这是在ApkIDE中Apk相关的处理命令工具，包括调用apktool反编译apk，调用apktool回编译apk，对生成的apk进行签名，调用Dex2jar对.dex反编译成.class文件，调用jad对.class文件进行反编译等。

using System;
using System.Collections.Generic;
using System.Text;
using System.Diagnostics;
using System.IO;
using System.Windows.Forms;

namespace Com.Popotu.ApkIDE
{
    /// <summary>
    /// Apk相关处理命令（使用Apktool2.0测试）
    /// ShellCmd类：http://www.jianshu.com/p/de99a6d99e31
    /// </summary>
    class ApkCmd
    {
        private static string GetApkToolCmdHead()
        {
            return "java -jar apktool.jar"; 
        }
        /// <summary>
        /// 使用apktool反编译apk文件
        /// </summary>
        /// <param name="apkFilePathForDecompile">要反编译的apk文件路径</param>
        /// <param name="smaliDirPathForOutput">反编译后smali源文件输出目录</param>
        /// <param name="frameworkList"></param>
        /// <param name="errinf"></param>
        /// <returns></returns>
        public static bool DecompileApk(string apkFilePathForDecompile, string smaliDirPathForOutput, List<string> frameworkList, out string errinf)
        {
            ShellCmd cmd = new ShellCmd();
            List<string> cmdList = new List<string>();
            cmdList.Add(string.Format("set path={0}", Path.Combine(Appres.JDK_HOME , "bin")));
            foreach (string framework in frameworkList)
                cmdList.Add(string.Format("{0} if \"{1}\"", GetApkToolCmdHead(), framework));         
            cmdList.Add(
                string.Format("{0} d -f \"{1}\" -o \"{3}\"",
                GetApkToolCmdHead(),
                apkFilePathForDecompile,
                smaliDirPathForOutput));
            cmd.Run(cmdList.ToArray());

            bool noerr = true;
            if (!string.IsNullOrEmpty(cmd.Errinf))
            {
                errinf = cmd.Errinf;
                noerr = !errinf.Contains("Exception in thread");
            }
            else errinf = string.Empty;
            return noerr && Directory.Exists(smaliDirPathForOutput);
        }

        /// <summary>
        /// 使用apktool将smali回编译为apk
        /// </summary>
        /// <param name="apkSourceDir">smali源文件夹</param>
        /// <param name="apkOutputFile">编译输出的apk文件路径</param>
        /// <param name="ingoreError">是否忽略错误（防卡死，但有副作用）</param>
        /// <returns></returns>
        public static bool CompileToApk(string smaliDirPathForCompile, string apkFilePathForOutput, List<string> frameworkList, bool ingoreError)
        {
            ShellCmd cmd = new ShellCmd();
            if (ingoreError) cmd.IngoreError = true;
            List<string> cmdList = new List<string>();
            cmdList.Add(string.Format("set path={0}", Path.Combine(Appres.JDK_HOME, "bin")));
            foreach (string framework in frameworkList)
                cmdList.Add(string.Format("{0} if \"{1}\"", GetApkToolCmdHead(), framework));
            
            cmdList.Add(
                string.Format("{0} b \"{1}\" -o \"{3}\"",
                GetApkToolCmdHead(),
                smaliDirPathForCompile,                
                apkFilePathForOutput));
            cmd.Run(cmdList.ToArray());
            bool success = File.Exists(apkFilePathForOutput);           
            return success;
        }

        /// <summary>
        /// 给apk签名
        /// </summary>
        /// <param name="apkFilePathForSigned">要签名的apk程序路径</param>
        /// <param name="getSignedApkFilePath"></param>
        /// <param name="useJarsigner">是否使用jarsigner来签名（需要设置keystore），否则使用signapk.jar签</param>
        /// <returns>是否成功</returns>
        public static bool SignApk(string apkFilePathForSigned, out string getSignedApkFilePath,
            bool useJarsigner = false, string keystoreFile = null, string storepass = null, string keypass = null, string alias = null)
        {
            string apkname = IOCommand.GetFileNameWithoutExt(apkFilePathForSigned);
            string signedApkOutputFilePath = Path.Combine(new FileInfo(apkFilePathForSigned).DirectoryName, apkname + "_Signed.apk");
            if (File.Exists(signedApkOutputFilePath)) File.Delete(signedApkOutputFilePath);
            ShellCmd cmd = new ShellCmd();
            if (string.IsNullOrEmpty(keystoreFile) || string.IsNullOrEmpty(storepass) || string.IsNullOrEmpty(keypass) || string.IsNullOrEmpty(alias)) useJarsigner = false;
            if (useJarsigner)//使用jarsigner.exe签名
            {
                string fmt = "jarsigner -keystore \"{0}\" -storepass {1} -keypass {2} \"{3}\" {4} {5}";
                fmt = string.Format(fmt, new string[]{
                    keystoreFile,
                    storepass,
                    keypass,
                    apkFilePathForSigned,
                    alias,
                    "-digestalg SHA1 -sigalg MD5withRSA" 
                });
                cmd.Run(new string[]{
                    string.Format("set path={0}", Path.Combine(Appres.JDK_HOME, "bin")),
                    fmt,
                    string.Format("zipalign -v 4 \"{0}\" \"{1}\"", apkFilePathForSigned, signedApkOutputFilePath)
                });
            }
            else//使用signapk.jar签名
            {
                string fmt = "testkey.x509.pem testkey.pk8 \"{0}\" \"{1}\"";
                fmt = string.Format(fmt, apkFilePathForSigned, signedApkOutputFilePath);
                cmd.Run(new string[] { 
                     string.Format("set path={0}", Path.Combine(Appres.JDK_HOME, "bin")),
                    "java -jar signapk.jar " + fmt 
                });
            }

            getSignedApkFilePath = signedApkOutputFilePath;
            bool success = File.Exists(getSignedApkFilePath);
            return success;
        }

        /// <summary>
        /// 将所有.class文件用jad反编译成.java文件
        /// </summary>
        /// <param name="dirPathOfClassFiles"></param>
        /// <param name="outputDirPathForJavaFiles"></param>
        public static void Classes2Javas(string dirPathOfClassFiles, string outputDirPathForJavaFiles)
        {
            List<string> cmdList = new List<string>();
            cmdList.Add(string.Format("jad -o -r -sjava -d\"{0}\" \"{1}\"/**/*.class", outputDirPathForJavaFiles, dirPathOfClassFiles));            
            ShellCmd cmd = new ShellCmd();
            cmd.IngoreError = true;
            cmd.Run(cmdList.ToArray());
        }
        /// <summary>
        /// 从apk反编译出.class代码文件
        /// </summary>
        /// <param name="apkFilePath"></param>
        /// <param name="outputDirPathForClassFiles"></param>
        /// <param name="errinf">错误信息</param>
        /// <exception cref="Exception">意外错误</exception>
        /// <returns></returns>
        public static bool Apk2Classes(string apkFilePath, string outputDirPathForClassFiles, out string errinf)
        {
            string dexFilePath = null;
            try
            {
                dexFilePath = Path.Combine(Application.StartupPath, "classes.dex");
                ApkZip.Unzip(apkFilePath, "classes.dex", dexFilePath);
                bool success = Dex2jar(dexFilePath, outputDirPathForClassFiles);
                errinf = string.Empty;
                return success;
            }
            catch (ApplicationException e)
            {
                errinf = e.Message;
                return false;
            }
            catch (Exception e)
            {
                throw e;
            }
            finally
            {
                try
                {
                    if (!string.IsNullOrEmpty(dexFilePath) && File.Exists(dexFilePath)) File.Delete(dexFilePath);
                }
                catch { }
            }
        }
        /// <summary>
        /// dex2jar
        /// </summary>
        /// <param name="dexFile"></param>
        /// <param name="outputDirPathForClassFiles"></param>
        /// <exception cref="ApplicationException"></exception>
        /// <returns></returns>
        public static bool Dex2jar(string dexFile,string outputDirPathForClassFiles)
        {
            //生成classes_dex2jar.jar
            List<string> cmdList = new List<string>();
            cmdList.Add(
                string.Format(
                "set path={0};{1}",
                Path.Combine(Appres.JDK_HOME, "bin"),
                Path.Combine(Application.StartupPath, "dex2jar")));
            cmdList.Add(
                string.Format(
                "d2j-dex2jar --force \"{0}\"", 
                dexFile));
            ShellCmd cmd = new ShellCmd();
            cmd.Run(cmdList.ToArray());
            string cd2jFile = Path.Combine(new FileInfo(dexFile).Directory.FullName ,IOCommand.GetFileNameWithoutExt(dexFile) + "-dex2jar.jar");
            try { if (Directory.Exists(outputDirPathForClassFiles)) Directory.Delete(outputDirPathForClassFiles, true); }
            catch { }
            ApkZip.Unzip(cd2jFile, outputDirPathForClassFiles);
            try { if (File.Exists(cd2jFile)) File.Delete(cd2jFile); }catch { }
            bool success = System.IO.Directory.Exists(outputDirPathForClassFiles);
            if (!success && !string.IsNullOrEmpty(cmd.Errinf))
            {
                throw new ApplicationException(cmd.Errinf);
            }
            return success;
        }

    }
}