diff --git a/src/com/google/javascript/jscomp/gwt/client/GwtRunner.java b/src/com/google/javascript/jscomp/gwt/client/GwtRunner.java
index f36c9cc209f..06bd47424b3 100644
--- a/src/com/google/javascript/jscomp/gwt/client/GwtRunner.java
+++ b/src/com/google/javascript/jscomp/gwt/client/GwtRunner.java
@@ -50,99 +50,70 @@ public final class GwtRunner implements EntryPoint {
 
   private GwtRunner() {}
 
-  /**
-   * Specifies flags and their defaults.
-   *
-   * You must specify defaults in the constructor (as of August 2016). Defaults specified
-   * alongside fields will cause falsey values to be optimized and inlined. Fix here-
-   *    https://gwt-review.googlesource.com/#/c/16600/
-   */
-  @JsType(namespace = JsPackage.GLOBAL, name = "Flags")
-  public static class Flags {
-    public boolean angularPass;
-    public boolean assumeFunctionWrapper;
-    public String compilationLevel;
-    public boolean dartPass;
-    public boolean exportLocalPropertyDefinitions;
-    public boolean generateExports;
-    public String languageIn;
-    public String languageOut;
-    public boolean checksOnly;
-    public boolean newTypeInf;
-    public boolean polymerPass;
-    public boolean preserveTypeAnnotations;
-    public boolean processCommonJsModules;
+  @JsType(namespace = JsPackage.GLOBAL, name = "Object", isNative = true)
+  private static class Flags {
+    boolean angularPass;
+    boolean assumeFunctionWrapper;
+    String compilationLevel;
+    boolean dartPass;
+    boolean exportLocalPropertyDefinitions;
+    boolean generateExports;
+    String languageIn;
+    String languageOut;
+    boolean checksOnly;
+    boolean newTypeInf;
+    boolean polymerPass;
+    boolean preserveTypeAnnotations;
+    boolean processCommonJsModules;
     public String renamePrefixNamespace;
-    public boolean rewritePolyfills;
-    public String warningLevel;
-    public boolean useTypesForOptimization;
-
-    // These flags do not match the Java jar release.
-    public File[] jsCode;
-    public File[] externs;
-    public boolean createSourceMap;
-
-    /**
-     * Flags constructor. Defaults must be specified here for every field.
-     */
-    public Flags() {
-      this.angularPass = false;
-      this.assumeFunctionWrapper = false;
-      this.compilationLevel = "SIMPLE";
-      this.dartPass = false;
-      this.exportLocalPropertyDefinitions = false;
-      this.generateExports = false;
-      this.languageIn = "ES6";
-      this.languageOut = "ES5";
-      this.checksOnly = false;
-      this.newTypeInf = false;
-      this.polymerPass = false;
-      this.preserveTypeAnnotations = false;
-      this.processCommonJsModules = false;
-      this.renamePrefixNamespace = null;
-      this.rewritePolyfills = true;
-      this.warningLevel = "DEFAULT";
-      this.useTypesForOptimization = true;
-      this.jsCode = null;
-      this.externs = null;
-      this.createSourceMap = false;
-    }
-
-    /**
-     * Updates this {@link Flags} with a raw {@link JavaScriptObject}.
-     *
-     * @param raw The raw flags passed to this program.
-     * @return A list of invalid/unhandled flags.
-     */
-    public native String[] update(JavaScriptObject raw) /*-{
-      var unhandled = [];
-      for (var k in raw) {
-        if (k in this) {
-          this[k] = raw[k];
-        } else {
-          unhandled.push(k);
-        }
-      }
-      return unhandled;
-    }-*/;
+    boolean rewritePolyfills;
+    String warningLevel;
+    boolean useTypesForOptimization;
+
+    // These flags do not match the Java compiler JAR.
+    File[] jsCode;
+    File[] externs;
+    boolean createSourceMap;
   }
 
   /**
-   * File object matching {@code AbstractCommandLineRunner.JsonFileSpec}. This is marked as the
-   * native {@code Object} type as it's not instantiated anywhere.
+   * defaultFlags must have a value set for each field. Otherwise, GWT has no way to create the
+   * fields inside Flags (as it's native). If Flags is not-native, GWT eats its field names
+   * anyway.
    */
+  private static final Flags defaultFlags = new Flags();
+  static {
+    defaultFlags.angularPass = false;
+    defaultFlags.assumeFunctionWrapper = false;
+    defaultFlags.compilationLevel = "SIMPLE";
+    defaultFlags.dartPass = false;
+    defaultFlags.exportLocalPropertyDefinitions = false;
+    defaultFlags.generateExports = false;
+    defaultFlags.languageIn = "ECMASCRIPT6";
+    defaultFlags.languageOut = "ECMASCRIPT5";
+    defaultFlags.checksOnly = false;
+    defaultFlags.newTypeInf = false;
+    defaultFlags.polymerPass = false;
+    defaultFlags.preserveTypeAnnotations = false;
+    defaultFlags.processCommonJsModules = false;
+    defaultFlags.renamePrefixNamespace = null;
+    defaultFlags.rewritePolyfills = true;
+    defaultFlags.warningLevel = "DEFAULT";
+    defaultFlags.useTypesForOptimization = true;
+    defaultFlags.jsCode = null;
+    defaultFlags.externs = null;
+    defaultFlags.createSourceMap = false;
+  }
+
   @JsType(namespace = JsPackage.GLOBAL, name = "Object", isNative = true)
-  public static class File {
+  private static class File {
     @JsProperty String path;
     @JsProperty String src;
     @JsProperty String sourceMap;
   }
 
-  /**
-   * Output type returned to caller.
-   */
-  @JsType(namespace = JsPackage.GLOBAL, name = "ModuleOutput")
-  public static class ModuleOutput {
+  @JsType(namespace = JsPackage.GLOBAL, name = "Object", isNative = true)
+  private static class ModuleOutput {
     @JsProperty String compiledCode;
     @JsProperty String sourceMap;
     @JsProperty JavaScriptObject[] errors;
@@ -199,16 +170,13 @@ private static void applyOptionsFromFlags(CompilerOptions options, Flags flags)
     warningLevel.setOptionsForWarningLevel(options);
 
     LanguageMode languageIn = LanguageMode.fromString(flags.languageIn);
-    if (languageIn == null) {
-      throw new RuntimeException("Bad value for languageIn: " + flags.languageIn);
+    if (languageIn != null) {
+      options.setLanguageIn(languageIn);
     }
-    options.setLanguageIn(languageIn);
-
     LanguageMode languageOut = LanguageMode.fromString(flags.languageOut);
-    if (languageOut == null) {
-      throw new RuntimeException("Bad value for languageOut: " + flags.languageOut);
+    if (languageOut != null) {
+      options.setLanguageOut(languageOut);
     }
-    options.setLanguageOut(languageOut);
 
     if (flags.createSourceMap) {
       options.setSourceMapOutputPath("%output%");
@@ -267,15 +235,30 @@ private static ImmutableMap<String, SourceMapInput> buildSourceMaps(
     return inputSourceMaps.build();
   }
 
+  /**
+   * Updates the destination flags (user input) with source flags (the defaults). Returns a list
+   * of flags that are on the destination, but not on the source.
+   */
+  private static native String[] updateFlags(Flags dst, Flags src) /*-{
+    for (var k in src) {
+      if (!(k in dst)) {
+        dst[k] = src[k];
+      }
+    }
+    var unhandled = [];
+    for (var k in dst) {
+      if (!(k in src)) {
+        unhandled.push(k);
+      }
+    }
+    return unhandled;
+  }-*/;
+
   /**
    * Public compiler call. Exposed in {@link #exportCompile}.
-   *
-   * @param raw The passed raw flags from the user.
-   * @return The output from the compile.
    */
-  public static ModuleOutput compile(JavaScriptObject raw) {
-    Flags flags = new Flags();
-    String[] unhandled = flags.update(raw);
+  public static ModuleOutput compile(Flags flags) {
+    String[] unhandled = updateFlags(flags, defaultFlags);
     if (unhandled.length > 0) {
       throw new RuntimeException("Unhandled flag: " + unhandled[0]);
     }
diff --git a/src/com/google/javascript/jscomp/gwt/linker/MinimalLinker.java b/src/com/google/javascript/jscomp/gwt/linker/MinimalLinker.java
index e18fee4fb6e..43030c0f1a1 100644
--- a/src/com/google/javascript/jscomp/gwt/linker/MinimalLinker.java
+++ b/src/com/google/javascript/jscomp/gwt/linker/MinimalLinker.java
@@ -29,11 +29,9 @@
 import com.google.gwt.dev.util.Util;
 
 /**
- * Simple single-script linker that doesn't add any dependencies on the browser.
- *
- * This is intended to generate JS for servers, Node, or inside browsers as a module. It doesn't
- * support permutations, nor does it allow late-loading code. It supports JSInterop, but it does not
- * automatically add anything to the external scope (see {@code $wnd} below).
+ * Simple single-script linker that doesn't add any dependence on the browser.
+ * This is intended to generate server-side runnable JS.  It doesn't support
+ * permutations, nor does it allow late-loading code.
  */
 @LinkerOrder(Order.PRIMARY)
 public class MinimalLinker extends AbstractLinker {
@@ -43,14 +41,10 @@ public class MinimalLinker extends AbstractLinker {
    * to invoke the {@code onModuleLoad} methods of loaded modules. The gwtOnLoad method then sets
    * {@code $moduleName} and {@code $moduleBase}, shadow them here so they don't leak into the
    * global scope.
-   *
-   * We also fake {@code $wnd} with an empty object (containg Error, to work around GWT using it
-   * statically in {@code StackTraceCreator}). JSInterop will export its objects here, which are
-   * then discarded at runtime. This is needed to avoid polluting our environments.
    */
   private static final String PREFIX =
-      "(function(){var $wnd={Error:{}}; var $doc={}; var $moduleName, $moduleBase;";
-  private static final String SUFFIX = "$wnd=this;typeof gwtOnLoad==='function'&&gwtOnLoad()})();";
+      "(function(){var $wnd=this; var $doc={}; var $moduleName, $moduleBase;";
+  private static final String SUFFIX = "typeof gwtOnLoad==='function'&&gwtOnLoad()})();";
 
   @Override
   public String getDescription() {