add support for automatically patch signatures

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

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

@@ -183,9 +183,11 @@ public class Main {
 		flags.put("verbose", false);
 		flags.put("framework", false);
 		flags.put("update", false);
+		flags.put("copyOriginal", false);
 
 		int i;
 		int skip = 0;
+
 		ExtFile mOrigApk = null;
 		String mAaptPath = "";
 		for (i = 0; i < args.length; i++) {
@@ -202,6 +204,8 @@ public class Main {
 			} else if ("-a".equals(opt) || "--aapt".equals(opt)) {
 				mAaptPath = args[i + 1];
 				skip = 1;
+			} else if ("-c".equals(opt) || "--copy-original".equals(opt)) {
+				flags.put("copyOriginal", true);
 			} else if ("--frame-path".equals(opt)) {
 			    i++;
 	        instance.setFrameworkFolder(args[i]);
@@ -329,6 +333,8 @@ public class Main {
 						+ "            Build in debug mode. Check project page for more info.\n"
 						+ "        -a, --aapt\n"
 						+ "            Loads aapt from specified location.\n"
+						+ "        -c, --copy-original\n"
+						+ "            Copies original AndroidManifest.xml and META-INF.\n"
             + "        --frame-path <dir>\n"
             + "            Use the specified directory for framework files\n"
 						+ "\n"

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

@@ -16,7 +16,6 @@
 
 package brut.androlib;
 
-import brut.androlib.err.InFileNotFoundException;
 import brut.androlib.java.AndrolibJava;
 import brut.androlib.res.AndrolibResources;
 import brut.androlib.res.data.ResPackage;
@@ -129,6 +128,27 @@ public class Androlib {
 		}
 	}
 
+	public void writeOriginalFiles(ExtFile apkFile, File outDir)
+			throws AndrolibException {
+		LOGGER.info("Copying original files...");
+		File originalDir = new File(outDir, "original");
+		if (!originalDir.exists()) {
+			originalDir.mkdirs();
+		}
+
+		try {
+			Directory in = apkFile.getDirectory();
+			if(in.containsFile("AndroidManifest.xml")) {
+				in.copyToDir(originalDir, "AndroidManifest.xml");
+			}
+			if (in.containsDir("META-INF")) {
+				in.copyToDir(originalDir, "META-INF");
+			}
+		} catch (DirectoryException ex) {
+			throw new AndrolibException(ex);
+		}
+	}
+
 	public void writeMetaFile(File mOutDir, Map<String, Object> meta)
 			throws AndrolibException {
 		DumperOptions options = new DumperOptions();
@@ -200,6 +220,7 @@ public class Androlib {
 		buildResources(appDir, flags,
 				(Map<String, Object>) meta.get("usesFramework"));
 		buildLib(appDir, flags);
+		buildCopyOriginalFiles(appDir, flags);
 		buildApk(appDir, outFile, flags);
 	}
 
@@ -424,6 +445,29 @@ public class Androlib {
 		}
 	}
 
+	public void buildCopyOriginalFiles(File appDir,
+			HashMap<String, Boolean> flags) throws AndrolibException {
+		if (flags.get("copyOriginal")) {
+			File originalDir = new File(appDir, "original");
+			if(originalDir.exists()) {
+				try {
+					LOGGER.info("Copy original files...");
+					Directory in = (new ExtFile(originalDir)).getDirectory();
+					if(in.containsFile("AndroidManifest.xml")) {
+						LOGGER.info("Copy AndroidManifest.xml...");
+						in.copyToDir(new File(appDir, APK_DIRNAME), "AndroidManifest.xml");
+					}
+					if (in.containsDir("META-INF")) {
+						LOGGER.info("Copy META-INF...");
+						in.copyToDir(new File(appDir, APK_DIRNAME), "META-INF");
+					}
+				} catch (DirectoryException ex) {
+					throw new AndrolibException(ex);
+				}
+			}
+		}
+	}
+
 	public void buildApk(File appDir, File outApk,
 			HashMap<String, Boolean> flags) throws AndrolibException {
 		LOGGER.info("Building apk file...");
@@ -514,16 +558,11 @@ public class Androlib {
 		}
 		return files;
 	}
-
-	public void setApkFile(File apkFile) {
-		mOrigApkFile = new ExtFile(apkFile);
-	}
 	
 	public void setFrameworkFolder(String path) {
 	  mAndRes.setFrameworkFolder(path);
 	}
 
-	private ExtFile mOrigApkFile = null;
 	private String mAaptPath = null;
 
 	private final static Logger LOGGER = Logger.getLogger(Androlib.class

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

@@ -133,6 +133,7 @@ public class ApkDecoder {
 		}
 
 		mAndrolib.decodeRawFiles(mApkFile, outDir);
+		mAndrolib.writeOriginalFiles(mApkFile, outDir);
 		writeMetaFile();
 	}
 

brut.apktool/apktool-lib/src/test/java/brut/androlib/BuildAndDecodeTest.java

@@ -184,6 +184,7 @@ public class BuildAndDecodeTest {
 		tmp.put("verbose", false);
 		tmp.put("framework", false);
 		tmp.put("update", false);
+		tmp.put("copyOriginal", false);
 
 		return tmp;
 	}