diff --git a/.idea/runConfigurations/Incremental_Compilation_Tests.xml b/.idea/runConfigurations/Incremental_Compilation_Tests.xml
deleted file mode 100644
index 73e4fa1f424..00000000000
--- a/.idea/runConfigurations/Incremental_Compilation_Tests.xml
+++ /dev/null
@@ -1,37 +0,0 @@
-<component name="ProjectRunConfigurationManager">
-  <configuration default="false" name="Incremental Compilation Tests" type="JUnit" factoryName="JUnit">
-    <extension name="coverage" enabled="false" merge="false" sample_coverage="true" runner="idea" />
-    <module name="jps-plugin" />
-    <option name="ALTERNATIVE_JRE_PATH_ENABLED" value="false" />
-    <option name="ALTERNATIVE_JRE_PATH" value="" />
-    <option name="PACKAGE_NAME" value="org.jetbrains.kotlin.jps.build" />
-    <option name="MAIN_CLASS_NAME" value="" />
-    <option name="METHOD_NAME" value="" />
-    <option name="TEST_OBJECT" value="pattern" />
-    <option name="VM_PARAMETERS" value="-ea -Xmx512m -XX:MaxPermSize=320m -Dkotlin.incremental.compilation=true" />
-    <option name="PARAMETERS" value="" />
-    <option name="WORKING_DIRECTORY" value="file://$PROJECT_DIR$" />
-    <option name="ENV_VARIABLES" />
-    <option name="PASS_PARENT_ENVS" value="true" />
-    <option name="TEST_SEARCH_SCOPE">
-      <value defaultName="moduleWithDependencies" />
-    </option>
-    <envs />
-    <patterns>
-      <pattern testClass="org.jetbrains.kotlin.jps.build.IncrementalJpsTestGenerated" />
-      <pattern testClass="org.jetbrains.kotlin.jps.build.IncrementalCacheVersionChangedTest" />
-      <pattern testClass="org.jetbrains.kotlin.jps.build.IncrementalConstantSearchTest" />
-    </patterns>
-    <RunnerSettings RunnerId="Debug">
-      <option name="DEBUG_PORT" value="" />
-      <option name="TRANSPORT" value="0" />
-      <option name="LOCAL" value="true" />
-    </RunnerSettings>
-    <RunnerSettings RunnerId="Run" />
-    <ConfigurationWrapper RunnerId="Debug" />
-    <ConfigurationWrapper RunnerId="Run" />
-    <method>
-      <option name="AntTarget" enabled="true" antfile="file://$PROJECT_DIR$/build.xml" target="dist-quick-compiler-only" />
-    </method>
-  </configuration>
-</component>
\ No newline at end of file
diff --git a/compiler/util/src/org/jetbrains/kotlin/config/IncrementalCompilation.java b/compiler/util/src/org/jetbrains/kotlin/config/IncrementalCompilation.java
index 5840c79425c..a44534feb0c 100644
--- a/compiler/util/src/org/jetbrains/kotlin/config/IncrementalCompilation.java
+++ b/compiler/util/src/org/jetbrains/kotlin/config/IncrementalCompilation.java
@@ -17,5 +17,5 @@
 package org.jetbrains.kotlin.config;
 
 public class IncrementalCompilation {
-    public static final boolean ENABLED = "true".equals(System.getProperty("kotlin.incremental.compilation"));
+    public static final boolean ENABLED = !"false".equals(System.getProperty("kotlin.incremental.compilation"));
 }
diff --git a/idea/testData/modules.xml/filtered.xml b/idea/testData/modules.xml/filtered.xml
index 21e59b08163..30ba6ca4746 100644
--- a/idea/testData/modules.xml/filtered.xml
+++ b/idea/testData/modules.xml/filtered.xml
@@ -5,10 +5,7 @@
         <sources path="s2"/>
         <!-- Java source roots -->
         <!-- Classpath -->
-        <!-- Output directory, commented out -->
-        <!-- 
-            <classpath path="cp1"/>
-        -->
+        <classpath path="cp1"/>
         <classpath path="cp2"/>
         <!-- External annotations -->
         <externalAnnotations path="a1/f1"/>
diff --git a/idea/testData/modules.xml/multiple.xml b/idea/testData/modules.xml/multiple.xml
index 59f09db520a..f2097e8b7fb 100644
--- a/idea/testData/modules.xml/multiple.xml
+++ b/idea/testData/modules.xml/multiple.xml
@@ -5,10 +5,7 @@
         <sources path="s2"/>
         <!-- Java source roots -->
         <!-- Classpath -->
-        <!-- Output directory, commented out -->
-        <!-- 
-            <classpath path="cp1"/>
-        -->
+        <classpath path="cp1"/>
         <classpath path="cp2"/>
         <!-- External annotations -->
         <externalAnnotations path="a1/f1"/>
@@ -20,10 +17,7 @@
         <sources path="s22"/>
         <!-- Java source roots -->
         <!-- Classpath -->
-        <!-- Output directory, commented out -->
-        <!-- 
-            <classpath path="cp12"/>
-        -->
+        <classpath path="cp12"/>
         <classpath path="cp22"/>
         <!-- External annotations -->
         <externalAnnotations path="a12/f12"/>
diff --git a/jps-plugin/test/org/jetbrains/kotlin/jps/build/AbstractIncrementalJpsTest.kt b/jps-plugin/test/org/jetbrains/kotlin/jps/build/AbstractIncrementalJpsTest.kt
index f01fc98f5d6..e4d8ac82c1a 100644
--- a/jps-plugin/test/org/jetbrains/kotlin/jps/build/AbstractIncrementalJpsTest.kt
+++ b/jps-plugin/test/org/jetbrains/kotlin/jps/build/AbstractIncrementalJpsTest.kt
@@ -219,10 +219,6 @@ public abstract class AbstractIncrementalJpsTest : JpsBuildTestCase() {
     }
 
     protected fun doTest(testDataPath: String) {
-        if (!IncrementalCompilation.ENABLED) {
-            return
-        }
-
         testDataDir = File(testDataPath)
         workDir = FileUtilRt.createTempDirectory(TEMP_DIRECTORY_TO_USE, "jps-build", null)
 
diff --git a/jps-plugin/test/org/jetbrains/kotlin/jps/build/KotlinJpsBuildTest.java b/jps-plugin/test/org/jetbrains/kotlin/jps/build/KotlinJpsBuildTest.java
index 697994f07c6..c2a386cc95f 100644
--- a/jps-plugin/test/org/jetbrains/kotlin/jps/build/KotlinJpsBuildTest.java
+++ b/jps-plugin/test/org/jetbrains/kotlin/jps/build/KotlinJpsBuildTest.java
@@ -20,6 +20,7 @@ import com.google.common.collect.Lists;
 import com.intellij.openapi.util.Condition;
 import com.intellij.openapi.util.io.FileUtil;
 import com.intellij.testFramework.LightVirtualFile;
+import com.intellij.util.ArrayUtil;
 import com.intellij.util.containers.ContainerUtil;
 import com.intellij.util.io.ZipUtil;
 import kotlin.KotlinPackage;
@@ -303,12 +304,16 @@ public class KotlinJpsBuildTest extends AbstractKotlinJpsBuildTestCase {
         checkWhen(touch("src/main.kt"), null, packageClasses("kotlinProject", "src/main.kt", "foo.FooPackage"));
         checkWhen(touch("src/boo.kt"), null, packageClasses("kotlinProject", "src/boo.kt", "boo.BooPackage"));
         checkWhen(touch("src/Bar.kt"),
-                  new String[] {"src/Bar.kt", "src/boo.kt", "src/main.kt"},
+                  new String[] {"src/Bar.kt"},
                   new String[] {klass("kotlinProject", "foo.Bar")});
 
         checkWhen(del("src/main.kt"),
                   new String[] {"src/Bar.kt", "src/boo.kt"},
-                  packageClasses("kotlinProject", "src/main.kt", "foo.FooPackage"));
+                  mergeArrays(
+                      packageClasses("kotlinProject", "src/main.kt", "foo.FooPackage"),
+                      packageClasses("kotlinProject", "src/boo.kt", "boo.BooPackage"),
+                      new String[]{ klass("kotlinProject", "foo.Bar") }
+                  ));
         assertFilesExistInOutput(module, "boo/BooPackage.class", "foo/Bar.class");
         assertFilesNotExistInOutput(module, "foo/FooPackage.class");
 
@@ -325,7 +330,7 @@ public class KotlinJpsBuildTest extends AbstractKotlinJpsBuildTestCase {
         checkWhen(touch("src/main.kt"), null, packageClasses("kotlinProject", "src/main.kt", "foo.FooPackage"));
         checkWhen(touch("src/boo.kt"), null, packageClasses("kotlinProject", "src/boo.kt", "boo.BooPackage"));
         checkWhen(touch("src/Bar.kt"),
-                  new String[] {"src/Bar.kt", "src/boo.kt", "src/main.kt"},
+                  new String[] {"src/Bar.kt"},
                   new String[] {
                           klass("kotlinProject", "foo.Bar"),
                           klass("kotlinProject", "foo.FooPackage"),
@@ -333,7 +338,12 @@ public class KotlinJpsBuildTest extends AbstractKotlinJpsBuildTestCase {
 
         checkWhen(del("src/main.kt"),
                   new String[] {"src/Bar.kt", "src/boo.kt"},
-                  packageClasses("kotlinProject", "src/main.kt", "foo.FooPackage"));
+                  mergeArrays(
+                          packageClasses("kotlinProject", "src/main.kt", "foo.FooPackage"),
+                          packageClasses("kotlinProject", "src/Bar.kt", "foo.FooPackage"),
+                          packageClasses("kotlinProject", "src/boo.kt", "boo.BooPackage"),
+                          new String[] {klass("kotlinProject", "foo.Bar")}
+                  ));
         assertFilesExistInOutput(module, "foo/FooPackage.class", "boo/BooPackage.class", "foo/Bar.class");
 
         checkWhen(touch("src/boo.kt"), null, packageClasses("kotlinProject", "src/boo.kt", "boo.BooPackage"));
@@ -618,6 +628,14 @@ public class KotlinJpsBuildTest extends AbstractKotlinJpsBuildTestCase {
         return klass(moduleName, AsmUtil.internalNameByFqNameWithoutInnerClasses(packagePartFqName));
     }
 
+    public static String[] mergeArrays(String[]... stringArrays) {
+        Set<String> result = new HashSet<String>();
+        for (String[] array : stringArrays) {
+            result.addAll(Arrays.asList(array));
+        }
+        return ArrayUtil.toStringArray(result);
+    }
+
     private enum Operation {
         CHANGE, DELETE
     }