Bugfix for issue mentioned here:

http://sourceforge.net/p/pmd/discussion/188192/thread/888425ac

pmd-eclipse-plugin/plugins/net.sourceforge.pmd.eclipse.plugin/src/net/sourceforge/pmd/eclipse/plugin/FileChangeReviewer.java

@@ -4,6 +4,7 @@ import java.util.HashSet;
 import java.util.Set;
 
 import name.herlin.command.CommandException;
+import net.sourceforge.pmd.eclipse.runtime.builder.MarkerUtil;
 import net.sourceforge.pmd.eclipse.runtime.cmd.ReviewCodeCmd;
 
 import org.eclipse.core.resources.IFile;
@@ -11,6 +12,7 @@ import org.eclipse.core.resources.IResource;
 import org.eclipse.core.resources.IResourceChangeEvent;
 import org.eclipse.core.resources.IResourceChangeListener;
 import org.eclipse.core.resources.IResourceDelta;
+import org.eclipse.core.runtime.CoreException;
 import org.eclipse.core.runtime.IProgressMonitor;
 import org.eclipse.core.runtime.IStatus;
 import org.eclipse.core.runtime.NullProgressMonitor;
@@ -79,10 +81,11 @@ public class FileChangeReviewer implements IResourceChangeListener {
 		if (itemsChanged.isEmpty()) return;
 		
 		ReviewCodeCmd cmd = new ReviewCodeCmd();	// separate one for each thread
+		cmd.clearExistingMarkersBeforeApplying(true);
 		cmd.reset();
 		
 		for (ResourceChange chg : itemsChanged) cmd.addResource(chg.file);
-		
+				
 		try {
 			cmd.performExecute();
 		} catch (CommandException e) {

pmd-eclipse-plugin/plugins/net.sourceforge.pmd.eclipse.plugin/src/net/sourceforge/pmd/eclipse/runtime/cmd/ReviewCodeCmd.java

@@ -49,6 +49,7 @@ import net.sourceforge.pmd.Rule;
 import net.sourceforge.pmd.RuleSet;
 import net.sourceforge.pmd.eclipse.plugin.PMDPlugin;
 import net.sourceforge.pmd.eclipse.runtime.PMDRuntimeConstants;
+import net.sourceforge.pmd.eclipse.runtime.builder.MarkerUtil;
 import net.sourceforge.pmd.eclipse.runtime.preferences.IPreferences;
 import net.sourceforge.pmd.eclipse.runtime.properties.IProjectProperties;
 import net.sourceforge.pmd.eclipse.runtime.properties.PropertiesException;
@@ -99,6 +100,7 @@ public class ReviewCodeCmd extends AbstractDefaultCommand {
     private int 						ruleCount;
     private int 						fileCount;
     private long 						pmdDuration;
+    private boolean						clearExistingMarkersBeforeApplying;
     private String						onErrorIssue = null;
 
     private static final long serialVersionUID = 1L;
@@ -116,6 +118,10 @@ public class ReviewCodeCmd extends AbstractDefaultCommand {
         setTerminated(false);
     }
 
+    public void clearExistingMarkersBeforeApplying(boolean flag) {
+    	clearExistingMarkersBeforeApplying = flag;
+    }
+    
     public Set<IFile> markedFiles() {
     	return markersByFile.keySet();
     }
@@ -523,7 +529,11 @@ public class ReviewCodeCmd extends AbstractDefaultCommand {
                 currentFile = file.getName();
 
                 Set<MarkerInfo2> markerInfoSet = markersByFile.get(file);
-  //              MarkerUtil.deleteAllMarkersIn(file);
+                
+                if (clearExistingMarkersBeforeApplying) {
+                	MarkerUtil.deleteAllMarkersIn(file);
+                }
+                
                 for (MarkerInfo2 markerInfo : markerInfoSet) { 
                 	markerInfo.addAsMarkerTo(file);
                     violationCount++;