diff --git a/src/vogar/ModeId.java b/src/vogar/ModeId.java
index 718c5e0..e3b94c2 100644
--- a/src/vogar/ModeId.java
+++ b/src/vogar/ModeId.java
@@ -75,8 +75,8 @@
      * generation.
      */
     private static final String[] APP_JARS = new String[] {
-            "ext",
             "framework",
+            "ext",
             "telephony-common",
             "voip-common",
             "ims-common",
diff --git a/src/vogar/android/AndroidSdk.java b/src/vogar/android/AndroidSdk.java
index b19f404..f59c9b9 100644
--- a/src/vogar/android/AndroidSdk.java
+++ b/src/vogar/android/AndroidSdk.java
@@ -28,6 +28,7 @@
 import java.util.jar.JarEntry;
 import java.util.jar.JarInputStream;
 import java.util.jar.JarOutputStream;
+
 import vogar.Classpath;
 import vogar.Dexer;
 import vogar.HostFileCache;
@@ -387,7 +388,14 @@
                 if (entry.getName().endsWith(".class")) {
                     continue;
                 }
+
+                // Skip directories as they can cause duplicates.
+                if (entry.isDirectory()) {
+                    continue;
+                }
+
                 outputJar.putNextEntry(entry);
+
                 int length;
                 while ((length = inputJar.read(buffer)) >= 0) {
                     if (length > 0) {