Patch APKTool to allow repeated entry offsets to appear

.gitignore

@@ -15,6 +15,7 @@ bin/
 # Tmp Files
 *.kate-swp
 *~
+*.DS_Store
 
 # IntelliJ
 *.iml
@@ -23,3 +24,6 @@ bin/
 
 # gradle/smali-patches patch smali/ into brut.apktool.smali/
 brut.apktool.smali/
+
+# Patches
+*.patch

brut.apktool/apktool-cli/src/main/java/brut/apktool/Main.java

@@ -127,6 +127,9 @@ private static void cmdDecode(CommandLine cli) throws AndrolibException {
         if (cli.hasOption("force-manifest")) {
             decoder.setForceDecodeManifest(ApkDecoder.FORCE_DECODE_MANIFEST_FULL);
         }
+        if (cli.hasOption("manifest-only")) {
+            decoder.setManifestOnly(true);
+        }
         if (cli.hasOption("no-assets")) {
             decoder.setDecodeAssets(ApkDecoder.DECODE_ASSETS_NONE);
         }
@@ -294,6 +297,11 @@ private static void _Options() {
                 .desc("Decode the APK's compiled manifest, even if decoding of resources is set to \"false\".")
                 .build();
 
+        Option manifestOnlyOption = Option.builder("mo")
+                .longOpt("manifest-only")
+                .desc("Only decode manifest.")
+                .build();
+
         Option noAssetOption = Option.builder()
                 .longOpt("no-assets")
                 .desc("Do not decode assets.")
@@ -431,6 +439,7 @@ private static void _Options() {
         DecodeOptions.addOption(forceDecOption);
         DecodeOptions.addOption(noSrcOption);
         DecodeOptions.addOption(noResOption);
+        DecodeOptions.addOption(manifestOnlyOption);
 
         // add basic build options
         BuildOptions.addOption(outputBuiOption);

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

@@ -100,6 +100,13 @@ public void decode() throws AndrolibException, IOException, DirectoryException {
 
             LOGGER.info("Using Apktool " + Androlib.getVersion() + " on " + mApkFile.getName());
 
+            if (mManifestOnly) {
+               setAnalysisMode(mAnalysisMode, true);
+               mAndrolib.decodeManifestWithResources(mApkFile, outDir, getResTable());
+               writeMetaFile();
+               return;
+            }
+
             if (hasResources()) {
                 switch (mDecodeResources) {
                     case DECODE_RESOURCES_NONE:
@@ -125,7 +132,7 @@ public void decode() throws AndrolibException, IOException, DirectoryException {
                         break;
                 }
             } else {
-                // if there's no resources.asrc, decode the manifest without looking
+                // if there's no resources.arsc, decode the manifest without looking
                 // up attribute references
                 if (hasManifest()) {
                     if (mDecodeResources == DECODE_RESOURCES_FULL
@@ -242,6 +249,10 @@ public void setForceDelete(boolean forceDelete) {
         mForceDelete = forceDelete;
     }
 
+    public void setManifestOnly(boolean manifestOnly) {
+        mManifestOnly = manifestOnly;
+    }
+
     public void setFrameworkTag(String tag) throws AndrolibException {
         mAndrolib.apkOptions.frameworkTag = tag;
     }
@@ -416,7 +427,7 @@ private void putUnknownInfo(MetaInfo meta) throws AndrolibException {
     }
 
     private void putFileCompressionInfo(MetaInfo meta) throws AndrolibException {
-        if (!mUncompressedFiles.isEmpty()) {
+        if (mUncompressedFiles != null && !mUncompressedFiles.isEmpty()) {
             meta.doNotCompress = mUncompressedFiles;
         }
     }
@@ -437,6 +448,7 @@ private void putSharedLibraryInfo(MetaInfo meta) throws AndrolibException {
     private short mForceDecodeManifest = FORCE_DECODE_MANIFEST_NONE;
     private short mDecodeAssets = DECODE_ASSETS_FULL;
     private boolean mForceDelete = false;
+    private boolean mManifestOnly = false;
     private boolean mKeepBrokenResources = false;
     private boolean mBakDeb = true;
     private Collection<String> mUncompressedFiles;

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

@@ -154,12 +154,12 @@ private ResTypeSpec readTableTypeSpec() throws AndrolibException, IOException {
 
         while (type == Header.TYPE_TYPE) {
             readTableType();
-            
+
             // skip "TYPE 8 chunks" and/or padding data at the end of this chunk
             if (mCountIn.getCount() < mHeader.endPosition) {
                 mCountIn.skip(mHeader.endPosition - mCountIn.getCount());
             }
-            
+
             type = nextChunk().type;
 
             addMissingResSpecs();
@@ -223,33 +223,55 @@ private ResType readTableType() throws IOException, AndrolibException {
         }
 
         mType = flags.isInvalid && !mKeepBroken ? null : mPkg.getOrCreateConfig(flags);
+        HashMap<Integer, EntryData> offsetsToEntryData =
+            new HashMap<Integer, EntryData>();
+
+        for (int offset : entryOffsets) {
+          if (offset == -1 || offsetsToEntryData.containsKey(offset)) {
+            continue;
+          }
+
+          offsetsToEntryData.put(offset, readEntryData());
+        }
 
         for (int i = 0; i < entryOffsets.length; i++) {
             if (entryOffsets[i] != -1) {
                 mMissingResSpecs[i] = false;
                 mResId = (mResId & 0xffff0000) | i;
-                readEntry();
+                EntryData entryData = offsetsToEntryData.get(entryOffsets[i]);
+                readEntry(entryData);
             }
         }
 
         return mType;
     }
 
-    private void readEntry() throws IOException, AndrolibException {
+    private class EntryData {
+        public short mFlags;
+        public int mSpecNamesId;
+        public ResValue mValue;
+    }
+
+    private EntryData readEntryData() throws IOException, AndrolibException {
         short size = mIn.readShort();
         if (size < 0) {
             throw new AndrolibException("Entry size is under 0 bytes.");
         }
+
         short flags = mIn.readShort();
         int specNamesId = mIn.readInt();
-
-        // If we are here, we probably already inserted any remaining dummy resources. No need to parse
-        // any resources that doesn't have type information
-        if (mCountIn.getCount() == mHeader.endPosition) {
-            return;
-        }
-
         ResValue value = (flags & ENTRY_FLAG_COMPLEX) == 0 ? readValue() : readComplexEntry();
+        EntryData entryData = new EntryData();
+        entryData.mFlags = flags;
+        entryData.mSpecNamesId = specNamesId;
+        entryData.mValue = value;
+        return entryData;
+    }
+
+    private void readEntry(EntryData entryData) throws AndrolibException {
+        short flags = entryData.mFlags;
+        int specNamesId = entryData.mSpecNamesId;
+        ResValue value = entryData.mValue;
 
         if (mTypeSpec.isString() && value instanceof ResFileValue) {
             value = new ResStringValue(value.toString(), ((ResFileValue) value).getRawIntValue());