diff --git a/platform/configuration-store-impl/src/ExportSettingsAction.kt b/platform/configuration-store-impl/src/ExportSettingsAction.kt
index d3e02082de94..0a30030bfa11 100644
--- a/platform/configuration-store-impl/src/ExportSettingsAction.kt
+++ b/platform/configuration-store-impl/src/ExportSettingsAction.kt
@@ -167,7 +167,6 @@ fun getExportableComponentsMap(onlyExisting: Boolean,
     }
   }
 
-  @Suppress("DEPRECATION")
   (ApplicationManager.getApplication() as ComponentManagerEx).getComponentInstancesOfType(ExportableApplicationComponent::class.java).forEach(processor)
   ServiceBean.loadServicesFromBeans(ExportableComponent.EXTENSION_POINT, ExportableComponent::class.java).forEach(processor)
 
diff --git a/platform/configuration-store-impl/src/ProjectStoreImpl.kt b/platform/configuration-store-impl/src/ProjectStoreImpl.kt
index e7a75bf87f87..69f51ce7e7ea 100644
--- a/platform/configuration-store-impl/src/ProjectStoreImpl.kt
+++ b/platform/configuration-store-impl/src/ProjectStoreImpl.kt
@@ -24,8 +24,11 @@ import com.intellij.openapi.application.invokeAndWaitIfNeed
 import com.intellij.openapi.application.runReadAction
 import com.intellij.openapi.components.*
 import com.intellij.openapi.components.StateStorage.SaveSession
+import com.intellij.openapi.components.ex.ComponentManagerEx
 import com.intellij.openapi.components.impl.stores.IComponentStore
 import com.intellij.openapi.components.impl.stores.IProjectStore
+import com.intellij.openapi.components.impl.stores.StoreUtil
+import com.intellij.openapi.diagnostic.catchAndLog
 import com.intellij.openapi.module.Module
 import com.intellij.openapi.module.ModuleManager
 import com.intellij.openapi.project.Project
@@ -40,8 +43,10 @@ import com.intellij.openapi.vfs.ReadonlyStatusHandler
 import com.intellij.openapi.vfs.VfsUtil
 import com.intellij.openapi.vfs.VirtualFile
 import com.intellij.util.*
+import com.intellij.util.containers.forEachGuaranteed
 import com.intellij.util.containers.isNullOrEmpty
 import com.intellij.util.lang.CompoundRuntimeException
+import org.jdom.Element
 import java.io.File
 import java.io.IOException
 import java.nio.file.Path
@@ -90,10 +95,11 @@ abstract class ProjectStoreBase(override final val project: ProjectImpl) : Compo
   override final fun loadProjectFromTemplate(defaultProject: Project) {
     defaultProject.save()
 
-    val element = (defaultProject.stateStore as DefaultProjectStoreImpl).getStateCopy()
-    if (element != null) {
-      (storageManager.getOrCreateStorage(PROJECT_FILE) as XmlElementStorage).setDefaultState(element)
+    val element = (defaultProject.stateStore as DefaultProjectStoreImpl).getStateCopy() ?: return
+    LOG.catchAndLog {
+      removeWorkspaceComponentConfiguration(defaultProject, element)
     }
+    (storageManager.getOrCreateStorage(PROJECT_FILE) as XmlElementStorage).setDefaultState(element)
   }
 
   override final fun getProjectBasePath(): String {
@@ -373,4 +379,34 @@ private fun useOldWorkspaceContent(filePath: String, ws: File) {
   catch (e: IOException) {
     LOG.error(e)
   }
+}
+
+// public only to test
+fun removeWorkspaceComponentConfiguration(defaultProject: Project, element: Element) {
+  val componentElements = element.getChildren("component")
+  if (componentElements.isEmpty()) {
+    return
+  }
+
+  val projectComponents = (defaultProject as ComponentManagerEx).getComponentInstancesOfType(PersistentStateComponent::class.java)
+  projectComponents.forEachGuaranteed {
+    val stateAnnotation = StoreUtil.getStateSpec(it.javaClass)
+    if (stateAnnotation == null || stateAnnotation.name.isNullOrEmpty()) {
+      return@forEachGuaranteed
+    }
+
+    val storage = stateAnnotation.storages.sortByDeprecated().firstOrNull() ?: return@forEachGuaranteed
+    if (storage.path != StoragePathMacros.WORKSPACE_FILE) {
+      return@forEachGuaranteed
+    }
+
+    val iterator = componentElements.iterator()
+    for (componentElement in iterator) {
+      if (componentElement.getAttributeValue("name") == stateAnnotation.name) {
+        iterator.remove()
+        break
+      }
+    }
+  }
+  return
 }
\ No newline at end of file
diff --git a/platform/configuration-store-impl/testSrc/DefaultProjectStoreTest.kt b/platform/configuration-store-impl/testSrc/DefaultProjectStoreTest.kt
index c7f023ac46a4..9468b817e5a3 100644
--- a/platform/configuration-store-impl/testSrc/DefaultProjectStoreTest.kt
+++ b/platform/configuration-store-impl/testSrc/DefaultProjectStoreTest.kt
@@ -10,10 +10,7 @@ import com.intellij.openapi.project.ProjectManager
 import com.intellij.openapi.util.JDOMUtil
 import com.intellij.openapi.vfs.LocalFileSystem
 import com.intellij.testFramework.*
-import com.intellij.util.delete
-import com.intellij.util.loadElement
-import com.intellij.util.refreshVfs
-import com.intellij.util.systemIndependentPath
+import com.intellij.util.*
 import org.assertj.core.api.Assertions.assertThat
 import org.jdom.Element
 import org.junit.ClassRule
@@ -24,7 +21,8 @@ import java.nio.file.Paths
 internal class DefaultProjectStoreTest {
   companion object {
     @JvmField
-    @ClassRule val projectRule = ProjectRule()
+    @ClassRule
+    val projectRule = ProjectRule()
 
     internal const val TEST_COMPONENT_NAME = "Foo"
 
@@ -100,4 +98,13 @@ internal class DefaultProjectStoreTest {
       stateStore.removeComponent(TEST_COMPONENT_NAME)
     }
   }
+
+  @Test fun `new project from default - remove workspace component configuration`() {
+    val element = loadElement("""
+    <state>
+      <component name="ProjectLevelVcsManager" settingsEditedManually="false" />
+    </state>""")
+    removeWorkspaceComponentConfiguration(ProjectManager.getInstance().defaultProject, element)
+    assertThat(element.isEmpty()).isTrue()
+  }
 }
\ No newline at end of file
diff --git a/platform/core-impl/src/com/intellij/openapi/components/ex/ComponentManagerEx.java b/platform/core-impl/src/com/intellij/openapi/components/ex/ComponentManagerEx.java
index a50c1810dcb6..ef6436d08561 100644
--- a/platform/core-impl/src/com/intellij/openapi/components/ex/ComponentManagerEx.java
+++ b/platform/core-impl/src/com/intellij/openapi/components/ex/ComponentManagerEx.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2000-2015 JetBrains s.r.o.
+ * Copyright 2000-2016 JetBrains s.r.o.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -29,8 +29,7 @@ public interface ComponentManagerEx extends ComponentManager {
   /**
    * Gets all components whose implementation class is derived from <code>baseClass</code>.
    *
-   * @return array of components
-   * @deprecated use extension points instead
+   * Consider using extension points instead.
    */
   @NotNull
   <T> List<T> getComponentInstancesOfType(@NotNull Class<T> baseClass);
diff --git a/platform/platform-resources/src/componentSets/VCS.xml b/platform/platform-resources/src/componentSets/VCS.xml
index fb451366bb6e..f10fbf8dd992 100644
--- a/platform/platform-resources/src/componentSets/VCS.xml
+++ b/platform/platform-resources/src/componentSets/VCS.xml
@@ -17,7 +17,6 @@
     <component>
       <interface-class>com.intellij.openapi.vcs.ProjectLevelVcsManager</interface-class>
       <implementation-class>com.intellij.openapi.vcs.impl.ProjectLevelVcsManagerImpl</implementation-class>
-      <option name="workspace" value="true"/>
       <loadForDefaultProject/>
     </component>
     <!-- <component>
diff --git a/platform/util/src/com/intellij/openapi/util/InvalidDataException.java b/platform/util/src/com/intellij/openapi/util/InvalidDataException.java
index c446c8bc3996..16922f35c5a2 100644
--- a/platform/util/src/com/intellij/openapi/util/InvalidDataException.java
+++ b/platform/util/src/com/intellij/openapi/util/InvalidDataException.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2000-2009 JetBrains s.r.o.
+ * Copyright 2000-2016 JetBrains s.r.o.
  *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
@@ -15,7 +15,7 @@
  */
 package com.intellij.openapi.util;
 
-public class InvalidDataException extends Exception {
+public class InvalidDataException extends RuntimeException {
   public InvalidDataException() {
     super();
   }
diff --git a/platform/vcs-impl/src/com/intellij/openapi/vcs/impl/ProjectLevelVcsManagerImpl.java b/platform/vcs-impl/src/com/intellij/openapi/vcs/impl/ProjectLevelVcsManagerImpl.java
index f2de19ddede3..61464dbf84c8 100644
--- a/platform/vcs-impl/src/com/intellij/openapi/vcs/impl/ProjectLevelVcsManagerImpl.java
+++ b/platform/vcs-impl/src/com/intellij/openapi/vcs/impl/ProjectLevelVcsManagerImpl.java
@@ -27,7 +27,7 @@ import com.intellij.openapi.actionSystem.ActionToolbar;
 import com.intellij.openapi.actionSystem.DefaultActionGroup;
 import com.intellij.openapi.application.ApplicationManager;
 import com.intellij.openapi.application.ModalityState;
-import com.intellij.openapi.components.ProjectComponent;
+import com.intellij.openapi.components.*;
 import com.intellij.openapi.diagnostic.Logger;
 import com.intellij.openapi.editor.markup.TextAttributes;
 import com.intellij.openapi.extensions.Extensions;
@@ -81,7 +81,8 @@ import java.awt.*;
 import java.util.*;
 import java.util.List;
 
-public class ProjectLevelVcsManagerImpl extends ProjectLevelVcsManagerEx implements ProjectComponent, JDOMExternalizable {
+@State(name = "ProjectLevelVcsManager", storages = @Storage(StoragePathMacros.WORKSPACE_FILE))
+public class ProjectLevelVcsManagerImpl extends ProjectLevelVcsManagerEx implements ProjectComponent, PersistentStateComponent<Element> {
   private static final Logger LOG = Logger.getInstance("#com.intellij.openapi.vcs.impl.ProjectLevelVcsManagerImpl");
   @NonNls public static final String SETTINGS_EDITED_MANUALLY = "settingsEditedManually";
 
@@ -596,10 +597,21 @@ public class ProjectLevelVcsManagerImpl extends ProjectLevelVcsManagerEx impleme
     VcsRootIterator.iterateVcsRoot(myProject, root, iterator, directoryFilter);
   }
 
+  @Nullable
   @Override
-  public void readExternal(Element element) throws InvalidDataException {
-    mySerialization.readExternalUtil(element, myOptionsAndConfirmations);
-    final Attribute attribute = element.getAttribute(SETTINGS_EDITED_MANUALLY);
+  public Element getState() {
+    Element element = new Element("state");
+    mySerialization.writeExternalUtil(element, myOptionsAndConfirmations);
+    if (myHaveLegacyVcsConfiguration) {
+      element.setAttribute(SETTINGS_EDITED_MANUALLY, "true");
+    }
+    return element;
+  }
+
+  @Override
+  public void loadState(Element state) {
+    mySerialization.readExternalUtil(state, myOptionsAndConfirmations);
+    final Attribute attribute = state.getAttribute(SETTINGS_EDITED_MANUALLY);
     if (attribute != null) {
       try {
         myHaveLegacyVcsConfiguration = attribute.getBooleanValue();
@@ -609,12 +621,6 @@ public class ProjectLevelVcsManagerImpl extends ProjectLevelVcsManagerEx impleme
     }
   }
 
-  @Override
-  public void writeExternal(Element element) throws WriteExternalException {
-    mySerialization.writeExternalUtil(element, myOptionsAndConfirmations);
-    element.setAttribute(SETTINGS_EDITED_MANUALLY, String.valueOf(myHaveLegacyVcsConfiguration));
-  }
-
   @Override
   @NotNull
   public VcsShowConfirmationOption getStandardConfirmation(@NotNull VcsConfiguration.StandardConfirmation option,