diff --git a/compiler/backend/src/org/jetbrains/jet/codegen/CodegenUtil.java b/compiler/backend/src/org/jetbrains/jet/codegen/CodegenUtil.java
index b5f4aeb7381..38753e4e0cf 100644
--- a/compiler/backend/src/org/jetbrains/jet/codegen/CodegenUtil.java
+++ b/compiler/backend/src/org/jetbrains/jet/codegen/CodegenUtil.java
@@ -18,7 +18,7 @@ package org.jetbrains.jet.codegen;
 
 import com.intellij.openapi.util.Condition;
 import com.intellij.openapi.util.io.FileUtil;
-import com.intellij.psi.PsiFile;
+import com.intellij.openapi.vfs.VirtualFile;
 import com.intellij.util.containers.ContainerUtil;
 import com.intellij.util.containers.Stack;
 import org.jetbrains.annotations.NotNull;
@@ -269,11 +269,11 @@ public class CodegenUtil {
         return ((ImplementationBodyCodegen) classBodyCodegen.getParentCodegen());
     }
 
-    static int getPathHashCode(@NotNull PsiFile file) {
+    static int getPathHashCode(@NotNull VirtualFile file) {
         // Conversion to system-dependent name seems to be unnecessary, but it's hard to check now:
         // it was introduced when fixing KT-2839, which appeared again (KT-3639).
         // If you try to remove it, run tests on Windows.
-        return FileUtil.toSystemDependentName(file.getVirtualFile().getPath()).hashCode();
+        return FileUtil.toSystemDependentName(file.getPath()).hashCode();
     }
 
     @Nullable
diff --git a/compiler/backend/src/org/jetbrains/jet/codegen/NamespaceCodegen.java b/compiler/backend/src/org/jetbrains/jet/codegen/NamespaceCodegen.java
index 7f21b86a083..3ba136af3e6 100644
--- a/compiler/backend/src/org/jetbrains/jet/codegen/NamespaceCodegen.java
+++ b/compiler/backend/src/org/jetbrains/jet/codegen/NamespaceCodegen.java
@@ -186,7 +186,7 @@ public class NamespaceCodegen extends MemberCodegen {
 
         if (!generateSrcClass) return null;
 
-        Type packageFragmentType = getNamespacePartType(getPackageClassFqName(name), file);
+        Type packageFragmentType = getNamespacePartType(getPackageClassFqName(name), file.getVirtualFile());
         ClassBuilder builder = state.getFactory().forPackageFragment(packageFragmentType, file);
 
         new NamespacePartCodegen(builder, file, packageFragmentType, packageFragmentContext, state).generate();
@@ -247,7 +247,7 @@ public class NamespaceCodegen extends MemberCodegen {
     }
 
     @NotNull
-    private static Type getNamespacePartType(@NotNull FqName facadeFqName, @NotNull PsiFile file) {
+    public static Type getNamespacePartType(@NotNull FqName facadeFqName, @NotNull VirtualFile file) {
         String fileName = FileUtil.getNameWithoutExtension(PathUtil.getFileName(file.getName()));
 
         // path hashCode to prevent same name / different path collision
@@ -267,6 +267,6 @@ public class NamespaceCodegen extends MemberCodegen {
     @NotNull
     public static String getNamespacePartInternalName(@NotNull JetFile file) {
         FqName packageFqName = JetPsiUtil.getFQName(file);
-        return getNamespacePartType(getPackageClassFqName(packageFqName), file).getInternalName();
+        return getNamespacePartType(getPackageClassFqName(packageFqName), file.getVirtualFile()).getInternalName();
     }
 }
diff --git a/compiler/backend/src/org/jetbrains/jet/codegen/SamWrapperCodegen.java b/compiler/backend/src/org/jetbrains/jet/codegen/SamWrapperCodegen.java
index 000f9c000a0..573adaea586 100644
--- a/compiler/backend/src/org/jetbrains/jet/codegen/SamWrapperCodegen.java
+++ b/compiler/backend/src/org/jetbrains/jet/codegen/SamWrapperCodegen.java
@@ -16,6 +16,7 @@
 
 package org.jetbrains.jet.codegen;
 
+import com.intellij.openapi.vfs.VirtualFile;
 import org.jetbrains.annotations.NotNull;
 import org.jetbrains.annotations.Nullable;
 import org.jetbrains.asm4.MethodVisitor;
@@ -134,11 +135,12 @@ public class SamWrapperCodegen extends ParentCodegenAwareImpl {
 
     private String getWrapperName(@NotNull JetFile containingFile) {
         NamespaceDescriptor namespace = state.getBindingContext().get(BindingContext.FILE_TO_NAMESPACE, containingFile);
-        assert namespace != null : "couldn't find namespace for file: " + containingFile.getVirtualFile();
+        VirtualFile virtualFile = containingFile.getVirtualFile();
+        assert namespace != null : "couldn't find namespace for file: " + virtualFile;
         FqName fqName = DescriptorUtils.getFQName(namespace).toSafe();
         String packageInternalName = JvmClassName.byFqNameWithoutInnerClasses(
                 PackageClassUtils.getPackageClassFqName(fqName)).getInternalName();
         return packageInternalName + "$sam$" + samInterface.getName().asString() + "$" +
-               Integer.toHexString(CodegenUtil.getPathHashCode(containingFile) * 31 + DescriptorUtils.getFQName(samInterface).hashCode());
+               Integer.toHexString(CodegenUtil.getPathHashCode(virtualFile) * 31 + DescriptorUtils.getFQName(samInterface).hashCode());
     }
 }
diff --git a/jps-plugin/jps-plugin.iml b/jps-plugin/jps-plugin.iml
index 83efc10247f..c3a06774179 100644
--- a/jps-plugin/jps-plugin.iml
+++ b/jps-plugin/jps-plugin.iml
@@ -14,6 +14,8 @@
     <orderEntry type="library" name="jps" level="project" />
     <orderEntry type="library" scope="TEST" name="jps-test" level="project" />
     <orderEntry type="library" scope="TEST" name="idea-full" level="project" />
+    <orderEntry type="module" module-name="backend" scope="TEST" />
+    <orderEntry type="module" module-name="descriptors" scope="TEST" />
   </component>
 </module>
 
diff --git a/jps-plugin/src/org/jetbrains/jet/jps/build/KotlinBuilder.java b/jps-plugin/src/org/jetbrains/jet/jps/build/KotlinBuilder.java
index 7b72857b7c6..70e32c89e5e 100644
--- a/jps-plugin/src/org/jetbrains/jet/jps/build/KotlinBuilder.java
+++ b/jps-plugin/src/org/jetbrains/jet/jps/build/KotlinBuilder.java
@@ -34,6 +34,7 @@ import org.jetbrains.jet.compiler.runner.SimpleOutputItem;
 import org.jetbrains.jet.jps.JpsKotlinCompilerSettings;
 import org.jetbrains.jet.utils.PathUtil;
 import org.jetbrains.jps.ModuleChunk;
+import org.jetbrains.jps.builders.BuildTarget;
 import org.jetbrains.jps.builders.DirtyFilesHolder;
 import org.jetbrains.jps.builders.java.JavaSourceRootDescriptor;
 import org.jetbrains.jps.incremental.*;
@@ -47,10 +48,7 @@ import java.io.File;
 import java.io.IOException;
 import java.lang.reflect.Field;
 import java.lang.reflect.Modifier;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.List;
-import java.util.Set;
+import java.util.*;
 
 import static org.jetbrains.jet.cli.common.messages.CompilerMessageSeverity.*;
 import static org.jetbrains.jet.compiler.runner.KotlinCompilerRunner.runK2JsCompiler;
@@ -165,9 +163,20 @@ public class KotlinBuilder extends ModuleLevelBuilder {
             runK2JvmCompiler(commonSettings, k2JvmSettings, messageCollector, environment, moduleFile, outputItemCollector);
         }
 
+        // If there's only one target, this map is empty: get() always returns null, and the representativeTarget will be used below
+        Map<File, BuildTarget<?>> sourceToTarget = new HashMap<File, BuildTarget<?>>();
+        if (chunk.getTargets().size() > 1) {
+            for (ModuleBuildTarget target : chunk.getTargets()) {
+                for (File file : KotlinSourceFileCollector.getAllKotlinSourceFiles(target)) {
+                    sourceToTarget.put(file, target);
+                }
+            }
+        }
+
         for (SimpleOutputItem outputItem : outputItemCollector.getOutputs()) {
+            BuildTarget<?> target = sourceToTarget.get(outputItem.getSourceFiles().iterator().next());
             outputConsumer.registerOutputFile(
-                    representativeTarget,
+                    target != null ? target : representativeTarget,
                     outputItem.getOutputFile(),
                     paths(outputItem.getSourceFiles()));
         }
diff --git a/jps-plugin/test/org/jetbrains/jet/jps/build/KotlinJpsBuildTestCase.java b/jps-plugin/test/org/jetbrains/jet/jps/build/KotlinJpsBuildTestCase.java
index 1a7320ee144..ac6b16c4fde 100644
--- a/jps-plugin/test/org/jetbrains/jet/jps/build/KotlinJpsBuildTestCase.java
+++ b/jps-plugin/test/org/jetbrains/jet/jps/build/KotlinJpsBuildTestCase.java
@@ -18,7 +18,10 @@ package org.jetbrains.jet.jps.build;
 
 import com.intellij.openapi.util.Condition;
 import com.intellij.openapi.util.io.FileUtil;
+import com.intellij.testFramework.LightVirtualFile;
 import com.intellij.util.containers.ContainerUtil;
+import org.jetbrains.jet.codegen.NamespaceCodegen;
+import org.jetbrains.jet.lang.resolve.name.FqName;
 import org.jetbrains.jps.builders.BuildResult;
 import org.jetbrains.jps.model.java.JpsJavaDependencyScope;
 import org.jetbrains.jps.model.java.JpsJavaExtensionService;
@@ -26,6 +29,7 @@ import org.jetbrains.jps.model.module.JpsModule;
 import org.jetbrains.jps.util.JpsPathUtil;
 
 import java.io.File;
+import java.io.IOException;
 
 public class KotlinJpsBuildTestCase extends AbstractKotlinJpsBuildTestCase {
     private static final String PROJECT_NAME = "kotlinProject";
@@ -36,6 +40,7 @@ public class KotlinJpsBuildTestCase extends AbstractKotlinJpsBuildTestCase {
         super.setUp();
         File sourceFilesRoot = new File(TEST_DATA_PATH + getTestName(false));
         workDir = copyTestDataToTmpDir(sourceFilesRoot);
+        getOrCreateProjectDir();
     }
 
     @Override
@@ -44,6 +49,11 @@ public class KotlinJpsBuildTestCase extends AbstractKotlinJpsBuildTestCase {
         super.tearDown();
     }
 
+    @Override
+    protected File doGetProjectDir() throws IOException {
+        return workDir;
+    }
+
     private void initProject() {
         addJdk(JDK_NAME);
         loadProject(workDir.getAbsolutePath() + File.separator + PROJECT_NAME + ".ipr");
@@ -62,6 +72,15 @@ public class KotlinJpsBuildTestCase extends AbstractKotlinJpsBuildTestCase {
 
     public void testKotlinProject() {
         doTest();
+
+        assertOutputDeleted("src/test1.kt", "_DefaultPackage", "kotlinProject");
+    }
+
+    public void testKotlinProjectTwoFilesInOnePackage() {
+        doTest();
+
+        assertOutputDeleted("src/test1.kt", "_DefaultPackage", "kotlinProject");
+        assertOutputDeleted("src/test2.kt", "_DefaultPackage", "kotlinProject");
     }
 
     public void testKotlinJavaProject() {
@@ -106,14 +125,9 @@ public class KotlinJpsBuildTestCase extends AbstractKotlinJpsBuildTestCase {
             }
         }
         result.assertSuccessful();
-    }
 
-    public void testTestDependencyLibrary() throws Throwable {
-        initProject();
-        addKotlinRuntimeDependency(JpsJavaDependencyScope.TEST, myProject.getModules(), false);
-        makeAll().assertSuccessful();
-        change(workDir + "/src/src.kt", "fun foo() { println() }");
-        makeAll().assertFailed();
+        assertOutputDeleted("src/kt2.kt", "kt2.Kt2Package", "kotlinProject");
+        assertOutputDeleted("module2/src/kt1.kt", "kt1.Kt1Package", "module2");
     }
 
     public void testReexportedDependency() {
@@ -133,7 +147,10 @@ public class KotlinJpsBuildTestCase extends AbstractKotlinJpsBuildTestCase {
         assertNotNull(outputUrl);
         File outputDir = new File(JpsPathUtil.urlToPath(outputUrl));
         File outputFile = new File(outputDir, relativePath);
-        assertTrue("Output not written: " + outputFile.getAbsolutePath() + "\n Directory contents: \n" + dirContents(outputFile.getParentFile()),
+        assertTrue("Output not written: " +
+                   outputFile.getAbsolutePath() +
+                   "\n Directory contents: \n" +
+                   dirContents(outputFile.getParentFile()),
                    outputFile.exists());
     }
 
@@ -148,4 +165,25 @@ public class KotlinJpsBuildTestCase extends AbstractKotlinJpsBuildTestCase {
         }
         return builder.toString();
     }
+
+    private void assertOutputDeleted(String sourceFileName, String packageClassFqName, String moduleName) {
+        File file = new File(workDir, sourceFileName);
+        change(file.getAbsolutePath());
+        makeAll();
+
+        String outputDirPrefix = "out/production/" + moduleName + "/";
+        assertDeleted(outputDirPrefix + packageClassFqName.replace('.', '/') + ".class",
+                      outputDirPrefix + getInternalNameForPackagePartClass(file, packageClassFqName) + ".class");
+    }
+
+    private static String getInternalNameForPackagePartClass(File sourceFile, String packageClassFqName) {
+        LightVirtualFile fakeVirtualFile = new LightVirtualFile(sourceFile.getPath()) {
+            @Override
+            public String getPath() {
+                // strip extra "/" from the beginning
+                return super.getPath().substring(1);
+            }
+        };
+        return NamespaceCodegen.getNamespacePartType(new FqName(packageClassFqName), fakeVirtualFile).getInternalName();
+    }
 }
diff --git a/jps-plugin/testData/KotlinProjectTwoFilesInOnePackage/kotlinProject.iml b/jps-plugin/testData/KotlinProjectTwoFilesInOnePackage/kotlinProject.iml
new file mode 100644
index 00000000000..a0cbe548242
--- /dev/null
+++ b/jps-plugin/testData/KotlinProjectTwoFilesInOnePackage/kotlinProject.iml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="JAVA_MODULE" version="4">
+  <component name="NewModuleRootManager" inherit-compiler-output="true">
+    <exclude-output />
+    <content url="file://$MODULE_DIR$">
+      <sourceFolder url="file://$MODULE_DIR$/src" isTestSource="false" />
+    </content>
+    <orderEntry type="jdk" jdkName="IDEA_JDK" jdkType="JavaSDK" />
+    <orderEntry type="sourceFolder" forTests="false" />
+    <orderEntry type="module" module-name="kotlinProject" />
+  </component>
+</module>
diff --git a/jps-plugin/testData/KotlinProjectTwoFilesInOnePackage/kotlinProject.ipr b/jps-plugin/testData/KotlinProjectTwoFilesInOnePackage/kotlinProject.ipr
new file mode 100644
index 00000000000..90747786771
--- /dev/null
+++ b/jps-plugin/testData/KotlinProjectTwoFilesInOnePackage/kotlinProject.ipr
@@ -0,0 +1,14 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="CompilerConfiguration">
+    <option name="DEFAULT_COMPILER" value="Javac" />
+  </component>
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/kotlinProject.iml" filepath="$PROJECT_DIR$/kotlinProject.iml" />
+    </modules>
+  </component>
+  <component name="ProjectRootManager" version="2" languageLevel="JDK_1_6" assert-keyword="true" jdk-15="true" project-jdk-name="IDEA_JDK" project-jdk-type="JavaSDK">
+    <output url="file://$PROJECT_DIR$/out" />
+  </component>
+</project>
\ No newline at end of file
diff --git a/jps-plugin/testData/KotlinProjectTwoFilesInOnePackage/src/test1.kt b/jps-plugin/testData/KotlinProjectTwoFilesInOnePackage/src/test1.kt
new file mode 100644
index 00000000000..a2c4e958bb5
--- /dev/null
+++ b/jps-plugin/testData/KotlinProjectTwoFilesInOnePackage/src/test1.kt
@@ -0,0 +1,3 @@
+fun foo() {
+
+}
\ No newline at end of file
diff --git a/jps-plugin/testData/KotlinProjectTwoFilesInOnePackage/src/test2.kt b/jps-plugin/testData/KotlinProjectTwoFilesInOnePackage/src/test2.kt
new file mode 100644
index 00000000000..6ec77d22887
--- /dev/null
+++ b/jps-plugin/testData/KotlinProjectTwoFilesInOnePackage/src/test2.kt
@@ -0,0 +1,3 @@
+fun bar() {
+
+}
\ No newline at end of file