPathEntriesForOldStyle() throws Exception {
+		p2 = CProjectHelper.createCCProject(PROJ_NAME_PREFIX + "b", null, IPDOMManager.ID_NO_INDEXER);
+		ICProjectDescriptionManager mngr = CoreModel.getDefault().getProjectDescriptionManager();
+		IProject project = p2.getProject();
+		ICProjectDescription des = mngr.getProjectDescription(project, false);
+		assertNotNull(des);
+		assertEquals(1, des.getConfigurations().length);
+		assertFalse(mngr.isNewStyleProject(des));
+		assertFalse(mngr.isNewStyleProject(project));
+		
+		IPathEntry[] entries = CoreModel.getRawPathEntries(p2);
+		entries = concatEntries(entries, new IPathEntry[]{
+			       CoreModel.newSourceEntry(project.getFullPath().append("test_src")),
+			       CoreModel.newOutputEntry(project.getFullPath().append("test_out")),});
+
+		CoreModel.setRawPathEntries(p2, entries, null);
+		
+		ICSourceEntry[] expectedSourceEntries = new ICSourceEntry[]{
+				new CSourceEntry(project.getFullPath(), new IPath[] {new Path("test_src")}, ICSettingEntry.RESOLVED),
+				new CSourceEntry(project.getFullPath().append("test_src"), null, ICSettingEntry.RESOLVED),
+		};
+
+		ICOutputEntry[] expectedOutputEntries = new ICOutputEntry[]{
+				new COutputEntry(project.getFullPath(), null, ICSettingEntry.RESOLVED | ICSettingEntry.VALUE_WORKSPACE_PATH),
+				new COutputEntry(project.getFullPath().append("test_out"), null, ICSettingEntry.RESOLVED | ICSettingEntry.VALUE_WORKSPACE_PATH),
+		};
+
+		des = mngr.getProjectDescription(project, false);
+		ICConfigurationDescription cfg = des.getDefaultSettingConfiguration();
+		ICSourceEntry[] sEntries = cfg.getSourceEntries();
+		ICOutputEntry[] oEntries = cfg.getBuildSetting().getOutputDirectories();
+		
+		checkCEntriesMatch(expectedSourceEntries, sEntries);
+		checkCEntriesMatch(expectedOutputEntries, oEntries);
+
+		des = mngr.getProjectDescription(project, true);
+		cfg = des.getDefaultSettingConfiguration();
+		sEntries = cfg.getSourceEntries();
+		oEntries = cfg.getBuildSetting().getOutputDirectories();
+		
+		checkCEntriesMatch(expectedSourceEntries, sEntries);
+		checkCEntriesMatch(expectedOutputEntries, oEntries);
+	}
+	
+	public static IPathEntry[] concatEntries(IPathEntry[] entries1, IPathEntry[] entries2){
+		List list = new ArrayList(entries1.length + entries2.length);
+		list.addAll(Arrays.asList(entries1));
+		list.addAll(Arrays.asList(entries2));
+		return (IPathEntry[])list.toArray(new IPathEntry[list.size()]);
+	}
+	
+	public static void checkCEntriesMatch(ICSettingEntry[] e1, ICSettingEntry[] e2){
+		if(e1.length != e2.length)
+			fail("entries num do not match");
+		
+		Set set = new HashSet(Arrays.asList(e1));
+		set.removeAll(Arrays.asList(e2));
+		if(set.size() != 0)
+			fail("entries do not match");
+	}
+	
+	public static void checkEntriesMatch(IPathEntry[] e1, IPathEntry[] e2){
 		if(e1.length != e2.length)
 			fail("entries arrays have different length \ne1: " + dumpArray(e1) +"\ne2:" + dumpArray(e2) + "\n");
 		
@@ -110,7 +230,7 @@ public class BackwardCompatibilityTests extends BaseTestCase {
 		}
 	}
 	
-	private String dumpArray(Object array[]){
+	public static String dumpArray(Object array[]){
 		if(array == null)
 			return "null";
 		

core/org.eclipse.cdt.core/model/org/eclipse/cdt/core/settings/model/extension/impl/CDataFacroty.java

@@ -128,6 +128,8 @@ public class CDataFacroty {
 	}
 
 	public void setModified(CDataObject data, boolean modified){
+		if(data == null)
+			return;
 		switch (data.getType()) {
 		case ICSettingBase.SETTING_CONFIGURATION:
 			((CDefaultConfigurationData)data).setModified(modified);

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

@@ -10,6 +10,7 @@
  *******************************************************************************/
 package org.eclipse.cdt.core.settings.model.util;
 
+import java.lang.reflect.Array;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.Collection;
@@ -758,7 +759,7 @@ public class CDataUtil {
 		return adjustEntries(entries, false, null);
 	}
 
-	private static ICSourceEntry[] getDefaultEntries(boolean absolute, IProject project){
+	private static ICSourceEntry[] getDefaultSourceEntries(boolean absolute, IProject project){
 		ICSourceEntry entry;
 		if(absolute){
 			if(project != null)
@@ -771,9 +772,29 @@ public class CDataUtil {
 		return new ICSourceEntry[]{entry};
 	}
 	
+	private static ICOutputEntry[] getDefaultOutputEntries(boolean absolute, IProject project){
+		ICOutputEntry entry;
+		if(absolute){
+			if(project != null)
+				entry = new COutputEntry(project.getFullPath(), null, ICSettingEntry.VALUE_WORKSPACE_PATH | ICSourceEntry.RESOLVED);
+			else
+				entry = new COutputEntry(Path.EMPTY, null, ICSettingEntry.VALUE_WORKSPACE_PATH | ICSourceEntry.RESOLVED);
+		} else {
+			entry = new COutputEntry(Path.EMPTY, null, ICSettingEntry.VALUE_WORKSPACE_PATH | ICSourceEntry.RESOLVED);
+		}
+		return new ICOutputEntry[]{entry};
+	}
+
+	public static ICOutputEntry[] adjustEntries(ICOutputEntry entries[], boolean makeAbsolute, IProject project){
+		if(entries == null || entries.length == 0)
+			return getDefaultOutputEntries(makeAbsolute, project);
+		
+		return makeAbsolute ? checkMakeAbsolute(project, entries) : checkMakeRelative(project, entries);
+	}
+
 	public static ICSourceEntry[] adjustEntries(ICSourceEntry entries[], boolean makeAbsolute, IProject project){
-		if(entries == null)
+		if(entries == null || entries.length == 0)
-			return getDefaultEntries(makeAbsolute, project);
+			return getDefaultSourceEntries(makeAbsolute, project);
 		
 		ICSourceEntry ei, ej;
 		LinkedHashMap map = new LinkedHashMap();
@@ -837,31 +858,35 @@ public class CDataUtil {
 	}
 
 	public static ICSourceEntry makeAbsolute(IProject project, ICSourceEntry entry){
-		if(project == null)
+		return (ICSourceEntry)makeAbsolute(project, entry, true);
-			return entry;
-		
-		IPath path = new Path(entry.getName());
-		if(path.isAbsolute())
-			return entry;
-		
-		path = project.getFullPath().append(path);
-		
-		return new CSourceEntry(path, entry.getExclusionPatterns(), entry.getFlags());
 	}
 
 	public static ICSourceEntry makeRelative(IProject project, ICSourceEntry entry){
-		IPath path = new Path(entry.getName());
+		return (ICSourceEntry)makeRelative(project, entry, true);
-		if(!path.isAbsolute())
+	}
-			return entry;
 
-//		if(project != null){
+	public static ICSourceEntry[] makeRelative(IProject project, ICSourceEntry[] entries){
-//			
+		return (ICSourceEntry[])makeRelative(project, entries, true);
-//			IPath projPath = project.getFullPath();
+	}
-//			
-//		}
-//		if(pro)
 
-		return new CSourceEntry(path.removeFirstSegments(1).makeRelative(), entry.getExclusionPatterns(), entry.getFlags());
+	public static ICSourceEntry[] makeAbsolute(IProject project, ICSourceEntry[] entries){
+		return (ICSourceEntry[])makeAbsolute(project, entries, true);
+	}
+
+	public static ICOutputEntry checkMakeAbsolute(IProject project, ICOutputEntry entry){
+		return (ICOutputEntry)makeAbsolute(project, entry, false);
+	}
+
+	public static ICOutputEntry checkMakeRelative(IProject project, ICOutputEntry entry){
+		return (ICOutputEntry)makeRelative(project, entry, false);
+	}
+
+	public static ICOutputEntry[] checkMakeAbsolute(IProject project, ICOutputEntry[] entries){
+		return (ICOutputEntry[])makeAbsolute(project, entries, false);
+	}
+
+	public static ICOutputEntry[] checkMakeRelative(IProject project, ICOutputEntry[] entries){
+		return (ICOutputEntry[])makeRelative(project, entries, false);
 	}
 
 	private static Collection removePrefix(IPath prefix, Collection paths, Collection result){
@@ -984,4 +1009,56 @@ public class CDataUtil {
 			set.removeAll(Arrays.asList(o2));
 		return set;
 	}
+	
+	public static ICExclusionPatternPathEntry makeAbsolute(IProject project, ICExclusionPatternPathEntry entry, boolean force){
+		if(!entry.isValueWorkspacePath() && !force)
+			return entry;
+
+		IPath path = new Path(entry.getName());
+		IPath projPath = project.getFullPath();
+		if(!path.isAbsolute() || (force && !projPath.isPrefixOf(path))){
+			path = projPath.append(path).makeAbsolute();
+			return (ICExclusionPatternPathEntry)CDataUtil.createEntry(entry.getKind(), path.toString(), null, entry.getExclusionPatterns(), entry.getFlags());
+		}
+		return entry;
+	}
+	
+	public static ICExclusionPatternPathEntry makeRelative(IProject project, ICExclusionPatternPathEntry entry, boolean force){
+		if(!entry.isValueWorkspacePath() && !force)
+			return entry;
+		
+		IPath path = new Path(entry.getName());
+		IPath projPath = project.getFullPath();
+		
+		if(path.isAbsolute()){
+			if(projPath.isPrefixOf(path))
+				path = path.removeFirstSegments(projPath.segmentCount()).makeRelative();
+			else if (force)
+				path = path.makeRelative();
+			return (ICExclusionPatternPathEntry)CDataUtil.createEntry(entry.getKind(), entry.getName(), entry.getValue(), entry.getExclusionPatterns(), entry.getFlags());
+		}
+		return entry;
+	}
+	
+	public static ICExclusionPatternPathEntry[] makeRelative(IProject project, ICExclusionPatternPathEntry[] entries, boolean force){
+		if(entries == null)
+			return null;
+		
+		ICExclusionPatternPathEntry[] relEntries = (ICExclusionPatternPathEntry[])Array.newInstance(entries.getClass().getComponentType(), entries.length);
+		for(int i = 0; i < entries.length; i++){
+			relEntries[i] = makeRelative(project, entries[i], force);
+		}
+		return relEntries;
+	}
+	
+	public static ICExclusionPatternPathEntry[] makeAbsolute(IProject project, ICExclusionPatternPathEntry[] entries, boolean force){
+		if(entries == null)
+			return null;
+		
+		ICExclusionPatternPathEntry[] relEntries = (ICExclusionPatternPathEntry[])Array.newInstance(entries.getClass().getComponentType(), entries.length);
+		for(int i = 0; i < entries.length; i++){
+			relEntries[i] = makeAbsolute(project, entries[i], force);
+		}
+		return relEntries;
+	}
 }

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

@@ -35,6 +35,7 @@ import org.eclipse.cdt.core.model.IIncludeFileEntry;
 import org.eclipse.cdt.core.model.ILibraryEntry;
 import org.eclipse.cdt.core.model.IMacroEntry;
 import org.eclipse.cdt.core.model.IMacroFileEntry;
+import org.eclipse.cdt.core.model.IOutputEntry;
 import org.eclipse.cdt.core.model.IPathEntry;
 import org.eclipse.cdt.core.model.ISourceEntry;
 import org.eclipse.cdt.core.resources.IPathEntryVariableManager;
@@ -44,6 +45,7 @@ import org.eclipse.cdt.core.settings.model.CIncludePathEntry;
 import org.eclipse.cdt.core.settings.model.CLibraryFileEntry;
 import org.eclipse.cdt.core.settings.model.CMacroEntry;
 import org.eclipse.cdt.core.settings.model.CMacroFileEntry;
+import org.eclipse.cdt.core.settings.model.COutputEntry;
 import org.eclipse.cdt.core.settings.model.CSourceEntry;
 import org.eclipse.cdt.core.settings.model.ICConfigurationDescription;
 import org.eclipse.cdt.core.settings.model.ICExclusionPatternPathEntry;
@@ -975,6 +977,7 @@ public class PathEntryTranslator {
 			Map nameKeyMap = getEntriesNameKeyMap(kind, true);
 			for(int i = 0; i < entries.length; i++){
 				ICExclusionPatternPathEntry entry = entries[i];
+				entry = CDataUtil.makeAbsolute(fProject, entry, kind == ICSettingEntry.SOURCE_PATH);
 				EntryNameKey nameKey = new EntryNameKey(entry);
 				PathEntryComposer old = (PathEntryComposer)nameKeyMap.get(nameKey);
 				if(old != null){
@@ -1510,6 +1513,7 @@ public class PathEntryTranslator {
 		List projList = new ArrayList();
 		List exportSettingsList = new ArrayList();
 		ICSourceEntry srcEntries[] = null;
+		ICOutputEntry outEntries[] = null;
 //		PathSettingsContainer child;
 		ResolvedEntry rEntry;
 		IPath projPath;
@@ -1525,7 +1529,7 @@ public class PathEntryTranslator {
 					srcList.add(rEntry.fEntry);
 					break;
 				case IPathEntry.CDT_OUTPUT:
-					outList.add(rEntry);
+					outList.add(rEntry.fEntry);
 					break;
 				case IPathEntry.CDT_PROJECT:
 					projList.add(rEntry);
@@ -1551,6 +1555,11 @@ public class PathEntryTranslator {
 		if(srcList.size() != 0){
 			srcEntries = toCSourceEntries(srcList);
 		} else {
+//			srcPaths = new IPath[]{new Path("")}; //$NON-NLS-1$
+		}
+		if(outList.size() != 0){
+			outEntries = toCOutputEntries(outList);
+		} else {
 //			srcPaths = new IPath[]{new Path("")}; //$NON-NLS-1$
 		}
 		
@@ -1575,6 +1584,7 @@ public class PathEntryTranslator {
 		//applying settings
 
 		//applySourcePaths(srcPaths, op);
+		applyOutputEntries(outEntries, op);
 		applySourceEntries(srcEntries, op);
 		applyLangSettings(cr, op);
 		
@@ -1611,6 +1621,15 @@ public class PathEntryTranslator {
 		return entries;
 	}
 	
+	private static ICOutputEntry[] toCOutputEntries(List list){
+		ICOutputEntry[] entries = new ICOutputEntry[list.size()];
+		for(int i = 0; i < entries.length; i++){
+			entries[i] = toCOutputEntry((IOutputEntry)list.get(i), true);
+		}
+		return entries;
+	}
+
+	
 	private static ICSourceEntry toCSourceEntry(ISourceEntry entry, boolean makeProjRelative){
 		IPath path = entry.getPath();
 		if(makeProjRelative && path.isAbsolute())
@@ -1621,6 +1640,16 @@ public class PathEntryTranslator {
 				| ICSourceEntry.RESOLVED);
 	}
 	
+	private static ICOutputEntry toCOutputEntry(IOutputEntry entry, boolean makeProjRelative){
+		IPath path = entry.getPath();
+		if(makeProjRelative && path.isAbsolute())
+			path = path.removeFirstSegments(1);
+		return new COutputEntry(path,
+				entry.getExclusionPatterns(), 
+				ICSettingEntry.VALUE_WORKSPACE_PATH
+				| ICSourceEntry.RESOLVED);
+	}
+	
 	private static ICSettingEntry[] replaceUserEntries(ICSettingEntry[] oldEntries, ICSettingEntry[] newUsrEntries){
 		Set set = new LinkedHashSet();
 		Class componentType = null;
@@ -1655,23 +1684,23 @@ public class PathEntryTranslator {
 
 	private void applySourceEntries(ICSourceEntry entries[], int op){
 		ICSourceEntry[] oldEntries = fCfgData.getSourceEntries();
+		oldEntries = (ICSourceEntry[])CDataUtil.makeRelative(fProject, oldEntries, true);
+		entries = (ICSourceEntry[])CDataUtil.makeRelative(fProject, entries, true);
 		entries = (ICSourceEntry[])replaceUserEntries(oldEntries, entries);
 		
 		switch (op) {
 		case OP_ADD:
 			if(entries != null && entries.length != 0){
-				ICSourceEntry curEntries[] = fCfgData.getSourceEntries();
 				Set set = new LinkedHashSet();
-				set.addAll(Arrays.asList(curEntries));
+				set.addAll(Arrays.asList(oldEntries));
 				set.addAll(Arrays.asList(entries));
 				fCfgData.setSourceEntries((ICSourceEntry[])set.toArray(new ICSourceEntry[set.size()]));
 			}
 			break;
 		case OP_REMOVE:
 			if(entries != null && entries.length != 0){
-				ICSourceEntry curEntries[] = fCfgData.getSourceEntries();
 				Set set = new HashSet();
-				set.addAll(Arrays.asList(curEntries));
+				set.addAll(Arrays.asList(oldEntries));
 				set.removeAll(Arrays.asList(entries));
 				fCfgData.setSourceEntries((ICSourceEntry[])set.toArray(new ICSourceEntry[set.size()]));
 			}
@@ -1687,6 +1716,46 @@ public class PathEntryTranslator {
 		}		
 	}
 	
+	private void applyOutputEntries(ICOutputEntry entries[], int op){
+		CBuildData bData = fCfgData.getBuildData();
+		if(bData == null){
+			CCorePlugin.log("PathEntryTranslator: failed to apply output entries: Build Data is null, ignoring..");
+			return;
+		}
+		
+		ICOutputEntry[] oldEntries = bData.getOutputDirectories();
+		oldEntries = (ICOutputEntry[])CDataUtil.makeRelative(fProject, oldEntries, false);
+		entries = (ICOutputEntry[])CDataUtil.makeRelative(fProject, entries, false);
+		entries = (ICOutputEntry[])replaceUserEntries(oldEntries, entries);
+		
+		switch (op) {
+		case OP_ADD:
+			if(entries != null && entries.length != 0){
+				Set set = new LinkedHashSet();
+				set.addAll(Arrays.asList(oldEntries));
+				set.addAll(Arrays.asList(entries));
+				bData.setOutputDirectories((ICOutputEntry[])set.toArray(new ICOutputEntry[set.size()]));
+			}
+			break;
+		case OP_REMOVE:
+			if(entries != null && entries.length != 0){
+				Set set = new HashSet();
+				set.addAll(Arrays.asList(oldEntries));
+				set.removeAll(Arrays.asList(entries));
+				bData.setOutputDirectories((ICOutputEntry[])set.toArray(new ICOutputEntry[set.size()]));
+			}
+			break;
+		case OP_REPLACE:
+		default:
+			if(entries != null){
+				bData.setOutputDirectories(entries);
+			} else {
+				bData.setOutputDirectories(new ICOutputEntry[0]);
+			}
+			break;
+		}		
+	}
+	
 	private void applyLangSettings(PathSettingsContainer cr, int op){
 		PathSettingsContainer crs[] = cr.getChildren(true);
 		for(int i = 0; i < crs.length; i++){
@@ -2492,7 +2561,4 @@ public class PathEntryTranslator {
 		PathEntryCollector cr = collectEntries(project, cfg);
 		return cr.getEntries(flags, cfg);
 	}
-//	
-//	private 
-
 }

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

@@ -0,0 +1,50 @@
+/*******************************************************************************
+ * Copyright (c) 2007 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.core.settings.model.util;
+
+import java.util.HashMap;
+import java.util.Map;
+
+public class ThreadLocalMap {
+	private ThreadLocal fLocal = new ThreadLocal();
+	
+	public Object get(Object key){
+		Map map = getMap(false);
+		return map != null ? map.get(key) : null;
+	}
+
+	public void set(Object key, Object value){
+		if(value == null)
+			clear(key);
+		else {
+			Map map = getMap(true);
+			map.put(key, value);
+		}
+	}
+
+	public void clear(Object key){
+		Map map = getMap(false);
+		if(map != null){
+			map.remove(key);
+			if(map == null)
+				fLocal.set(null);
+		}
+	}
+
+	private Map getMap(boolean create){
+		Map map = (Map)fLocal.get();
+		if(map == null && create){
+			map = new HashMap();
+			fLocal.set(map);
+		}
+		return map;
+	}
+}

core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/model/PathEntryManager.java

@@ -53,6 +53,7 @@ import org.eclipse.cdt.core.resources.IPathEntryStoreListener;
 import org.eclipse.cdt.core.resources.PathEntryStoreChangedEvent;
 import org.eclipse.cdt.core.settings.model.util.PathEntryResolveInfo;
 import org.eclipse.cdt.core.settings.model.util.PathEntryResolveInfoElement;
+import org.eclipse.cdt.core.settings.model.util.ThreadLocalMap;
 import org.eclipse.cdt.internal.core.settings.model.AbstractCExtensionProxy;
 import org.eclipse.cdt.internal.core.settings.model.ConfigBasedPathEntryStore;
 import org.eclipse.core.resources.IMarker;
@@ -112,6 +113,7 @@ public class PathEntryManager implements IPathEntryStoreListener, IElementChange
 	// Synchronized the access of the cache entries.
 	protected Map resolvedMap = new Hashtable();
 	private Map resolvedInfoMap = new Hashtable();
+	private ThreadLocalMap resolveInfoValidState = new ThreadLocalMap(); 
 
 	// Accessing the map is synch with the class
 	private Map storeMap = new HashMap();
@@ -415,10 +417,23 @@ public class PathEntryManager implements IPathEntryStoreListener, IElementChange
 		if(info == null){
 			getResolvedPathEntries(cproject);
 			info = (PathEntryResolveInfo)resolvedInfoMap.get(cproject);
+		} else if(!getResolveInfoValidState(cproject)){
+			Object[] resolved = getResolvedPathEntries(cproject, false, false);
+			if(resolved != null)
+				info = (PathEntryResolveInfo)resolved[1]; 
 		}
 		return info;
 	}
 	
+	private void setResolveInfoValidState(ICProject cproject, boolean valid){
+		Object v = valid ? null : Boolean.FALSE;
+		resolveInfoValidState.set(cproject, v);
+	}
+	
+	private boolean getResolveInfoValidState(ICProject cproject){
+		return resolveInfoValidState.get(cproject) == null;
+	}
+	
 	protected IPathEntry[] removeCachedResolvedPathEntries(ICProject cproject) {
 		ArrayList resolvedListEntries = (ArrayList)resolvedMap.remove(cproject);
 		resolvedInfoMap.remove(cproject);
@@ -485,7 +500,19 @@ public class PathEntryManager implements IPathEntryStoreListener, IElementChange
 	 * @throws CModelException
 	 */
 	private ArrayList getResolvedPathEntries(ICProject cproject, boolean generateMarkers) throws CModelException {
-		ArrayList resolvedEntries = (ArrayList)resolvedMap.get(cproject);
+		Object[] result = getResolvedPathEntries(cproject, generateMarkers, true);
+		if(result != null)
+			return (ArrayList)result[0];
+		return null;
+	}
+
+	private Object[] getResolvedPathEntries(ICProject cproject, boolean generateMarkers, boolean useCache) throws CModelException {
+		ArrayList resolvedEntries = null;
+		PathEntryResolveInfo rInfo = null;
+		if(useCache){
+			resolvedEntries = (ArrayList)resolvedMap.get(cproject);
+			rInfo = (PathEntryResolveInfo)resolvedInfoMap.get(cproject);
+		}
 		if (resolvedEntries == null) {
 			List resolveInfoList = new ArrayList();
 			IPath projectPath = cproject.getPath();
@@ -561,10 +588,13 @@ public class PathEntryManager implements IPathEntryStoreListener, IElementChange
 				resolvedEntries.removeAll(dups);
 			}
 
+			rInfo = new PathEntryResolveInfo(resolveInfoList);
+			if(useCache){
 				resolvedMap.put(cproject, resolvedEntries);
-			resolvedInfoMap.put(cproject, new PathEntryResolveInfo(resolveInfoList));
+				resolvedInfoMap.put(cproject, rInfo);
 			}
-		return resolvedEntries;
+		}
+		return new Object[]{resolvedEntries, rInfo};
 	}
 
 	public void setRawPathEntries(ICProject cproject, IPathEntry[] newEntries, IProgressMonitor monitor) throws CModelException {
@@ -944,7 +974,9 @@ public class PathEntryManager implements IPathEntryStoreListener, IElementChange
 			list.toArray(newRawEntries);
 			IProject project = cproject.getProject();
 			IPathEntryStore store = getPathEntryStore(project, true);
+			setResolveInfoValidState(cproject, false);
 			store.setRawPathEntries(newRawEntries);
+			setResolveInfoValidState(cproject, true);
 		} catch (CoreException e) {
 			throw new CModelException(e);
 		}

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

@@ -16,6 +16,7 @@ import org.eclipse.cdt.core.settings.model.ICOutputEntry;
 import org.eclipse.cdt.core.settings.model.ICSettingBase;
 import org.eclipse.cdt.core.settings.model.extension.CBuildData;
 import org.eclipse.cdt.core.settings.model.util.CDataUtil;
+import org.eclipse.core.resources.IProject;
 import org.eclipse.core.runtime.IPath;
 
 public class CBuildSetting extends CDataProxy implements ICBuildSetting {
@@ -40,7 +41,10 @@ public class CBuildSetting extends CDataProxy implements ICBuildSetting {
 
 	public ICOutputEntry[] getOutputDirectories() {
 		CBuildData data = getBuildData(false);
-		return data.getOutputDirectories();
+		ICOutputEntry[] entries = data.getOutputDirectories();
+		IProject project = getProject();
+		entries = CDataUtil.adjustEntries(entries, true, project);
+		return entries;
 	}
 
 	public void setBuilderCWD(IPath path) {
@@ -55,6 +59,11 @@ public class CBuildSetting extends CDataProxy implements ICBuildSetting {
 
 	public void setOutputDirectories(ICOutputEntry[] entries) {
 		CBuildData data = getBuildData(true);
+		IProject project = getProject();
+		if(entries != null){
+			entries = CDataUtil.adjustEntries(entries, false, project);
+		}
+
 		data.setOutputDirectories(entries);
 		if(entries == null){
 			CExternalSettingsManager.getInstance().restoreOutputEntryDefaults(getConfiguration());

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

@@ -20,6 +20,7 @@ import org.eclipse.cdt.core.settings.model.extension.impl.CDefaultBuildData;
 import org.eclipse.cdt.core.settings.model.util.CDataUtil;
 import org.eclipse.cdt.internal.core.envvar.EnvironmentVariableManager;
 import org.eclipse.cdt.utils.envvar.StorableEnvironment;
+import org.eclipse.core.resources.IProject;
 import org.eclipse.core.runtime.IPath;
 
 public class CBuildSettingCache extends CDefaultBuildData implements
@@ -27,6 +28,7 @@ public class CBuildSettingCache extends CDefaultBuildData implements
 	private CConfigurationDescriptionCache fCfgCache;
 	private StorableEnvironment fEnvironment;
 	private StorableEnvironment fResolvedEnvironment;
+	private ICOutputEntry[] fProjOutputEntries;
 	private ICOutputEntry[] fResolvedOutputEntries;
 
 	CBuildSettingCache(CBuildData base, CConfigurationDescriptionCache cfgCache){
@@ -97,4 +99,22 @@ public class CBuildSettingCache extends CDefaultBuildData implements
 		return fResolvedOutputEntries;
 	}
 	
+	public ICOutputEntry[] getOutputDirectories() {
+		initOutputEntries();
+		return (ICOutputEntry[])fProjOutputEntries.clone();
+	}
+	
+	private void initOutputEntries(){
+		if(fProjOutputEntries == null){
+			IProject project = getProject(); 
+			fProjOutputEntries = CDataUtil.adjustEntries(fOutputEntries, true, project);
+		}
+	}
+	
+	private IProject getProject(){
+		ICConfigurationDescription cfg = getConfiguration();
+		return cfg.isPreferenceConfiguration() ? null : cfg.getProjectDescription().getProject();
+	}
+
+	
 }

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

@@ -476,130 +476,15 @@ public class CConfigurationDescription extends CDataProxyContainer implements IC
 	public void setSourceEntries(ICSourceEntry[] entries) throws CoreException {
 		CConfigurationData data = getConfigurationData(true);
 		IProject project = fIsPreference ? null : getProjectDescription().getProject();
-		boolean restoreDefault = false;
+		if(entries != null){
-		if(entries == null)
-			restoreDefault = true;
-		else if(entries.length == 0)
-			entries = null;
 			entries = CDataUtil.adjustEntries(entries, false, project);
+		}
+		
 		data.setSourceEntries(entries);
 
-		if(restoreDefault){
+		if(entries == null){
 			CExternalSettingsManager.getInstance().restoreSourceEntryDefaults(this);
 		}
-//		ICSourceEntry entry;
-//		IPath entryPath;
-//		IPath paths[];
-//		PathSettingsContainer cr = PathSettingsContainer.createRootContainer();
-//		cr.setValue(Boolean.valueOf(getRootFolderDescription().isExcluded()));
-//		Set srcPathSet = new HashSet();
-//		IProject project = fIsPreference ? null : getProjectDescription().getProject();
-//		IPath projPath = project != null ? project.getFullPath() : null;
-////		Map exclusionMap = new HashMap();
-//		
-////		HashSet pathSet = new HashSet();
-//		
-//		if(entries == null){
-//			IPath pasePath = projPath != null ? projPath : Path.EMPTY;
-//			entries = new ICSourceEntry[]{new CSourceEntry(pasePath, null, ICLanguageSettingEntry.RESOLVED | ICLanguageSettingEntry.VALUE_WORKSPACE_PATH)};
-//		}
-//
-//		for(int i = 0 ; i < entries.length; i++){
-//			entry = entries[i];
-//			entryPath = entry.getFullPath();
-//			if(projPath != null){
-//				if(projPath.isPrefixOf(entryPath)){
-//					entryPath = entryPath.removeFirstSegments(projPath.segmentCount());
-//				} else {
-//					continue;
-//				}
-//			} 
-////			else {
-////				if(entryPath.segmentCount() > 0)
-////					entryPath = entryPath.removeFirstSegments(1);
-////				else
-////					continue;
-////			}
-//			if(srcPathSet.add(entryPath)){
-//	//			exclusionMap.put(entryPath, Boolean.TRUE);
-//				PathSettingsContainer entryCr = cr.getChildContainer(entryPath, true, true);
-//				entryCr.setValue(Boolean.TRUE);
-//	
-//				
-//				paths = entry.getExclusionPatterns();
-//				
-//				
-//				for(int j = 0; j < paths.length; j++){
-//					IPath path = paths[j];
-//					PathSettingsContainer exclusion = entryCr.getChildContainer(path, true, true);
-//					if(exclusion.getValue() == null)
-//						exclusion.setValue(Boolean.FALSE);
-//	//				if(null == exclusionMap.get(path))
-//	//					exclusionMap.put(path, Boolean.FALSE);
-//				}
-//			}
-//		}
-//
-//		CConfigurationData data = getConfigurationData(true);
-//		data.setSourcePaths((IPath[])srcPathSet.toArray(new IPath[srcPathSet.size()]));
-//		ICResourceDescription rcDess[] = getResourceDescriptions();
-//		ICResourceDescription rcDes;
-//		Set pathSet = new HashSet();
-//		
-//		for(int i = 0; i < rcDess.length; i++){
-//			rcDes = rcDess[i];
-//			IPath path  = rcDes.getPath();
-//			pathSet.add(path);
-////			Boolean b = (Boolean)exclusionMap.remove(path);
-//			Boolean b = (Boolean)cr.getChildContainer(path, false, false).getValue();
-//			assert (b != null);
-//			if(Boolean.TRUE == b) {
-//				if(rcDes.isExcluded())
-//					rcDes.setExcluded(false);
-//			} else {
-//				if(/*(rcDes.getType() == ICSettingBase.SETTING_FILE
-//						|| !((ICFolderDescription)rcDes).isRoot())
-//						   &&*/ !rcDes.isExcluded())
-//					rcDes.setExcluded(true);
-//			}
-//		}
-//		
-//		PathSettingsContainer crs[] = cr.getChildren(true);
-//		for(int i= 0; i < crs.length; i++){
-//			PathSettingsContainer c = crs[i];
-//			IPath path = c.getPath();
-//			if(!pathSet.remove(path)){
-//				Boolean b = (Boolean)c.getValue();
-//				assert (b != null);
-//				ICResourceDescription base = getResourceDescription(path, false);
-//				if(b == Boolean.TRUE){
-//					if(base.isExcluded()){
-//						ICResourceDescription newDes = createResourceDescription(path, base);
-//						if(newDes == null){
-//							ICResourceDescription fo = getResourceDescription(path, false);
-//							if(fo.getType() == ICSettingBase.SETTING_FILE){
-//								fo = getResourceDescription(path.removeLastSegments(1), false);
-//							}
-//							newDes = createFolderDescription(path, (ICFolderDescription)fo);
-//						}
-//						newDes.setExcluded(false);
-//					}
-//				} else {
-//					if(!base.isExcluded()){
-//						ICResourceDescription newDes = createResourceDescription(path, base);
-//						if(newDes == null){
-//							ICResourceDescription fo = getResourceDescription(path, false);
-//							if(fo.getType() == ICSettingBase.SETTING_FILE){
-//								fo = getResourceDescription(path.removeLastSegments(1), false);
-//							}
-//							newDes = createFolderDescription(path, (ICFolderDescription)fo);
-//						}
-//						newDes.setExcluded(true);
-//					}
-//				}
-//			}
-//		}
-//		
 	}
 	
 //	private ICResourceDescription createResourceDescription(IPath path, ICResourceDescription base){

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

@@ -11,9 +11,11 @@
 package org.eclipse.cdt.internal.core.settings.model;
 
 import org.eclipse.cdt.core.settings.model.ICConfigurationDescription;
+import org.eclipse.cdt.core.settings.model.ICProjectDescription;
 import org.eclipse.cdt.core.settings.model.ICSettingContainer;
 import org.eclipse.cdt.core.settings.model.ICSettingObject;
 import org.eclipse.cdt.core.settings.model.extension.CDataObject;
+import org.eclipse.core.resources.IProject;
 
 public abstract class CDataProxy implements ICSettingObject {
 	protected ICDataProxyContainer fParent;
@@ -152,4 +154,16 @@ public abstract class CDataProxy implements ICSettingObject {
 	public boolean isReadOnly() {
 		return false;
 	}
+	
+	protected IProject getProject(){
+		ICConfigurationDescription cfg = getConfiguration();
+		if(cfg == null)
+			return null;
+		
+		ICProjectDescription projDes = cfg.getProjectDescription();
+		if(projDes == null)
+			return null;
+		
+		return projDes.getProject();
+	}
 }

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

@@ -91,10 +91,6 @@ public class CLanguageSetting extends CDataProxy implements
 		return (getSupportedEntryKinds() & kind) == kind;
 	}
 	
-	private IProject getProject(){
-		return getConfiguration().getProjectDescription().getProject();
-	}
-
 /*	public String[] getHeaderExtensions() {
 		CLanguageData data = getCLanguageData(false);
 		IContentType type = data.getHeaderContentType();

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

@@ -216,6 +216,7 @@ public class CProjectDescription implements ICProjectDescription, ICDataProxyCon
 				cache.applyData(factory);
 			} catch (CoreException e) {
 				CCorePlugin.log(e);
+				e.printStackTrace();
 				iter.remove();
 			}
 		}

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

@@ -422,7 +422,7 @@ public class CProjectDescriptionManager implements ICProjectDescriptionManager {
 		
 		des = getDescriptionApplying(project);
 		
-		if(des == null)
+		if(des == null && project.isOpen())
 			des = getLoaddedDescription(project);
 
 		if(des == null)
@@ -892,10 +892,15 @@ public class CProjectDescriptionManager implements ICProjectDescriptionManager {
 		if(!overwriteIfExists && fDescriptionMap.get(project) != null)
 			return false;
 		
-		if(des != null)
+		if(des != null){
+			if(project.exists() && project.isOpen()){
 				fDescriptionMap.put(project, des);
-		else
+			} else {
+				CCorePlugin.log("attempt to set description for the non-openned project");
+			}
+		}else {
 			fDescriptionMap.remove(project);
+		}
 
 		return true;
 ////		try {
@@ -2527,7 +2532,7 @@ public class CProjectDescriptionManager implements ICProjectDescriptionManager {
 //			}
 			ICConfigurationDescription oldIndexCfg = oldDes.getDefaultSettingConfiguration();
 			ICDescriptionDelta indexDelta;
-			if(oldIndexCfg.getId().equals(indexCfg.getId())){
+			if(oldIndexCfg != null && oldIndexCfg.getId().equals(indexCfg.getId())){
 				indexDelta = findDelta(indexCfg.getId(), projDesDelta);
 			} else {
 				indexDelta = createDelta(indexCfg, oldIndexCfg);

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

@@ -235,9 +235,13 @@ public class PathEntryConfigurationDataProvider extends
 			IProgressMonitor monitor)
 			throws CoreException {
 		//TODO: check external/reference info here as well.
-		if(!fFactory.isModified(base))
+		if(!fFactory.isModified(base)){
+			try {
+				return createData(des);
+			} catch (Exception e){
+			}
 			return base;
-		
+		}
 		
 		
 		IProject project = des.getProjectDescription().getProject();
@@ -250,7 +254,7 @@ public class PathEntryConfigurationDataProvider extends
 		List list = new ArrayList();
 		list.addAll(Arrays.asList(entries));
 		for(int i = 0; i < curRawEntries.length; i++){
-			if(curRawEntries[i].getEntryKind() == IPathEntry.CDT_CONTAINER){
+			if(curRawEntries[i].getEntryKind() != IPathEntry.CDT_CONTAINER){
 				list.add(curRawEntries[i]);
 			}
 		}