diff --git a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CConfigurationSpecSettings.java b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CConfigurationSpecSettings.java
index d1e432a448a..852bfc4e5c0 100644
--- a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CConfigurationSpecSettings.java
+++ b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CConfigurationSpecSettings.java
@@ -279,11 +279,11 @@ public class CConfigurationSpecSettings implements ICSettingsStorage{
 	void doneInitialization(){
 		if(isReadOnly()){
 			if(fRootStorageElement != null)
-				((InternalXmlStorageElement)fRootStorageElement).setReadOnly(true);
+				((InternalXmlStorageElement)fRootStorageElement).setReadOnly(true, false);
 			if(fSettingsStorageElement != null)
-				((InternalXmlStorageElement)fSettingsStorageElement).setReadOnly(true);
+				((InternalXmlStorageElement)fSettingsStorageElement).setReadOnly(true, false);
 			if(fStorage != null)
-				fStorage.setReadOnly(true);
+				fStorage.setReadOnly(true, false);
 		}
 	}
 	
@@ -492,7 +492,16 @@ public class CConfigurationSpecSettings implements ICSettingsStorage{
 		if(isReadOnly())
 			throw ExceptionFactory.createIsReadOnlyException();
 		fIsModified = modified;
+		
+		if(!modified){
+			if(fMacros != null)
+				fMacros.setDirty(false);
+			
+			if(fEnvironment != null)
+				fEnvironment.setDirty(false);
+		}
 	}
+
 	void setModified(){
 		setModified(true);
 	}
diff --git a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CProjectDescription.java b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CProjectDescription.java
index 9c8c790b028..aa2824cee49 100644
--- a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CProjectDescription.java
+++ b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CProjectDescription.java
@@ -232,11 +232,16 @@ public class CProjectDescription implements ICProjectDescription, ICDataProxyCon
 		return modified;
 	}
 	
-	
-
 	void doneApplying(){
 		doneInitializing();
 		fIsApplying = false;
+		
+		try {
+			((InternalXmlStorageElement)getRootStorageElement()).setReadOnly(true, false);
+		} catch (CoreException e1) {
+		}
+		
+		setModified(false);
 	}
 
 	void doneLoadding(){
@@ -502,6 +507,20 @@ public class CProjectDescription implements ICProjectDescription, ICDataProxyCon
 		}
 		return false;
 	}
+	
+	private void setModified(boolean modified){
+		fIsModified = modified;
+		
+		if(!modified){
+			fActiveCfgInfo.fIsModified = false;
+
+			fSettingCfgInfo.fIsModified = false;
+
+			fPrefs.setModified(false);
+
+			//no need to do that for config cache since they always maintain the "isModified == false"
+		}
+	}
 
 	public boolean isReadOnly() {
 		return fIsReadOnly && !(fIsLoadding || fIsApplying);
diff --git a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CProjectDescriptionManager.java b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CProjectDescriptionManager.java
index f999bf20f0f..6ba684f7e68 100644
--- a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CProjectDescriptionManager.java
+++ b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CProjectDescriptionManager.java
@@ -709,11 +709,6 @@ public class CProjectDescriptionManager implements ICProjectDescriptionManager {
 				} finally {
 					clearDescriptionApplying(project);
 				}
-				
-				try {
-					((InternalXmlStorageElement)des.getRootStorageElement()).setReadOnly(true);
-				} catch (CoreException e1) {
-				}
 			}
 		}finally{
 			CProjectDescription d = clearDescriptionLoadding(project);
diff --git a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CProjectDescriptionPreferences.java b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CProjectDescriptionPreferences.java
index de33cd528a5..d0c9d7bb020 100644
--- a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CProjectDescriptionPreferences.java
+++ b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CProjectDescriptionPreferences.java
@@ -95,6 +95,10 @@ public class CProjectDescriptionPreferences implements ICProjectDescriptionPrefe
 					&& !fSuperPreference.settingsEqual((CProjectDescriptionPreferences)CProjectDescriptionManager.getInstance().getProjectDescriptionWorkspacePreferences(false)));
 	}
 	
+	void setModified(boolean modified){
+		fIsModified = modified;
+	}
+	
 	public boolean isReadOnly(){
 		return fIsReadOnly;
 	}
diff --git a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CStorage.java b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CStorage.java
index 67b21924b0c..acd862b0c6f 100644
--- a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CStorage.java
+++ b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/CStorage.java
@@ -170,11 +170,12 @@ public class CStorage implements ICSettingsStorage{
 		return false;
 	}
 	
-	void setReadOnly(boolean readOnly){
+	void setReadOnly(boolean readOnly, boolean keepModify){
 		fIsReadOnly = readOnly;
+		fIsDirty &= keepModify;
 		for(Iterator iter = fStorageElementMap.values().iterator(); iter.hasNext();){
 			InternalXmlStorageElement el = (InternalXmlStorageElement)iter.next();
-			el.setReadOnly(readOnly);
+			el.setReadOnly(readOnly, keepModify);
 		}
 	}
 
diff --git a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/InternalXmlStorageElement.java b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/InternalXmlStorageElement.java
index 446d88aa8df..35d2762ccd7 100644
--- a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/InternalXmlStorageElement.java
+++ b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/InternalXmlStorageElement.java
@@ -61,11 +61,16 @@ public class InternalXmlStorageElement extends XmlStorageElement {
 	}
 	
 	public void setReadOnly(boolean readOnly){
+		setReadOnly(readOnly, true);
+	}
+	
+	public void setReadOnly(boolean readOnly, boolean keepModify){
 		fIsReadOnly = readOnly;
+		fIsDirty &= keepModify;
 
 		ICStorageElement children[] = getChildren(false);
 		for(int i = 0; i < children.length; i++){
-			((InternalXmlStorageElement)children[i]).setReadOnly(readOnly);
+			((InternalXmlStorageElement)children[i]).setReadOnly(readOnly, keepModify);
 		}
 
 	}
diff --git a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/SetCProjectDescriptionOperation.java b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/SetCProjectDescriptionOperation.java
index 7df2215b456..78775696bf2 100644
--- a/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/SetCProjectDescriptionOperation.java
+++ b/core/org.eclipse.cdt.core/model/org/eclipse/cdt/internal/core/settings/model/SetCProjectDescriptionOperation.java
@@ -45,11 +45,14 @@ public class SetCProjectDescriptionOperation extends CModelOperation {
 		mngr.notifyListeners(event);
 		CProjectDescription fNewDescriptionCache = null;
 		SettingsContext context = new SettingsContext(project);
-		boolean modified;
+		boolean modified = false;
+		
 		if(fSetDescription != null){
 			InternalXmlStorageElement el = null;
 			try {
-				el = mngr.copyElement((InternalXmlStorageElement)fSetDescription.getRootStorageElement(), false);
+				InternalXmlStorageElement base = (InternalXmlStorageElement)fSetDescription.getRootStorageElement();
+				modified = base.isDirty();
+				el = mngr.copyElement(base, false);
 			} catch (CoreException e2) {
 			}
 	
@@ -63,7 +66,7 @@ public class SetCProjectDescriptionOperation extends CModelOperation {
 			fNewDescriptionCache = new CProjectDescription(fSetDescription, true, el, creating);
 			try {
 				mngr.setDescriptionApplying(project, fNewDescriptionCache);
-				modified = fNewDescriptionCache.applyDatas(context);
+				modified |= fNewDescriptionCache.applyDatas(context);
 			} finally {
 				mngr.clearDescriptionApplying(project);
 			}
@@ -105,11 +108,6 @@ public class SetCProjectDescriptionOperation extends CModelOperation {
 //		ExternalSettingsManager.getInstance().updateDepentents(delta);
 		
 		if(fNewDescriptionCache != null){
-			try {
-				((InternalXmlStorageElement)fNewDescriptionCache.getRootStorageElement()).setReadOnly(true);
-			} catch (CoreException e1) {
-			}
-	
 			fNewDescriptionCache.doneApplying();
 		}