diff --git a/java/execution/impl/src/com/intellij/execution/application/ApplicationConfiguration.java b/java/execution/impl/src/com/intellij/execution/application/ApplicationConfiguration.java
index b31c26425f6f..0148402611bd 100644
--- a/java/execution/impl/src/com/intellij/execution/application/ApplicationConfiguration.java
+++ b/java/execution/impl/src/com/intellij/execution/application/ApplicationConfiguration.java
@@ -42,6 +42,7 @@ import com.intellij.psi.PsiElement;
 import com.intellij.psi.PsiJavaModule;
 import com.intellij.psi.util.PsiMethodUtil;
 import com.intellij.refactoring.listeners.RefactoringElementListener;
+import com.intellij.util.PathsList;
 import org.jdom.Element;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
@@ -299,7 +300,9 @@ public class ApplicationConfiguration extends ModuleBasedConfiguration<JavaRunCo
           PsiJavaModule mainModule = JavaModuleGraphUtil.findDescriptorByElement(mainClass);
           if (mainModule != null) {
             params.setModuleName(mainModule.getModuleName());
-            params.getModulePath().addAll(params.getClassPath().getPathList());
+            PathsList classPath = params.getClassPath(), modulePath = params.getModulePath();
+            modulePath.addAll(classPath.getPathList());
+            classPath.clear();
           }
         }
       }
diff --git a/platform/core-api/src/com/intellij/util/PathsList.java b/platform/core-api/src/com/intellij/util/PathsList.java
index 2e5ef730428c..08d94d4a3f9d 100644
--- a/platform/core-api/src/com/intellij/util/PathsList.java
+++ b/platform/core-api/src/com/intellij/util/PathsList.java
@@ -77,6 +77,12 @@ public class PathsList  {
     myPathSet.remove(path);
   }
 
+  public void clear() {
+    myPath.clear();
+    myPathTail.clear();
+    myPathSet.clear();
+  }
+
   public void add(VirtualFile file) {
     add(LOCAL_PATH.fun(file));
   }