diff --git a/jps/jps-builders/src/org/jetbrains/jps/builders/BuildTarget.java b/jps/jps-builders/src/org/jetbrains/jps/builders/BuildTarget.java
index 2750aefcfdf5..a4fd3e2f263f 100644
--- a/jps/jps-builders/src/org/jetbrains/jps/builders/BuildTarget.java
+++ b/jps/jps-builders/src/org/jetbrains/jps/builders/BuildTarget.java
@@ -7,6 +7,7 @@ import org.jetbrains.jps.indices.IgnoredFileIndex;
 import org.jetbrains.jps.indices.ModuleExcludeIndex;
 import org.jetbrains.jps.model.JpsModel;
 
+import java.io.File;
 import java.io.PrintWriter;
 import java.util.Collection;
 import java.util.List;
@@ -44,6 +45,9 @@ public abstract class BuildTarget<R extends BuildRootDescriptor> {
   @NotNull
   public abstract String getPresentableName();
 
+  @Nullable
+  public abstract File getOutputDir(BuildDataPaths paths);
+
   @Override
   public String toString() {
     return getPresentableName();
diff --git a/jps/jps-builders/src/org/jetbrains/jps/incremental/IncProjectBuilder.java b/jps/jps-builders/src/org/jetbrains/jps/incremental/IncProjectBuilder.java
index 189e121d34ac..adb6a8b674d8 100644
--- a/jps/jps-builders/src/org/jetbrains/jps/incremental/IncProjectBuilder.java
+++ b/jps/jps-builders/src/org/jetbrains/jps/incremental/IncProjectBuilder.java
@@ -305,31 +305,19 @@ public class IncProjectBuilder {
   }
 
   private void clearOutputs(CompileContext context) throws ProjectBuildException, IOException {
-    final MultiMap<File, ModuleBuildTarget> rootsToDelete = new MultiMapBasedOnSet<File, ModuleBuildTarget>();
-    final Set<File> annotationOutputs = new HashSet<File>(); // separate collection because no root intersection checks needed for annotation generated sources
+    final MultiMap<File, BuildTarget<?>> rootsToDelete = new MultiMapBasedOnSet<File,BuildTarget<?>>();
     final Set<File> allSourceRoots = new HashSet<File>();
 
     final ProjectPaths paths = context.getProjectPaths();
 
-    for (JavaModuleBuildTargetType type : JavaModuleBuildTargetType.ALL_TYPES) {
-      for (ModuleBuildTarget target : context.getProjectDescriptor().getBuildTargetIndex().getAllTargets(type)) {
-        final File out = paths.getModuleOutputDir(target.getModule(), target.isTests());
-        if (out != null) {
-          rootsToDelete.putValue(out, target);
-        }
-
-        final ProcessorConfigProfile profile = context.getAnnotationProcessingProfile(target.getModule());
-        if (profile.isEnabled()) {
-          File annotationOut =
-            paths.getAnnotationProcessorGeneratedSourcesOutputDir(target.getModule(), target.isTests(), profile.getGeneratedSourcesDirectoryName());
-          if (annotationOut != null) {
-            annotationOutputs.add(annotationOut);
-          }
-        }
+    ProjectDescriptor projectDescriptor = context.getProjectDescriptor();
+    for (BuildTarget<?> target : projectDescriptor.getBuildTargetIndex().getAllTargets()) {
+      File outputDir = target.getOutputDir(projectDescriptor.dataManager.getDataPaths());
+      if (outputDir != null) {
+        rootsToDelete.putValue(outputDir, target);
       }
     }
 
-    ProjectDescriptor projectDescriptor = context.getProjectDescriptor();
     for (BuildTargetType<?> type : JavaModuleBuildTargetType.ALL_TYPES) {
       for (BuildTarget<?> target : projectDescriptor.getBuildTargetIndex().getAllTargets(type)) {
         for (BuildRootDescriptor descriptor : projectDescriptor.getBuildRootIndex().getTargetRoots(target, context)) {
@@ -340,7 +328,7 @@ public class IncProjectBuilder {
 
     // check that output and source roots are not overlapping
     final List<File> filesToDelete = new ArrayList<File>();
-    for (Map.Entry<File, Collection<ModuleBuildTarget>> entry : rootsToDelete.entrySet()) {
+    for (Map.Entry<File, Collection<BuildTarget<?>>> entry : rootsToDelete.entrySet()) {
       context.checkCanceled();
       boolean okToDelete = true;
       final File outputRoot = entry.getKey();
@@ -366,12 +354,24 @@ public class IncProjectBuilder {
       else {
         context.processMessage(new CompilerMessage(BUILD_NAME, BuildMessage.Kind.WARNING, "Output path " + outputRoot.getPath() + " intersects with a source root. The output cannot be cleaned."));
         // clean only those files we are aware of
-        for (ModuleBuildTarget target : entry.getValue()) {
+        for (BuildTarget<?> target : entry.getValue()) {
           clearOutputFiles(context, target);
         }
       }
     }
 
+    final Set<File> annotationOutputs = new HashSet<File>(); // separate collection because no root intersection checks needed for annotation generated sources
+    for (JavaModuleBuildTargetType type : JavaModuleBuildTargetType.ALL_TYPES) {
+      for (ModuleBuildTarget target : projectDescriptor.getBuildTargetIndex().getAllTargets(type)) {
+        final ProcessorConfigProfile profile = context.getAnnotationProcessingProfile(target.getModule());
+        if (profile.isEnabled()) {
+          File annotationOut = paths.getAnnotationProcessorGeneratedSourcesOutputDir(target.getModule(), target.isTests(), profile.getGeneratedSourcesDirectoryName());
+          if (annotationOut != null) {
+            annotationOutputs.add(annotationOut);
+          }
+        }
+      }
+    }
     for (File annotationOutput : annotationOutputs) {
       // do not delete output root itself to avoid lots of unnecessary "roots_changed" events in IDEA
       final File[] children = annotationOutput.listFiles();
@@ -649,26 +649,23 @@ public class IncProjectBuilder {
   }
 
   private static void createClasspathIndex(final ModuleChunk chunk) {
-    final Set<File> outputPaths = new LinkedHashSet<File>();
+    final Set<File> outputDirs = new THashSet<File>(FileUtil.FILE_HASHING_STRATEGY);
     for (ModuleBuildTarget target : chunk.getTargets()) {
-      final File outputDir = JpsJavaExtensionService.getInstance().getOutputDirectory(target.getModule(), target.isTests());
-      if (outputDir != null) {
-        outputPaths.add(outputDir);
-      }
-    }
-    for (File outputRoot : outputPaths) {
-      try {
-        BufferedWriter writer = new BufferedWriter(new FileWriter(new File(outputRoot, CLASSPATH_INDEX_FINE_NAME)));
+      File outputDir = target.getOutputDir();
+      if (outputDir != null && outputDirs.add(outputDir)) {
         try {
-          writeIndex(writer, outputRoot, "");
+          BufferedWriter writer = new BufferedWriter(new FileWriter(new File(outputDir, CLASSPATH_INDEX_FINE_NAME)));
+          try {
+            writeIndex(writer, outputDir, "");
+          }
+          finally {
+            writer.close();
+          }
         }
-        finally {
-          writer.close();
+        catch (IOException e) {
+          // Ignore. Failed to create optional classpath index
         }
       }
-      catch (IOException e) {
-        // Ignore. Failed to create optional classpath index
-      }
     }
   }
 
@@ -964,7 +961,7 @@ public class IncProjectBuilder {
         if (context.isMake()) {
           if (pd.fsState.markInitialScanPerformed(target)) {
             boolean forceMarkDirty = false;
-            final File currentOutput = context.getProjectPaths().getModuleOutputDir(target.getModule(), target.isTests());
+            final File currentOutput = target.getOutputDir();
             if (currentOutput != null) {
               final Pair<String, String> outputsPair = pd.dataManager.getOutputRootsLayout().getState(target.getModuleName());
               if (outputsPair != null) {
@@ -1011,7 +1008,7 @@ public class IncProjectBuilder {
   }
 
   private static void updateOutputRootsLayout(CompileContext context, ModuleBuildTarget target) throws IOException {
-    final File currentOutput = context.getProjectPaths().getModuleOutputDir(target.getModule(), target.isTests());
+    final File currentOutput = target.getOutputDir();
     if (currentOutput == null) {
       return;
     }
diff --git a/jps/jps-builders/src/org/jetbrains/jps/incremental/ModuleBuildTarget.java b/jps/jps-builders/src/org/jetbrains/jps/incremental/ModuleBuildTarget.java
index 99f5a4bc23a9..16803ac7a2a1 100644
--- a/jps/jps-builders/src/org/jetbrains/jps/incremental/ModuleBuildTarget.java
+++ b/jps/jps-builders/src/org/jetbrains/jps/incremental/ModuleBuildTarget.java
@@ -3,12 +3,12 @@ package org.jetbrains.jps.incremental;
 import com.intellij.util.Consumer;
 import com.intellij.util.containers.ContainerUtil;
 import org.jetbrains.annotations.NotNull;
-import org.jetbrains.jps.builders.storage.BuildDataPaths;
-import org.jetbrains.jps.util.JpsPathUtil;
+import org.jetbrains.annotations.Nullable;
 import org.jetbrains.jps.builders.BuildRootIndex;
 import org.jetbrains.jps.builders.BuildTarget;
 import org.jetbrains.jps.builders.java.JavaModuleBuildTargetType;
 import org.jetbrains.jps.builders.java.JavaSourceRootDescriptor;
+import org.jetbrains.jps.builders.storage.BuildDataPaths;
 import org.jetbrains.jps.indices.IgnoredFileIndex;
 import org.jetbrains.jps.indices.ModuleExcludeIndex;
 import org.jetbrains.jps.model.JpsModel;
@@ -19,6 +19,7 @@ import org.jetbrains.jps.model.java.JpsJavaDependenciesEnumerator;
 import org.jetbrains.jps.model.java.JpsJavaExtensionService;
 import org.jetbrains.jps.model.module.JpsModule;
 import org.jetbrains.jps.model.module.JpsTypedModuleSourceRoot;
+import org.jetbrains.jps.util.JpsPathUtil;
 
 import java.io.File;
 import java.util.ArrayList;
@@ -41,6 +42,17 @@ public class ModuleBuildTarget extends BuildTarget<JavaSourceRootDescriptor> {
     myModule = module;
   }
 
+  @Nullable
+  public File getOutputDir() {
+    return JpsJavaExtensionService.getInstance().getOutputDirectory(myModule, myTargetType.isTests());
+  }
+
+  @Nullable
+  @Override
+  public File getOutputDir(BuildDataPaths paths) {
+    return getOutputDir();
+  }
+
   @NotNull
   public JpsModule getModule() {
     return myModule;
diff --git a/jps/jps-builders/src/org/jetbrains/jps/incremental/artifacts/ArtifactBuildTarget.java b/jps/jps-builders/src/org/jetbrains/jps/incremental/artifacts/ArtifactBuildTarget.java
index 5cbffd1bc4f3..e4b4d5487548 100644
--- a/jps/jps-builders/src/org/jetbrains/jps/incremental/artifacts/ArtifactBuildTarget.java
+++ b/jps/jps-builders/src/org/jetbrains/jps/incremental/artifacts/ArtifactBuildTarget.java
@@ -1,8 +1,10 @@
 package org.jetbrains.jps.incremental.artifacts;
 
+import com.intellij.openapi.util.io.FileUtil;
 import com.intellij.openapi.util.text.StringUtil;
 import com.intellij.util.Processor;
 import org.jetbrains.annotations.NotNull;
+import org.jetbrains.annotations.Nullable;
 import org.jetbrains.jps.builders.BuildRootDescriptor;
 import org.jetbrains.jps.builders.BuildRootIndex;
 import org.jetbrains.jps.builders.BuildTarget;
@@ -17,6 +19,7 @@ import org.jetbrains.jps.model.artifact.JpsArtifact;
 import org.jetbrains.jps.model.artifact.elements.JpsArtifactOutputPackagingElement;
 import org.jetbrains.jps.model.artifact.elements.JpsPackagingElement;
 
+import java.io.File;
 import java.io.PrintWriter;
 import java.util.Collection;
 import java.util.LinkedHashSet;
@@ -110,4 +113,11 @@ public class ArtifactBuildTarget extends BuildTarget<ArtifactRootDescriptor> {
   public String getPresentableName() {
     return "Artifact '" + myArtifact.getName() + "'";
   }
+
+  @Nullable
+  @Override
+  public File getOutputDir(BuildDataPaths paths) {
+    String outputPath = myArtifact.getOutputPath();
+    return !StringUtil.isEmpty(outputPath) ? new File(FileUtil.toSystemDependentName(outputPath)) : null;
+  }
 }
diff --git a/jps/jps-builders/src/org/jetbrains/jps/incremental/java/JavaBuilder.java b/jps/jps-builders/src/org/jetbrains/jps/incremental/java/JavaBuilder.java
index a9c87ffb6413..6b2a6cc45b16 100644
--- a/jps/jps-builders/src/org/jetbrains/jps/incremental/java/JavaBuilder.java
+++ b/jps/jps-builders/src/org/jetbrains/jps/incremental/java/JavaBuilder.java
@@ -368,11 +368,13 @@ public class JavaBuilder extends ModuleLevelBuilder {
                 instrumentForms(context, chunk, chunkSourcePath, finder, forms, outputSink);
                 JpsUiDesignerConfiguration configuration = JpsUiDesignerExtensionService.getInstance().getUiDesignerConfiguration(
                   pd.getProject());
-                if (configuration != null && configuration.isCopyFormsRuntimeToOutput() && !chunk.containsTests()) {
-                  for (JpsModule module : chunk.getModules()) {
-                    final File outputDir = paths.getModuleOutputDir(module, false);
-                    if (outputDir != null) {
-                      CopyResourcesUtil.copyFormsRuntime(outputDir.getAbsolutePath(), false);
+                if (configuration != null && configuration.isCopyFormsRuntimeToOutput()) {
+                  for (ModuleBuildTarget target : chunk.getTargets()) {
+                    if (!target.isTests()) {
+                      final File outputDir = target.getOutputDir();
+                      if (outputDir != null) {
+                        CopyResourcesUtil.copyFormsRuntime(outputDir.getAbsolutePath(), false);
+                      }
                     }
                   }
                 }
@@ -888,7 +890,7 @@ public class JavaBuilder extends ModuleLevelBuilder {
   private static Map<File, Set<File>> buildOutputDirectoriesMap(CompileContext context, ModuleChunk chunk) {
     final Map<File, Set<File>> map = new LinkedHashMap<File, Set<File>>();
     for (ModuleBuildTarget target : chunk.getTargets()) {
-      final File outputDir = JpsJavaExtensionService.getInstance().getOutputDirectory(target.getModule(), target.isTests());
+      final File outputDir = target.getOutputDir();
       if (outputDir == null) {
         continue;
       }
diff --git a/jps/jps-builders/testSrc/org/jetbrains/jps/incremental/artifacts/ArtifactBuilderTest.java b/jps/jps-builders/testSrc/org/jetbrains/jps/incremental/artifacts/ArtifactBuilderTest.java
index fc8d6dd00d27..506004b2853e 100644
--- a/jps/jps-builders/testSrc/org/jetbrains/jps/incremental/artifacts/ArtifactBuilderTest.java
+++ b/jps/jps-builders/testSrc/org/jetbrains/jps/incremental/artifacts/ArtifactBuilderTest.java
@@ -2,10 +2,10 @@ package org.jetbrains.jps.incremental.artifacts;
 
 import com.intellij.openapi.util.io.FileUtil;
 import com.intellij.util.PathUtil;
-import org.jetbrains.jps.util.JpsPathUtil;
 import org.jetbrains.jps.model.artifact.JpsArtifact;
 import org.jetbrains.jps.model.library.JpsLibrary;
 import org.jetbrains.jps.model.module.JpsModule;
+import org.jetbrains.jps.util.JpsPathUtil;
 
 import java.io.File;
 import java.io.IOException;
@@ -269,4 +269,15 @@ public class ArtifactBuilderTest extends ArtifactBuilderTestCase {
     }
   }
 
+  public void testClearOutputOnRebuild() throws IOException {
+    String file = createFile("d/a.txt");
+    JpsArtifact a = addArtifact(root().parentDirCopy(file));
+    buildAll();
+    new File(a.getOutputPath(), "b.txt").createNewFile();
+    buildAllAndAssertUpToDate();
+    assertOutput(a, fs().file("a.txt").file("b.txt"));
+
+    rebuildAll();
+    assertOutput(a, fs().file("a.txt"));
+  }
 }
diff --git a/jps/model-impl/src/org/jetbrains/jps/model/java/impl/compiler/JpsJavaCompilerConfigurationImpl.java b/jps/model-impl/src/org/jetbrains/jps/model/java/impl/compiler/JpsJavaCompilerConfigurationImpl.java
index db50e4297b2f..e805d539edbf 100644
--- a/jps/model-impl/src/org/jetbrains/jps/model/java/impl/compiler/JpsJavaCompilerConfigurationImpl.java
+++ b/jps/model-impl/src/org/jetbrains/jps/model/java/impl/compiler/JpsJavaCompilerConfigurationImpl.java
@@ -18,7 +18,7 @@ import java.util.*;
 public class JpsJavaCompilerConfigurationImpl extends JpsCompositeElementBase<JpsJavaCompilerConfigurationImpl> implements JpsJavaCompilerConfiguration {
   public static final JpsElementChildRole<JpsJavaCompilerConfiguration> ROLE = JpsElementChildRoleBase.create("compiler configuration");
   private boolean myAddNotNullAssertions = true;
-  private boolean myClearOutputDirectoryOnRebuild;
+  private boolean myClearOutputDirectoryOnRebuild = true;
   private JpsCompilerExcludes myCompilerExcludes = new JpsCompilerExcludesImpl();
   private List<String> myResourcePatterns = new ArrayList<String>();
   private List<ProcessorConfigProfile> myAnnotationProcessingProfiles = new ArrayList<ProcessorConfigProfile>();
diff --git a/plugins/android/jps-plugin/src/org/jetbrains/jps/android/builder/AndroidProjectBuildTarget.java b/plugins/android/jps-plugin/src/org/jetbrains/jps/android/builder/AndroidProjectBuildTarget.java
index 63be2b1e1b27..3f079a4e6cfd 100644
--- a/plugins/android/jps-plugin/src/org/jetbrains/jps/android/builder/AndroidProjectBuildTarget.java
+++ b/plugins/android/jps-plugin/src/org/jetbrains/jps/android/builder/AndroidProjectBuildTarget.java
@@ -29,6 +29,7 @@ import org.jetbrains.jps.indices.ModuleExcludeIndex;
 import org.jetbrains.jps.model.JpsModel;
 import org.jetbrains.jps.model.module.JpsModule;
 
+import java.io.File;
 import java.util.*;
 
 /**
@@ -105,7 +106,13 @@ public class AndroidProjectBuildTarget extends BuildTarget<BuildRootDescriptor>
   public String getPresentableName() {
     return "Android " + myKind.name();
   }
-  
+
+  @Nullable
+  @Override
+  public File getOutputDir(BuildDataPaths paths) {
+    return null;
+  }
+
   public static class TargetType extends BuildTargetType<AndroidProjectBuildTarget> {
     public static final TargetType INSTANCE = new TargetType();
 
diff --git a/plugins/groovy/jps-plugin/src/org/jetbrains/jps/incremental/groovy/GroovyBuilder.java b/plugins/groovy/jps-plugin/src/org/jetbrains/jps/incremental/groovy/GroovyBuilder.java
index c6a67bc14898..6eb82bcd3908 100644
--- a/plugins/groovy/jps-plugin/src/org/jetbrains/jps/incremental/groovy/GroovyBuilder.java
+++ b/plugins/groovy/jps-plugin/src/org/jetbrains/jps/incremental/groovy/GroovyBuilder.java
@@ -189,7 +189,7 @@ public class GroovyBuilder extends ModuleLevelBuilder {
   private static Map<ModuleBuildTarget, String> getCanonicalModuleOutputs(CompileContext context, ModuleChunk chunk) {
     Map<ModuleBuildTarget, String> finalOutputs = new HashMap<ModuleBuildTarget, String>();
     for (ModuleBuildTarget target : chunk.getTargets()) {
-      File moduleOutputDir = context.getProjectPaths().getModuleOutputDir(target.getModule(), target.isTests());
+      File moduleOutputDir = target.getOutputDir();
       if (moduleOutputDir == null) {
         context.processMessage(new CompilerMessage(BUILDER_NAME, BuildMessage.Kind.ERROR, "Output directory not specified for module " + target.getModuleName()));
         return null;