diff --git a/build.gradle b/build.gradle
index 63513ce..c6fdf8d 100644
--- a/build.gradle
+++ b/build.gradle
@@ -435,6 +435,20 @@
     }
 }
 
+task maindex(type: Jar) {
+    from sourceSets.main.output
+    baseName 'maindex'
+    manifest {
+      attributes 'Main-Class': 'com.android.tools.r8.GenerateMainDexList'
+    }
+    // In order to build without dependencies, pass the exclude_deps property using:
+    // gradle -Pexclude_deps maindex
+    if (!project.hasProperty('exclude_deps')) {
+        // Also include dependencies
+        from { configurations.compile.collect { it.isDirectory() ? it : zipTree(it) } }
+    }
+}
+
 task ExtractMarker(type: Jar) {
     from sourceSets.main.output
     baseName 'extractmarker'
diff --git a/src/main/java/com/android/tools/r8/BaseCommand.java b/src/main/java/com/android/tools/r8/BaseCommand.java
index debe8a1..cbd8dd6 100644
--- a/src/main/java/com/android/tools/r8/BaseCommand.java
+++ b/src/main/java/com/android/tools/r8/BaseCommand.java
@@ -3,51 +3,33 @@
 // BSD-style license that can be found in the LICENSE file.
 package com.android.tools.r8;
 
-import com.android.tools.r8.dex.Constants;
 import com.android.tools.r8.utils.AndroidApp;
-import com.android.tools.r8.utils.FileUtils;
 import com.android.tools.r8.utils.InternalOptions;
-import com.android.tools.r8.utils.OutputMode;
 import java.io.IOException;
 import java.nio.file.Path;
 import java.util.Collection;
 
+/**
+ * Base class for commands and command builders for applications/tools which take an Android
+ * application (and a main-dex list) as input.
+ */
 abstract class BaseCommand {
 
   private final boolean printHelp;
   private final boolean printVersion;
 
   private final AndroidApp app;
-  private final Path outputPath;
-  private final OutputMode outputMode;
-  private final CompilationMode mode;
-  private final int minApiLevel;
 
   BaseCommand(boolean printHelp, boolean printVersion) {
     this.printHelp = printHelp;
     this.printVersion = printVersion;
     // All other fields are initialized with stub/invalid values.
     this.app = null;
-    this.outputPath = null;
-    this.outputMode = OutputMode.Indexed;
-    this.mode = null;
-    this.minApiLevel = 0;
   }
 
-  BaseCommand(
-      AndroidApp app,
-      Path outputPath,
-      OutputMode outputMode,
-      CompilationMode mode,
-      int minApiLevel) {
+  BaseCommand(AndroidApp app) {
     assert app != null;
-    assert mode != null;
-    assert minApiLevel > 0;
     this.app = app;
-    this.outputPath = outputPath;
-    this.outputMode = outputMode;
-    this.mode = mode;
-    this.minApiLevel = minApiLevel;
     // Print options are not set.
     printHelp = false;
     printVersion = false;
@@ -69,48 +51,27 @@
   // Internal access to the internal options.
   abstract InternalOptions getInternalOptions();
 
-  public Path getOutputPath() {
-    return outputPath;
-  }
-
-  public CompilationMode getMode() {
-    return mode;
-  }
-
-  public int getMinApiLevel() {
-    return minApiLevel;
-  }
-
-  public OutputMode getOutputMode() {
-    return outputMode;
-  }
-
-  abstract static class Builder<C extends BaseCommand, B extends Builder<C, B>> {
+  abstract public static class Builder<C extends BaseCommand, B extends Builder<C, B>> {
 
     private boolean printHelp = false;
     private boolean printVersion = false;
     private final AndroidApp.Builder app;
-    private Path outputPath = null;
-    private OutputMode outputMode = OutputMode.Indexed;
-    private CompilationMode mode;
-    private int minApiLevel = Constants.DEFAULT_ANDROID_API;
 
-    // Internal flag used by CompatDx to ignore dex files in archives.
-    protected boolean ignoreDexInArchive = false;
+    protected Builder() {
+      this(AndroidApp.builder(), false);
+    }
 
-    protected Builder(CompilationMode mode) {
-      this(AndroidApp.builder(), mode);
+    protected Builder(boolean ignoreDexInArchive) {
+      this(AndroidApp.builder(), ignoreDexInArchive);
     }
 
     // Internal constructor for testing.
     Builder(AndroidApp app, CompilationMode mode) {
-      this(AndroidApp.builder(app), mode);
+      this(AndroidApp.builder(app), false);
     }
 
-    private Builder(AndroidApp.Builder builder, CompilationMode mode) {
-      assert mode != null;
+    protected Builder(AndroidApp.Builder builder, boolean ignoreDexInArchive) {
       this.app = builder;
-      this.mode = mode;
       app.setIgnoreDexInArchive(ignoreDexInArchive);
     }
 
@@ -177,52 +138,6 @@
       return self();
     }
 
-    /** Get current compilation mode. */
-    public CompilationMode getMode() {
-      return mode;
-    }
-
-    /** Set compilation mode. */
-    public B setMode(CompilationMode mode) {
-      assert mode != null;
-      this.mode = mode;
-      return self();
-    }
-
-    /** Get the output path. Null if not set. */
-    public Path getOutputPath() {
-      return outputPath;
-    }
-
-    /** Get the output mode. */
-    public OutputMode getOutputMode() {
-      return outputMode;
-    }
-
-    /** Set an output path. Must be an existing directory or a zip file. */
-    public B setOutputPath(Path outputPath) {
-      this.outputPath = outputPath;
-      return self();
-    }
-
-    /** Set an output mode. */
-    public B setOutputMode(OutputMode outputMode) {
-      this.outputMode = outputMode;
-      return self();
-    }
-
-    /** Get the minimum API level (aka SDK version). */
-    public int getMinApiLevel() {
-      return minApiLevel;
-    }
-
-    /** Set the minimum required API level (aka SDK version). */
-    public B setMinApiLevel(int minApiLevel) {
-      assert minApiLevel > 0;
-      this.minApiLevel = minApiLevel;
-      return self();
-    }
-
     /**
      * Add main-dex list files.
      *
@@ -296,11 +211,7 @@
     }
 
     protected void validate() throws CompilationException {
-      if (app.hasMainDexList() && outputMode == OutputMode.FilePerClass) {
-        throw new CompilationException(
-            "Option --main-dex-list cannot be used with --file-per-class");
-      }
-      FileUtils.validateOutputFile(outputPath);
+      // Currently does nothing.
     }
   }
 }
diff --git a/src/main/java/com/android/tools/r8/BaseCompilerCommand.java b/src/main/java/com/android/tools/r8/BaseCompilerCommand.java
new file mode 100644
index 0000000..5e8f975
--- /dev/null
+++ b/src/main/java/com/android/tools/r8/BaseCompilerCommand.java
@@ -0,0 +1,146 @@
+// Copyright (c) 2017, the R8 project authors. Please see the AUTHORS file
+// for details. All rights reserved. Use of this source code is governed by a
+// BSD-style license that can be found in the LICENSE file.
+package com.android.tools.r8;
+
+import com.android.tools.r8.dex.Constants;
+import com.android.tools.r8.utils.AndroidApp;
+import com.android.tools.r8.utils.FileUtils;
+import com.android.tools.r8.utils.OutputMode;
+import java.nio.file.Path;
+
+/**
+ * Base class for commands and command builders for compiler applications/tools which besides an
+ * Android application (and a main-dex list) also takes compilation output, compilation mode and
+ * min API level as input.
+ */
+abstract class BaseCompilerCommand extends BaseCommand {
+
+  private final Path outputPath;
+  private final OutputMode outputMode;
+  private final CompilationMode mode;
+  private final int minApiLevel;
+
+  BaseCompilerCommand(boolean printHelp, boolean printVersion) {
+    super(printHelp, printVersion);
+
+    this.outputPath = null;
+    this.outputMode = OutputMode.Indexed;
+    this.mode = null;
+    this.minApiLevel = 0;
+  }
+
+  BaseCompilerCommand(
+      AndroidApp app,
+      Path outputPath,
+      OutputMode outputMode,
+      CompilationMode mode,
+      int minApiLevel) {
+    super(app);
+    assert mode != null;
+    assert minApiLevel > 0;
+    this.outputPath = outputPath;
+    this.outputMode = outputMode;
+    this.mode = mode;
+    this.minApiLevel = minApiLevel;
+  }
+
+  public Path getOutputPath() {
+    return outputPath;
+  }
+
+  public CompilationMode getMode() {
+    return mode;
+  }
+
+  public int getMinApiLevel() {
+    return minApiLevel;
+  }
+
+  public OutputMode getOutputMode() {
+    return outputMode;
+  }
+
+  abstract public static class Builder<C extends BaseCompilerCommand, B extends Builder<C, B>>
+      extends BaseCommand.Builder<C, B> {
+
+    private Path outputPath = null;
+    private OutputMode outputMode = OutputMode.Indexed;
+    private CompilationMode mode;
+    private int minApiLevel = Constants.DEFAULT_ANDROID_API;
+
+    protected Builder(CompilationMode mode) {
+      this(AndroidApp.builder(), mode, false);
+    }
+
+    protected Builder(CompilationMode mode, boolean ignoreDexInArchive) {
+      this(AndroidApp.builder(), mode, ignoreDexInArchive);
+    }
+
+    // Internal constructor for testing.
+    Builder(AndroidApp app, CompilationMode mode) {
+      this(AndroidApp.builder(app), mode, false);
+    }
+
+    private Builder(AndroidApp.Builder builder, CompilationMode mode, boolean ignoreDexInArchive) {
+      super(builder, ignoreDexInArchive);
+      assert mode != null;
+      this.mode = mode;
+    }
+
+    /** Get current compilation mode. */
+    public CompilationMode getMode() {
+      return mode;
+    }
+
+    /** Set compilation mode. */
+    public B setMode(CompilationMode mode) {
+      assert mode != null;
+      this.mode = mode;
+      return self();
+    }
+
+    /** Get the output path. Null if not set. */
+    public Path getOutputPath() {
+      return outputPath;
+    }
+
+    /** Get the output mode. */
+    public OutputMode getOutputMode() {
+      return outputMode;
+    }
+
+    /** Set an output path. Must be an existing directory or a zip file. */
+    public B setOutputPath(Path outputPath) {
+      this.outputPath = outputPath;
+      return self();
+    }
+
+    /** Set an output mode. */
+    public B setOutputMode(OutputMode outputMode) {
+      this.outputMode = outputMode;
+      return self();
+    }
+
+    /** Get the minimum API level (aka SDK version). */
+    public int getMinApiLevel() {
+      return minApiLevel;
+    }
+
+    /** Set the minimum required API level (aka SDK version). */
+    public B setMinApiLevel(int minApiLevel) {
+      assert minApiLevel > 0;
+      this.minApiLevel = minApiLevel;
+      return self();
+    }
+
+    protected void validate() throws CompilationException {
+      super.validate();
+      if (getAppBuilder().hasMainDexList() && outputMode == OutputMode.FilePerClass) {
+        throw new CompilationException(
+            "Option --main-dex-list cannot be used with --file-per-class");
+      }
+      FileUtils.validateOutputFile(outputPath);
+    }
+  }
+}
diff --git a/src/main/java/com/android/tools/r8/D8.java b/src/main/java/com/android/tools/r8/D8.java
index f7e65d9..e7a1d6e 100644
--- a/src/main/java/com/android/tools/r8/D8.java
+++ b/src/main/java/com/android/tools/r8/D8.java
@@ -55,7 +55,7 @@
  */
 public final class D8 {
 
-  private static final String VERSION = "v0.1.10";
+  private static final String VERSION = "v0.1.11";
   private static final int STATUS_ERROR = 1;
 
   private D8() {}
diff --git a/src/main/java/com/android/tools/r8/D8Command.java b/src/main/java/com/android/tools/r8/D8Command.java
index cb8c170..5b2e5cf 100644
--- a/src/main/java/com/android/tools/r8/D8Command.java
+++ b/src/main/java/com/android/tools/r8/D8Command.java
@@ -27,15 +27,19 @@
  *     .build();
  * </pre>
  */
-public class D8Command extends BaseCommand {
+public class D8Command extends BaseCompilerCommand {
 
   /**
    * Builder for constructing a D8Command.
    */
-  public static class Builder extends BaseCommand.Builder<D8Command, Builder> {
+  public static class Builder extends BaseCompilerCommand.Builder<D8Command, Builder> {
 
     private boolean intermediate = false;
 
+    protected Builder(boolean ignoreDexInArchive) {
+      super(CompilationMode.DEBUG, ignoreDexInArchive);
+    }
+
     protected Builder() {
       super(CompilationMode.DEBUG);
     }
diff --git a/src/main/java/com/android/tools/r8/DexSegments.java b/src/main/java/com/android/tools/r8/DexSegments.java
index 3827cae..24c1789 100644
--- a/src/main/java/com/android/tools/r8/DexSegments.java
+++ b/src/main/java/com/android/tools/r8/DexSegments.java
@@ -8,11 +8,9 @@
 import com.android.tools.r8.shaking.ProguardRuleParserException;
 import com.android.tools.r8.utils.AndroidApp;
 import com.android.tools.r8.utils.InternalOptions;
-import com.android.tools.r8.utils.OutputMode;
 import com.google.common.collect.ImmutableList;
 import com.google.common.io.Closer;
 import java.io.IOException;
-import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.HashMap;
 import java.util.Map;
@@ -24,10 +22,6 @@
     public static class Builder
         extends BaseCommand.Builder<Command, Builder> {
 
-      private Builder() {
-        super(CompilationMode.RELEASE);
-      }
-
       @Override
       Command.Builder self() {
         return this;
@@ -40,8 +34,7 @@
           return new Command(isPrintHelp());
         }
         validate();
-        return new Command(
-            getAppBuilder().build(), getOutputPath(), getOutputMode(), getMode(), getMinApiLevel());
+        return new Command(getAppBuilder().build());
       }
     }
 
@@ -79,13 +72,8 @@
       }
     }
 
-    private Command(
-        AndroidApp inputApp,
-        Path outputPath,
-        OutputMode outputMode,
-        CompilationMode mode,
-        int minApiLevel) {
-      super(inputApp, outputPath, outputMode, mode, minApiLevel);
+    private Command(AndroidApp inputApp) {
+      super(inputApp);
     }
 
     private Command(boolean printHelp) {
diff --git a/src/main/java/com/android/tools/r8/Disassemble.java b/src/main/java/com/android/tools/r8/Disassemble.java
index 2f1d523..6b7df77 100644
--- a/src/main/java/com/android/tools/r8/Disassemble.java
+++ b/src/main/java/com/android/tools/r8/Disassemble.java
@@ -6,7 +6,6 @@
 import com.android.tools.r8.shaking.ProguardRuleParserException;
 import com.android.tools.r8.utils.AndroidApp;
 import com.android.tools.r8.utils.InternalOptions;
-import com.android.tools.r8.utils.OutputMode;
 import com.google.common.collect.ImmutableList;
 import java.io.IOException;
 import java.nio.file.Path;
@@ -16,13 +15,13 @@
 public class Disassemble {
   public static class DisassembleCommand extends BaseCommand {
 
+    private final Path outputPath;
+
     public static class Builder
         extends BaseCommand.Builder<DisassembleCommand, DisassembleCommand.Builder> {
-      private boolean useSmali = false;
 
-      private Builder() {
-        super(CompilationMode.RELEASE);
-      }
+      private Path outputPath = null;
+      private boolean useSmali = false;
 
       @Override
       DisassembleCommand.Builder self() {
@@ -34,6 +33,15 @@
         return this;
       }
 
+      public Path getOutputPath() {
+        return outputPath;
+      }
+
+      public DisassembleCommand.Builder setOutputPath(Path outputPath) {
+        this.outputPath = outputPath;
+        return this;
+      }
+
       public DisassembleCommand.Builder setUseSmali(boolean useSmali) {
         this.useSmali = useSmali;
         return this;
@@ -47,13 +55,7 @@
         }
 
         validate();
-        return new DisassembleCommand(
-            getAppBuilder().build(),
-            getOutputPath(),
-            getOutputMode(),
-            getMode(),
-            getMinApiLevel(),
-            useSmali);
+        return new DisassembleCommand(getAppBuilder().build(), getOutputPath(), useSmali);
       }
     }
 
@@ -94,6 +96,9 @@
           builder.setUseSmali(true);
         } else if (arg.equals("--pg-map")) {
           builder.setProguardMapFile(Paths.get(args[++i]));
+        } else if (arg.equals("--output")) {
+          String outputPath = args[++i];
+          builder.setOutputPath(Paths.get(outputPath));
         } else {
           if (arg.startsWith("--")) {
             throw new CompilationException("Unknown option: " + arg);
@@ -103,23 +108,22 @@
       }
     }
 
-    private DisassembleCommand(
-        AndroidApp inputApp,
-        Path outputPath,
-        OutputMode outputMode,
-        CompilationMode mode,
-        int minApiLevel,
-        boolean useSmali) {
-      super(inputApp, outputPath, outputMode, mode, minApiLevel);
-      assert getOutputMode() == OutputMode.Indexed : "Only regular mode is supported in R8";
+    private DisassembleCommand(AndroidApp inputApp, Path outputPath, boolean useSmali) {
+      super(inputApp);
+      this.outputPath = outputPath;
       this.useSmali = useSmali;
     }
 
     private DisassembleCommand(boolean printHelp, boolean printVersion) {
       super(printHelp, printVersion);
+      this.outputPath = null;
       this.useSmali = false;
     }
 
+    public Path getOutputPath() {
+      return outputPath;
+    }
+
     public boolean useSmali() {
       return useSmali;
     }
diff --git a/src/main/java/com/android/tools/r8/ExtractMarker.java b/src/main/java/com/android/tools/r8/ExtractMarker.java
index c1234b8..bf3b919 100644
--- a/src/main/java/com/android/tools/r8/ExtractMarker.java
+++ b/src/main/java/com/android/tools/r8/ExtractMarker.java
@@ -3,19 +3,15 @@
 // BSD-style license that can be found in the LICENSE file.
 package com.android.tools.r8;
 
-import com.google.common.collect.ImmutableList;
-
 import com.android.tools.r8.dex.ApplicationReader;
 import com.android.tools.r8.dex.Marker;
 import com.android.tools.r8.graph.DexApplication;
 import com.android.tools.r8.shaking.ProguardRuleParserException;
 import com.android.tools.r8.utils.AndroidApp;
 import com.android.tools.r8.utils.InternalOptions;
-import com.android.tools.r8.utils.OutputMode;
 import com.android.tools.r8.utils.Timing;
-
+import com.google.common.collect.ImmutableList;
 import java.io.IOException;
-import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.concurrent.ExecutionException;
 
@@ -25,10 +21,6 @@
     public static class Builder
         extends BaseCommand.Builder<ExtractMarker.Command, ExtractMarker.Command.Builder> {
 
-      private Builder() {
-        super(CompilationMode.RELEASE);
-      }
-
       @Override
       ExtractMarker.Command.Builder self() {
         return this;
@@ -41,8 +33,7 @@
           return new ExtractMarker.Command(isPrintHelp());
         }
         validate();
-        return new ExtractMarker.Command(
-            getAppBuilder().build(), getOutputPath(), getOutputMode(), getMode(), getMinApiLevel());
+        return new ExtractMarker.Command(getAppBuilder().build());
       }
     }
 
@@ -80,13 +71,8 @@
       }
     }
 
-    private Command(
-        AndroidApp inputApp,
-        Path outputPath,
-        OutputMode outputMode,
-        CompilationMode mode,
-        int minApiLevel) {
-      super(inputApp, outputPath, outputMode, mode, minApiLevel);
+    private Command(AndroidApp inputApp) {
+      super(inputApp);
     }
 
     private Command(boolean printHelp) {
diff --git a/src/main/java/com/android/tools/r8/GenerateMainDexList.java b/src/main/java/com/android/tools/r8/GenerateMainDexList.java
new file mode 100644
index 0000000..44d523e
--- /dev/null
+++ b/src/main/java/com/android/tools/r8/GenerateMainDexList.java
@@ -0,0 +1,124 @@
+// Copyright (c) 2017, the R8 project authors. Please see the AUTHORS file
+// for details. All rights reserved. Use of this source code is governed by a
+// BSD-style license that can be found in the LICENSE file.
+package com.android.tools.r8;
+
+import com.android.tools.r8.dex.ApplicationReader;
+import com.android.tools.r8.graph.AppInfoWithSubtyping;
+import com.android.tools.r8.graph.DexApplication;
+import com.android.tools.r8.graph.DexType;
+import com.android.tools.r8.shaking.Enqueuer;
+import com.android.tools.r8.shaking.MainDexListBuilder;
+import com.android.tools.r8.shaking.ProguardRuleParserException;
+import com.android.tools.r8.shaking.RootSetBuilder;
+import com.android.tools.r8.shaking.RootSetBuilder.RootSet;
+import com.android.tools.r8.utils.AndroidApp;
+import com.android.tools.r8.utils.InternalOptions;
+import com.android.tools.r8.utils.ThreadUtils;
+import com.android.tools.r8.utils.Timing;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.PrintWriter;
+import java.nio.file.Files;
+import java.nio.file.StandardOpenOption;
+import java.util.List;
+import java.util.Set;
+import java.util.concurrent.ExecutionException;
+import java.util.concurrent.ExecutorService;
+import java.util.stream.Collectors;
+
+public class GenerateMainDexList {
+  private static final String VERSION = "v0.2.0";
+  private final Timing timing = new Timing("maindex");
+  private final InternalOptions options;
+
+  private GenerateMainDexList(InternalOptions options) {
+    this.options = options;
+  }
+
+  private List<String> run(AndroidApp app) throws IOException, ExecutionException {
+    ExecutorService executor = ThreadUtils.getExecutorService(options);
+    DexApplication application = new ApplicationReader(app, options, timing).read(executor);
+    AppInfoWithSubtyping appInfo = new AppInfoWithSubtyping(application);
+    RootSet mainDexRootSet =
+        new RootSetBuilder(application, appInfo, options.mainDexKeepRules).run(executor);
+    Set<DexType> mainDexBaseClasses = new Enqueuer(appInfo).traceMainDex(mainDexRootSet, timing);
+    Set<DexType> mainDexClasses = new MainDexListBuilder(mainDexBaseClasses, application).run();
+
+    List<String> result = mainDexClasses.stream()
+        .map(c -> c.toSourceString().replace('.', '/') + ".class")
+        .sorted()
+        .collect(Collectors.toList());
+
+    if (options.printMainDexListFile != null) {
+      try (OutputStream mainDexOut = Files.newOutputStream(options.printMainDexListFile,
+          StandardOpenOption.CREATE, StandardOpenOption.TRUNCATE_EXISTING)) {
+        PrintWriter writer = new PrintWriter(mainDexOut);
+        result.forEach(writer::println);
+        writer.flush();
+      }
+    }
+
+    return result;
+  }
+
+  /**
+   * Main API entry for computing the main-dex list.
+   *
+   * The main-dex list is represented as a list of strings, each string specifies one class to
+   * keep in the primary dex file (<code>classes.dex</code>).
+   *
+   * A class is specified using the following format: "com/example/MyClass.class". That is
+   * "/" as separator between package components, and a trailing ".class".
+   *
+   * @param command main dex-list generator command.
+   * @return classes to keep in the primary dex file.
+   */
+  public static List<String> run(GenerateMainDexListCommand command)
+      throws IOException, ExecutionException {
+    ExecutorService executorService = ThreadUtils.getExecutorService(command.getInternalOptions());
+    try {
+      return run(command, executorService);
+    } finally {
+      executorService.shutdown();
+    }
+  }
+
+  /**
+   * Main API entry for computing the main-dex list.
+   *
+   * The main-dex list is represented as a list of strings, each string specifies one class to
+   * keep in the primary dex file (<code>classes.dex</code>).
+   *
+   * A class is specified using the following format: "com/example/MyClass.class". That is
+   * "/" as separator between package components, and a trailing ".class".
+   *
+   * @param command main dex-list generator command.
+   * @param executor executor service from which to get threads for multi-threaded processing.
+   * @return classes to keep in the primary dex file.
+   */
+  public static List<String> run(GenerateMainDexListCommand command, ExecutorService executor)
+      throws IOException, ExecutionException {
+    AndroidApp app = command.getInputApp();
+    InternalOptions options = command.getInternalOptions();
+    return new GenerateMainDexList(options).run(app);
+  }
+
+  public static void main(String[] args)
+      throws IOException, ProguardRuleParserException, CompilationException, ExecutionException {
+    GenerateMainDexListCommand.Builder builder = GenerateMainDexListCommand.parse(args);
+    GenerateMainDexListCommand command = builder.build();
+    if (command.isPrintHelp()) {
+      System.out.println(GenerateMainDexListCommand.USAGE_MESSAGE);
+      return;
+    }
+    if (command.isPrintVersion()) {
+      System.out.println("MainDexListGenerator " + VERSION);
+      return;
+    }
+    List<String> result = run(command);
+    if (command.getMainDexListOutputPath() == null) {
+      result.forEach(System.out::println);
+    }
+  }
+}
diff --git a/src/main/java/com/android/tools/r8/GenerateMainDexListCommand.java b/src/main/java/com/android/tools/r8/GenerateMainDexListCommand.java
new file mode 100644
index 0000000..76d7d56
--- /dev/null
+++ b/src/main/java/com/android/tools/r8/GenerateMainDexListCommand.java
@@ -0,0 +1,200 @@
+// Copyright (c) 2017, the R8 project authors. Please see the AUTHORS file
+// for details. All rights reserved. Use of this source code is governed by a
+// BSD-style license that can be found in the LICENSE file.
+package com.android.tools.r8;
+
+import com.android.tools.r8.graph.DexItemFactory;
+import com.android.tools.r8.shaking.ProguardConfigurationParser;
+import com.android.tools.r8.shaking.ProguardConfigurationRule;
+import com.android.tools.r8.shaking.ProguardConfigurationSource;
+import com.android.tools.r8.shaking.ProguardConfigurationSourceFile;
+import com.android.tools.r8.shaking.ProguardConfigurationSourceStrings;
+import com.android.tools.r8.shaking.ProguardRuleParserException;
+import com.android.tools.r8.utils.AndroidApp;
+import com.android.tools.r8.utils.InternalOptions;
+import com.google.common.collect.ImmutableList;
+import java.io.IOException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.List;
+
+public class GenerateMainDexListCommand extends BaseCommand {
+
+  private final ImmutableList<ProguardConfigurationRule> mainDexKeepRules;
+  private final Path mainDexListOutput;
+  private final DexItemFactory factory;
+
+  /**
+   * Get the output path for the main-dex list. Null if not set.
+   */
+  public Path getMainDexListOutputPath() {
+    return mainDexListOutput;
+  }
+
+  public static class Builder extends BaseCommand.Builder<GenerateMainDexListCommand, Builder> {
+
+    private final DexItemFactory factory = new DexItemFactory();
+    private final List<ProguardConfigurationSource> mainDexRules = new ArrayList<>();
+    private Path mainDexListOutput = null;
+
+    @Override
+    GenerateMainDexListCommand.Builder self() {
+      return this;
+    }
+
+    /**
+     * Add proguard configuration file resources for automatic main dex list calculation.
+     */
+    public GenerateMainDexListCommand.Builder addMainDexRulesFiles(Path... paths) {
+      for (Path path : paths) {
+        mainDexRules.add(new ProguardConfigurationSourceFile(path));
+      }
+      return self();
+    }
+
+    /**
+     * Add proguard configuration file resources for automatic main dex list calculation.
+     */
+    public GenerateMainDexListCommand.Builder addMainDexRulesFiles(List<Path> paths) {
+      for (Path path : paths) {
+        mainDexRules.add(new ProguardConfigurationSourceFile(path));
+      }
+      return self();
+    }
+
+    /**
+     * Add proguard configuration for automatic main dex list calculation.
+     */
+    public GenerateMainDexListCommand.Builder addMainDexRules(List<String> lines) {
+      mainDexRules.add(new ProguardConfigurationSourceStrings(lines));
+      return self();
+    }
+
+    /**
+     * Get the output path for the main-dex list. Null if not set.
+     */
+    public Path getMainDexListOutputPath() {
+      return mainDexListOutput;
+    }
+
+    /**
+     * Set the output file for the main-dex list.
+     *
+     * If the file exists it will be overwritten.
+     */
+    public GenerateMainDexListCommand.Builder setMainDexListOutputPath(Path mainDexListOutputPath) {
+      mainDexListOutput = mainDexListOutputPath;
+      return self();
+    }
+
+
+    @Override
+    public GenerateMainDexListCommand build() throws CompilationException, IOException {
+      // If printing versions ignore everything else.
+      if (isPrintHelp() || isPrintVersion()) {
+        return new GenerateMainDexListCommand(isPrintHelp(), isPrintVersion());
+      }
+
+      validate();
+      ImmutableList<ProguardConfigurationRule> mainDexKeepRules;
+      if (this.mainDexRules.isEmpty()) {
+        mainDexKeepRules = ImmutableList.of();
+      } else {
+        ProguardConfigurationParser parser = new ProguardConfigurationParser(factory);
+        try {
+          parser.parse(mainDexRules);
+        } catch (ProguardRuleParserException e) {
+          throw new CompilationException(e.getMessage(), e.getCause());
+        }
+        mainDexKeepRules = parser.getConfig().getRules();
+      }
+
+      return new GenerateMainDexListCommand(
+          factory,
+          getAppBuilder().build(),
+          mainDexKeepRules,
+          mainDexListOutput);
+    }
+  }
+
+  static final String USAGE_MESSAGE = String.join("\n", ImmutableList.of(
+      "Usage: maindex [options] <input-files>",
+      " where <input-files> are JAR files",
+      " and options are:",
+      "  --main-dex-rules <file>  # Proguard keep rules for classes to place in the",
+      "                           # primary dex file.",
+      "  --main-dex-list <file>   # List of classes to place in the primary dex file.",
+      "  --main-dex-list-output <file>  # Output the full main-dex list in <file>.",
+      "  --version                # Print the version.",
+      "  --help                   # Print this message."));
+
+
+  public static GenerateMainDexListCommand.Builder builder() {
+    return new GenerateMainDexListCommand.Builder();
+  }
+
+  public static GenerateMainDexListCommand.Builder parse(String[] args)
+      throws CompilationException, IOException {
+    GenerateMainDexListCommand.Builder builder = builder();
+    parse(args, builder);
+    return builder;
+  }
+
+  private static void parse(String[] args, GenerateMainDexListCommand.Builder builder)
+      throws CompilationException, IOException {
+    for (int i = 0; i < args.length; i++) {
+      String arg = args[i].trim();
+      if (arg.length() == 0) {
+        continue;
+      } else if (arg.equals("--help")) {
+        builder.setPrintHelp(true);
+      } else if (arg.equals("--version")) {
+        builder.setPrintVersion(true);
+      } else if (arg.equals("--main-dex-rules")) {
+        builder.addMainDexRulesFiles(Paths.get(args[++i]));
+      } else if (arg.equals("--main-dex-list")) {
+        builder.addMainDexListFiles(Paths.get(args[++i]));
+      } else if (arg.equals("--main-dex-list-output")) {
+        builder.setMainDexListOutputPath(Paths.get(args[++i]));
+      } else {
+        if (arg.startsWith("--")) {
+          throw new CompilationException("Unknown option: " + arg);
+        }
+        builder.addProgramFiles(Paths.get(arg));
+      }
+    }
+  }
+
+  private GenerateMainDexListCommand(
+      DexItemFactory factory,
+      AndroidApp inputApp,
+      ImmutableList<ProguardConfigurationRule> mainDexKeepRules,
+      Path mainDexListOutput) {
+    super(inputApp);
+    this.factory = factory;
+    this.mainDexKeepRules = mainDexKeepRules;
+    this.mainDexListOutput = mainDexListOutput;
+  }
+
+  private GenerateMainDexListCommand(boolean printHelp, boolean printVersion) {
+    super(printHelp, printVersion);
+    this.factory = new DexItemFactory();
+    this.mainDexKeepRules = ImmutableList.of();
+    this.mainDexListOutput = null;
+  }
+
+  @Override
+  InternalOptions getInternalOptions() {
+    InternalOptions internal = new InternalOptions(factory);
+    internal.mainDexKeepRules = mainDexKeepRules;
+    if (mainDexListOutput != null) {
+      internal.printMainDexListFile = mainDexListOutput;
+    }
+    internal.minimalMainDex = internal.debug;
+    internal.removeSwitchMaps = false;
+    internal.inlineAccessors = false;
+    return internal;
+  }
+}
+
diff --git a/src/main/java/com/android/tools/r8/R8.java b/src/main/java/com/android/tools/r8/R8.java
index edfe01e..6e7e36d 100644
--- a/src/main/java/com/android/tools/r8/R8.java
+++ b/src/main/java/com/android/tools/r8/R8.java
@@ -71,7 +71,7 @@
 
 public class R8 {
 
-  private static final String VERSION = "v0.1.10";
+  private static final String VERSION = "v0.1.11";
   private final Timing timing = new Timing("R8");
   private final InternalOptions options;
 
diff --git a/src/main/java/com/android/tools/r8/R8Command.java b/src/main/java/com/android/tools/r8/R8Command.java
index ec040a5..14b53c2 100644
--- a/src/main/java/com/android/tools/r8/R8Command.java
+++ b/src/main/java/com/android/tools/r8/R8Command.java
@@ -8,6 +8,9 @@
 import com.android.tools.r8.shaking.ProguardConfiguration.Builder;
 import com.android.tools.r8.shaking.ProguardConfigurationParser;
 import com.android.tools.r8.shaking.ProguardConfigurationRule;
+import com.android.tools.r8.shaking.ProguardConfigurationSource;
+import com.android.tools.r8.shaking.ProguardConfigurationSourceFile;
+import com.android.tools.r8.shaking.ProguardConfigurationSourceStrings;
 import com.android.tools.r8.shaking.ProguardRuleParserException;
 import com.android.tools.r8.utils.AndroidApp;
 import com.android.tools.r8.utils.FileUtils;
@@ -18,19 +21,18 @@
 import java.nio.file.Path;
 import java.nio.file.Paths;
 import java.util.ArrayList;
-import java.util.Collections;
 import java.util.List;
 import java.util.Optional;
 import java.util.function.Consumer;
 
-public class R8Command extends BaseCommand {
+public class R8Command extends BaseCompilerCommand {
 
-  public static class Builder extends BaseCommand.Builder<R8Command, Builder> {
+  public static class Builder extends BaseCompilerCommand.Builder<R8Command, Builder> {
 
-    private final List<Path> mainDexRules = new ArrayList<>();
+    private final List<ProguardConfigurationSource> mainDexRules = new ArrayList<>();
     private Path mainDexListOutput = null;
     private Consumer<ProguardConfiguration.Builder> proguardConfigurationConsumer = null;
-    private final List<Path> proguardConfigFiles = new ArrayList<>();
+    private final List<ProguardConfigurationSource> proguardConfigs = new ArrayList<>();
     private Optional<Boolean> treeShaking = Optional.empty();
     private Optional<Boolean> minification = Optional.empty();
     private boolean ignoreMissingClasses = false;
@@ -68,16 +70,28 @@
     /**
      * Add proguard configuration file resources for automatic main dex list calculation.
      */
-    public Builder addMainDexRules(Path... paths) {
-      Collections.addAll(mainDexRules, paths);
+    public Builder addMainDexRulesFiles(Path... paths) {
+      for (Path path : paths) {
+        mainDexRules.add(new ProguardConfigurationSourceFile(path));
+      }
       return self();
     }
 
     /**
      * Add proguard configuration file resources for automatic main dex list calculation.
      */
-    public Builder addMainDexRules(List<Path> paths) {
-      mainDexRules.addAll(paths);
+    public Builder addMainDexRulesFiles(List<Path> paths) {
+      for (Path path : paths) {
+        mainDexRules.add(new ProguardConfigurationSourceFile(path));
+      }
+      return self();
+    }
+
+    /**
+     * Add proguard configuration for automatic main dex list calculation.
+     */
+    public Builder addMainDexRules(List<String> lines) {
+      mainDexRules.add(new ProguardConfigurationSourceStrings(lines));
       return self();
     }
 
@@ -90,7 +104,9 @@
      * Add proguard configuration file resources.
      */
     public Builder addProguardConfigurationFiles(Path... paths) {
-      Collections.addAll(proguardConfigFiles, paths);
+      for (Path path : paths) {
+        proguardConfigs.add(new ProguardConfigurationSourceFile(path));
+      }
       return self();
     }
 
@@ -98,7 +114,17 @@
      * Add proguard configuration file resources.
      */
     public Builder addProguardConfigurationFiles(List<Path> paths) {
-      proguardConfigFiles.addAll(paths);
+      for (Path path : paths) {
+        proguardConfigs.add(new ProguardConfigurationSourceFile(path));
+      }
+      return self();
+    }
+
+    /**
+     * Add proguard configuration.
+     */
+    public Builder addProguardConfiguration(List<String> lines) {
+      proguardConfigs.add(new ProguardConfigurationSourceStrings(lines));
       return self();
     }
 
@@ -176,12 +202,12 @@
         mainDexKeepRules = parser.getConfig().getRules();
       }
       ProguardConfiguration configuration;
-      if (proguardConfigFiles.isEmpty()) {
+      if (proguardConfigs.isEmpty()) {
         configuration = ProguardConfiguration.defaultConfiguration(factory);
       } else {
         ProguardConfigurationParser parser = new ProguardConfigurationParser(factory);
         try {
-          parser.parse(proguardConfigFiles);
+          parser.parse(proguardConfigs);
         } catch (ProguardRuleParserException e) {
           throw new CompilationException(e.getMessage(), e.getCause());
         }
@@ -308,7 +334,7 @@
       } else if (arg.equals("--no-minification")) {
         builder.setMinification(false);
       } else if (arg.equals("--main-dex-rules")) {
-        builder.addMainDexRules(Paths.get(args[++i]));
+        builder.addMainDexRulesFiles(Paths.get(args[++i]));
       } else if (arg.equals("--main-dex-list")) {
         builder.addMainDexListFiles(Paths.get(args[++i]));
       } else if (arg.equals("--main-dex-list-output")) {
diff --git a/src/main/java/com/android/tools/r8/compatdx/CompatDxCommandBuilder.java b/src/main/java/com/android/tools/r8/compatdx/CompatDxCommandBuilder.java
index ba9daec..55206a4 100644
--- a/src/main/java/com/android/tools/r8/compatdx/CompatDxCommandBuilder.java
+++ b/src/main/java/com/android/tools/r8/compatdx/CompatDxCommandBuilder.java
@@ -8,6 +8,6 @@
 
 public class CompatDxCommandBuilder extends D8Command.Builder {
   CompatDxCommandBuilder() {
-    ignoreDexInArchive = true;
+    super(true);
   }
 }
diff --git a/src/main/java/com/android/tools/r8/shaking/ProguardConfigurationParser.java b/src/main/java/com/android/tools/r8/shaking/ProguardConfigurationParser.java
index 4fb7357..2667f79 100644
--- a/src/main/java/com/android/tools/r8/shaking/ProguardConfigurationParser.java
+++ b/src/main/java/com/android/tools/r8/shaking/ProguardConfigurationParser.java
@@ -22,11 +22,8 @@
 import java.io.FileNotFoundException;
 import java.io.IOException;
 import java.nio.CharBuffer;
-import java.nio.charset.StandardCharsets;
-import java.nio.file.Files;
 import java.nio.file.NoSuchFileException;
 import java.nio.file.Path;
-import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
@@ -85,31 +82,32 @@
   }
 
   public void parse(Path path) throws ProguardRuleParserException, IOException {
-    parse(Collections.singletonList(path));
+    parse(ImmutableList.of(new ProguardConfigurationSourceFile(path)));
   }
 
-  public void parse(List<Path> pathList) throws ProguardRuleParserException, IOException {
-    for (Path path : pathList) {
-      new ProguardFileParser(path).parse();
+  public void parse(ProguardConfigurationSource source)
+      throws ProguardRuleParserException, IOException {
+    parse(ImmutableList.of(source));
+  }
+
+  public void parse(List<ProguardConfigurationSource> sources)
+      throws ProguardRuleParserException, IOException {
+    for (ProguardConfigurationSource source : sources) {
+      new ProguardFileParser(source).parse();
     }
   }
 
   private class ProguardFileParser {
 
-    private final Path path;
+    private final String name;
     private final String contents;
     private int position = 0;
     private Path baseDirectory;
 
-    ProguardFileParser(Path path) throws IOException {
-      this.path = path;
-      contents = new String(Files.readAllBytes(path), StandardCharsets.UTF_8);
-      baseDirectory = path.getParent();
-      if (baseDirectory == null) {
-        // path parent can be null only if it's root dir or if its a one element path relative to
-        // current directory.
-        baseDirectory = Paths.get(".");
-      }
+    ProguardFileParser(ProguardConfigurationSource source) throws IOException {
+      contents = source.get();
+      baseDirectory = source.getBaseDirectory();
+      name = source.getName();
     }
 
     public void parse() throws ProguardRuleParserException {
@@ -267,7 +265,7 @@
     private void parseInclude() throws ProguardRuleParserException {
       Path included = parseFileName();
       try {
-        new ProguardFileParser(included).parse();
+        new ProguardFileParser(new ProguardConfigurationSourceFile(included)).parse();
       } catch (FileNotFoundException | NoSuchFileException e) {
         throw parseError("Included file '" + included.toString() + "' not found", e);
       } catch (IOException e) {
@@ -1033,12 +1031,12 @@
         String line = lines[lineNumber];
         if (remaining <= line.length() || lineNumber == lines.length - 1) {
           String arrow = CharBuffer.allocate(remaining).toString().replace( '\0', ' ' ) + '^';
-          return path.toString() + ":" + (lineNumber + 1) + ":" + remaining + "\n" + line
+          return name + ":" + (lineNumber + 1) + ":" + remaining + "\n" + line
               + '\n' + arrow;
         }
         remaining -= (line.length() + 1); // Include newline.
       }
-      return path.toString();
+      return name;
     }
 
     private ProguardRuleParserException parseError(String message) {
diff --git a/src/main/java/com/android/tools/r8/shaking/ProguardConfigurationSource.java b/src/main/java/com/android/tools/r8/shaking/ProguardConfigurationSource.java
new file mode 100644
index 0000000..b0375c0
--- /dev/null
+++ b/src/main/java/com/android/tools/r8/shaking/ProguardConfigurationSource.java
@@ -0,0 +1,14 @@
+// Copyright (c) 2017, the R8 project authors. Please see the AUTHORS file
+// for details. All rights reserved. Use of this source code is governed by a
+// BSD-style license that can be found in the LICENSE file.
+
+package com.android.tools.r8.shaking;
+
+import java.io.IOException;
+import java.nio.file.Path;
+
+public interface ProguardConfigurationSource {
+  String get() throws IOException;
+  Path getBaseDirectory();
+  String getName();
+}
diff --git a/src/main/java/com/android/tools/r8/shaking/ProguardConfigurationSourceFile.java b/src/main/java/com/android/tools/r8/shaking/ProguardConfigurationSourceFile.java
new file mode 100644
index 0000000..058c14f
--- /dev/null
+++ b/src/main/java/com/android/tools/r8/shaking/ProguardConfigurationSourceFile.java
@@ -0,0 +1,37 @@
+// Copyright (c) 2017, the R8 project authors. Please see the AUTHORS file
+// for details. All rights reserved. Use of this source code is governed by a
+// BSD-style license that can be found in the LICENSE file.
+
+package com.android.tools.r8.shaking;
+
+import java.io.IOException;
+import java.nio.charset.StandardCharsets;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+
+public class ProguardConfigurationSourceFile implements ProguardConfigurationSource {
+  private final Path path;
+
+  public ProguardConfigurationSourceFile(Path path) {
+    this.path = path;
+  }
+
+  public String get() throws IOException{
+    return new String(Files.readAllBytes(path), StandardCharsets.UTF_8);
+  }
+
+  public Path getBaseDirectory() {
+    Path baseDirectory = path.getParent();
+    if (baseDirectory == null) {
+      // Path parent can be null only if it's root dir or if its a one element path relative to
+      // current directory.
+      baseDirectory = Paths.get(".");
+    }
+    return baseDirectory;
+  }
+
+  public String getName() {
+    return path.toString();
+  }
+}
diff --git a/src/main/java/com/android/tools/r8/shaking/ProguardConfigurationSourceStrings.java b/src/main/java/com/android/tools/r8/shaking/ProguardConfigurationSourceStrings.java
new file mode 100644
index 0000000..ac5f0ab
--- /dev/null
+++ b/src/main/java/com/android/tools/r8/shaking/ProguardConfigurationSourceStrings.java
@@ -0,0 +1,31 @@
+// Copyright (c) 2017, the R8 project authors. Please see the AUTHORS file
+// for details. All rights reserved. Use of this source code is governed by a
+// BSD-style license that can be found in the LICENSE file.
+
+package com.android.tools.r8.shaking;
+
+import java.io.IOException;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.List;
+import joptsimple.internal.Strings;
+
+public class ProguardConfigurationSourceStrings implements ProguardConfigurationSource {
+  private final List<String> config;
+
+  public ProguardConfigurationSourceStrings(List<String> config) {
+    this.config = config;
+  }
+
+  public String get() throws IOException{
+    return Strings.join(config, "\n");
+  }
+
+  public Path getBaseDirectory() {
+    return Paths.get(".");
+  }
+
+  public String getName() {
+    return "<no file>";
+  }
+}
diff --git a/src/main/java/com/android/tools/r8/shaking/RootSetBuilder.java b/src/main/java/com/android/tools/r8/shaking/RootSetBuilder.java
index 0fa5051..d40da61 100644
--- a/src/main/java/com/android/tools/r8/shaking/RootSetBuilder.java
+++ b/src/main/java/com/android/tools/r8/shaking/RootSetBuilder.java
@@ -28,6 +28,7 @@
 import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
+import java.util.Comparator;
 import java.util.HashSet;
 import java.util.IdentityHashMap;
 import java.util.List;
@@ -582,5 +583,29 @@
       return Collections
           .unmodifiableMap(dependentNoShrinking.getOrDefault(item, Collections.emptyMap()));
     }
+
+    @Override
+    public String toString() {
+      StringBuilder builder = new StringBuilder();
+      builder.append("RootSet");
+
+      builder.append("\nnoShrinking: " + noShrinking.size());
+      builder.append("\nnoOptimization: " + noOptimization.size());
+      builder.append("\nnoObfuscation: " + noObfuscation.size());
+      builder.append("\nreasonAsked: " + reasonAsked.size());
+      builder.append("\nkeepPackageName: " + keepPackageName.size());
+      builder.append("\ncheckDiscarded: " + checkDiscarded.size());
+      builder.append("\nnoSideEffects: " + noSideEffects.size());
+      builder.append("\nassumedValues: " + assumedValues.size());
+      builder.append("\ndependentNoShrinking: " + dependentNoShrinking.size());
+
+      builder.append("\n\nNo Shrinking:");
+      noShrinking.keySet().stream()
+          .sorted(Comparator.comparing(DexItem::toSourceString))
+          .forEach(a -> builder
+              .append("\n").append(a.toSourceString()).append(" ").append(noShrinking.get(a)));
+      builder.append("\n");
+      return builder.toString();
+    }
   }
 }
diff --git a/src/test/java/com/android/tools/r8/ToolHelper.java b/src/test/java/com/android/tools/r8/ToolHelper.java
index 8b83058..e91870d 100644
--- a/src/test/java/com/android/tools/r8/ToolHelper.java
+++ b/src/test/java/com/android/tools/r8/ToolHelper.java
@@ -448,7 +448,9 @@
       return ProguardConfiguration.defaultConfiguration(factory);
     }
     ProguardConfigurationParser parser = new ProguardConfigurationParser(factory);
-    parser.parse(configPaths);
+    for (Path configPath : configPaths) {
+      parser.parse(configPath);
+    }
     return parser.getConfig();
   }
 
@@ -597,13 +599,31 @@
         .toArray(new String[0]));
   }
 
+  public static ProcessResult forkGenerateMainDexList(Path dir, List<String> args1, String... args2)
+      throws IOException, InterruptedException {
+    List<String> args = new ArrayList<>();
+    args.addAll(args1);
+    args.addAll(Arrays.asList(args2));
+    return forkJava(dir, GenerateMainDexList.class, args);
+  }
+
+  public static ProcessResult forkGenerateMainDexList(Path dir, String... args)
+      throws IOException, InterruptedException {
+    return forkJava(dir, GenerateMainDexList.class, args);
+  }
+
   private static ProcessResult forkJava(Path dir, Class clazz, String... args)
       throws IOException, InterruptedException {
+    return forkJava(dir, clazz, Arrays.asList(args));
+  }
+
+  private static ProcessResult forkJava(Path dir, Class clazz, List<String> args)
+      throws IOException, InterruptedException {
     List<String> command = new ImmutableList.Builder<String>()
         .add(getJavaExecutable())
         .add("-cp").add(System.getProperty("java.class.path"))
         .add(clazz.getCanonicalName())
-        .addAll(Arrays.asList(args))
+        .addAll(args)
         .build();
     return runProcess(new ProcessBuilder(command).directory(dir.toFile()));
   }
diff --git a/src/test/java/com/android/tools/r8/compatdx/CompatDxTests.java b/src/test/java/com/android/tools/r8/compatdx/CompatDxTests.java
index dbe776d..3222734 100644
--- a/src/test/java/com/android/tools/r8/compatdx/CompatDxTests.java
+++ b/src/test/java/com/android/tools/r8/compatdx/CompatDxTests.java
@@ -6,33 +6,33 @@
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertNotEquals;
 import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
 
 import com.android.tools.r8.ToolHelper;
+import com.android.tools.r8.ToolHelper.ProcessResult;
 import com.android.tools.r8.dex.Constants;
-import com.android.tools.r8.errors.CompilationError;
-import com.android.tools.r8.maindexlist.MainDexListTests;
-import com.android.tools.r8.utils.AndroidApp;
 import com.android.tools.r8.utils.FileUtils;
-import com.android.tools.r8.utils.OutputMode;
 import com.android.tools.r8.utils.StringUtils;
 import com.android.tools.r8.utils.StringUtils.BraceType;
 import com.google.common.collect.ImmutableList;
+import com.google.common.collect.ImmutableMap;
 import java.io.IOException;
+import java.net.URI;
+import java.nio.file.FileSystem;
+import java.nio.file.FileSystems;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
+import java.nio.file.StandardCopyOption;
+import java.nio.file.StandardOpenOption;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 import java.util.Set;
-import java.util.concurrent.ExecutionException;
 import java.util.stream.Collectors;
 import java.util.zip.ZipEntry;
 import java.util.zip.ZipFile;
 import org.junit.Rule;
 import org.junit.Test;
-import org.junit.rules.ExpectedException;
 import org.junit.rules.TemporaryFolder;
 
 public class CompatDxTests {
@@ -100,40 +100,28 @@
   }
 
   @Test
-  public void singleDexProgramFull() throws IOException, ExecutionException {
-    // Generate an application that fills the whole dex file.
-    AndroidApp generated =
-        MainDexListTests.generateApplication(
-            ImmutableList.of("A"), Constants.ANDROID_L_API, MAX_METHOD_COUNT + 1);
-    Path applicationJar = temp.newFile("application.jar").toPath();
-    generated.write(applicationJar, OutputMode.Indexed);
-    runDexer(applicationJar.toString());
-  }
-
-  @Test
-  public void singleDexProgramIsTooLarge() throws IOException, ExecutionException {
-    // Generate an application that will not fit into a single dex file.
-    AndroidApp generated = MainDexListTests.generateApplication(
-        ImmutableList.of("A", "B"), Constants.ANDROID_L_API, MAX_METHOD_COUNT / 2 + 2);
-    Path applicationJar = temp.newFile("application.jar").toPath();
-    generated.write(applicationJar, OutputMode.Indexed);
-    try {
-      runDexer(applicationJar.toString());
-      fail("Expect to fail, for there are many classes while multidex is not enabled.");
-    } catch (CompilationError e) {
-      // Make sure {@link MonoDexDistributor} was used.
-      assertTrue(e.getMessage().contains("single dex file"));
-      // Make sure what exceeds the limit is the number of methods.
-      assertTrue(e.getMessage().contains("# methods: "
-          + String.valueOf((MAX_METHOD_COUNT / 2 + 2) * 2)));
-    }
-  }
-
-  @Test
   public void keepClassesTest() throws IOException {
     runDexerWithOutput("out.zip", "--keep-classes", EXAMPLE_JAR_FILE1);
   }
 
+  @Test
+  public void ignoreDexInArchiveTest() throws IOException {
+    // Create a JAR with both a .class and a .dex file (the .dex file is just empty).
+    Path jarWithClassesAndDex = temp.newFile("test.jar").toPath();
+    Files.copy(Paths.get(EXAMPLE_JAR_FILE1), jarWithClassesAndDex,
+        StandardCopyOption.REPLACE_EXISTING);
+    URI uri = URI.create("jar:" + jarWithClassesAndDex.toUri());
+    FileSystem fileSystem = FileSystems.newFileSystem(uri, ImmutableMap.of("create", "true"));
+    Path dexFile = fileSystem.getPath("classes.dex");
+    Files.newOutputStream(dexFile, StandardOpenOption.CREATE).close();
+    fileSystem.close();
+
+    // Only test this with CompatDx, as dx does not like the empty .dex file.
+    List<String> d8Args =ImmutableList.of(
+        "--output=" + temp.newFolder("out").toString(), jarWithClassesAndDex.toString());
+    CompatDx.main(d8Args.toArray(new String[d8Args.size()]));
+  }
+
   private void runDexer(String... args) throws IOException {
     runDexerWithOutput("", args);
   }
@@ -178,7 +166,8 @@
     }
     Collections.addAll(dxArgs, args);
     System.out.println("running: dx " + StringUtils.join(dxArgs, " "));
-    ToolHelper.runDX(dxArgs.toArray(new String[dxArgs.size()]));
+    ProcessResult result = ToolHelper.runDX(dxArgs.toArray(new String[dxArgs.size()]));
+    assertEquals(result.stderr, 0, result.exitCode);
 
     if (out == null) {
       // Can't check output if explicitly not writing any.
diff --git a/src/test/java/com/android/tools/r8/maindexlist/MainDexListOutputTest.java b/src/test/java/com/android/tools/r8/maindexlist/MainDexListOutputTest.java
index dfc20f9..1039475 100644
--- a/src/test/java/com/android/tools/r8/maindexlist/MainDexListOutputTest.java
+++ b/src/test/java/com/android/tools/r8/maindexlist/MainDexListOutputTest.java
@@ -38,7 +38,7 @@
     Path mainDexListOutput = temp.getRoot().toPath().resolve("main-dex-output.txt");
     R8Command command =
         ToolHelper.prepareR8CommandBuilder(readClasses(HelloWorldMain.class))
-            .addMainDexRules(mainDexRules)
+            .addMainDexRulesFiles(mainDexRules)
             .setMainDexListOutputPath(mainDexListOutput)
             .build();
     ToolHelper.runR8(command);
diff --git a/src/test/java/com/android/tools/r8/maindexlist/MainDexTracingTest.java b/src/test/java/com/android/tools/r8/maindexlist/MainDexTracingTest.java
index 57c8cf6..ba5092f 100644
--- a/src/test/java/com/android/tools/r8/maindexlist/MainDexTracingTest.java
+++ b/src/test/java/com/android/tools/r8/maindexlist/MainDexTracingTest.java
@@ -9,16 +9,18 @@
 import static com.android.tools.r8.utils.FileUtils.ZIP_EXTENSION;
 
 import com.android.tools.r8.CompilationResult;
+import com.android.tools.r8.GenerateMainDexList;
+import com.android.tools.r8.GenerateMainDexListCommand;
 import com.android.tools.r8.R8Command;
 import com.android.tools.r8.ToolHelper;
 import com.android.tools.r8.graph.DexClass;
 import com.android.tools.r8.graph.DexType;
+import com.android.tools.r8.utils.DescriptorUtils;
 import com.android.tools.r8.utils.InternalOptions;
 import java.nio.charset.StandardCharsets;
 import java.nio.file.Files;
 import java.nio.file.Path;
 import java.nio.file.Paths;
-import java.util.Collections;
 import java.util.List;
 import java.util.concurrent.ExecutionException;
 import java.util.function.Consumer;
@@ -107,7 +109,6 @@
         mainDexRules,
         expectedMainDexList,
         minSdk,
-        R8Command.builder(),
         (options) -> {
           options.inlineAccessors = false;
         });
@@ -120,48 +121,86 @@
       Path mainDexRules,
       Path expectedMainDexList,
       int minSdk,
-      R8Command.Builder builder,
       Consumer<InternalOptions> optionsConsumer)
       throws Throwable {
     Path out = temp.getRoot().toPath().resolve(testName + ZIP_EXTENSION);
 
     Path inputJar = Paths.get(buildDir, packageName + JAR_EXTENSION);
-    builder.setMinApiLevel(minSdk);
     try {
-      R8Command command = builder
+      // Build main-dex list using GenerateMainDexList.
+      GenerateMainDexListCommand.Builder mdlCommandBuilder = GenerateMainDexListCommand.builder();
+      GenerateMainDexListCommand command2 = mdlCommandBuilder
           .addProgramFiles(inputJar)
-          .addLibraryFiles(Paths.get(EXAMPLE_BUILD_DIR, "multidexfakeframeworks" + JAR_EXTENSION),
-              Paths.get(ToolHelper.getAndroidJar(minSdk)))
+          .addProgramFiles(Paths.get(EXAMPLE_BUILD_DIR, "multidexfakeframeworks" + JAR_EXTENSION))
+          .addMainDexRulesFiles(mainDexRules)
+          .build();
+      List<String> mainDexGeneratorMainDexList =
+          GenerateMainDexList.run(command2).stream()
+              .map(this::mainDexStringToDescriptor)
+              .sorted()
+              .collect(Collectors.toList());
+
+      // Build main-dex list using R8.
+      R8Command.Builder r8CommandBuilder = R8Command.builder();
+      R8Command command = r8CommandBuilder
+          .setMinApiLevel(minSdk)
+          .addProgramFiles(inputJar)
+          .addProgramFiles(Paths.get(EXAMPLE_BUILD_DIR, "multidexfakeframeworks" + JAR_EXTENSION))
+          .addLibraryFiles(Paths.get(ToolHelper.getAndroidJar(minSdk)))
           .setOutputPath(out)
-          .addMainDexRules(mainDexRules)
+          .addMainDexRulesFiles(mainDexRules)
           .build();
       CompilationResult result = ToolHelper.runR8WithFullResult(command, optionsConsumer);
-      List<String> resultMainDexList =
+      List<String> r8MainDexList =
           result.dexApplication.mainDexList.stream()
               .filter(dexType -> isApplicationClass(dexType, result))
               .map(dexType -> dexType.descriptor.toString())
+              .sorted()
               .collect(Collectors.toList());
-      Collections.sort(resultMainDexList);
+
+      // Check that both generated lists are the same as the reference list, except for lambda
+      // classes which are only produced when running R8.
       String[] refList = new String(Files.readAllBytes(
           expectedMainDexList), StandardCharsets.UTF_8).split("\n");
+      int nonLambdaOffset = 0;
       for (int i = 0; i < refList.length; i++) {
         String reference = refList[i].trim();
-        String computed = resultMainDexList.get(i);
-        if (reference.contains("-$$Lambda$")) {
-          // For lambda classes we check that there is a lambda class for the right containing
-          // class. However, we do not check the hash for the generated lambda class. The hash
-          // changes for different compiler versions because different compiler versions generate
-          // different lambda implementation method names.
-          reference = reference.substring(0, reference.lastIndexOf('$'));
-          computed = computed.substring(0, computed.lastIndexOf('$'));
+        checkSameMainDexEntry(reference, r8MainDexList.get(i));
+        // The main dex list generator does not do any lambda desugaring.
+        if (!isLambda(reference)) {
+          checkSameMainDexEntry(reference, mainDexGeneratorMainDexList.get(i - nonLambdaOffset));
+        } else {
+          nonLambdaOffset++;
         }
-        Assert.assertEquals(reference, computed);
       }
     } catch (ExecutionException e) {
       throw e.getCause();
     }
   }
 
+  private boolean isLambda(String mainDexEntry) {
+    return mainDexEntry.contains("-$$Lambda$");
+  }
+
+  private String mainDexStringToDescriptor(String mainDexString) {
+    final String CLASS_EXTENSION = ".class";
+    Assert.assertTrue(mainDexString.endsWith(CLASS_EXTENSION));
+    return DescriptorUtils.getDescriptorFromClassBinaryName(
+        mainDexString.substring(0, mainDexString.length() - CLASS_EXTENSION.length()));
+  }
+
+  private void checkSameMainDexEntry(String reference, String computed) {
+    if (isLambda(reference)) {
+      // For lambda classes we check that there is a lambda class for the right containing
+      // class. However, we do not check the hash for the generated lambda class. The hash
+      // changes for different compiler versions because different compiler versions generate
+      // different lambda implementation method names.
+      reference = reference.substring(0, reference.lastIndexOf('$'));
+      computed = computed.substring(0, computed.lastIndexOf('$'));
+    }
+    Assert.assertEquals(reference, computed);
+  }
+
   private boolean isApplicationClass(DexType dexType, CompilationResult result) {
     DexClass clazz = result.appInfo.definitionFor(dexType);
     return clazz != null && clazz.isProgramClass();
diff --git a/src/test/java/com/android/tools/r8/shaking/ProguardConfigurationParserTest.java b/src/test/java/com/android/tools/r8/shaking/ProguardConfigurationParserTest.java
index ea28214..3d6ab69 100644
--- a/src/test/java/com/android/tools/r8/shaking/ProguardConfigurationParserTest.java
+++ b/src/test/java/com/android/tools/r8/shaking/ProguardConfigurationParserTest.java
@@ -14,6 +14,7 @@
 import com.android.tools.r8.ToolHelper;
 import com.android.tools.r8.graph.DexAccessFlags;
 import com.android.tools.r8.graph.DexItemFactory;
+import com.android.tools.r8.utils.FileUtils;
 import com.android.tools.r8.utils.InternalOptions.PackageObfuscationMode;
 import java.io.IOException;
 import java.nio.file.Path;
@@ -98,11 +99,22 @@
 
   @Test
   public void parse() throws IOException, ProguardRuleParserException {
-    ProguardConfigurationParser parser = new ProguardConfigurationParser(new DexItemFactory());
+    ProguardConfigurationParser parser;
+
+    // Parse from file.
+    parser = new ProguardConfigurationParser(new DexItemFactory());
     parser.parse(Paths.get(PROGUARD_SPEC_FILE));
     List<ProguardConfigurationRule> rules = parser.getConfig().getRules();
     assertEquals(24, rules.size());
     assertEquals(1, rules.get(0).getMemberRules().size());
+
+    // Parse from strings.
+    parser = new ProguardConfigurationParser(new DexItemFactory());
+    List<String> lines = FileUtils.readTextFile(Paths.get(PROGUARD_SPEC_FILE));
+    parser.parse(new ProguardConfigurationSourceStrings(lines));
+    rules = parser.getConfig().getRules();
+    assertEquals(24, rules.size());
+    assertEquals(1, rules.get(0).getMemberRules().size());
   }
 
   @Test
diff --git a/src/test/java/com/android/tools/r8/utils/GenerateMainDexListCommandTest.java b/src/test/java/com/android/tools/r8/utils/GenerateMainDexListCommandTest.java
new file mode 100644
index 0000000..64e7a5b
--- /dev/null
+++ b/src/test/java/com/android/tools/r8/utils/GenerateMainDexListCommandTest.java
@@ -0,0 +1,144 @@
+// Copyright (c) 2017, the R8 project authors. Please see the AUTHORS file
+// for details. All rights reserved. Use of this source code is governed by a
+// BSD-style license that can be found in the LICENSE file.
+package com.android.tools.r8.utils;
+
+import static com.android.tools.r8.utils.FileUtils.JAR_EXTENSION;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+
+import com.android.tools.r8.GenerateMainDexListCommand;
+import com.android.tools.r8.ToolHelper;
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.PrintWriter;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.nio.file.StandardOpenOption;
+import java.util.ArrayList;
+import java.util.List;
+import org.junit.Rule;
+import org.junit.Test;
+import org.junit.rules.ExpectedException;
+import org.junit.rules.TemporaryFolder;
+
+public class GenerateMainDexListCommandTest {
+
+  @Rule
+  public ExpectedException thrown = ExpectedException.none();
+
+  @Rule
+  public TemporaryFolder temp = ToolHelper.getTemporaryFolderForTest();
+
+  @Test
+  public void emptyCommand() throws Throwable {
+    verifyEmptyCommand(GenerateMainDexListCommand.builder().build());
+    verifyEmptyCommand(parse());
+    verifyEmptyCommand(parse(""));
+    verifyEmptyCommand(parse("", ""));
+    verifyEmptyCommand(parse(" "));
+    verifyEmptyCommand(parse(" ", " "));
+    verifyEmptyCommand(parse("\t"));
+    verifyEmptyCommand(parse("\t", "\t"));
+  }
+
+  private void verifyEmptyCommand(GenerateMainDexListCommand command) throws IOException {
+    assertEquals(0, ToolHelper.getApp(command).getDexProgramResources().size());
+    assertEquals(0, ToolHelper.getApp(command).getClassProgramResources().size());
+    assertFalse(ToolHelper.getApp(command).hasMainDexListResources());
+  }
+
+  // Add the jars used in the com.android.tools.r8.maindexlist.MainDexTracingTest test.
+  private void addInputJarsToCommandLine(List<String> args) {
+    args.add(Paths.get(ToolHelper.EXAMPLES_BUILD_DIR, "multidex001" + JAR_EXTENSION)
+        .toAbsolutePath().toString());
+    args.add(Paths.get(ToolHelper.EXAMPLES_BUILD_DIR, "multidexfakeframeworks" + JAR_EXTENSION)
+        .toAbsolutePath().toString());
+  }
+
+  // Add main-dex rules used in the com.android.tools.r8.maindexlist.MainDexTracingTest test.
+  private void addMainDexRuleToCommandLine(List<String> args) {
+    args.add("--main-dex-rules");
+    args.add(Paths.get(ToolHelper.EXAMPLES_DIR, "multidex", "main-dex-rules.txt")
+        .toAbsolutePath().toString());
+  }
+
+  @Test
+  public void defaultOutIsCwd() throws Throwable {
+    Path working = temp.getRoot().toPath();
+    String mainDexListOutput = "main-dex-list.txt";
+    Path output = working.resolve(mainDexListOutput);
+    assertFalse(Files.exists(output));
+    List<String> args = new ArrayList<>();
+    addInputJarsToCommandLine(args);
+    addMainDexRuleToCommandLine(args);
+    assertEquals(0, ToolHelper.forkGenerateMainDexList(
+        working, args, "--main-dex-list-output", mainDexListOutput).exitCode);
+    assertTrue(Files.exists(output));
+    assertTrue(Files.size(output) > 0);
+  }
+
+  @Test
+  public void validOutputPath() throws Throwable {
+    Path existingFile = temp.getRoot().toPath().resolve("existing_output");
+    try (OutputStream existingFileOut = Files.newOutputStream(existingFile,
+        StandardOpenOption.CREATE, StandardOpenOption.TRUNCATE_EXISTING)) {
+      PrintWriter writer = new PrintWriter(existingFileOut);
+      writer.println("Hello, world!");
+      writer.flush();
+    }
+    Path nonExistingFile = temp.getRoot().toPath().resolve("non_existing_output");
+    assertEquals(
+        existingFile,
+        GenerateMainDexListCommand.builder().setMainDexListOutputPath(existingFile).build()
+            .getMainDexListOutputPath());
+    assertEquals(
+        nonExistingFile,
+        GenerateMainDexListCommand.builder().setMainDexListOutputPath(nonExistingFile).build()
+            .getMainDexListOutputPath());
+    assertEquals(
+        existingFile,
+        parse("--main-dex-list-output", existingFile.toString()).getMainDexListOutputPath());
+    assertEquals(
+        nonExistingFile,
+        parse("--main-dex-list-output", nonExistingFile.toString()).getMainDexListOutputPath());
+  }
+
+  @Test
+  public void nonExistingOutputFileInNonExistingDir() throws Throwable {
+    Path nonExistingFileInNonExistingDir =
+        temp.getRoot().toPath().resolve("a/path/that/does/not/exist");
+    assertEquals(
+        nonExistingFileInNonExistingDir,
+        GenerateMainDexListCommand.builder()
+            .setMainDexListOutputPath(nonExistingFileInNonExistingDir).build()
+            .getMainDexListOutputPath());
+    assertEquals(
+        nonExistingFileInNonExistingDir,
+        parse("--main-dex-list-output",
+            nonExistingFileInNonExistingDir.toString()).getMainDexListOutputPath());
+  }
+
+  @Test
+  public void mainDexRules() throws Throwable {
+    Path mainDexRules1 = temp.newFile("main-dex-1.rules").toPath();
+    Path mainDexRules2 = temp.newFile("main-dex-2.rules").toPath();
+    parse("--main-dex-rules", mainDexRules1.toString());
+    parse(
+        "--main-dex-rules", mainDexRules1.toString(), "--main-dex-rules", mainDexRules2.toString());
+  }
+
+  @Test
+  public void mainDexList() throws Throwable {
+    Path mainDexList1 = temp.newFile("main-dex-list-1.txt").toPath();
+    Path mainDexList2 = temp.newFile("main-dex-list-2.txt").toPath();
+    parse("--main-dex-list", mainDexList1.toString());
+    parse("--main-dex-list", mainDexList1.toString(), "--main-dex-list", mainDexList2.toString());
+  }
+
+  private GenerateMainDexListCommand parse(String... args) throws Throwable {
+    return GenerateMainDexListCommand.parse(args).build();
+  }
+}