diff --git a/compiler/cli/src/org/jetbrains/kotlin/cli/js/K2JSCompiler.java b/compiler/cli/src/org/jetbrains/kotlin/cli/js/K2JSCompiler.java
index 1854d6f0030..4c1bf991ec2 100644
--- a/compiler/cli/src/org/jetbrains/kotlin/cli/js/K2JSCompiler.java
+++ b/compiler/cli/src/org/jetbrains/kotlin/cli/js/K2JSCompiler.java
@@ -45,10 +45,10 @@ import org.jetbrains.kotlin.cli.common.messages.CompilerMessageSeverity;
 import org.jetbrains.kotlin.cli.common.messages.MessageCollector;
 import org.jetbrains.kotlin.cli.common.output.outputUtils.OutputUtilsPackage;
 import org.jetbrains.kotlin.cli.jvm.JVMConfigurationKeys;
-import org.jetbrains.kotlin.cli.jvm.compiler.CompileEnvironmentUtil;
 import org.jetbrains.kotlin.cli.jvm.compiler.CompilerJarLocator;
 import org.jetbrains.kotlin.cli.jvm.compiler.EnvironmentConfigFiles;
 import org.jetbrains.kotlin.cli.jvm.compiler.JetCoreEnvironment;
+import org.jetbrains.kotlin.config.CommonConfigurationKeys;
 import org.jetbrains.kotlin.config.CompilerConfiguration;
 import org.jetbrains.kotlin.config.Services;
 import org.jetbrains.kotlin.js.analyze.TopDownAnalyzerFacadeForJS;
@@ -103,7 +103,7 @@ public class K2JSCompiler extends CLICompiler<K2JSCompilerArguments> {
             configuration.put(JVMConfigurationKeys.COMPILER_JAR_LOCATOR, locator);
         }
 
-        CompileEnvironmentUtil.addSourceFilesCheckingForDuplicates(configuration, arguments.freeArgs);
+        configuration.addAll(CommonConfigurationKeys.SOURCE_ROOTS_KEY, arguments.freeArgs);
         JetCoreEnvironment environmentForJS =
                 JetCoreEnvironment.createForProduction(rootDisposable, configuration, EnvironmentConfigFiles.JS_CONFIG_FILES);
 
diff --git a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/K2JVMCompiler.java b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/K2JVMCompiler.java
index d2f2a7c665e..9cb6863f094 100644
--- a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/K2JVMCompiler.java
+++ b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/K2JVMCompiler.java
@@ -99,7 +99,7 @@ public class K2JVMCompiler extends CLICompiler<K2JVMCompilerArguments> {
             configuration.add(CommonConfigurationKeys.SOURCE_ROOTS_KEY, arguments.freeArgs.get(0));
         }
         else if (arguments.module == null) {
-            CompileEnvironmentUtil.addSourceFilesCheckingForDuplicates(configuration, arguments.freeArgs);
+            configuration.addAll(CommonConfigurationKeys.SOURCE_ROOTS_KEY, arguments.freeArgs);
 
             // Adding all directory sources to classpath to resolve Java symbols from Kotlin
             for (String source : arguments.freeArgs) {
diff --git a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/CompileEnvironmentUtil.java b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/CompileEnvironmentUtil.java
index 37ad12ef390..b1b40f1d5ea 100644
--- a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/CompileEnvironmentUtil.java
+++ b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/CompileEnvironmentUtil.java
@@ -64,6 +64,7 @@ import java.net.MalformedURLException;
 import java.net.URL;
 import java.net.URLClassLoader;
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.List;
 import java.util.Set;
 import java.util.jar.*;
@@ -271,7 +272,7 @@ public class CompileEnvironmentUtil {
     @NotNull
     public static List<JetFile> getJetFiles(
             @NotNull final Project project,
-            @NotNull List<String> sourceRoots,
+            @NotNull Collection<String> sourceRoots,
             @NotNull Function1<String, Unit> reportError
     ) {
         final VirtualFileSystem localFileSystem = VirtualFileManager.getInstance().getFileSystem(StandardFileSystems.FILE_PROTOCOL);
@@ -314,23 +315,4 @@ public class CompileEnvironmentUtil {
 
         return result;
     }
-
-    public static void addSourceFilesCheckingForDuplicates(@NotNull CompilerConfiguration configuration, @NotNull List<String> sourceRoots) {
-        MessageCollector messageCollector = configuration.get(CLIConfigurationKeys.MESSAGE_COLLECTOR_KEY);
-        assert messageCollector != null : "messageCollector should be set: " + configuration;
-
-        Set<String> uniqueSourceRoots = Sets.newLinkedHashSet();
-
-        for (String sourceRoot : sourceRoots) {
-            if (!uniqueSourceRoots.add(sourceRoot)) {
-                messageCollector.report(
-                        CompilerMessageSeverity.WARNING,
-                        "Duplicate source roots: " + sourceRoot,
-                        NO_LOCATION
-                );
-            }
-        }
-
-        configuration.put(CommonConfigurationKeys.SOURCE_ROOTS_KEY, new ArrayList<String>(uniqueSourceRoots));
-    }
 }
diff --git a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/JetCoreEnvironment.java b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/JetCoreEnvironment.java
index 6a2c116d9a8..050000cfcd8 100644
--- a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/JetCoreEnvironment.java
+++ b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/JetCoreEnvironment.java
@@ -16,6 +16,7 @@
 
 package org.jetbrains.kotlin.cli.jvm.compiler;
 
+import com.google.common.collect.Sets;
 import com.intellij.codeInsight.ExternalAnnotationsManager;
 import com.intellij.core.CoreApplicationEnvironment;
 import com.intellij.core.CoreJavaFileManager;
@@ -62,9 +63,7 @@ import org.jetbrains.kotlin.resolve.lazy.declarations.DeclarationProviderFactory
 import org.jetbrains.kotlin.utils.PathUtil;
 
 import java.io.File;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.List;
+import java.util.*;
 
 import static org.jetbrains.kotlin.cli.common.messages.CompilerMessageSeverity.ERROR;
 import static org.jetbrains.kotlin.cli.common.messages.CompilerMessageSeverity.WARNING;
@@ -231,17 +230,22 @@ public class JetCoreEnvironment {
             addExternalAnnotationsRoot(path);
         }
         sourceFiles.addAll(
-                CompileEnvironmentUtil
-                        .getJetFiles(getProject(), configuration.getList(CommonConfigurationKeys.SOURCE_ROOTS_KEY),
-                                     new Function1<String, Unit>() {
-                                         @Override
-                                         public Unit invoke(String s) {
-                                             report(ERROR, s);
-                                             return Unit.INSTANCE$;
-                                         }
-                                     }));
+                CompileEnvironmentUtil.getJetFiles(
+                        getProject(),
+                        getSourceRootsCheckingForDuplicates(),
+                        new Function1<String, Unit>() {
+                            @Override
+                            public Unit invoke(String s) {
+                                report(ERROR, s);
+                                return Unit.INSTANCE$;
+                            }
+                        }
+                )
+        );
+
         JetScriptDefinitionProvider.getInstance(project).addScriptDefinitions(
-                configuration.getList(CommonConfigurationKeys.SCRIPT_DEFINITIONS_KEY));
+                configuration.getList(CommonConfigurationKeys.SCRIPT_DEFINITIONS_KEY)
+        );
 
         project.registerService(VirtualFileFinderFactory.class, new CliVirtualFileFinderFactory(classPath));
     }
@@ -315,6 +319,19 @@ public class JetCoreEnvironment {
         }
     }
 
+    @NotNull
+    private Collection<String> getSourceRootsCheckingForDuplicates() {
+        Set<String> uniqueSourceRoots = Sets.newLinkedHashSet();
+
+        for (String sourceRoot : configuration.getList(CommonConfigurationKeys.SOURCE_ROOTS_KEY)) {
+            if (!uniqueSourceRoots.add(sourceRoot)) {
+                report(WARNING, "Duplicate source root: " + sourceRoot);
+            }
+        }
+
+        return uniqueSourceRoots;
+    }
+
     @NotNull
     public List<JetFile> getSourceFiles() {
         return sourceFiles;
diff --git a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinToJVMBytecodeCompiler.java b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinToJVMBytecodeCompiler.java
index bc797ea9368..4529bd71b31 100644
--- a/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinToJVMBytecodeCompiler.java
+++ b/compiler/cli/src/org/jetbrains/kotlin/cli/jvm/compiler/KotlinToJVMBytecodeCompiler.java
@@ -41,6 +41,7 @@ import org.jetbrains.kotlin.cli.jvm.JVMConfigurationKeys;
 import org.jetbrains.kotlin.codegen.*;
 import org.jetbrains.kotlin.codegen.state.GenerationState;
 import org.jetbrains.kotlin.codegen.state.Progress;
+import org.jetbrains.kotlin.config.CommonConfigurationKeys;
 import org.jetbrains.kotlin.config.CompilerConfiguration;
 import org.jetbrains.kotlin.context.ContextPackage;
 import org.jetbrains.kotlin.descriptors.impl.ModuleDescriptorImpl;
@@ -161,10 +162,8 @@ public class KotlinToJVMBytecodeCompiler {
     ) {
         CompilerConfiguration configuration = base.copy();
 
-        List<String> sourceRoots = Lists.newArrayList();
-
         for (Module module : chunk) {
-            sourceRoots.addAll(getAbsolutePaths(directory, module));
+            configuration.addAll(CommonConfigurationKeys.SOURCE_ROOTS_KEY, getAbsolutePaths(directory, module));
 
             for (String classpathRoot : module.getClasspathRoots()) {
                 configuration.add(JVMConfigurationKeys.CLASSPATH_KEY, new File(classpathRoot));
@@ -177,8 +176,6 @@ public class KotlinToJVMBytecodeCompiler {
             configuration.add(JVMConfigurationKeys.MODULE_IDS, module.getModuleName());
         }
 
-        CompileEnvironmentUtil.addSourceFilesCheckingForDuplicates(configuration, sourceRoots);
-
         return configuration;
     }
 
diff --git a/compiler/testData/cli/jvm/duplicateSources.out b/compiler/testData/cli/jvm/duplicateSources.out
index 3fa46d66e7c..633de589487 100644
--- a/compiler/testData/cli/jvm/duplicateSources.out
+++ b/compiler/testData/cli/jvm/duplicateSources.out
@@ -1,2 +1,2 @@
-WARNING: Duplicate source roots: compiler/testData/cli/jvm/simple.kt
+WARNING: Duplicate source root: compiler/testData/cli/jvm/simple.kt
 OK
\ No newline at end of file
diff --git a/compiler/testData/cli/jvm/duplicateSourcesInModule.out b/compiler/testData/cli/jvm/duplicateSourcesInModule.out
index 963b2b6e862..5bb55eaa0b3 100644
--- a/compiler/testData/cli/jvm/duplicateSourcesInModule.out
+++ b/compiler/testData/cli/jvm/duplicateSourcesInModule.out
@@ -1,2 +1,2 @@
-WARNING: Duplicate source roots: $TESTDATA_DIR$/duplicateSourcesInModule.kt
+WARNING: Duplicate source root: $TESTDATA_DIR$/duplicateSourcesInModule.kt
 OK
\ No newline at end of file