chore(release): 2.6.0 [skip ci]

# [2.6.0](https://github.com/revanced/revanced-cli/compare/v2.5.3...v2.6.0) (2022-07-18)

### Features

* more efficient zipalign ([a942a57](a942a57364))

.github/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,24 @@
+---
+name: Bug report
+about: Create a bug report on the CLI. Do not submit suggestions for patches here.
+title: 'problem: some problem'
+labels: bug
+assignees: ''
+
+---
+
+## 🐞 Issue
+
+<!-- Describe your issue in detail here -->
+
+## ⚙ Reproduce
+
+<!-- Include your environment and steps to reproduce the issue as detailed as possible -->
+
+## 🛠 Solution
+
+<!-- If applicable, add a possible solution -->
+
+## ⚠ Additional context
+
+<!-- Add any other context about the problem here -->

.github/ISSUE_TEMPLATE/feature_request.md

@@ -0,0 +1,24 @@
+---
+name: Feature request
+about: Suggest a change to the CLI. Do not submit suggestions for patches here.
+title: 'feat: some feature'
+labels: feature-request
+assignees: ''
+
+---
+
+## 🐞 Issue
+
+<!-- Describe your issue in detail here -->
+
+## ⚙ Reproduce
+
+<!-- Include your environment and steps to reproduce the issue as detailed as possible -->
+
+## 🛠 Solution
+
+<!-- If applicable, add a possible solution -->
+
+## ⚠ Additional context
+
+<!-- Add any other context about the problem here -->

.github/workflows/release.yml

@@ -1,5 +1,6 @@
 name: Release
 on:
+  workflow_dispatch:
   push:
     branches:
       - main
@@ -27,12 +28,10 @@ jobs:
         uses: actions/setup-node@v2
         with:
           node-version: "lts/*"
-      - name: Make gradlew executable
-        run: chmod +x gradlew
       - name: Build with Gradle
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: ./gradlew build
+        run: ./gradlew build clean
       - name: Setup semantic-release
         run: npm install -g semantic-release @semantic-release/git @semantic-release/changelog gradle-semantic-release-plugin -D
       - name: Release

.releaserc

@@ -7,7 +7,11 @@
     }
   ],
   "plugins": [
-    "@semantic-release/commit-analyzer",
+    ["@semantic-release/commit-analyzer", {
+      "releaseRules": [
+        {"type": "build", "release": "patch"}
+      ]
+    }],
     "@semantic-release/release-notes-generator",
     "@semantic-release/changelog",
     "gradle-semantic-release-plugin",
@@ -20,6 +24,15 @@
         ]
       }
     ],
-    "@semantic-release/github"
+    [
+      "@semantic-release/github",
+      {
+        "assets": [
+          {
+            "path": "build/libs/*all.jar"
+          }
+        ]
+      }
+    ]
   ]
-}
+}

build.gradle.kts

@@ -1,42 +1,36 @@
 plugins {
-    kotlin("jvm") version "1.6.21"
+    kotlin("jvm") version "1.7.0"
     id("com.github.johnrengelman.shadow") version "7.1.2"
-    java
-    `maven-publish`
 }
 
 group = "app.revanced"
 
+val githubUsername: String = project.findProperty("gpr.user") as? String ?: System.getenv("GITHUB_ACTOR")
+val githubPassword: String = project.findProperty("gpr.key") as? String ?: System.getenv("GITHUB_TOKEN")
+
 repositories {
     mavenCentral()
     mavenLocal()
     maven {
-        url = uri("https://maven.pkg.github.com/revanced/multidexlib2")
+        url = uri("https://maven.pkg.github.com/revanced/revanced-patcher")
         credentials {
-            username = project.findProperty("gpr.user") as String? ?: System.getenv("GITHUB_ACTOR") // DO NOT CHANGE!
-            password = project.findProperty("gpr.key") as String? ?: System.getenv("GITHUB_TOKEN") // DO NOT CHANGE!
+            username = githubUsername
+            password = githubPassword
         }
     }
-    maven {
-        url = uri("https://jitpack.io")
-    }
+    maven { url = uri("https://jitpack.io") }
+    google()
 }
 
 dependencies {
-    implementation("org.jetbrains.kotlin:kotlin-stdlib:1.6.21")
-    implementation("app.revanced:revanced-patcher:+")
-    implementation("app.revanced:revanced-patches:+")
+    implementation(kotlin("stdlib"))
+    implementation(kotlin("reflect"))
 
+    implementation("app.revanced:revanced-patcher:2.4.0")
     implementation("info.picocli:picocli:4.6.3")
-
-    implementation("com.github.li-wjohnson:jadb:master-SNAPSHOT") // using a fork instead.
+    implementation("com.android.tools.build:apksig:7.2.1")
+    implementation("com.github.revanced:jadb:master-SNAPSHOT") // updated fork
     implementation("org.bouncycastle:bcpkix-jdk15on:1.70")
-    implementation("org.jetbrains.kotlin:kotlin-reflect:1.6.21")
-}
-
-java {
-    withSourcesJar()
-    withJavadocJar()
 }
 
 tasks {
@@ -45,27 +39,17 @@ tasks {
     }
     shadowJar {
         manifest {
-            attributes("Main-Class" to "app.revanced.cli.MainKt")
+            attributes("Main-Class" to "app.revanced.cli.main.MainKt")
             attributes("Implementation-Title" to project.name)
             attributes("Implementation-Version" to project.version)
         }
     }
+    // Dummy task to fix the Gradle semantic-release plugin.
+    // Remove this if you forked it to support building only.
+    // Tracking issue: https://github.com/KengoTODA/gradle-semantic-release-plugin/issues/435
+    register<DefaultTask>("publish") {
+        group = "publish"
+        description = "Dummy task"
+        dependsOn(build)
+    }
 }
-
-publishing {
-    repositories {
-        maven {
-            name = "GitHubPackages"
-            url = uri("https://maven.pkg.github.com/revanced/revanced-cli")
-            credentials {
-                username = System.getenv("GITHUB_ACTOR")
-                password = System.getenv("GITHUB_TOKEN")
-            }
-        }
-    }
-    publications {
-        register<MavenPublication>("gpr") {
-            from(components["java"])
-        }
-    }
-}

gradle.properties

@@ -1,2 +1,2 @@
 kotlin.code.style = official
-version = 1.1.3
+version = 2.6.0

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.1.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-7.4.2-all.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

src/main/kotlin/app/revanced/cli/MainCommand.kt

@@ -1,96 +0,0 @@
-package app.revanced.cli
-
-import app.revanced.patcher.annotation.Name
-import app.revanced.patcher.extensions.findAnnotationRecursively
-import app.revanced.patcher.util.patch.PatchLoader
-import app.revanced.utils.adb.Adb
-import app.revanced.utils.patcher.addPatchesFiltered
-import app.revanced.utils.signature.Signature
-import picocli.CommandLine.*
-import java.io.File
-
-@Command(
-    name = "ReVanced-CLI", version = ["1.0.0"], mixinStandardHelpOptions = true
-)
-internal object MainCommand : Runnable {
-    @Parameters(
-        paramLabel = "INCLUDE",
-        description = ["Which patches to include. If none is specified, all compatible patches will be included"]
-    )
-    internal var includedPatches = arrayOf<String>()
-
-    @Option(names = ["-p", "--patches"], description = ["One or more bundles of patches"])
-    internal var patchBundles = arrayOf<File>()
-
-    @Option(names = ["-t", "--temp-dir"], description = ["Temporal resource cache directory"], required = true)
-    internal lateinit var cacheDirectory: String
-
-    @Option(names = ["-r", "--resource-patcher"], description = ["Enable patching resources"])
-    internal var patchResources: Boolean = false
-
-    @Option(
-        names = ["-c", "--clean"],
-        description = ["Clean the temporal resource cache directory. This will be done anyways when running the patcher"]
-    )
-    internal var clean: Boolean = false
-
-    @Option(names = ["-l", "--list"], description = ["List patches only"])
-    internal var listOnly: Boolean = false
-
-    @Option(names = ["-s", "--signature-checker"], description = ["Check signatures of all patches"])
-    internal var signatureCheck: Boolean = false
-
-    @Option(names = ["-m", "--merge"], description = ["One or more dex file containers to merge"])
-    internal var mergeFiles = listOf<File>()
-
-    @Option(names = ["-a", "--apk"], description = ["Input file to be patched"], required = true)
-    internal lateinit var inputFile: File
-
-    @Option(names = ["-o", "--out"], description = ["Output file path"], required = true)
-    internal lateinit var outputPath: String
-
-    @Option(names = ["-d", "--deploy-on"], description = ["If specified, deploy to adb device with given name"])
-    internal var deploy: String? = null
-
-    override fun run() {
-        if (listOnly) {
-            for (patchBundle in patchBundles)
-                for (it in PatchLoader.loadFromFile(patchBundle))
-                    println(
-                        "[available] ${
-                            it.javaClass.findAnnotationRecursively(
-                                Name::class.java
-                            )?.name ?: Name::class.java.name
-                        }"
-                    )
-            return
-        }
-
-        val patcher = app.revanced.patcher.Patcher(
-            inputFile, cacheDirectory, patchResources
-        )
-
-        if (signatureCheck) {
-            patcher.addPatchesFiltered()
-            Signature.checkSignatures(patcher)
-            return
-        }
-
-        val outputFile = File(outputPath)
-
-        var adb: Adb? = null
-        deploy?.let {
-            adb = Adb(
-                outputFile, patcher.packageName, deploy!!
-            )
-        }
-
-        Patcher.start(patcher)
-
-        if (clean) File(cacheDirectory).deleteRecursively()
-
-        adb?.deploy()
-      
-        if (clean) outputFile.delete()
-    }
-}

src/main/kotlin/app/revanced/cli/Patcher.kt

@@ -1,54 +0,0 @@
-package app.revanced.cli
-
-import app.revanced.utils.filesystem.FileSystemUtils
-import app.revanced.utils.patcher.addPatchesFiltered
-import app.revanced.utils.patcher.applyPatchesPrint
-import app.revanced.utils.patcher.mergeFiles
-import app.revanced.utils.signing.Signer
-import java.io.File
-import java.io.FileFilter
-
-internal class Patcher {
-    internal companion object {
-        internal fun start(patcher: app.revanced.patcher.Patcher) {
-            // merge files like necessary integrations
-            patcher.mergeFiles()
-            // add patches, but filter incompatible or excluded patches
-            patcher.addPatchesFiltered(includeFilter = MainCommand.includedPatches.isNotEmpty())
-            // apply patches
-            patcher.applyPatchesPrint()
-
-            // write output file
-            val outFile = File(MainCommand.outputPath)
-            if (outFile.exists()) outFile.delete()
-            MainCommand.inputFile.copyTo(outFile)
-
-            val zipFileSystem = FileSystemUtils(outFile)
-
-            // replace all dex files
-            for ((name, data) in patcher.save()) {
-                zipFileSystem.replaceFile(name, data.data)
-            }
-
-            if (MainCommand.patchResources) {
-                for (file in File(MainCommand.cacheDirectory).resolve("build/").listFiles(FileFilter { it.isDirectory })?.first()?.listFiles()!!) {
-                    if (!file.isDirectory) {
-                        zipFileSystem.replaceFile(file.name, file.readBytes())
-                        continue
-                    }
-                    zipFileSystem.replaceDirectory(file)
-                }
-            }
-
-            // finally close the stream
-            zipFileSystem.close()
-
-            // and sign the apk file
-            Signer.signApk(outFile)
-
-            println("[done]")
-        }
-
-
-    }
-}

src/main/kotlin/app/revanced/cli/command/MainCommand.kt

@@ -0,0 +1,219 @@
+package app.revanced.cli.command
+
+import app.revanced.cli.logging.impl.DefaultCliLogger
+import app.revanced.cli.patcher.Patcher
+import app.revanced.cli.patcher.logging.impl.PatcherLogger
+import app.revanced.cli.signing.Signing
+import app.revanced.cli.signing.SigningOptions
+import app.revanced.patcher.PatcherOptions
+import app.revanced.patcher.extensions.PatchExtensions.compatiblePackages
+import app.revanced.patcher.extensions.PatchExtensions.description
+import app.revanced.patcher.extensions.PatchExtensions.patchName
+import app.revanced.patcher.util.patch.implementation.JarPatchBundle
+import app.revanced.utils.adb.Adb
+import picocli.CommandLine.*
+import java.io.File
+import java.nio.file.Files
+
+private class CLIVersionProvider : IVersionProvider {
+    override fun getVersion() = arrayOf(
+        MainCommand::class.java.`package`.implementationVersion ?: "unknown"
+    )
+}
+
+@Command(
+    name = "ReVanced-CLI",
+    mixinStandardHelpOptions = true,
+    versionProvider = CLIVersionProvider::class
+)
+internal object MainCommand : Runnable {
+    val logger = DefaultCliLogger()
+
+    @ArgGroup(exclusive = false, multiplicity = "1")
+    lateinit var args: Args
+
+    class Args {
+        @Option(names = ["-a", "--apk"], description = ["Input file to be patched"], required = true)
+        lateinit var inputFile: File
+
+        @Option(names = ["--uninstall"], description = ["Uninstall the mount variant"])
+        var uninstall: Boolean = false
+
+        @Option(names = ["-d", "--deploy-on"], description = ["If specified, deploy to adb device with given name"])
+        var deploy: String? = null
+
+        @ArgGroup(exclusive = false)
+        var sArgs: StartPatcherArgs? = null
+    }
+
+    class StartPatcherArgs {
+        @Option(names = ["-b", "--bundles"], description = ["One or more bundles of patches"], required = true)
+        var patchBundles = arrayOf<String>()
+
+        @ArgGroup(exclusive = false)
+        var lArgs: ListingArgs? = null
+
+        @ArgGroup(exclusive = false)
+        var pArgs: PatchingArgs? = null
+    }
+
+    class ListingArgs {
+        @Option(names = ["-l", "--list"], description = ["List patches only"], required = true)
+        var listOnly: Boolean = false
+
+        @Option(names = ["--with-versions"], description = ["List patches with compatible versions"])
+        var withVersions: Boolean = false
+
+        @Option(names = ["--with-packages"], description = ["List patches with compatible packages"])
+        var withPackages: Boolean = false
+
+        @Option(names = ["--with-descriptions"], description = ["List patches with their descriptions"])
+        var withDescriptions: Boolean = true
+    }
+
+    class PatchingArgs {
+        @Option(names = ["-o", "--out"], description = ["Output file path"], required = true)
+        lateinit var outputPath: String
+
+        @Option(names = ["-e", "--exclude"], description = ["Explicitly exclude patches"])
+        var excludedPatches = arrayOf<String>()
+
+        @Option(names = ["--exclusive"], description = ["Only installs the patches you include, not including any patch by default"])
+        var defaultExclude = false
+
+        @Option(names = ["-i", "--include"], description = ["Include patches"])
+        var includedPatches = arrayOf<String>()
+
+        @Option(names = ["-r", "--resource-patcher"], description = ["Disable patching resources"])
+        var disableResourcePatching: Boolean = false
+
+        @Option(names = ["--experimental"], description = ["Disable patch version compatibility patch"])
+        var experimental: Boolean = false
+
+        @Option(names = ["-m", "--merge"], description = ["One or more dex file containers to merge"])
+        var mergeFiles = listOf<File>()
+
+        @Option(names = ["--mount"], description = ["If specified, instead of installing, mount"])
+        var mount: Boolean = false
+
+        @Option(names = ["--cn"], description = ["Overwrite the default CN for the signed file"])
+        var cn = "ReVanced"
+
+        @Option(names = ["--keystore"], description = ["File path to your keystore"])
+        var keystorePath: String? = null
+
+        @Option(names = ["-p", "--password"], description = ["Overwrite the default password for the signed file"])
+        var password = "ReVanced"
+
+        @Option(names = ["-t", "--temp-dir"], description = ["Temporal resource cache directory"])
+        var cacheDirectory = "revanced-cache"
+
+        @Option(
+            names = ["-c", "--clean"],
+            description = ["Clean the temporal resource cache directory. This will be done anyways when running the patcher"]
+        )
+        var clean: Boolean = false
+    }
+
+    override fun run() {
+        if (args.sArgs?.lArgs?.listOnly == true) {
+            printListOfPatches()
+            return
+        }
+
+        if (args.uninstall) {
+            // temporarily get package name using Patcher method
+            // fix: abstract options in patcher
+            val patcher = app.revanced.patcher.Patcher(
+                PatcherOptions(
+                    args.inputFile,
+                    "uninstaller-cache",
+                    false
+                )
+            )
+            File("uninstaller-cache").deleteRecursively()
+
+            val adb: Adb? = args.deploy?.let {
+                Adb(File("placeholder_file"), patcher.data.packageMetadata.packageName, args.deploy!!, false)
+            }
+            adb?.uninstall()
+
+            return
+        }
+
+        val _args = args
+        val args = args.sArgs?.pArgs ?: return
+
+        val patcher = app.revanced.patcher.Patcher(
+            PatcherOptions(
+                _args.inputFile,
+                args.cacheDirectory,
+                !args.disableResourcePatching,
+                logger = PatcherLogger
+            )
+        )
+
+        val outputFile = File(args.outputPath)
+
+        val adb: Adb? = _args.deploy?.let {
+            Adb(outputFile, patcher.data.packageMetadata.packageName, _args.deploy!!, !args.mount)
+        }
+        val patchedFile = if (args.mount) outputFile
+        else File(args.cacheDirectory).resolve("${outputFile.nameWithoutExtension}_raw.apk")
+
+        Patcher.start(patcher, patchedFile)
+
+        if (!args.mount) {
+            Signing.start(
+                patchedFile,
+                outputFile,
+                SigningOptions(
+                    args.cn,
+                    args.password,
+                    args.keystorePath ?: outputFile.absoluteFile.parentFile
+                        .resolve("${outputFile.nameWithoutExtension}.keystore")
+                        .canonicalPath
+                )
+            )
+        }
+
+        if (args.clean) File(args.cacheDirectory).deleteRecursively()
+
+        adb?.deploy()
+
+        if (args.clean && _args.deploy != null) Files.delete(outputFile.toPath())
+
+        logger.info("Finished")
+    }
+
+    private fun printListOfPatches() {
+        for (patchBundlePath in args.sArgs?.patchBundles!!) for (patch in JarPatchBundle(patchBundlePath).loadPatches()) {
+            for (compatiblePackage in patch.compatiblePackages!!) {
+                val packageEntryStr = buildString {
+                    // Add package if flag is set
+                    if (args.sArgs?.lArgs?.withPackages == true) {
+                        val packageName = compatiblePackage.name.substringAfterLast(".").padStart(10)
+                        append(packageName)
+                        append("\t")
+                    }
+                    // Add patch name
+                    val patchName = patch.patchName.padStart(25)
+                    append(patchName)
+                    // Add description if flag is set.
+                    if (args.sArgs?.lArgs?.withDescriptions == true) {
+                        append("\t")
+                        append(patch.description)
+                    }
+                    // Add compatible versions, if flag is set
+                    if (args.sArgs?.lArgs?.withVersions == true) {
+                        val compatibleVersions = compatiblePackage.versions.joinToString(separator = ", ")
+                        append("\t")
+                        append(compatibleVersions)
+                    }
+
+                }
+                logger.info(packageEntryStr)
+            }
+        }
+    }
+}

src/main/kotlin/app/revanced/cli/logging/CliLogger.kt

@@ -0,0 +1,8 @@
+package app.revanced.cli.logging
+
+internal interface CliLogger {
+     fun error(msg: String)
+     fun info(msg: String)
+     fun trace(msg: String)
+     fun warn(msg: String)
+}

src/main/kotlin/app/revanced/cli/logging/impl/DefaultCliLogger.kt

@@ -0,0 +1,30 @@
+package app.revanced.cli.logging.impl
+
+import app.revanced.cli.command.MainCommand
+import app.revanced.cli.logging.CliLogger
+import java.util.logging.Logger
+import java.util.logging.SimpleFormatter
+
+internal class DefaultCliLogger(
+    private val logger: Logger = Logger.getLogger(MainCommand::class.java.name),
+    private val errorLogger: Logger = Logger.getLogger(logger.name + "Err")
+) : CliLogger {
+
+    init {
+        logger.useParentHandlers = false
+        if (logger.handlers.isEmpty()) {
+            logger.addHandler(FlushingStreamHandler(System.out, SimpleFormatter()))
+        }
+    }
+
+    companion object {
+        init {
+            System.setProperty("java.util.logging.SimpleFormatter.format", "%4\$s: %5\$s %n")
+        }
+    }
+
+    override fun error(msg: String) = errorLogger.severe(msg)
+    override fun info(msg: String) = logger.info(msg)
+    override fun trace(msg: String) = logger.finest(msg)
+    override fun warn(msg: String) = errorLogger.warning(msg)
+}

src/main/kotlin/app/revanced/cli/logging/impl/FlushingStreamHandler.kt

@@ -0,0 +1,13 @@
+package app.revanced.cli.logging.impl
+
+import java.io.OutputStream
+import java.util.logging.Formatter
+import java.util.logging.LogRecord
+import java.util.logging.StreamHandler
+
+internal class FlushingStreamHandler(out: OutputStream, format: Formatter) : StreamHandler(out, format) {
+    override fun publish(record: LogRecord) {
+        super.publish(record)
+        flush()
+    }
+}

src/main/kotlin/app/revanced/cli/main/Main.kt

@@ -1,5 +1,6 @@
-package app.revanced.cli
+package app.revanced.cli.main
 
+import app.revanced.cli.command.MainCommand
 import picocli.CommandLine
 
 internal fun main(args: Array<String>) {

src/main/kotlin/app/revanced/cli/patcher/Patcher.kt

@@ -0,0 +1,48 @@
+package app.revanced.cli.patcher
+
+import app.revanced.cli.command.MainCommand.args
+import app.revanced.cli.command.MainCommand.logger
+import app.revanced.utils.filesystem.ZipFileSystemUtils
+import app.revanced.utils.patcher.addPatchesFiltered
+import app.revanced.utils.patcher.applyPatchesVerbose
+import app.revanced.utils.patcher.mergeFiles
+import java.io.File
+import java.nio.file.Files
+
+internal object Patcher {
+    internal fun start(patcher: app.revanced.patcher.Patcher, output: File) {
+        val inputFile = args.inputFile
+        val args = args.sArgs?.pArgs!!
+
+        // merge files like necessary integrations
+        patcher.mergeFiles()
+        // add patches, but filter incompatible or excluded patches
+        patcher.addPatchesFiltered()
+        // apply patches
+        patcher.applyPatchesVerbose()
+
+        // write output file
+        if (output.exists()) Files.delete(output.toPath())
+        inputFile.copyTo(output)
+
+        val result = patcher.save()
+        ZipFileSystemUtils(output).use { outputFileSystem ->
+            // replace all dex files
+            result.dexFiles.forEach {
+                logger.info("Writing dex file ${it.name}")
+                outputFileSystem.write(it.name, it.dexFileInputStream.readAllBytes())
+            }
+
+            if (!args.disableResourcePatching) {
+                logger.info("Writing resources...")
+
+                ZipFileSystemUtils(result.resourceFile!!).use { resourceFileSystem ->
+                    val resourceFiles = resourceFileSystem.getFile(File.separator)
+                    outputFileSystem.writePathRecursively(resourceFiles)
+                }
+            }
+
+            result.doNotCompress?.let { outputFileSystem.uncompress(*it.toTypedArray()) }
+        }
+    }
+}

src/main/kotlin/app/revanced/cli/patcher/logging/impl/PatcherLogger.kt

@@ -0,0 +1,13 @@
+package app.revanced.cli.patcher.logging.impl
+
+import app.revanced.cli.logging.impl.DefaultCliLogger
+import java.util.logging.Logger
+
+internal object PatcherLogger : app.revanced.patcher.logging.Logger{
+    private val logger = DefaultCliLogger(Logger.getLogger(app.revanced.patcher.Patcher::class.java.name))
+
+    override fun error(msg: String) = logger.error(msg)
+    override fun info(msg: String) = logger.info(msg)
+    override fun warn(msg: String)= logger.warn(msg)
+    override fun trace(msg: String)= logger.trace(msg)
+}

src/main/kotlin/app/revanced/cli/signing/Signing.kt

@@ -0,0 +1,28 @@
+package app.revanced.cli.signing
+
+import app.revanced.cli.command.MainCommand.args
+import app.revanced.cli.command.MainCommand.logger
+import app.revanced.utils.signing.Signer
+import app.revanced.utils.signing.align.ZipAligner
+import java.io.File
+
+object Signing {
+    fun start(inputFile: File, outputFile: File, signingOptions: SigningOptions) {
+        val cacheDirectory = File(args.sArgs?.pArgs?.cacheDirectory)
+        val alignedOutput = cacheDirectory.resolve("${outputFile.nameWithoutExtension}_aligned.apk")
+        val signedOutput = cacheDirectory.resolve("${outputFile.nameWithoutExtension}_signed.apk")
+
+        // align the inputFile and write to alignedOutput
+        logger.info("Aligning ${inputFile.name}")
+        ZipAligner.align(inputFile, alignedOutput)
+        // sign the alignedOutput and write to signedOutput
+        // the reason is, in case the signer fails
+        // it does not damage the output file
+        logger.info("Signing ${alignedOutput.name}")
+        Signer(signingOptions).signApk(alignedOutput, signedOutput)
+
+        // afterwards copy over the file to the output
+        logger.info("Copying ${signedOutput.name} to ${outputFile.name}")
+        signedOutput.copyTo(outputFile, true)
+    }
+}

src/main/kotlin/app/revanced/cli/signing/SigningOptions.kt

@@ -0,0 +1,7 @@
+package app.revanced.cli.signing
+
+data class SigningOptions(
+    val cn: String,
+    val password: String,
+    val keyStoreFilePath: String
+)

src/main/kotlin/app/revanced/utils/adb/Adb.kt

@@ -1,14 +1,17 @@
 package app.revanced.utils.adb
 
+import app.revanced.cli.command.MainCommand.logger
 import se.vidstige.jadb.JadbConnection
 import se.vidstige.jadb.JadbDevice
+import se.vidstige.jadb.managers.PackageManager
 import java.io.File
 import java.util.concurrent.Executors
 
 internal class Adb(
-    private val apk: File,
+    private val file: File,
     private val packageName: String,
     deviceName: String,
+    private val modeInstall: Boolean = false,
     private val logging: Boolean = true
 ) {
     private val device: JadbDevice
@@ -17,49 +20,65 @@ internal class Adb(
         device = JadbConnection().devices.find { it.serial == deviceName }
             ?: throw IllegalArgumentException("No such device with name $deviceName")
 
-        if (device.run("su -h", false) != 0)
-            throw IllegalArgumentException("Root required on $deviceName. Deploying failed.")
+        if (!modeInstall && device.run("su -h", false) != 0)
+            throw IllegalArgumentException("Root required on $deviceName. Task failed")
     }
 
-    private fun String.replacePlaceholder(): String {
-        return this.replace(Constants.PLACEHOLDER, packageName)
+    private fun String.replacePlaceholder(with: String? = null): String {
+        return this.replace(Constants.PLACEHOLDER, with ?: packageName)
     }
 
     internal fun deploy() {
-        // create revanced path
-        device.run("${Constants.COMMAND_CREATE_DIR} ${Constants.PATH_REVANCED}")
+        if (modeInstall) {
+            logger.info("Installing without mounting")
 
-        // push patched file
-        device.copy(Constants.PATH_INIT_PUSH, apk)
-        // install apk
-        device.run(Constants.COMMAND_INSTALL_APK.replacePlaceholder())
+            PackageManager(device).install(file)
+        } else {
+            logger.info("Installing by mounting")
 
-        // push mount script
-        device.createFile(
-            Constants.PATH_INIT_PUSH,
-            Constants.CONTENT_MOUNT_SCRIPT.replacePlaceholder()
-        )
-        // install mount script
-        device.run(Constants.COMMAND_INSTALL_MOUNT.replacePlaceholder())
+            // push patched file
+            device.copy(Constants.PATH_INIT_PUSH, file)
 
-        // push umount script
-        device.createFile(
-            Constants.PATH_INIT_PUSH,
-            Constants.CONTENT_UMOUNT_SCRIPT.replacePlaceholder()
-        )
-        // install mount script
-        device.run(Constants.COMMAND_INSTALL_UMOUNT.replacePlaceholder())
+            // create revanced folder path
+            device.run("${Constants.COMMAND_CREATE_DIR} ${Constants.PATH_REVANCED}")
 
-        // unmount the apk for sanity
-        device.run(Constants.PATH_UMOUNT.replacePlaceholder())
-        // mount the apk
-        device.run(Constants.PATH_MOUNT.replacePlaceholder())
+            // prepare mounting the apk
+            device.run(Constants.COMMAND_PREPARE_MOUNT_APK.replacePlaceholder())
 
-        // relaunch app
-        device.run(Constants.COMMAND_RESTART.replacePlaceholder())
+            // push mount script
+            device.createFile(
+                Constants.PATH_INIT_PUSH,
+                Constants.CONTENT_MOUNT_SCRIPT.replacePlaceholder()
+            )
+            // install mount script
+            device.run(Constants.COMMAND_INSTALL_MOUNT.replacePlaceholder())
 
-        // log the app
-        log()
+            // unmount the apk for sanity
+            device.run(Constants.COMMAND_UMOUNT.replacePlaceholder())
+            // mount the apk
+            device.run(Constants.PATH_MOUNT.replacePlaceholder())
+
+            // relaunch app
+            device.run(Constants.COMMAND_RESTART.replacePlaceholder())
+
+            // log the app
+            log()
+        }
+    }
+
+    internal fun uninstall() {
+        logger.info("Uninstalling by unmounting")
+
+        // unmount the apk
+        device.run(Constants.COMMAND_UMOUNT.replacePlaceholder())
+
+        // delete revanced app
+        device.run(Constants.COMMAND_DELETE.replacePlaceholder(Constants.PATH_REVANCED_APP).replacePlaceholder())
+
+        // delete mount script
+        device.run(Constants.COMMAND_DELETE.replacePlaceholder(Constants.PATH_MOUNT).replacePlaceholder())
+
+        logger.info("Finished uninstalling")
     }
 
     private fun log() {
@@ -84,11 +103,11 @@ internal class Adb(
                 }
                 break
             } catch (e: Exception) {
-                throw RuntimeException("An error occurred while monitoring state of app", e)
+                throw RuntimeException("An error occurred while monitoring the state of app", e)
             }
         }
-        println("App closed, continuing.")
+        logger.info("Stopped logging because the app was closed")
         process.destroy()
         executor.shutdown()
     }
-}
+}

src/main/kotlin/app/revanced/utils/adb/Constants.kt

@@ -15,37 +15,31 @@ internal object Constants {
     private const val NAME_MOUNT_SCRIPT = "mount_revanced_$PLACEHOLDER.sh"
 
     // initial directory to push files to via adb push
-    internal const val PATH_INIT_PUSH = "/sdcard/revanced.delete"
+    internal const val PATH_INIT_PUSH = "/data/local/tmp/revanced.delete"
 
     // revanced path
     internal const val PATH_REVANCED = "/data/adb/revanced/"
 
     // revanced apk path
-    private const val PATH_REVANCED_APP = "$PATH_REVANCED$PLACEHOLDER.apk"
+    internal const val PATH_REVANCED_APP = "$PATH_REVANCED$PLACEHOLDER.apk"
 
-    // (un)mount script paths
+    // delete command
+    internal const val COMMAND_DELETE = "rm -rf $PLACEHOLDER"
+
+    // mount script path
     internal const val PATH_MOUNT = "/data/adb/service.d/$NAME_MOUNT_SCRIPT"
-    internal const val PATH_UMOUNT = "/data/adb/post-fs-data.d/un$NAME_MOUNT_SCRIPT"
 
     // move to revanced apk path & set permissions
-    internal const val COMMAND_INSTALL_APK =
+    internal const val COMMAND_PREPARE_MOUNT_APK =
         "base_path=\"$PATH_REVANCED_APP\" && mv $PATH_INIT_PUSH ${'$'}base_path && chmod 644 ${'$'}base_path && chown system:system ${'$'}base_path && chcon u:object_r:apk_data_file:s0  ${'$'}base_path"
 
+    // unmount command
+    internal const val COMMAND_UMOUNT =
+        "stock_path=${'$'}( pm path $PLACEHOLDER | grep base | sed 's/package://g' ) && umount -l ${'$'}stock_path"
+
     // install mount script & set permissions
     internal const val COMMAND_INSTALL_MOUNT = "mv $PATH_INIT_PUSH $PATH_MOUNT && $COMMAND_CHMOD_MOUNT $PATH_MOUNT"
 
-    // install umount script & set permissions
-    internal const val COMMAND_INSTALL_UMOUNT = "mv $PATH_INIT_PUSH $PATH_UMOUNT && $COMMAND_CHMOD_MOUNT $PATH_UMOUNT"
-
-    // unmount script
-    internal val CONTENT_UMOUNT_SCRIPT =
-        """
-            #!/system/bin/sh
-            
-            stock_path=${'$'}( pm path $PLACEHOLDER | grep base | sed 's/package://g' )
-            umount -l ${'$'}stock_path
-        """.trimIndent()
-
     // mount script
     internal val CONTENT_MOUNT_SCRIPT =
         """
@@ -54,6 +48,8 @@ internal object Constants {
             
             base_path="$PATH_REVANCED_APP"
             stock_path=${'$'}( pm path $PLACEHOLDER | grep base | sed 's/package://g' )
+
+            chcon u:object_r:apk_data_file:s0  ${'$'}base_path
             mount -o bind ${'$'}base_path ${'$'}stock_path
         """.trimIndent()
 }

src/main/kotlin/app/revanced/utils/filesystem/FileSystemUtils.kt

@@ -1,63 +0,0 @@
-package app.revanced.utils.filesystem
-
-import java.io.Closeable
-import java.io.File
-import java.nio.file.FileSystem
-import java.nio.file.FileSystems
-import java.nio.file.Files
-
-internal class FileSystemUtils(
-    file: File
-) : Closeable {
-    private var fileSystem: FileSystem
-
-    init {
-        fileSystem = FileSystems.newFileSystem(file.toPath(), null as ClassLoader?)
-    }
-
-    private fun deleteDirectory(dirPath: String) {
-        val files = Files.walk(fileSystem.getPath("$dirPath/"))
-
-        files
-            .sorted(Comparator.reverseOrder())
-            .forEach {
-
-                Files.delete(it)
-            }
-
-        files.close()
-    }
-
-
-    internal fun replaceDirectory(replacement: File) {
-        if (!replacement.isDirectory) throw Exception("${replacement.name} is not a directory.")
-
-        // FIXME: make this delete the directory recursively
-        //deleteDirectory(replacement.name)
-        //val path = Files.createDirectory(fileSystem.getPath(replacement.name))
-
-        val excludeFromPath = replacement.path.removeSuffix(replacement.name)
-        for (path in Files.walk(replacement.toPath())) {
-            val file = path.toFile()
-            if (file.isDirectory) {
-                val relativePath = path.toString().removePrefix(excludeFromPath)
-                val fileSystemPath = fileSystem.getPath(relativePath)
-                if (!Files.exists(fileSystemPath)) Files.createDirectory(fileSystemPath)
-
-                continue
-            }
-
-            replaceFile(path.toString().removePrefix(excludeFromPath), file.readBytes())
-        }
-    }
-
-    internal fun replaceFile(sourceFile: String, content: ByteArray) {
-        val path = fileSystem.getPath(sourceFile)
-        Files.deleteIfExists(path)
-        Files.write(path, content)
-    }
-
-    override fun close() {
-        fileSystem.close()
-    }
-}

src/main/kotlin/app/revanced/utils/filesystem/ZipFileSystemUtils.kt

@@ -0,0 +1,64 @@
+package app.revanced.utils.filesystem
+
+import java.io.Closeable
+import java.io.File
+import java.nio.file.FileSystems
+import java.nio.file.Files
+import java.nio.file.Path
+import java.util.zip.ZipEntry
+
+internal class ZipFileSystemUtils(
+    file: File
+) : Closeable {
+    private var zipFileSystem = FileSystems.newFileSystem(file.toPath(), mapOf("noCompression" to true))
+
+    private fun Path.deleteRecursively() {
+        if (!Files.exists(this)) {
+            throw IllegalStateException("File exists in real folder but not in zip file system")
+        }
+
+        if (Files.isDirectory(this)) {
+            Files.list(this).forEach { path ->
+                path.deleteRecursively()
+            }
+        }
+
+        Files.delete(this)
+    }
+
+    internal fun getFile(path: String) = zipFileSystem.getPath(path)
+
+    internal fun writePathRecursively(path: Path) {
+        Files.list(path).use { fileStream ->
+            fileStream.forEach { filePath ->
+                val fileSystemPath = filePath.getRelativePath(path)
+                fileSystemPath.deleteRecursively()
+            }
+        }
+
+        Files.walk(path).use { fileStream ->
+            // don't include build directory
+            // by skipping the root node.
+            fileStream.skip(1).forEach { filePath ->
+                val relativePath = filePath.getRelativePath(path)
+
+                if (Files.isDirectory(filePath)) {
+                    Files.createDirectory(relativePath)
+                    return@forEach
+                }
+
+                Files.copy(filePath, relativePath)
+            }
+        }
+    }
+
+    internal fun write(path: String, content: ByteArray) = Files.write(zipFileSystem.getPath(path), content)
+
+    private fun Path.getRelativePath(path: Path): Path = zipFileSystem.getPath(path.relativize(this).toString())
+
+    // TODO: figure out why the file system is uncompressed by default and how to fix it
+    internal fun uncompress(vararg paths: String) =
+        paths.forEach { Files.setAttribute(zipFileSystem.getPath(it), "zip:method", ZipEntry.STORED) }
+
+    override fun close() = zipFileSystem.close()
+}

src/main/kotlin/app/revanced/utils/patcher/Patcher.kt

@@ -1,71 +1,78 @@
 package app.revanced.utils.patcher
 
-import app.revanced.cli.MainCommand
+import app.revanced.cli.command.MainCommand
+import app.revanced.cli.command.MainCommand.args
+import app.revanced.cli.command.MainCommand.logger
 import app.revanced.patcher.Patcher
-import app.revanced.patcher.annotation.Compatibility
-import app.revanced.patcher.annotation.Name
-import app.revanced.patcher.data.base.Data
-import app.revanced.patcher.extensions.findAnnotationRecursively
-import app.revanced.patcher.patch.base.Patch
-import app.revanced.patcher.util.patch.PatchLoader
+import app.revanced.patcher.data.Data
+import app.revanced.patcher.extensions.PatchExtensions.compatiblePackages
+import app.revanced.patcher.extensions.PatchExtensions.include
+import app.revanced.patcher.extensions.PatchExtensions.patchName
+import app.revanced.patcher.patch.Patch
+import app.revanced.patcher.util.patch.implementation.JarPatchBundle
 
-fun Patcher.addPatchesFiltered(
-    packageCompatibilityFilter: Boolean = true,
-    packageVersionCompatibilityFilter: Boolean = true,
-    includeFilter: Boolean = false
-) {
-    val packageName = this.packageName
-    val packageVersion = this.packageVersion
+fun Patcher.addPatchesFiltered() {
+    val packageName = this.data.packageMetadata.packageName
+    val packageVersion = this.data.packageMetadata.packageVersion
 
-    MainCommand.patchBundles.forEach { bundle ->
-        val includedPatches = mutableListOf<Patch<Data>>()
-        PatchLoader.loadFromFile(bundle).forEach patch@{ p ->
-            val patch = p.getDeclaredConstructor().newInstance()
+    args.sArgs?.patchBundles!!.forEach { bundle ->
+        val includedPatches = mutableListOf<Class<out Patch<Data>>>()
+        JarPatchBundle(bundle).loadPatches().forEach patch@{ patch ->
+            val compatiblePackages = patch.compatiblePackages
+            val patchName = patch.patchName
 
-            val compatibilityAnnotation = patch.javaClass.findAnnotationRecursively(Compatibility::class.java)
+            val prefix = "Skipping $patchName"
 
-            val patchName = patch.javaClass.findAnnotationRecursively(Name::class.java)?.name ?: Name::class.java.name
+            val args = MainCommand.args.sArgs?.pArgs!!
 
-            val prefix = "[skipped] $patchName"
-
-            if (includeFilter && !MainCommand.includedPatches.contains(patchName)) {
-                println(prefix)
+            if (args.excludedPatches.contains(patchName)) {
+                logger.info("$prefix: Explicitely excluded")
+                return@patch
+            } else if ((!patch.include || args.defaultExclude) && !args.includedPatches.contains(patchName)) {
+                logger.info("$prefix: Not explicitly included")
                 return@patch
             }
 
-            if (packageVersionCompatibilityFilter || packageCompatibilityFilter) {
-
-                if (compatibilityAnnotation == null) {
-                    println("$prefix: Missing compatibility annotation.")
+            if (compatiblePackages == null) logger.warn("$prefix: Missing compatibility annotation. Continuing.")
+            else {
+                if (!compatiblePackages.any { it.name == packageName }) {
+                    logger.warn("$prefix: Incompatible with $packageName. This patch is only compatible with ${
+                        compatiblePackages.joinToString(
+                            ", "
+                        ) { it.name }
+                    }")
                     return@patch
                 }
 
-
-                for (compatiblePackage in compatibilityAnnotation.compatiblePackages) {
-                    if (packageCompatibilityFilter && compatiblePackage.name != packageName) {
-                        println("$prefix: Package name not matching ${compatiblePackage.name}.")
-                        return@patch
-                    }
-
-                    if (!packageVersionCompatibilityFilter || compatiblePackage.versions.any { it == packageVersion }) continue
-                    println("$prefix: Unsupported version.")
+                if (!(args.experimental || compatiblePackages.any { it.versions.isEmpty() || it.versions.any { version -> version == packageVersion } })) {
+                    val compatibleWith = compatiblePackages.map { _package ->
+                        "${_package.name}: ${_package.versions.joinToString(", ")}"
+                    }.joinToString(";")
+                    logger.warn("$prefix: Incompatible with version $packageVersion. This patch is only compatible with version $compatibleWith")
                     return@patch
                 }
             }
 
+            logger.trace("Adding $patchName")
             includedPatches.add(patch)
-            println("[added] $patchName")
         }
         this.addPatches(includedPatches)
     }
 }
 
-fun Patcher.applyPatchesPrint() {
-    for ((patch, result) in this.applyPatches()) {
-        println("[${if (result.isFailure) "error" else "success"}] $patch")
+fun Patcher.applyPatchesVerbose() {
+    this.applyPatches().forEach { (patch, result) ->
+        if (result.isSuccess) {
+            logger.info("$patch succeeded")
+            return@forEach
+        }
+        logger.error("$patch failed:")
+        result.exceptionOrNull()!!.printStackTrace()
     }
 }
 
 fun Patcher.mergeFiles() {
-    this.addFiles(MainCommand.mergeFiles)
+    this.addFiles(args.sArgs?.pArgs!!.mergeFiles) { file ->
+        logger.info("Merging $file")
+    }
 }

src/main/kotlin/app/revanced/utils/signature/Signature.kt

@@ -1,58 +0,0 @@
-package app.revanced.utils.signature
-
-import app.revanced.patcher.Patcher
-import app.revanced.patcher.extensions.findAnnotationRecursively
-import app.revanced.patcher.signature.implementation.method.annotation.FuzzyPatternScanMethod
-import app.revanced.patcher.signature.implementation.method.annotation.MatchingMethod
-import org.jf.dexlib2.iface.Method
-
-object Signature {
-
-    fun checkSignatures(patcher: Patcher) {
-        val failed = mutableListOf<String>()
-        for (signature in patcher.resolveSignatures()) {
-            val signatureClass = signature::class.java
-            val signatureName =
-                signatureClass.findAnnotationRecursively(app.revanced.patcher.annotation.Name::class.java)?.name
-                    ?: signatureClass.name
-            if (!signature.resolved) {
-                failed.add(signatureName)
-                continue
-            }
-
-            val method = signature.result!!.method
-            val matchingMethod =
-                signatureClass.findAnnotationRecursively(MatchingMethod::class.java) ?: MatchingMethod()
-
-            println(
-                """
-                    [Signature] $signatureName
-                    [Method] ${matchingMethod.definingClass}->${matchingMethod.name}
-                    [Match] ${method.definingClass}->${method.toStr()}
-                """.trimIndent()
-            )
-
-            signatureClass.findAnnotationRecursively(FuzzyPatternScanMethod::class.java)?.let {
-                val warnings = signature.result!!.scanResult.warnings!!
-                println(
-                    """
-                        [Warnings: ${warnings.count()}]
-                        ${warnings.joinToString(separator = "\n") { warning -> "${warning.instructionIndex} / ${warning.patternIndex}: ${warning.wrongOpcode} (expected: ${warning.correctOpcode})" }}
-                    """.trimIndent()
-                )
-            }
-        }
-
-        println(
-            """
-                ${"=".repeat(50)}
-                [Failed signatures: ${failed.size}]
-                ${failed.joinToString(separator = "\n") { it }}
-        """.trimIndent()
-        )
-    }
-
-    private fun Method.toStr(): String {
-        return "${this.name}(${this.parameterTypes.joinToString("")})${this.returnType}"
-    }
-}

src/main/kotlin/app/revanced/utils/signing/KeySet.kt

@@ -1,9 +0,0 @@
-package app.revanced.utils.signing
-
-import java.security.PrivateKey
-import java.security.cert.X509Certificate
-
-data class KeySet(
-    val publicKey: X509Certificate,
-    val privateKey: PrivateKey
-)

src/main/kotlin/app/revanced/utils/signing/Signer.kt

@@ -1,65 +1,42 @@
-/*
- * Copyright (c) 2021 Juby210 & Vendicated
- * Licensed under the Open Software License version 3.0
- */
-
 package app.revanced.utils.signing
 
+import app.revanced.cli.command.MainCommand.logger
+import app.revanced.cli.signing.SigningOptions
+import com.android.apksig.ApkSigner
 import org.bouncycastle.asn1.x500.X500Name
 import org.bouncycastle.asn1.x509.SubjectPublicKeyInfo
 import org.bouncycastle.cert.X509v3CertificateBuilder
-import org.bouncycastle.cert.jcajce.JcaCertStore
 import org.bouncycastle.cert.jcajce.JcaX509CertificateConverter
-import org.bouncycastle.cms.*
-import org.bouncycastle.cms.jcajce.JcaSignerInfoGeneratorBuilder
 import org.bouncycastle.jce.provider.BouncyCastleProvider
 import org.bouncycastle.operator.ContentSigner
-import org.bouncycastle.operator.DigestCalculatorProvider
 import org.bouncycastle.operator.jcajce.JcaContentSignerBuilder
-import org.bouncycastle.operator.jcajce.JcaDigestCalculatorProviderBuilder
-import org.bouncycastle.util.encoders.Base64
-import java.io.ByteArrayOutputStream
 import java.io.File
 import java.io.FileInputStream
 import java.io.FileOutputStream
 import java.math.BigInteger
-import java.nio.file.FileSystems
-import java.nio.file.Files
-import java.nio.file.Path
 import java.security.*
 import java.security.cert.X509Certificate
 import java.util.*
-import java.util.jar.Attributes
-import java.util.jar.JarFile
-import java.util.jar.Manifest
-import java.util.regex.Pattern
 
-
-const val CN = "ReVanced"
-val PASSWORD = "revanced".toCharArray() // TODO: make it secure; random password should be enough
-
-/**
- * APK Signer.
- * @author Aliucord authors
- * @author ReVanced team
- */
-object Signer {
+internal class Signer(
+    private val signingOptions: SigningOptions
+) {
+    private val passwordCharArray = signingOptions.password.toCharArray()
     private fun newKeystore(out: File) {
-        val key = createKey()
+        val (publicKey, privateKey) = createKey()
         val privateKS = KeyStore.getInstance("BKS", "BC")
-        privateKS.load(null, PASSWORD)
-        privateKS.setKeyEntry("alias", key.privateKey, PASSWORD, arrayOf(key.publicKey))
-        privateKS.store(FileOutputStream(out), PASSWORD)
+        privateKS.load(null, passwordCharArray)
+        privateKS.setKeyEntry("alias", privateKey, passwordCharArray, arrayOf(publicKey))
+        privateKS.store(FileOutputStream(out), passwordCharArray)
     }
 
-    private fun createKey(): KeySet {
+    private fun createKey(): Pair<X509Certificate, PrivateKey> {
         val gen = KeyPairGenerator.getInstance("RSA")
         gen.initialize(2048)
         val pair = gen.generateKeyPair()
         var serialNumber: BigInteger
-        do serialNumber =
-            BigInteger.valueOf(SecureRandom().nextLong()) while (serialNumber < BigInteger.ZERO)
-        val x500Name = X500Name("CN=$CN")
+        do serialNumber = BigInteger.valueOf(SecureRandom().nextLong()) while (serialNumber < BigInteger.ZERO)
+        val x500Name = X500Name("CN=${signingOptions.cn}")
         val builder = X509v3CertificateBuilder(
             x500Name,
             serialNumber,
@@ -69,143 +46,34 @@ object Signer {
             x500Name,
             SubjectPublicKeyInfo.getInstance(pair.public.encoded)
         )
-        val signer: ContentSigner = JcaContentSignerBuilder("SHA1withRSA").build(pair.private)
-        return KeySet(JcaX509CertificateConverter().getCertificate(builder.build(signer)), pair.private)
+        val signer: ContentSigner = JcaContentSignerBuilder("SHA256withRSA").build(pair.private)
+        return JcaX509CertificateConverter().getCertificate(builder.build(signer)) to pair.private
     }
 
-    private val stripPattern: Pattern = Pattern.compile("^META-INF/(.*)[.](MF|SF|RSA|DSA)$")
-
-    // based on https://gist.github.com/mmuszkow/10288441
-    // and https://github.com/fornwall/apksigner/blob/master/src/main/java/net/fornwall/apksigner/ZipSigner.java
-    fun signApk(apkFile: File) {
+    fun signApk(input: File, output: File) {
         Security.addProvider(BouncyCastleProvider())
 
-        val ks = File(apkFile.parent, "revanced-cli.keystore")
-        if (!ks.exists()) newKeystore(ks)
+        // TODO: keystore should be saved securely
+        val ks = File(signingOptions.keyStoreFilePath)
+        if (!ks.exists()) newKeystore(ks) else {
+            logger.info("Found existing keystore: ${ks.nameWithoutExtension}")
+        }
 
         val keyStore = KeyStore.getInstance("BKS", "BC")
         FileInputStream(ks).use { fis -> keyStore.load(fis, null) }
         val alias = keyStore.aliases().nextElement()
-        val keySet = KeySet(
-            (keyStore.getCertificate(alias) as X509Certificate),
-            (keyStore.getKey(alias, PASSWORD) as PrivateKey)
-        )
 
-        val zip = FileSystems.newFileSystem(apkFile.toPath(), null as ClassLoader?)
+        val config = ApkSigner.SignerConfig.Builder(
+            signingOptions.cn,
+            keyStore.getKey(alias, passwordCharArray) as PrivateKey,
+            listOf(keyStore.getCertificate(alias) as X509Certificate)
+        ).build()
 
-        val dig = MessageDigest.getInstance("SHA1")
-        val digests: MutableMap<String, String> = LinkedHashMap()
+        val signer = ApkSigner.Builder(listOf(config))
+        signer.setCreatedBy(signingOptions.cn)
+        signer.setInputApk(input)
+        signer.setOutputApk(output)
 
-        for (entry in zip.allEntries) {
-            val name = entry.toString()
-            if (stripPattern.matcher(name).matches()) {
-                Files.delete(entry)
-            } else {
-                digests[name] = toBase64(dig.digest(Files.readAllBytes(entry)))
-            }
-        }
-
-        val sectionDigests: MutableMap<String, String> = LinkedHashMap()
-        var manifest = Manifest()
-        var attrs = manifest.mainAttributes
-        attrs[Attributes.Name.MANIFEST_VERSION] = "1.0"
-        attrs[Attributes.Name("Created-By")] = CN
-
-        val digestAttr = Attributes.Name("SHA1-Digest")
-        for ((name, value) in digests) {
-            val attributes = Attributes()
-            attributes[digestAttr] = value
-            manifest.entries[name] = attributes
-            sectionDigests[name] = hashEntrySection(name, attributes, dig)
-        }
-        ByteArrayOutputStream().use { baos ->
-            manifest.write(baos)
-            zip.writeFile(JarFile.MANIFEST_NAME, baos.toByteArray())
-        }
-
-        val manifestHash = getManifestHash(manifest, dig)
-        val tmpManifest = Manifest()
-        tmpManifest.mainAttributes.putAll(attrs)
-        val manifestMainHash = getManifestHash(tmpManifest, dig)
-
-        manifest = Manifest()
-        attrs = manifest.mainAttributes
-        attrs[Attributes.Name.SIGNATURE_VERSION] = "1.0"
-        attrs[Attributes.Name("Created-By")] = CN
-        attrs[Attributes.Name("SHA1-Digest-Manifest")] = manifestHash
-        attrs[Attributes.Name("SHA1-Digest-Manifest-Main-Attributes")] = manifestMainHash
-
-        for ((key, value) in sectionDigests) {
-            val attributes = Attributes()
-            attributes[digestAttr] = value
-            manifest.entries[key] = attributes
-        }
-        var sigBytes: ByteArray
-        ByteArrayOutputStream().use { sigStream ->
-            manifest.write(sigStream)
-            sigBytes = sigStream.toByteArray()
-            zip.writeFile("META-INF/CERT.SF", sigBytes)
-        }
-
-        val signature = signSigFile(keySet, sigBytes)
-        zip.writeFile("META-INF/CERT.RSA", signature)
-
-        zip.close()
+        signer.build().sign()
     }
-
-    private fun hashEntrySection(name: String, attrs: Attributes, dig: MessageDigest): String {
-        val manifest = Manifest()
-        manifest.mainAttributes[Attributes.Name.MANIFEST_VERSION] = "1.0"
-        ByteArrayOutputStream().use { baos ->
-            manifest.write(baos)
-            val emptyLen = baos.toByteArray().size
-            manifest.entries[name] = attrs
-            baos.reset()
-            manifest.write(baos)
-            var ob = baos.toByteArray()
-            ob = Arrays.copyOfRange(ob, emptyLen, ob.size)
-            return toBase64(dig.digest(ob))
-        }
-    }
-
-    private fun getManifestHash(manifest: Manifest, dig: MessageDigest): String {
-        ByteArrayOutputStream().use { baos ->
-            manifest.write(baos)
-            return toBase64(dig.digest(baos.toByteArray()))
-        }
-    }
-
-    private fun signSigFile(keySet: KeySet, content: ByteArray): ByteArray {
-        val msg: CMSTypedData = CMSProcessableByteArray(content)
-        val certs = JcaCertStore(Collections.singletonList(keySet.publicKey))
-        val gen = CMSSignedDataGenerator()
-        val jcaContentSignerBuilder = JcaContentSignerBuilder("SHA1withRSA")
-        val sha1Signer: ContentSigner = jcaContentSignerBuilder.build(keySet.privateKey)
-        val jcaDigestCalculatorProviderBuilder = JcaDigestCalculatorProviderBuilder()
-        val digestCalculatorProvider: DigestCalculatorProvider = jcaDigestCalculatorProviderBuilder.build()
-        val jcaSignerInfoGeneratorBuilder = JcaSignerInfoGeneratorBuilder(digestCalculatorProvider)
-        jcaSignerInfoGeneratorBuilder.setDirectSignature(true)
-        val signerInfoGenerator: SignerInfoGenerator = jcaSignerInfoGeneratorBuilder.build(sha1Signer, keySet.publicKey)
-        gen.addSignerInfoGenerator(signerInfoGenerator)
-        gen.addCertificates(certs)
-        val sigData: CMSSignedData = gen.generate(msg, false)
-        return sigData.toASN1Structure().getEncoded("DER")
-    }
-
-    private fun toBase64(data: ByteArray): String {
-        return String(Base64.encode(data))
-    }
-}
-
-private val java.nio.file.FileSystem.allEntries: List<Path>
-    get() = buildList {
-        this@allEntries.rootDirectories.forEach { dir ->
-            Files.walk(dir).filter(Files::isRegularFile).forEach { file ->
-                this@buildList.add(file)
-            }
-        }
-    }
-
-private fun java.nio.file.FileSystem.writeFile(path: String, bytes: ByteArray) {
-    Files.write(this.getPath("/$path"), bytes)
 }

src/main/kotlin/app/revanced/utils/signing/align/ZipAligner.kt

@@ -0,0 +1,28 @@
+package app.revanced.utils.signing.align
+
+import app.revanced.utils.signing.align.zip.ZipFile
+import java.io.File
+
+internal object ZipAligner {
+    private const val DEFAULT_ALIGNMENT = 4
+    private const val LIBRARY_ALIGNMENT = 4096
+
+    fun align(input: File, output: File) {
+        val inputZip = ZipFile(input)
+        val outputZip = ZipFile(output)
+
+        for (entry in inputZip.entries) {
+            val data = inputZip.getDataForEntry(entry)
+
+            if (entry.compression == 0.toUShort()) {
+                val alignment = if (entry.fileName.endsWith(".so")) LIBRARY_ALIGNMENT else DEFAULT_ALIGNMENT
+
+                outputZip.addEntryAligned(entry, data, alignment)
+            } else {
+                outputZip.addEntry(entry, data)
+            }
+        }
+
+        outputZip.finish()
+    }
+}

src/main/kotlin/app/revanced/utils/signing/align/zip/Extensions.kt

@@ -0,0 +1,33 @@
+package app.revanced.utils.signing.align.zip
+
+import java.io.DataInput
+import java.io.DataOutput
+import java.nio.ByteBuffer
+
+fun UInt.toLittleEndian() =
+    (((this.toInt() and 0xff000000.toInt()) shr 24) or ((this.toInt() and 0x00ff0000) shr 8) or ((this.toInt() and 0x0000ff00) shl 8) or (this.toInt() shl 24)).toUInt()
+
+fun UShort.toLittleEndian() = (this.toUInt() shl 16).toLittleEndian().toUShort()
+
+fun UInt.toBigEndian() = (((this.toInt() and 0xff) shl 24) or ((this.toInt() and 0xff00) shl 8)
+        or ((this.toInt() and 0x00ff0000) ushr 8) or (this.toInt() ushr 24)).toUInt()
+
+fun UShort.toBigEndian() = (this.toUInt() shl 16).toBigEndian().toUShort()
+
+fun ByteBuffer.getUShort() = this.getShort().toUShort()
+fun ByteBuffer.getUInt() = this.getInt().toUInt()
+
+fun ByteBuffer.putUShort(ushort: UShort) = this.putShort(ushort.toShort())
+fun ByteBuffer.putUInt(uint: UInt) = this.putInt(uint.toInt())
+
+fun DataInput.readUShort() = this.readShort().toUShort()
+fun DataInput.readUInt() = this.readInt().toUInt()
+
+fun DataOutput.writeUShort(ushort: UShort) = this.writeShort(ushort.toInt())
+fun DataOutput.writeUInt(uint: UInt) = this.writeInt(uint.toInt())
+
+fun DataInput.readUShortLE() = this.readUShort().toBigEndian()
+fun DataInput.readUIntLE() = this.readUInt().toBigEndian()
+
+fun DataOutput.writeUShortLE(ushort: UShort) = this.writeUShort(ushort.toLittleEndian())
+fun DataOutput.writeUIntLE(uint: UInt) = this.writeUInt(uint.toLittleEndian())

src/main/kotlin/app/revanced/utils/signing/align/zip/ZipFile.kt

@@ -0,0 +1,130 @@
+package app.revanced.utils.signing.align.zip
+
+import app.revanced.utils.signing.align.zip.structures.ZipEndRecord
+import app.revanced.utils.signing.align.zip.structures.ZipEntry
+import java.io.File
+import java.io.RandomAccessFile
+import java.nio.ByteBuffer
+import java.nio.channels.FileChannel
+
+class ZipFile(val file: File) {
+    var entries: MutableList<ZipEntry> = mutableListOf()
+
+    private val filePointer: RandomAccessFile = RandomAccessFile(file, "rw")
+
+    init {
+        //if file isn't empty try to load entries
+        if (file.length() > 0) {
+            val endRecord = findEndRecord()
+
+            if (endRecord.diskNumber > 0u || endRecord.totalEntries != endRecord.diskEntries)
+                throw IllegalArgumentException("Multi-file archives are not supported")
+
+            entries = readEntries(endRecord).toMutableList()
+        }
+
+        //seek back to start for writing
+        filePointer.seek(0)
+    }
+
+    private fun findEndRecord(): ZipEndRecord {
+        //look from end to start since end record is at the end
+        for (i in filePointer.length() - 1 downTo 0) {
+            filePointer.seek(i)
+            //possible beginning of signature
+            if (filePointer.readByte() == 0x50.toByte()) {
+                //seek back to get the full int
+                filePointer.seek(i)
+                val possibleSignature = filePointer.readUIntLE()
+                if (possibleSignature == ZipEndRecord.ECD_SIGNATURE) {
+                    filePointer.seek(i)
+                    return ZipEndRecord.fromECD(filePointer)
+                }
+            }
+        }
+
+        throw Exception("Couldn't find end record")
+    }
+
+    private fun readEntries(endRecord: ZipEndRecord): List<ZipEntry> {
+        filePointer.seek(endRecord.centralDirectoryStartOffset.toLong())
+
+        val numberOfEntries = endRecord.diskEntries.toInt()
+
+        return buildList(numberOfEntries) {
+            for (i in 1..numberOfEntries) {
+                add(ZipEntry.fromCDE(filePointer).also
+                {
+                    //for some reason the local extra field can be different from the central one
+                    it.readLocalExtra(
+                        filePointer.channel.map(
+                            FileChannel.MapMode.READ_ONLY,
+                            it.localHeaderOffset.toLong() + 28,
+                            2
+                        )
+                    )
+                })
+            }
+        }
+    }
+
+    private fun writeCDE() {
+        val CDEStart = filePointer.channel.position().toUInt()
+
+        entries.forEach {
+            filePointer.channel.write(it.toCDE())
+        }
+
+        val entriesCount = entries.size.toUShort()
+
+        val endRecord = ZipEndRecord(
+            0u,
+            0u,
+            entriesCount,
+            entriesCount,
+            filePointer.channel.position().toUInt() - CDEStart,
+            CDEStart,
+            ""
+        )
+
+        filePointer.channel.write(endRecord.toECD())
+    }
+
+    fun addEntry(entry: ZipEntry, data: ByteBuffer) {
+        entry.localHeaderOffset = filePointer.channel.position().toUInt()
+
+        filePointer.channel.write(entry.toLFH())
+        filePointer.channel.write(data)
+
+        entries.add(entry)
+    }
+
+    fun addEntryAligned(entry: ZipEntry, data: ByteBuffer, alignment: Int) {
+        //calculate where data would end up
+        val dataOffset = filePointer.filePointer + entry.LFHSize
+
+        val mod = dataOffset % alignment
+
+        //wrong alignment
+        if (mod != 0L) {
+            //add padding at end of extra field
+            entry.localExtraField =
+                entry.localExtraField.copyOf((entry.localExtraField.size + (alignment - mod)).toInt())
+        }
+
+        addEntry(entry, data)
+    }
+
+    fun getDataForEntry(entry: ZipEntry): ByteBuffer {
+        return filePointer.channel.map(
+            FileChannel.MapMode.READ_ONLY,
+            entry.dataOffset.toLong(),
+            entry.compressedSize.toLong()
+        )
+    }
+
+    fun finish() {
+        writeCDE()
+        filePointer.close()
+    }
+}

src/main/kotlin/app/revanced/utils/signing/align/zip/structures/ZipEndRecord.kt

@@ -0,0 +1,77 @@
+package app.revanced.utils.signing.align.zip.structures
+
+import app.revanced.utils.signing.align.zip.putUInt
+import app.revanced.utils.signing.align.zip.putUShort
+import app.revanced.utils.signing.align.zip.readUIntLE
+import app.revanced.utils.signing.align.zip.readUShortLE
+import java.io.DataInput
+import java.nio.ByteBuffer
+import java.nio.ByteOrder
+
+data class ZipEndRecord(
+    val diskNumber: UShort,
+    val startingDiskNumber: UShort,
+    val diskEntries: UShort,
+    val totalEntries: UShort,
+    val centralDirectorySize: UInt,
+    val centralDirectoryStartOffset: UInt,
+    val fileComment: String,
+) {
+
+    companion object {
+        const val ECD_HEADER_SIZE = 22
+        const val ECD_SIGNATURE = 0x06054b50u
+
+        fun fromECD(input: DataInput): ZipEndRecord {
+            val signature = input.readUIntLE()
+
+            if (signature != ECD_SIGNATURE)
+                throw IllegalArgumentException("Input doesn't start with end record signature")
+
+            val diskNumber = input.readUShortLE()
+            val startingDiskNumber = input.readUShortLE()
+            val diskEntries = input.readUShortLE()
+            val totalEntries = input.readUShortLE()
+            val centralDirectorySize = input.readUIntLE()
+            val centralDirectoryStartOffset = input.readUIntLE()
+            val fileCommentLength = input.readUShortLE()
+            var fileComment = ""
+
+            if (fileCommentLength > 0u) {
+                val fileCommentBytes = ByteArray(fileCommentLength.toInt())
+                input.readFully(fileCommentBytes)
+                fileComment = fileCommentBytes.toString(Charsets.UTF_8)
+            }
+
+            return ZipEndRecord(
+                diskNumber,
+                startingDiskNumber,
+                diskEntries,
+                totalEntries,
+                centralDirectorySize,
+                centralDirectoryStartOffset,
+                fileComment
+            )
+        }
+    }
+
+    fun toECD(): ByteBuffer {
+        val commentBytes = fileComment.toByteArray(Charsets.UTF_8)
+
+        val buffer = ByteBuffer.allocate(ECD_HEADER_SIZE + commentBytes.size).also { it.order(ByteOrder.LITTLE_ENDIAN) }
+
+        buffer.putUInt(ECD_SIGNATURE)
+        buffer.putUShort(diskNumber)
+        buffer.putUShort(startingDiskNumber)
+        buffer.putUShort(diskEntries)
+        buffer.putUShort(totalEntries)
+        buffer.putUInt(centralDirectorySize)
+        buffer.putUInt(centralDirectoryStartOffset)
+        buffer.putUShort(commentBytes.size.toUShort())
+
+        buffer.put(commentBytes)
+
+        buffer.flip()
+        return buffer
+    }
+}