I checked a fix for the missing AndroidManifest.xml issue, please pull it into the master repository if you think it's ok

apktool-lib/src/main/java/brut/androlib/Androlib.java

@@ -77,6 +77,22 @@ public void decodeSourcesJava(ExtFile apkFile, File outDir, boolean debug)
         new AndrolibJava().decode(apkFile, outDir);
     }
 
+    public void decodeManifestRaw(ExtFile apkFile, File outDir)
+            throws AndrolibException {
+        try {
+            Directory apk = apkFile.getDirectory();
+            LOGGER.info("Copying raw manifest...");
+            apkFile.getDirectory().copyToDir(outDir, APK_MANIFEST_FILENAME);
+        } catch (DirectoryException ex) {
+            throw new AndrolibException(ex);
+        }
+    }
+
+    public void decodeManifestFull(ExtFile apkFile, File outDir)
+            throws AndrolibException {
+        mAndRes.decodeManifest(apkFile, outDir);
+    }
+
     public void decodeResourcesRaw(ExtFile apkFile, File outDir)
             throws AndrolibException {
         try {
@@ -436,5 +452,6 @@ private File[] newFiles(String[] names, File dir) {
         new String[]{"resources.arsc", "AndroidManifest.xml"};
     private final static String[] APP_RESOURCES_FILENAMES =
         new String[]{"AndroidManifest.xml", "res"};
+    private final static String APK_MANIFEST_FILENAME = "AndroidManifest.xml";
     private final static String VERSION = "1.3.2";
 }

apktool-lib/src/main/java/brut/androlib/ApkDecoder.java

@@ -89,6 +89,7 @@ public void decode() throws AndrolibException {
                     break;
             }
         }
+
         if (hasResources()) {
             switch (mDecodeResources) {
                 case DECODE_RESOURCES_NONE:
@@ -99,7 +100,21 @@ public void decode() throws AndrolibException {
                         getResTable());
                     break;
             }
+        } else {
+            // if there's no resources.asrc, decode the manifest without looking up
+            // attribute references
+            if (hasManifest()) {
+                switch (mDecodeResources) {
+                case DECODE_RESOURCES_NONE:
+                    mAndrolib.decodeManifestRaw(mApkFile, outDir);
+                    break;
+                case DECODE_RESOURCES_FULL:
+                    mAndrolib.decodeManifestFull(mApkFile, outDir);
+                    break;
+                }
+            }
         }
+
         mAndrolib.decodeRawFiles(mApkFile, outDir);
         writeMetaFile();
     }
@@ -159,6 +174,14 @@ public boolean hasSources() throws AndrolibException {
         }
     }
 
+    public boolean hasManifest() throws AndrolibException {
+        try {
+            return mApkFile.getDirectory().containsFile("AndroidManifest.xml");
+        } catch (DirectoryException ex) {
+            throw new AndrolibException(ex);
+        }
+    }
+
     public boolean hasResources() throws AndrolibException {
         try {
             return mApkFile.getDirectory().containsFile("resources.arsc");

apktool-lib/src/main/java/brut/androlib/res/AndrolibResources.java

@@ -97,6 +97,27 @@ public ResPackage loadFrameworkPkg(ResTable resTable, int id,
         return pkg;
     }
 
+    public void decodeManifest(ExtFile apkFile, File outDir)
+            throws AndrolibException {
+
+        Duo<ResFileDecoder, AXmlResourceParser> duo = getManifestFileDecoder();
+        ResFileDecoder fileDecoder = duo.m1;
+
+        Directory inApk, out;
+        try {
+            inApk = apkFile.getDirectory();
+            out = new FileDirectory(outDir);
+
+            LOGGER.info("Decoding AndroidManifest.xml without resources...");
+            fileDecoder.decode(
+                inApk, "AndroidManifest.xml", out, "AndroidManifest.xml",
+                "xml");
+
+        } catch (DirectoryException ex) {
+            throw new AndrolibException(ex);
+        }
+    }
+
     public void decode(ResTable resTable, ExtFile apkFile, File outDir)
             throws AndrolibException {
         Duo<ResFileDecoder, AXmlResourceParser> duo = getResFileDecoder();
@@ -111,6 +132,7 @@ public void decode(ResTable resTable, ExtFile apkFile, File outDir)
             inApk = apkFile.getDirectory();
             out = new FileDirectory(outDir);
 
+            LOGGER.info("Decoding AndroidManifest.xml with resources...");
             fileDecoder.decode(
                 inApk, "AndroidManifest.xml", out, "AndroidManifest.xml",
                 "xml");
@@ -238,6 +260,19 @@ public Duo<ResFileDecoder, AXmlResourceParser> getResFileDecoder() {
             new ResFileDecoder(decoders), axmlParser);
     }
 
+    public Duo<ResFileDecoder, AXmlResourceParser> getManifestFileDecoder() {
+        ResStreamDecoderContainer decoders =
+            new ResStreamDecoderContainer();
+
+        AXmlResourceParser axmlParser = new AXmlResourceParser();
+
+        decoders.setDecoder("xml",
+            new XmlPullStreamDecoder(axmlParser, getResXmlSerializer()));
+
+        return new Duo<ResFileDecoder, AXmlResourceParser>(
+            new ResFileDecoder(decoders), axmlParser);
+    }
+
     public ExtMXSerializer getResXmlSerializer() {
         ExtMXSerializer serial = new ExtMXSerializer();
         serial.setProperty(ExtXmlSerializer.PROPERTY_SERIALIZER_INDENTATION

apktool-lib/src/main/java/brut/androlib/res/decoder/AXmlResourceParser.java

@@ -325,6 +325,10 @@ public String getAttributeValue(int index) {
                     valueData
                 ), ex);
             }
+        } else {
+            if (valueType==TypedValue.TYPE_STRING) {
+                return m_strings.getString(valueRaw);
+            }
         }
 
         return TypedValue.coerceToString(valueType, valueData);
@@ -370,7 +374,7 @@ public int getAttributeResourceValue(int index, int defaultValue) {
     public String getAttributeValue(String namespace, String attribute) {
         int index = findAttribute(namespace, attribute);
         if (index == -1) {
-            return null;
+            return "";
         }
         return getAttributeValue(index);
     }