chore(release): 3.0.0-dev.1 [skip ci]

# [3.0.0-dev.1](https://github.com/ReVanced/revanced-cli/compare/v2.23.0-dev.5...v3.0.0-dev.1) (2023-08-23)

### Bug Fixes

* do not use absolute path from custom AAPT2 binary option ([a9c2a5f](a9c2a5f096))
* use correct option name ([f8972ea](f8972eac3e))

* refactor!: restructure code ([07da528](07da528ce2))

### Features

* add options command ([9edbbf3](9edbbf3163))
* use better logging text ([b0e748d](b0e748daff))
* use separate command to list patches ([b74213f](b74213f66e))
* use separate command to patch ([32da961](32da961d57))
* use separate command to uninstall ([c0cc909](c0cc909626))
* use simpler log ([ba758f0](ba758f00f4))

### BREAKING CHANGES

* This introduces major changes to how ReVanced CLI is used from the command line.

.gitattributes

@@ -0,0 +1,9 @@
+#
+# https://help.github.com/articles/dealing-with-line-endings/
+#
+# Linux start script should use lf
+/gradlew        text eol=lf
+
+# These are Windows script files and should use crlf
+*.bat           text eol=crlf
+

.github/workflows/release.yml

@@ -23,17 +23,20 @@ jobs:
           # https://github.com/cycjimmy/semantic-release-action#private-packages
           persist-credentials: false
           fetch-depth: 0
-      - name: Setup JDK
-        uses: actions/setup-java@v3
+      - name: Cache
+        uses: actions/cache@v3
         with:
-          java-version: '17'
-          distribution: 'zulu'
-          cache: gradle
-      - name: Setup Node.js
-        uses: actions/setup-node@v3
-        with:
-          node-version: "18"
-          cache: 'npm'
+          path: |
+            ${{ runner.home }}/.gradle/caches
+            ${{ runner.home }}/.gradle/wrapper
+            .gradle
+            build
+            node_modules
+          key: ${{ runner.os }}-gradle-npm-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties', 'package-lock.json') }}
+      - name: Build with Gradle
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: ./gradlew clean --no-daemon
       - name: Setup semantic-release
         run: npm install
       - name: Release

.releaserc

@@ -10,7 +10,7 @@
     [
       "@semantic-release/commit-analyzer", {
         "releaseRules": [
-          { "type": "build", "scope": "revanced-patcher", "release": "patch" }
+          { "type": "build", "scope": "Needs bump", "release": "patch" }
         ]
       }
     ],

CHANGELOG.md

@@ -1,3 +1,98 @@
+# [3.0.0-dev.1](https://github.com/ReVanced/revanced-cli/compare/v2.23.0-dev.5...v3.0.0-dev.1) (2023-08-23)
+
+
+### Bug Fixes
+
+* do not use absolute path from custom AAPT2 binary option ([a9c2a5f](https://github.com/ReVanced/revanced-cli/commit/a9c2a5f096627dbbf8ab1b8da26fb14529ce6bc3))
+* use correct option name ([f8972ea](https://github.com/ReVanced/revanced-cli/commit/f8972eac3e5ee0a4a186c12cbe711925656d657b))
+
+
+* refactor!: restructure code ([07da528](https://github.com/ReVanced/revanced-cli/commit/07da528ce2223582f84bf64d2fec69714c647ddc))
+
+
+### Features
+
+* add options command ([9edbbf3](https://github.com/ReVanced/revanced-cli/commit/9edbbf31635603f89fc7bc5dcc6c023d4cdbb5a6))
+* use better logging text ([b0e748d](https://github.com/ReVanced/revanced-cli/commit/b0e748daff527ee7f417b3069882e074896fc131))
+* use separate command to list patches ([b74213f](https://github.com/ReVanced/revanced-cli/commit/b74213f66e0d04d3a0ae6197d069631388e06580))
+* use separate command to patch ([32da961](https://github.com/ReVanced/revanced-cli/commit/32da961d57537e99b39fd92b625a1c73f8314bc6))
+* use separate command to uninstall ([c0cc909](https://github.com/ReVanced/revanced-cli/commit/c0cc90962646cfffd5e2730ae556423271a7990b))
+* use simpler log ([ba758f0](https://github.com/ReVanced/revanced-cli/commit/ba758f00f4ce18791439b7e72fe1ad2e7f11f8af))
+
+
+### BREAKING CHANGES
+
+* This introduces major changes to how ReVanced CLI is used from the command line.
+
+# [2.23.0-dev.5](https://github.com/ReVanced/revanced-cli/compare/v2.23.0-dev.4...v2.23.0-dev.5) (2023-08-14)
+
+# [2.23.0-dev.4](https://github.com/ReVanced/revanced-cli/compare/v2.23.0-dev.3...v2.23.0-dev.4) (2023-08-13)
+
+
+### Features
+
+* show full package name when listing patches ([#240](https://github.com/ReVanced/revanced-cli/issues/240)) ([7174364](https://github.com/ReVanced/revanced-cli/commit/7174364ef8ef5d6ce8351a8340f9c1a5b58eac3c))
+
+# [2.23.0-dev.3](https://github.com/ReVanced/revanced-cli/compare/v2.23.0-dev.2...v2.23.0-dev.3) (2023-08-03)
+
+# [2.23.0-dev.2](https://github.com/ReVanced/revanced-cli/compare/v2.23.0-dev.1...v2.23.0-dev.2) (2023-08-03)
+
+# [2.23.0-dev.1](https://github.com/ReVanced/revanced-cli/compare/v2.22.1-dev.1...v2.23.0-dev.1) (2023-07-30)
+
+
+### Features
+
+* Improve command line argument descriptions ([f9cf7d2](https://github.com/ReVanced/revanced-cli/commit/f9cf7d21b7f1c2f11234d604a1047b9d2b165f83))
+
+## [2.22.1-dev.1](https://github.com/ReVanced/revanced-cli/compare/v2.22.0...v2.22.1-dev.1) (2023-07-24)
+
+
+### Bug Fixes
+
+* print original instead of kebab cased names ([5eaad33](https://github.com/ReVanced/revanced-cli/commit/5eaad33dc1fbd24c36e1498f04e21d068e85f53e))
+
+# [2.22.0](https://github.com/revanced/revanced-cli/compare/v2.21.5...v2.22.0) (2023-07-11)
+
+
+### Features
+
+* use new patch naming convention ([f6c221d](https://github.com/revanced/revanced-cli/commit/f6c221d72dc43ebea00e5eba6bfa02751ae8ad77))
+
+# [2.22.0-dev.1](https://github.com/revanced/revanced-cli/compare/v2.21.5...v2.22.0-dev.1) (2023-07-10)
+
+
+### Features
+
+* use new patch naming convention ([e4908c7](https://github.com/revanced/revanced-cli/commit/e4908c71051a535f8ce3406427cebbb0941464df))
+
+## [2.21.5](https://github.com/revanced/revanced-cli/compare/v2.21.4...v2.21.5) (2023-07-01)
+
+## [2.21.5-dev.2](https://github.com/revanced/revanced-cli/compare/v2.21.5-dev.1...v2.21.5-dev.2) (2023-07-01)
+
+## [2.21.5-dev.1](https://github.com/revanced/revanced-cli/compare/v2.21.4...v2.21.5-dev.1) (2023-06-27)
+
+## [2.21.4](https://github.com/revanced/revanced-cli/compare/v2.21.3...v2.21.4) (2023-06-21)
+
+
+### Bug Fixes
+
+* remove duplicate options entries. ([d0fc886](https://github.com/revanced/revanced-cli/commit/d0fc8864286adc2677f91a319a11a90272c1001d))
+
+## [2.21.4-dev.1](https://github.com/revanced/revanced-cli/compare/v2.21.3...v2.21.4-dev.1) (2023-06-18)
+
+
+### Bug Fixes
+
+* remove duplicate options entries. ([d0fc886](https://github.com/revanced/revanced-cli/commit/d0fc8864286adc2677f91a319a11a90272c1001d))
+
+## [2.21.3](https://github.com/revanced/revanced-cli/compare/v2.21.2...v2.21.3) (2023-06-12)
+
+## [2.21.3-dev.1](https://github.com/revanced/revanced-cli/compare/v2.21.2...v2.21.3-dev.1) (2023-06-07)
+
+## [2.21.2](https://github.com/revanced/revanced-cli/compare/v2.21.1...v2.21.2) (2023-05-24)
+
+## [2.21.2-dev.2](https://github.com/revanced/revanced-cli/compare/v2.21.2-dev.1...v2.21.2-dev.2) (2023-05-15)
+
 ## [2.21.2-dev.1](https://github.com/revanced/revanced-cli/compare/v2.21.1...v2.21.2-dev.1) (2023-05-07)
 
 ## [2.21.1](https://github.com/revanced/revanced-cli/compare/v2.21.0...v2.21.1) (2023-05-06)

README.md

@@ -0,0 +1,3 @@
+# 💻 ReVanced CLI
+
+Command line application to use ReVanced.

build.gradle.kts

@@ -1,42 +1,23 @@
 plugins {
-    kotlin("jvm") version "1.8.10"
-    id("com.github.johnrengelman.shadow") version "7.1.2"
+    kotlin("jvm") version "1.8.20"
+    alias(libs.plugins.shadow)
 }
 
 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/revanced-patcher")
-        credentials {
-            username = githubUsername
-            password = githubPassword
-        }
-    }
-    maven { url = uri("https://jitpack.io") }
-    google()
-}
-
 dependencies {
-    implementation("org.jetbrains.kotlin:kotlin-reflect:1.8.20-RC")
-
-    implementation("app.revanced:revanced-patcher:7.1.1")
-    implementation("info.picocli:picocli:4.7.1")
-    implementation("com.github.revanced:jadb:2531a28109") // updated fork
-    implementation("com.android.tools.build:apksig:8.1.0-alpha09")
-    implementation("org.bouncycastle:bcpkix-jdk15on:1.70")
-    implementation("com.fasterxml.jackson.module:jackson-module-kotlin:2.14.+")
-    testImplementation("org.jetbrains.kotlin:kotlin-test:1.8.20-RC")
+    implementation(libs.revanced.patcher)
+    implementation(libs.kotlin.reflect)
+    implementation(libs.kotlinx.coroutines.core)
+    implementation(libs.picocli)
+    implementation(libs.jadb) // Updated fork
+    implementation(libs.apksig)
+    implementation(libs.bcpkix.jdk15on)
+    implementation(libs.jackson.module.kotlin)
+    testImplementation(libs.kotlin.test)
 }
 
-kotlin {
-    jvmToolchain(11)
-}
+kotlin { jvmToolchain(11) }
 
 tasks {
     test {
@@ -45,9 +26,15 @@ tasks {
             events("PASSED", "SKIPPED", "FAILED")
         }
     }
+
+    processResources {
+        expand("projectVersion" to project.version)
+    }
+
     build {
         dependsOn(shadowJar)
     }
+
     shadowJar {
         manifest {
             attributes("Main-Class" to "app.revanced.cli.main.MainKt")
@@ -58,12 +45,12 @@ tasks {
             exclude(dependency("app.revanced:.*"))
         }
     }
+
     // 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)
     }
 }

docs/0_prerequisites.md

@@ -1,15 +1,17 @@
 # 💼 Prerequisites
 
-To use ReVanced CLI, you will need to fulfill certain requirements.
+To use ReVanced CLI, you will need to fulfil specific requirements.
 
 ## 🤝 Requirements
 
-- [Android Debug Bridge (adb)](https://developer.android.com/studio/command-line/adb) if you want to deploy the patched APK file on your device
+- Java SDK 11 (Azul Zulu JDK or OpenJDK)
+- [Android Debug Bridge (adb)](https://developer.android.com/studio/command-line/adb) if you want to install the patched APK file on your device
 - An ABI other than ARMv7 such as x86 or x86-64 (or a custom AAPT binary that supports ARMv7)
-- Java SDK 17 or higher (Azul JDK or OpenJDK)
+- ReVanced Patches
+- ReVanced Integrations, if the patches require it
 
 ## ⏭️ Whats next
 
-The next section will show, how to use [ReVanced CLI](https://github.com/revanced/revanced-cli).
+The following section will show you how to use ReVanced CLI.
 
-Continue: [🛠️ Using ReVanced CLI](1_usage.md)
+Continue: [🛠️ Using ReVanced CLI](1_usage.md)

docs/1_usage.md

@@ -2,73 +2,98 @@
 
 Learn how to ReVanced CLI.
 
-## ⚡ Setup (optional)
+## ⚡ Setup ADB
 
-1. Make sure your device is connected
+1. Ensure that ADB is working
 
    ```bash
    adb shell exit
    ```
 
-   If you plan to use the root variant, check if you have root access
+   Optionally, you can install the patched APK file on your device by mounting it on top of the original APK file. 
+   You will need root permissions for this. Check if you have root permissions by running the following command:
 
    ```bash
    adb shell su -c exit
    ```
 
-2. Copy the ADB device name
+2. Get your device serial
 
    ```bash
    adb devices
    ```
 
-## 🔨 ReVanced CLI Usage
+## 🔨 Using ReVanced CLI
 
-- ### Show all available options for ReVanced CLI
+- ### ⚙️ Show all available options for ReVanced CLI
 
   ```bash
   java -jar revanced-cli.jar -h
   ```
 
-- ### List all available patches from supplied patch bundles
+- ### 📃 List patches from supplied patch bundles
 
   ```bash
-  java -jar revanced-cli.jar \
-      -b revanced-patches.jar \
-      -l
+  java -jar revanced-cli.jar list-patches \
+   --with-packages \
+   --with-versions \
+   --with-options \
+   revanced-patches.jar [<patch-bundle> ...]
   ```
 
-- ### Use ReVanced CLI without root permissions
+- ### ⚙️ Generate options from patches using ReVanced CLI
+
+  This will generate an `options.json` file for the patches from a list of supplied patch bundles.
+  The file can be supplied to ReVanced CLI later on.
+ 
+- ```bash
+  java -jar revanced-cli.jar options \
+   --path options.json \
+   --overwrite \
+   revanced-patches.jar [<patch-bundle> ...]
+  ```
+
+  > **Note**: A default `options.json` file will be automatically generated, if it does not exist 
+  without any need of intervention when using the `patch` command.
 
   ```bash
-  java -jar revanced-cli.jar \
-   -a input.apk \
-   -o patched-output.apk \
-   -b revanced-patches.jar
-  ```
 
-- ### Mount the patched application with root permissions over the installed application
+- ### 💉 Use ReVanced CLI to patch an APK file but install without root permissions
+
+  This will install the patched APK file regularly on your device.
 
   ```bash
-  adb install input.apk # make sure the same version is installed
-  java -jar revanced-cli.jar \
-      -a input.apk \
-      -d device-name \
-      -o patched-output.apk \
-      -b revanced-patches.jar \
-      -e vanced-microg-support \
-      --mount
+  java -jar revanced-cli.jar patch \
+   --patch-bundle revanced-patches.jar \
+   --out output.apk \
+   --device-serial <device-serial> \
+   input.apk
   ```
 
-> **Note**:
->
-> - If you want to exclude patches, you can use the option `-e`. In the case of YouTube, you can exclude
-    the `vanced-microg-support` patch from [ReVanced Patches](https://github.com/revanced/revanced-patches) with the
-    option `-e vanced-microg-support` when mounting for example.
->
-> - Some patches from [ReVanced Patches](https://github.com/revanced/revanced-patches) also might require
-    [ReVanced Integrations](https://github.com/revanced/revanced-integrations). Supply them with the option `-m`.
-    > The integrations will be merged, if necessary automatically, if supplied.
->
-> - If you supplied a device with the option `-d`, the patched application will be automatically installed on the
-    device.
+- ### 👾 Use ReVanced CLI to patch an APK file but install with root permissions
+
+  This will install the patched APK file on your device by mounting it on top of the original APK file.
+
+  ```bash
+  adb install input.apk
+  java -jar revanced-cli.jar patch \
+   --patch-bundle revanced-patches.jar \
+   --include some-other-patch \
+   --exclude some-patch \
+   --out patched-output.apk \
+   --device-serial <device-serial> \
+   --mount \
+   input.apk
+  ```
+
+  > **Note**: Some patches may require integrations
+  such as [ReVanced Integrations](https://github.com/revanced/revanced-integrations). 
+  Supply them with the option `-m`. If any patches accepted by ReVanced Patcher require ReVanced Integrations, 
+  they will be merged into the APK file automatically.
+
+- ### 🗑️ Uninstall a patched 
+  ```bash
+  java -jar revanced-cli.jar uninstall \
+   --package-name <package-name> \
+   <device-serial>
+  ```

gradle.properties

@@ -1,2 +1,4 @@
+org.gradle.parallel = true
+org.gradle.caching = true
 kotlin.code.style = official
-version = 2.21.2-dev.1
+version = 3.0.0-dev.1

gradle/libs.versions.toml

@@ -0,0 +1,25 @@
+[versions]
+shadow = "8.1.1"
+apksig = "8.1.0"
+bcpkix-jdk15on = "1.70"
+jackson-module-kotlin = "2.14.3"
+jadb = "2531a28109"
+kotlin-reflect = "1.9.0"
+kotlin-test = "1.8.20-RC"
+kotlinx-coroutines-core = "1.7.1"
+picocli = "4.7.3"
+revanced-patcher = "14.0.0"
+
+[libraries]
+apksig = { module = "com.android.tools.build:apksig", version.ref = "apksig" }
+bcpkix-jdk15on = { module = "org.bouncycastle:bcpkix-jdk15on", version.ref = "bcpkix-jdk15on" }
+jackson-module-kotlin = { module = "com.fasterxml.jackson.module:jackson-module-kotlin", version.ref = "jackson-module-kotlin" }
+jadb = { module = "com.github.revanced:jadb", version.ref = "jadb" }
+kotlin-reflect = { module = "org.jetbrains.kotlin:kotlin-reflect", version.ref = "kotlin-reflect" }
+kotlin-test = { module = "org.jetbrains.kotlin:kotlin-test", version.ref = "kotlin-test" }
+kotlinx-coroutines-core = { module = "org.jetbrains.kotlinx:kotlinx-coroutines-core", version.ref = "kotlinx-coroutines-core" }
+picocli = { module = "info.picocli:picocli", version.ref = "picocli" }
+revanced-patcher = { module = "app.revanced:revanced-patcher", version.ref = "revanced-patcher" }
+
+[plugins]
+shadow = { id = "com.github.johnrengelman.shadow", version.ref = "shadow" }

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,7 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-8.1.1-all.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.2-bin.zip
+networkTimeout=10000
+validateDistributionUrl=true
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

gradlew

@@ -1,7 +1,7 @@
-#!/usr/bin/env sh
+#!/bin/sh
 
 #
-# Copyright 2015 the original author or authors.
+# Copyright © 2015-2021 the original authors.
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -17,67 +17,98 @@
 #
 
 ##############################################################################
-##
-##  Gradle start up script for UN*X
-##
+#
+#   Gradle start up script for POSIX generated by Gradle.
+#
+#   Important for running:
+#
+#   (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is
+#       noncompliant, but you have some other compliant shell such as ksh or
+#       bash, then to run this script, type that shell name before the whole
+#       command line, like:
+#
+#           ksh Gradle
+#
+#       Busybox and similar reduced shells will NOT work, because this script
+#       requires all of these POSIX shell features:
+#         * functions;
+#         * expansions «$var», «${var}», «${var:-default}», «${var+SET}»,
+#           «${var#prefix}», «${var%suffix}», and «$( cmd )»;
+#         * compound commands having a testable exit status, especially «case»;
+#         * various built-in commands including «command», «set», and «ulimit».
+#
+#   Important for patching:
+#
+#   (2) This script targets any POSIX shell, so it avoids extensions provided
+#       by Bash, Ksh, etc; in particular arrays are avoided.
+#
+#       The "traditional" practice of packing multiple parameters into a
+#       space-separated string is a well documented source of bugs and security
+#       problems, so this is (mostly) avoided, by progressively accumulating
+#       options in "$@", and eventually passing that to Java.
+#
+#       Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS,
+#       and GRADLE_OPTS) rely on word-splitting, this is performed explicitly;
+#       see the in-line comments for details.
+#
+#       There are tweaks for specific operating systems such as AIX, CygWin,
+#       Darwin, MinGW, and NonStop.
+#
+#   (3) This script is generated from the Groovy template
+#       https://github.com/gradle/gradle/blob/HEAD/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt
+#       within the Gradle project.
+#
+#       You can find Gradle at https://github.com/gradle/gradle/.
+#
 ##############################################################################
 
 # Attempt to set APP_HOME
+
 # Resolve links: $0 may be a link
-PRG="$0"
-# Need this for relative symlinks.
-while [ -h "$PRG" ] ; do
-    ls=`ls -ld "$PRG"`
-    link=`expr "$ls" : '.*-> \(.*\)$'`
-    if expr "$link" : '/.*' > /dev/null; then
-        PRG="$link"
-    else
-        PRG=`dirname "$PRG"`"/$link"
-    fi
+app_path=$0
+
+# Need this for daisy-chained symlinks.
+while
+    APP_HOME=${app_path%"${app_path##*/}"}  # leaves a trailing /; empty if no leading path
+    [ -h "$app_path" ]
+do
+    ls=$( ls -ld "$app_path" )
+    link=${ls#*' -> '}
+    case $link in             #(
+      /*)   app_path=$link ;; #(
+      *)    app_path=$APP_HOME$link ;;
+    esac
 done
-SAVED="`pwd`"
-cd "`dirname \"$PRG\"`/" >/dev/null
-APP_HOME="`pwd -P`"
-cd "$SAVED" >/dev/null
 
-APP_NAME="Gradle"
-APP_BASE_NAME=`basename "$0"`
-
-# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
-DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+# This is normally unused
+# shellcheck disable=SC2034
+APP_BASE_NAME=${0##*/}
+APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit
 
 # Use the maximum available, or set MAX_FD != -1 to use that value.
-MAX_FD="maximum"
+MAX_FD=maximum
 
 warn () {
     echo "$*"
-}
+} >&2
 
 die () {
     echo
     echo "$*"
     echo
     exit 1
-}
+} >&2
 
 # OS specific support (must be 'true' or 'false').
 cygwin=false
 msys=false
 darwin=false
 nonstop=false
-case "`uname`" in
-  CYGWIN* )
-    cygwin=true
-    ;;
-  Darwin* )
-    darwin=true
-    ;;
-  MSYS* | MINGW* )
-    msys=true
-    ;;
-  NONSTOP* )
-    nonstop=true
-    ;;
+case "$( uname )" in                #(
+  CYGWIN* )         cygwin=true  ;; #(
+  Darwin* )         darwin=true  ;; #(
+  MSYS* | MINGW* )  msys=true    ;; #(
+  NONSTOP* )        nonstop=true ;;
 esac
 
 CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
@@ -87,9 +118,9 @@ CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar
 if [ -n "$JAVA_HOME" ] ; then
     if [ -x "$JAVA_HOME/jre/sh/java" ] ; then
         # IBM's JDK on AIX uses strange locations for the executables
-        JAVACMD="$JAVA_HOME/jre/sh/java"
+        JAVACMD=$JAVA_HOME/jre/sh/java
     else
-        JAVACMD="$JAVA_HOME/bin/java"
+        JAVACMD=$JAVA_HOME/bin/java
     fi
     if [ ! -x "$JAVACMD" ] ; then
         die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME
@@ -98,88 +129,120 @@ Please set the JAVA_HOME variable in your environment to match the
 location of your Java installation."
     fi
 else
-    JAVACMD="java"
-    which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
+    JAVACMD=java
+    if ! command -v java >/dev/null 2>&1
+    then
+        die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
 
 Please set the JAVA_HOME variable in your environment to match the
 location of your Java installation."
+    fi
 fi
 
 # Increase the maximum file descriptors if we can.
-if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then
-    MAX_FD_LIMIT=`ulimit -H -n`
-    if [ $? -eq 0 ] ; then
-        if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then
-            MAX_FD="$MAX_FD_LIMIT"
-        fi
-        ulimit -n $MAX_FD
-        if [ $? -ne 0 ] ; then
-            warn "Could not set maximum file descriptor limit: $MAX_FD"
-        fi
-    else
-        warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT"
-    fi
-fi
-
-# For Darwin, add options to specify how the application appears in the dock
-if $darwin; then
-    GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
-fi
-
-# For Cygwin or MSYS, switch paths to Windows format before running java
-if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
-    APP_HOME=`cygpath --path --mixed "$APP_HOME"`
-    CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
-
-    JAVACMD=`cygpath --unix "$JAVACMD"`
-
-    # We build the pattern for arguments to be converted via cygpath
-    ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null`
-    SEP=""
-    for dir in $ROOTDIRSRAW ; do
-        ROOTDIRS="$ROOTDIRS$SEP$dir"
-        SEP="|"
-    done
-    OURCYGPATTERN="(^($ROOTDIRS))"
-    # Add a user-defined pattern to the cygpath arguments
-    if [ "$GRADLE_CYGPATTERN" != "" ] ; then
-        OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)"
-    fi
-    # Now convert the arguments - kludge to limit ourselves to /bin/sh
-    i=0
-    for arg in "$@" ; do
-        CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -`
-        CHECK2=`echo "$arg"|egrep -c "^-"`                                 ### Determine if an option
-
-        if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then                    ### Added a condition
-            eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"`
-        else
-            eval `echo args$i`="\"$arg\""
-        fi
-        i=`expr $i + 1`
-    done
-    case $i in
-        0) set -- ;;
-        1) set -- "$args0" ;;
-        2) set -- "$args0" "$args1" ;;
-        3) set -- "$args0" "$args1" "$args2" ;;
-        4) set -- "$args0" "$args1" "$args2" "$args3" ;;
-        5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
-        6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
-        7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
-        8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
-        9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
+if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then
+    case $MAX_FD in #(
+      max*)
+        # In POSIX sh, ulimit -H is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC3045
+        MAX_FD=$( ulimit -H -n ) ||
+            warn "Could not query maximum file descriptor limit"
+    esac
+    case $MAX_FD in  #(
+      '' | soft) :;; #(
+      *)
+        # In POSIX sh, ulimit -n is undefined. That's why the result is checked to see if it worked.
+        # shellcheck disable=SC3045
+        ulimit -n "$MAX_FD" ||
+            warn "Could not set maximum file descriptor limit to $MAX_FD"
     esac
 fi
 
-# Escape application args
-save () {
-    for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
-    echo " "
-}
-APP_ARGS=`save "$@"`
+# Collect all arguments for the java command, stacking in reverse order:
+#   * args from the command line
+#   * the main class name
+#   * -classpath
+#   * -D...appname settings
+#   * --module-path (only if needed)
+#   * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables.
 
-# Collect all arguments for the java command, following the shell quoting and substitution rules
-eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if "$cygwin" || "$msys" ; then
+    APP_HOME=$( cygpath --path --mixed "$APP_HOME" )
+    CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" )
+
+    JAVACMD=$( cygpath --unix "$JAVACMD" )
+
+    # Now convert the arguments - kludge to limit ourselves to /bin/sh
+    for arg do
+        if
+            case $arg in                                #(
+              -*)   false ;;                            # don't mess with options #(
+              /?*)  t=${arg#/} t=/${t%%/*}              # looks like a POSIX filepath
+                    [ -e "$t" ] ;;                      #(
+              *)    false ;;
+            esac
+        then
+            arg=$( cygpath --path --ignore --mixed "$arg" )
+        fi
+        # Roll the args list around exactly as many times as the number of
+        # args, so each arg winds up back in the position where it started, but
+        # possibly modified.
+        #
+        # NB: a `for` loop captures its iteration list before it begins, so
+        # changing the positional parameters here affects neither the number of
+        # iterations, nor the values presented in `arg`.
+        shift                   # remove old arg
+        set -- "$@" "$arg"      # push replacement arg
+    done
+fi
+
+
+# Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script.
+DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"'
+
+# Collect all arguments for the java command;
+#   * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of
+#     shell script including quotes and variable substitutions, so put them in
+#     double quotes to make sure that they get re-expanded; and
+#   * put everything else in single quotes, so that it's not re-expanded.
+
+set -- \
+        "-Dorg.gradle.appname=$APP_BASE_NAME" \
+        -classpath "$CLASSPATH" \
+        org.gradle.wrapper.GradleWrapperMain \
+        "$@"
+
+# Stop when "xargs" is not available.
+if ! command -v xargs >/dev/null 2>&1
+then
+    die "xargs is not available"
+fi
+
+# Use "xargs" to parse quoted args.
+#
+# With -n1 it outputs one arg per line, with the quotes and backslashes removed.
+#
+# In Bash we could simply go:
+#
+#   readarray ARGS < <( xargs -n1 <<<"$var" ) &&
+#   set -- "${ARGS[@]}" "$@"
+#
+# but POSIX shell has neither arrays nor command substitution, so instead we
+# post-process each arg (as a line of input to sed) to backslash-escape any
+# character that might be a shell metacharacter, then use eval to reverse
+# that process (while maintaining the separation between arguments), and wrap
+# the whole thing up as a single "set" statement.
+#
+# This will of course break if any of these variables contains a newline or
+# an unmatched quote.
+#
+
+eval "set -- $(
+        printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" |
+        xargs -n1 |
+        sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' |
+        tr '\n' ' '
+    )" '"$@"'
 
 exec "$JAVACMD" "$@"

gradlew.bat

@@ -14,7 +14,7 @@
 @rem limitations under the License.
 @rem
 
-@if "%DEBUG%" == "" @echo off
+@if "%DEBUG%"=="" @echo off
 @rem ##########################################################################
 @rem
 @rem  Gradle startup script for Windows
@@ -25,7 +25,8 @@
 if "%OS%"=="Windows_NT" setlocal
 
 set DIRNAME=%~dp0
-if "%DIRNAME%" == "" set DIRNAME=.
+if "%DIRNAME%"=="" set DIRNAME=.
+@rem This is normally unused
 set APP_BASE_NAME=%~n0
 set APP_HOME=%DIRNAME%
 
@@ -40,7 +41,7 @@ if defined JAVA_HOME goto findJavaFromJavaHome
 
 set JAVA_EXE=java.exe
 %JAVA_EXE% -version >NUL 2>&1
-if "%ERRORLEVEL%" == "0" goto execute
+if %ERRORLEVEL% equ 0 goto execute
 
 echo.
 echo ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH.
@@ -75,13 +76,15 @@ set CLASSPATH=%APP_HOME%\gradle\wrapper\gradle-wrapper.jar
 
 :end
 @rem End local scope for the variables with windows NT shell
-if "%ERRORLEVEL%"=="0" goto mainEnd
+if %ERRORLEVEL% equ 0 goto mainEnd
 
 :fail
 rem Set variable GRADLE_EXIT_CONSOLE if you need the _script_ return code instead of
 rem the _cmd.exe /c_ return code!
-if  not "" == "%GRADLE_EXIT_CONSOLE%" exit 1
-exit /b 1
+set EXIT_CODE=%ERRORLEVEL%
+if %EXIT_CODE% equ 0 set EXIT_CODE=1
+if not ""=="%GRADLE_EXIT_CONSOLE%" exit %EXIT_CODE%
+exit /b %EXIT_CODE%
 
 :mainEnd
 if "%OS%"=="Windows_NT" endlocal

settings.gradle.kts

@@ -1 +1,23 @@
+val githubUsername: String = providers.gradleProperty("gpr.user").orNull ?: System.getenv("GITHUB_ACTOR")
+val githubPassword: String = providers.gradleProperty("gpr.key").orNull ?: System.getenv("GITHUB_TOKEN")
+
+dependencyResolutionManagement {
+    repositoriesMode.set(RepositoriesMode.FAIL_ON_PROJECT_REPOS)
+    repositories {
+        mavenCentral()
+        mavenLocal()
+        google()
+        maven { url = uri("https://jitpack.io") }
+        listOf("revanced-patcher", "jadb").forEach { repo ->
+            maven {
+                url = uri("https://maven.pkg.github.com/revanced/$repo")
+                credentials {
+                    username = githubUsername
+                    password = githubPassword
+                }
+            }
+        }
+    }
+}
+
 rootProject.name = "revanced-cli"

src/main/kotlin/app/revanced/cli/aligning/Aligning.kt

@@ -1,37 +0,0 @@
-package app.revanced.cli.aligning
-
-import app.revanced.cli.command.MainCommand.logger
-import app.revanced.patcher.PatcherResult
-import app.revanced.utils.signing.align.ZipAligner
-import app.revanced.utils.signing.align.zip.ZipFile
-import app.revanced.utils.signing.align.zip.structures.ZipEntry
-import java.io.File
-
-object Aligning {
-    fun align(result: PatcherResult, inputFile: File, outputFile: File) {
-        logger.info("Aligning ${inputFile.name} to ${outputFile.name}")
-
-        if (outputFile.exists()) outputFile.delete()
-
-        ZipFile(outputFile).use { file ->
-            result.dexFiles.forEach {
-                file.addEntryCompressData(
-                    ZipEntry.createWithName(it.name),
-                    it.stream.readBytes()
-                )
-            }
-
-            result.resourceFile?.let {
-                file.copyEntriesFromFileAligned(
-                    ZipFile(it),
-                    ZipAligner::getEntryAlignment
-                )
-            }
-
-            file.copyEntriesFromFileAligned(
-                ZipFile(inputFile),
-                ZipAligner::getEntryAlignment
-            )
-        }
-    }
-}

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

@@ -0,0 +1,94 @@
+package app.revanced.cli.command
+
+import app.revanced.patcher.PatchBundleLoader
+import app.revanced.patcher.annotation.Package
+import app.revanced.patcher.extensions.PatchExtensions.compatiblePackages
+import app.revanced.patcher.extensions.PatchExtensions.description
+import app.revanced.patcher.extensions.PatchExtensions.options
+import app.revanced.patcher.extensions.PatchExtensions.patchName
+import app.revanced.patcher.patch.PatchClass
+import app.revanced.patcher.patch.PatchOption
+import picocli.CommandLine.*
+import picocli.CommandLine.Help.Visibility.ALWAYS
+import java.io.File
+
+
+@Command(name = "list-patches", description = ["List patches from supplied patch bundles"])
+internal object ListPatchesCommand : Runnable {
+    @Parameters(
+        description = ["Paths to patch bundles"],
+        arity = "1..*"
+    )
+    lateinit var patchBundles: Array<File>
+
+    @Option(
+        names = ["-d", "--with-descriptions"],
+        description = ["List their descriptions"],
+        showDefaultValue = ALWAYS
+    )
+    var withDescriptions: Boolean = true
+
+    @Option(
+        names = ["-p", "--with-packages"],
+        description = ["List the packages the patches are compatible with"],
+        showDefaultValue = ALWAYS
+    )
+    var withPackages: Boolean = false
+
+    @Option(
+        names = ["-v", "--with-versions"],
+        description = ["List the versions of the packages the patches are compatible with"],
+        showDefaultValue = ALWAYS
+    )
+    var withVersions: Boolean = false
+
+    @Option(
+        names = ["-o", "--with-options"],
+        description = ["List the options of the patches"],
+        showDefaultValue = ALWAYS
+    )
+    var withOptions: Boolean = false
+
+    override fun run() {
+        fun Package.buildString() = buildString {
+            if (withVersions && versions.isNotEmpty()) {
+                appendLine("Package name: $name")
+                appendLine("Compatible versions:")
+                append(versions.joinToString("\n") { version -> version }.prependIndent("\t"))
+            } else
+                append("Package name: $name")
+        }
+
+        fun PatchOption<*>.buildString() = buildString {
+            appendLine("Title: $title")
+            appendLine("Description: $description")
+
+            value?.let {
+                appendLine("Key: $key")
+                append("Value: $it")
+            } ?: append("Key: $key")
+        }
+
+        fun PatchClass.buildString() = buildString {
+            append("Name: $patchName")
+
+            if (withDescriptions) append("\nDescription: $description")
+
+            if (withOptions && options != null) {
+                appendLine("\nOptions:")
+                append(
+                    options!!.joinToString("\n\n") { option -> option.buildString() }.prependIndent("\t")
+                )
+            }
+
+            if (withPackages && compatiblePackages != null) {
+                appendLine("\nCompatible packages:")
+                append(
+                    compatiblePackages!!.joinToString("\n") { it.buildString() }.prependIndent("\t")
+                )
+            }
+        }
+
+        logger.info(PatchBundleLoader.Jar(*patchBundles).joinToString("\n\n") { it.buildString() })
+    }
+}

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

@@ -0,0 +1,40 @@
+package app.revanced.cli.command
+
+import app.revanced.cli.logging.impl.DefaultCliLogger
+import app.revanced.patcher.patch.PatchClass
+import picocli.CommandLine
+import picocli.CommandLine.Command
+import picocli.CommandLine.IVersionProvider
+import java.util.*
+
+fun main(args: Array<String>) {
+    CommandLine(Main).execute(*args)
+}
+
+internal typealias PatchList = List<PatchClass>
+
+internal val logger = DefaultCliLogger()
+
+object CLIVersionProvider : IVersionProvider {
+    override fun getVersion(): Array<String> {
+        Properties().apply {
+            load(Main::class.java.getResourceAsStream("/app/revanced/cli/version.properties"))
+        }.let {
+            return arrayOf("ReVanced CLI v${it.getProperty("version")}")
+        }
+    }
+}
+
+@Command(
+    name = "revanced-cli",
+    description = ["Command line application to use ReVanced"],
+    mixinStandardHelpOptions = true,
+    versionProvider = CLIVersionProvider::class,
+    subcommands = [
+        ListPatchesCommand::class,
+        PatchCommand::class,
+        UninstallCommand::class,
+        OptionsCommand::class,
+    ]
+)
+internal object Main

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

@@ -1,264 +0,0 @@
-package app.revanced.cli.command
-
-import app.revanced.cli.aligning.Aligning
-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.data.Context
-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.patch.Patch
-import app.revanced.patcher.util.patch.PatchBundle
-import app.revanced.utils.Options
-import app.revanced.utils.Options.setOptions
-import app.revanced.utils.adb.Adb
-import picocli.CommandLine.*
-import java.io.File
-import java.nio.file.Files
-
-/**
- * Alias for return type of [PatchBundle.loadPatches].
- */
-internal typealias PatchList = List<Class<out Patch<Context>>>
-
-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 APK 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 device over ADB with given name"]
-        )
-        var deploy: String? = null
-
-        @ArgGroup(exclusive = false)
-        var patchArgs: PatchArgs? = null
-    }
-
-    class PatchArgs {
-        @Option(names = ["-b", "--bundle"], description = ["One or more bundles of patches"], required = true)
-        var patchBundles = arrayOf<String>()
-
-        @Option(names = ["--options"], description = ["Path to patch options JSON file"])
-        var optionsFile: File = File("options.json")
-
-        @ArgGroup(exclusive = false)
-        var listingArgs: ListingArgs? = null
-
-        @ArgGroup(exclusive = false)
-        var patchingArgs: PatchingArgs? = null
-    }
-
-    class ListingArgs {
-        @Option(names = ["-l", "--list"], description = ["List patches"], 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
-    }
-
-    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 exclusive = false
-
-        @Option(names = ["-i", "--include"], description = ["Include patches"])
-        var includedPatches = arrayOf<String>()
-
-        @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 = ["Temporary resource cache directory"])
-        var cacheDirectory = "revanced-cache"
-
-        @Option(
-            names = ["-c", "--clean"],
-            description = ["Clean the temporary resource cache directory. This will be done anyways when running the patcher"]
-        )
-        var clean: Boolean = false
-
-        @Option(names = ["--custom-aapt2-binary"], description = ["Path to custom aapt2 binary"])
-        var aaptPath: String = ""
-    }
-
-    override fun run() {
-        if (args.patchArgs?.listingArgs?.listOnly == true) return printListOfPatches()
-        if (args.uninstall) return uninstall()
-
-        val pArgs = this.args.patchArgs?.patchingArgs ?: return
-        val outputFile = File(pArgs.outputPath) // the file to write to
-
-        val allPatches = args.patchArgs!!.patchBundles.flatMap { bundle ->
-            PatchBundle.Jar(bundle).loadPatches()
-        }
-
-        args.patchArgs!!.optionsFile.let {
-            if (it.exists()) allPatches.setOptions(it, logger)
-            else Options.serialize(allPatches, prettyPrint = true).let(it::writeText)
-        }
-
-        val patcher = app.revanced.patcher.Patcher(
-            PatcherOptions(
-                args.inputFile.also { if (!it.exists()) return logger.error("Input file ${args.inputFile} does not exist.") },
-                pArgs.cacheDirectory,
-                pArgs.aaptPath,
-                pArgs.cacheDirectory,
-                PatcherLogger
-            )
-        )
-
-        // prepare adb
-        val adb: Adb? = args.deploy?.let {
-            Adb(outputFile, patcher.context.packageMetadata.packageName, args.deploy!!, !pArgs.mount)
-        }
-
-        // start the patcher
-        val result = Patcher.start(patcher, allPatches)
-
-        val cacheDirectory = File(pArgs.cacheDirectory)
-
-        // align the file
-        val alignedFile = cacheDirectory.resolve("${outputFile.nameWithoutExtension}_aligned.apk")
-        Aligning.align(result, args.inputFile, alignedFile)
-
-        // sign the file
-        val finalFile = if (!pArgs.mount) {
-            val signedOutput = cacheDirectory.resolve("${outputFile.nameWithoutExtension}_signed.apk")
-            Signing.sign(
-                alignedFile,
-                signedOutput,
-                SigningOptions(
-                    pArgs.cn,
-                    pArgs.password,
-                    pArgs.keystorePath ?: outputFile.absoluteFile.parentFile
-                        .resolve("${outputFile.nameWithoutExtension}.keystore")
-                        .canonicalPath
-                )
-            )
-
-            signedOutput
-        } else
-            alignedFile
-
-        // finally copy to the specified output file
-        logger.info("Copying ${finalFile.name} to ${outputFile.name}")
-        finalFile.copyTo(outputFile, overwrite = true)
-
-        // clean up the cache directory if needed
-        if (pArgs.clean)
-            cleanUp(pArgs.cacheDirectory)
-
-        // deploy if specified
-        adb?.deploy()
-
-        if (pArgs.clean && args.deploy != null) Files.delete(outputFile.toPath())
-
-        logger.info("Finished")
-    }
-
-    private fun cleanUp(cacheDirectory: String) {
-        val result = if (File(cacheDirectory).deleteRecursively())
-            "Cleaned up cache directory"
-        else
-            "Failed to clean up cache directory"
-        logger.info(result)
-    }
-
-    private fun uninstall() {
-        val adb: Adb? = args.deploy?.let {
-            Adb(
-                File("placeholder_file"),
-                app.revanced.patcher.Patcher(PatcherOptions(args.inputFile, "")).context.packageMetadata.packageName,
-                args.deploy!!,
-                false
-            )
-        }
-        adb?.uninstall()
-    }
-
-    private fun printListOfPatches() {
-        val logged = mutableListOf<String>()
-        for (patchBundlePath in args.patchArgs?.patchBundles!!) for (patch in PatchBundle.Jar(patchBundlePath)
-            .loadPatches()) {
-            if (patch.patchName in logged) continue
-            for (compatiblePackage in patch.compatiblePackages ?: continue) {
-                val packageEntryStr = buildString {
-                    // Add package if flag is set
-                    if (args.patchArgs?.listingArgs?.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.
-                    append("\t")
-                    append(patch.description)
-
-                    // Add compatible versions, if flag is set
-                    if (args.patchArgs?.listingArgs?.withVersions == true) {
-                        val compatibleVersions = compatiblePackage.versions.joinToString(separator = ", ")
-                        append("\t")
-                        append(compatibleVersions)
-                    }
-                }
-
-                logged.add(patch.patchName)
-                logger.info(packageEntryStr)
-            }
-        }
-    }
-}

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

@@ -0,0 +1,50 @@
+package app.revanced.cli.command
+
+import app.revanced.patcher.PatchBundleLoader
+import app.revanced.utils.Options
+import app.revanced.utils.Options.setOptions
+import picocli.CommandLine
+import picocli.CommandLine.Help.Visibility.ALWAYS
+import java.io.File
+
+@CommandLine.Command(
+    name = "options",
+    description = ["Generate options file from patches"],
+)
+internal object OptionsCommand : Runnable {
+    @CommandLine.Parameters(
+        description = ["Paths to patch bundles"],
+        arity = "1..*"
+    )
+    lateinit var patchBundles: Array<File>
+
+    @CommandLine.Option(
+        names = ["-p", "--path"],
+        description = ["Path to patch options JSON file"],
+        showDefaultValue = ALWAYS
+    )
+    var path: File = File("options.json")
+
+    @CommandLine.Option(
+        names = ["-o", "--overwrite"],
+        description = ["Overwrite existing options file"],
+        showDefaultValue = ALWAYS
+    )
+    var overwrite: Boolean = false
+
+    @CommandLine.Option(
+        names = ["-u", "--update"],
+        description = ["Update existing options by adding missing and removing non-existent options"],
+        showDefaultValue = ALWAYS
+    )
+    var update: Boolean = false
+
+    override fun run() = if (!path.exists() || overwrite)
+        with(PatchBundleLoader.Jar(*patchBundles)) {
+            if (update) setOptions(path, logger)
+
+            Options.serialize(this, prettyPrint = true)
+                .let(path::writeText)
+        }
+    else logger.error("Options file already exists, use --override to override it")
+}

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

@@ -0,0 +1,412 @@
+package app.revanced.cli.command
+
+import app.revanced.cli.patcher.logging.impl.PatcherLogger
+import app.revanced.patcher.PatchBundleLoader
+import app.revanced.patcher.Patcher
+import app.revanced.patcher.PatcherOptions
+import app.revanced.patcher.PatcherResult
+import app.revanced.patcher.extensions.PatchExtensions.compatiblePackages
+import app.revanced.patcher.extensions.PatchExtensions.include
+import app.revanced.patcher.extensions.PatchExtensions.patchName
+import app.revanced.utils.Options
+import app.revanced.utils.Options.setOptions
+import app.revanced.utils.adb.AdbManager
+import app.revanced.utils.align.ZipAligner
+import app.revanced.utils.align.zip.ZipFile
+import app.revanced.utils.align.zip.structures.ZipEntry
+import app.revanced.utils.signing.ApkSigner
+import app.revanced.utils.signing.SigningOptions
+import kotlinx.coroutines.runBlocking
+import picocli.CommandLine
+import picocli.CommandLine.Help.Visibility.ALWAYS
+import java.io.File
+
+
+@CommandLine.Command(
+    name = "patch",
+    description = ["Patch the supplied APK file with the supplied patches and integrations"]
+)
+internal object PatchCommand: Runnable {
+    @CommandLine.Parameters(
+        description = ["APK file to be patched"],
+        arity = "1..1"
+    )
+    lateinit var apk: File
+
+    @CommandLine.Option(
+        names = ["-b", "--patch-bundle"],
+        description = ["One or more bundles of patches"],
+        required = true
+    )
+    var patchBundles = emptyList<File>()
+
+    @CommandLine.Option(
+        names = ["-m", "--merge"],
+        description = ["One or more DEX files or containers to merge into the APK"]
+    )
+    var integrations = listOf<File>()
+
+    @CommandLine.Option(
+        names = ["-i", "--include"],
+        description = ["List of patches to include"]
+    )
+    var includedPatches = arrayOf<String>()
+
+    @CommandLine.Option(
+        names = ["-e", "--exclude"],
+        description = ["List of patches to exclude"]
+    )
+    var excludedPatches = arrayOf<String>()
+
+    @CommandLine.Option(
+        names = ["--options"],
+        description = ["Path to patch options JSON file"],
+        showDefaultValue = ALWAYS
+    )
+    var optionsFile: File = File("options.json")
+
+    @CommandLine.Option(
+        names = ["--exclusive"],
+        description = ["Only include patches that are explicitly specified to be included"],
+        showDefaultValue = ALWAYS
+    )
+    var exclusive = false
+
+    @CommandLine.Option(
+        names = ["--experimental"],
+        description = ["Ignore patches incompatibility to versions"],
+        showDefaultValue = ALWAYS
+    )
+    var experimental: Boolean = false
+
+    @CommandLine.Option(
+        names = ["-o", "--out"],
+        description = ["Path to save the patched APK file to"],
+        required = true
+    )
+    lateinit var outputFilePath: File
+
+    @CommandLine.Option(
+        names = ["-d", "--device-serial"],
+        description = ["ADB device serial to install to"],
+        showDefaultValue = ALWAYS
+    )
+    var deviceSerial: String? = null
+
+    @CommandLine.Option(
+        names = ["--mount"],
+        description = ["Install by mounting the patched package"],
+        showDefaultValue = ALWAYS
+    )
+    var mount: Boolean = false
+
+    @CommandLine.Option(
+        names = ["--common-name"],
+        description = ["The common name of the signer of the patched APK file"],
+        showDefaultValue = ALWAYS
+
+    )
+    var commonName = "ReVanced"
+
+    @CommandLine.Option(
+        names = ["--keystore"],
+        description = ["Path to the keystore to sign the patched APK file with"]
+    )
+    var keystorePath: String? = null
+
+    @CommandLine.Option(
+        names = ["--password"],
+        description = ["The password of the keystore to sign the patched APK file with"]
+    )
+    var password = "ReVanced"
+
+    @CommandLine.Option(
+        names = ["-r", "--resource-cache"],
+        description = ["Path to temporary resource cache directory"],
+        showDefaultValue = ALWAYS
+    )
+    var resourceCachePath = File("revanced-resource-cache")
+
+    @CommandLine.Option(
+        names = ["--custom-aapt2-binary"],
+        description = ["Path to a custom AAPT binary to compile resources with"]
+    )
+    var aaptBinaryPath = File("")
+
+    @CommandLine.Option(
+        names = ["-p", "--purge"],
+        description = ["Purge the temporary resource cache directory after patching"],
+        showDefaultValue = ALWAYS
+    )
+    var purge: Boolean = false
+
+    override fun run() {
+        // region Prepare
+
+        if (!apk.exists()) {
+            logger.error("Input file ${apk.name} does not exist")
+            return
+        }
+
+        val adbManager = deviceSerial?.let { serial ->
+            if (mount) AdbManager.RootAdbManager(serial, logger) else AdbManager.UserAdbManager(
+                serial,
+                logger
+            )
+        }
+
+        // endregion
+
+        // region Load patches
+
+        logger.info("Loading patches")
+
+        val patches = PatchBundleLoader.Jar(*patchBundles.toTypedArray())
+        val integrations = integrations
+
+        logger.info("Setting patch options")
+
+        optionsFile.let {
+            if (it.exists()) patches.setOptions(it, logger)
+            else Options.serialize(patches, prettyPrint = true).let(it::writeText)
+        }
+
+        // endregion
+
+        // region Patch
+
+        val patcher = Patcher(
+            PatcherOptions(
+                apk,
+                resourceCachePath,
+                aaptBinaryPath.path,
+                resourceCachePath.absolutePath,
+                PatcherLogger
+            )
+        )
+
+        val result = patcher.apply {
+            acceptIntegrations(integrations)
+            acceptPatches(filterPatchSelection(patches))
+
+            // Execute patches.
+            runBlocking {
+                apply(false).collect { patchResult ->
+                    patchResult.exception?.let {
+                        logger.error("${patchResult.patchName} failed:\n${patchResult.exception}")
+                    } ?: logger.info("${patchResult.patchName} succeeded")
+                }
+            }
+        }.get()
+
+        patcher.close()
+
+        // endregion
+
+        // region Finish
+
+        val alignAndSignedFile = sign(
+            apk.newAlignedFile(
+                result,
+                resourceCachePath.resolve("${outputFilePath.nameWithoutExtension}_aligned.apk")
+            )
+        )
+
+        logger.info("Copying to ${outputFilePath.name}")
+        alignAndSignedFile.copyTo(outputFilePath, overwrite = true)
+
+        adbManager?.install(AdbManager.Apk(outputFilePath, patcher.context.packageMetadata.packageName))
+
+        if (purge) {
+            logger.info("Purging temporary files")
+            outputFilePath.delete()
+            purge(resourceCachePath)
+        }
+
+        // endregion
+    }
+
+
+    /**
+     * Filter the patches to be added to the patcher. The filter is based on the following:
+     * - [includedPatches] (explicitly included)
+     * - [excludedPatches] (explicitly excluded)
+     * - [exclusive] (only include patches that are explicitly included)
+     * - [experimental] (ignore patches incompatibility to versions)
+     * - package name and version of the input APK file (if [experimental] is false)
+     *
+     * @param patches The patches to filter.
+     * @return The filtered patches.
+     */
+    private fun Patcher.filterPatchSelection(patches: PatchList) = buildList {
+        val packageName = context.packageMetadata.packageName
+        val packageVersion = context.packageMetadata.packageVersion
+
+        patches.forEach patch@{ patch ->
+            val formattedPatchName = patch.patchName.lowercase().replace(" ", "-")
+
+            /**
+             * Check if the patch is explicitly excluded.
+             *
+             * Cases:
+             *  1. -e patch.name
+             *  2. -i patch.name -e patch.name
+             */
+
+            /**
+             * Check if the patch is explicitly excluded.
+             *
+             * Cases:
+             *  1. -e patch.name
+             *  2. -i patch.name -e patch.name
+             */
+
+            val excluded = excludedPatches.contains(formattedPatchName)
+            if (excluded) return@patch logger.info("Excluding ${patch.patchName}")
+
+            /**
+             * Check if the patch is constrained to packages.
+             */
+
+            /**
+             * Check if the patch is constrained to packages.
+             */
+
+            patch.compatiblePackages?.let { packages ->
+                packages.singleOrNull { it.name == packageName }?.let { `package` ->
+                    /**
+                     * Check if the package version matches.
+                     * If experimental is true, version matching will be skipped.
+                     */
+
+                    /**
+                     * Check if the package version matches.
+                     * If experimental is true, version matching will be skipped.
+                     */
+
+                    val matchesVersion = experimental || `package`.versions.let {
+                        it.isEmpty() || it.any { version -> version == packageVersion }
+                    }
+
+                    if (!matchesVersion) return@patch logger.warn(
+                        "${patch.patchName} is incompatible with version $packageVersion. " +
+                                "This patch is only compatible with version " +
+                                packages.joinToString(";") { pkg ->
+                                    "${pkg.name}: ${pkg.versions.joinToString(", ")}"
+                                }
+                    )
+
+                } ?: return@patch logger.trace(
+                    "${patch.patchName} is incompatible with $packageName. " +
+                            "This patch is only compatible with " +
+                            packages.joinToString(", ") { `package` -> `package`.name }
+                )
+
+                return@let
+            } ?: logger.trace("$formattedPatchName: No constraint on packages.")
+
+            /**
+             * Check if the patch is explicitly included.
+             *
+             * Cases:
+             *  1. --exclusive
+             *  2. --exclusive -i patch.name
+             */
+
+            /**
+             * Check if the patch is explicitly included.
+             *
+             * Cases:
+             *  1. --exclusive
+             *  2. --exclusive -i patch.name
+             */
+
+            val explicitlyIncluded = includedPatches.contains(formattedPatchName)
+
+            val implicitlyIncluded = !exclusive && patch.include // Case 3.
+            val exclusivelyIncluded = exclusive && explicitlyIncluded // Case 2.
+
+            val included = implicitlyIncluded || exclusivelyIncluded
+            if (!included) return@patch logger.info("${patch.patchName} excluded by default") // Case 1.
+
+            logger.trace("Adding $formattedPatchName")
+
+            add(patch)
+        }
+    }
+
+    /**
+     * Create a new aligned APK file.
+     *
+     * @param result The result of the patching process.
+     * @param outputFile The file to save the aligned APK to.
+     */
+    private fun File.newAlignedFile(
+        result: PatcherResult,
+        outputFile: File
+    ): File {
+        logger.info("Aligning $name")
+
+        if (outputFile.exists()) outputFile.delete()
+
+        ZipFile(outputFile).use { file ->
+            result.dexFiles.forEach {
+                file.addEntryCompressData(
+                    ZipEntry.createWithName(it.name),
+                    it.stream.readBytes()
+                )
+            }
+
+            result.resourceFile?.let {
+                file.copyEntriesFromFileAligned(
+                    ZipFile(it),
+                    ZipAligner::getEntryAlignment
+                )
+            }
+
+            // TODO: Do not compress result.doNotCompress
+
+            file.copyEntriesFromFileAligned(
+                ZipFile(this),
+                ZipAligner::getEntryAlignment
+            )
+        }
+
+        return outputFile
+    }
+
+    /**
+     * Sign the APK file.
+     *
+     * @param inputFile The APK file to sign.
+     * @return The signed APK file. If [mount] is true, the input file will be returned.
+     */
+    private fun sign(inputFile: File) = if (mount)
+        inputFile
+    else {
+        logger.info("Signing ${inputFile.name}")
+
+        val keyStoreFilePath = keystorePath ?: outputFilePath
+            .absoluteFile.parentFile.resolve("${outputFilePath.nameWithoutExtension}.keystore").canonicalPath
+
+        val options = SigningOptions(
+            commonName,
+            password,
+            keyStoreFilePath
+        )
+
+        ApkSigner(options)
+            .signApk(
+                inputFile,
+                resourceCachePath.resolve("${outputFilePath.nameWithoutExtension}_signed.apk")
+            )
+    }
+
+    private fun purge(resourceCachePath: File) {
+        val result = if (resourceCachePath.deleteRecursively())
+            "Purged resource cache directory"
+        else
+            "Failed to purge resource cache directory"
+        logger.info(result)
+    }
+}

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

@@ -0,0 +1,44 @@
+package app.revanced.cli.command
+
+import app.revanced.utils.adb.AdbManager
+import picocli.CommandLine.*
+import picocli.CommandLine.Help.Visibility.ALWAYS
+
+
+@Command(
+    name = "uninstall",
+    description = ["Uninstall a patched APK file from the devices with the supplied ADB device serials"]
+)
+internal object UninstallCommand : Runnable {
+    @Parameters(
+        description = ["ADB device serials"],
+        arity = "1..*"
+    )
+    lateinit var deviceSerials: Array<String>
+
+    @Option(
+        names = ["-p", "--package-name"],
+        description = ["Package name to uninstall"],
+        required = true
+    )
+    lateinit var packageName: String
+
+    @Option(
+        names = ["-u", "--unmount"],
+        description = ["Uninstall by unmounting the patched package"],
+        showDefaultValue = ALWAYS
+    )
+    var unmount: Boolean = false
+
+    override fun run() = try {
+        deviceSerials.forEach {deviceSerial ->
+            if (unmount) {
+                AdbManager.RootAdbManager(deviceSerial, logger)
+            } else {
+                AdbManager.UserAdbManager(deviceSerial, logger)
+            }.uninstall(packageName)
+        }
+    } catch (e: AdbManager.DeviceNotFoundException) {
+        logger.error(e.toString())
+    }
+}

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

@@ -1,12 +1,12 @@
 package app.revanced.cli.logging.impl
 
-import app.revanced.cli.command.MainCommand
+import app.revanced.cli.command.Main
 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 logger: Logger = Logger.getLogger(Main::class.java.name),
     private val errorLogger: Logger = Logger.getLogger(logger.name + "Err")
 ) : CliLogger {
 

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

@@ -1,8 +0,0 @@
-package app.revanced.cli.main
-
-import app.revanced.cli.command.MainCommand
-import picocli.CommandLine
-
-internal fun main(args: Array<String>) {
-    CommandLine(MainCommand).execute(*args)
-}

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

@@ -1,23 +0,0 @@
-package app.revanced.cli.patcher
-
-import app.revanced.cli.command.PatchList
-import app.revanced.patcher.PatcherResult
-import app.revanced.utils.patcher.addPatchesFiltered
-import app.revanced.utils.patcher.applyPatchesVerbose
-import app.revanced.utils.patcher.mergeFiles
-
-internal object Patcher {
-    internal fun start(
-        patcher: app.revanced.patcher.Patcher,
-        allPatches: PatchList
-    ): PatcherResult {
-        // merge files like necessary integrations
-        patcher.mergeFiles()
-        // add patches, but filter incompatible or excluded patches
-        patcher.addPatchesFiltered(allPatches)
-        // apply patches
-        patcher.applyPatchesVerbose()
-
-        return patcher.save()
-    }
-}

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

@@ -1,12 +0,0 @@
-package app.revanced.cli.signing
-
-import app.revanced.cli.command.MainCommand.logger
-import app.revanced.utils.signing.Signer
-import java.io.File
-
-object Signing {
-    fun sign(alignedFile: File, signedOutput: File, signingOptions: SigningOptions) {
-        logger.info("Signing ${alignedFile.name} to ${signedOutput.name}")
-        Signer(signingOptions).signApk(alignedFile, signedOutput)
-    }
-}

src/main/kotlin/app/revanced/utils/Options.kt

@@ -5,6 +5,7 @@ import app.revanced.cli.logging.CliLogger
 import app.revanced.patcher.extensions.PatchExtensions.options
 import app.revanced.patcher.extensions.PatchExtensions.patchName
 import app.revanced.patcher.patch.NoSuchOptionException
+import app.revanced.utils.Options.PatchOption.Option
 import com.fasterxml.jackson.module.kotlin.jacksonObjectMapper
 import java.io.File
 
@@ -25,9 +26,12 @@ internal object Options {
         .map { patch ->
             PatchOption(
                 patch.patchName,
-                patch.options!!.map { option -> PatchOption.Option(option.key, option.value) }
+                patch.options!!.map { option -> Option(option.key, option.value) }
             )
-        }.let {
+        }
+        // See https://github.com/revanced/revanced-patches/pull/2434/commits/60e550550b7641705e81aa72acfc4faaebb225e7.
+        .distinctBy { it.patchName }
+        .let {
             if (prettyPrint)
                 mapper.writerWithDefaultPrettyPrinter().writeValueAsString(it)
             else

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

@@ -1,113 +0,0 @@
-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 file: File,
-    private val packageName: String,
-    deviceName: String,
-    private val modeInstall: Boolean = false,
-    private val logging: Boolean = true
-) {
-    private val device: JadbDevice
-
-    init {
-        device = JadbConnection().devices.let { device -> device.find { it.serial == deviceName } ?: device.first() }
-            ?: throw IllegalArgumentException("No such device with name $deviceName")
-
-        if (!modeInstall && device.run("su -h", false) != 0)
-            throw IllegalArgumentException("Root required on $deviceName. Task failed")
-    }
-
-    private fun String.replacePlaceholder(with: String? = null): String {
-        return this.replace(Constants.PLACEHOLDER, with ?: packageName)
-    }
-
-    internal fun deploy() {
-        if (modeInstall) {
-            logger.info("Installing without mounting")
-
-            PackageManager(device).install(file)
-        } else {
-            logger.info("Installing by mounting")
-
-            // push patched file
-            device.copy(Constants.PATH_INIT_PUSH, file)
-
-            // create revanced folder path
-            device.run("${Constants.COMMAND_CREATE_DIR} ${Constants.PATH_REVANCED}")
-
-            // prepare mounting the apk
-            device.run(Constants.COMMAND_PREPARE_MOUNT_APK.replacePlaceholder())
-
-            // push mount script
-            device.createFile(
-                Constants.PATH_INIT_PUSH,
-                Constants.CONTENT_MOUNT_SCRIPT.replacePlaceholder()
-            )
-            // install mount script
-            device.run(Constants.COMMAND_INSTALL_MOUNT.replacePlaceholder())
-
-            // unmount the apk for sanity
-            device.run(Constants.COMMAND_UMOUNT.replacePlaceholder())
-            // mount the apk
-            device.run(Constants.PATH_MOUNT.replacePlaceholder())
-
-            // relaunch app
-            device.run(Constants.COMMAND_RESTART.replacePlaceholder())
-
-            // log the app
-            log()
-        }
-    }
-
-    internal fun uninstall() {
-        logger.info("Uninstalling by unmounting")
-
-        // unmount the apk
-        device.run(Constants.COMMAND_UMOUNT.replacePlaceholder())
-
-        // delete revanced app
-        device.run(Constants.COMMAND_DELETE.replacePlaceholder(Constants.PATH_REVANCED_APP).replacePlaceholder())
-
-        // delete mount script
-        device.run(Constants.COMMAND_DELETE.replacePlaceholder(Constants.PATH_MOUNT).replacePlaceholder())
-
-        logger.info("Finished uninstalling")
-    }
-
-    private fun log() {
-        val executor = Executors.newSingleThreadExecutor()
-        val pipe = if (logging) {
-            ProcessBuilder.Redirect.INHERIT
-        } else {
-            ProcessBuilder.Redirect.PIPE
-        }
-
-        val process = device.buildCommand(Constants.COMMAND_LOGCAT.replacePlaceholder())
-            .redirectOutput(pipe)
-            .redirectError(pipe)
-            .useExecutor(executor)
-            .start()
-
-        Thread.sleep(500) // give the app some time to start up.
-        while (true) {
-            try {
-                while (device.run("${Constants.COMMAND_PID_OF} $packageName") == 0) {
-                    Thread.sleep(1000)
-                }
-                break
-            } catch (e: Exception) {
-                throw RuntimeException("An error occurred while monitoring the state of app", e)
-            }
-        }
-        logger.info("Stopped logging because the app was closed")
-        process.destroy()
-        executor.shutdown()
-    }
-}

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

@@ -0,0 +1,135 @@
+package app.revanced.utils.adb
+
+import app.revanced.cli.logging.CliLogger
+import app.revanced.utils.adb.AdbManager.Apk
+import app.revanced.utils.adb.Constants.COMMAND_CREATE_DIR
+import app.revanced.utils.adb.Constants.COMMAND_DELETE
+import app.revanced.utils.adb.Constants.COMMAND_INSTALL_MOUNT
+import app.revanced.utils.adb.Constants.COMMAND_PREPARE_MOUNT_APK
+import app.revanced.utils.adb.Constants.COMMAND_RESTART
+import app.revanced.utils.adb.Constants.COMMAND_UMOUNT
+import app.revanced.utils.adb.Constants.CONTENT_MOUNT_SCRIPT
+import app.revanced.utils.adb.Constants.PATH_INIT_PUSH
+import app.revanced.utils.adb.Constants.PATH_INSTALLATION
+import app.revanced.utils.adb.Constants.PATH_MOUNT
+import app.revanced.utils.adb.Constants.PATH_PATCHED_APK
+import app.revanced.utils.adb.Constants.PLACEHOLDER
+import se.vidstige.jadb.JadbConnection
+import se.vidstige.jadb.managers.Package
+import se.vidstige.jadb.managers.PackageManager
+import java.io.Closeable
+import java.io.File
+
+/**
+ * Adb manager. Used to install and uninstall [Apk] files.
+ *
+ * @param deviceSerial The serial of the device.
+ */
+internal sealed class AdbManager(deviceSerial: String? = null, protected val logger: CliLogger? = null) : Closeable {
+    protected val device = JadbConnection().devices.find { device -> device.serial == deviceSerial }
+        ?: throw DeviceNotFoundException(deviceSerial)
+
+    init {
+        logger?.trace("Established connection to $deviceSerial")
+    }
+
+    /**
+     * Installs the [Apk] file.
+     *
+     * @param apk The [Apk] file.
+     */
+    open fun install(apk: Apk) {
+        logger?.info("Finished installing ${apk.file.name}")
+    }
+
+    /**
+     * Uninstalls the package.
+     *
+     * @param packageName The package name.
+     */
+    open fun uninstall(packageName: String) {
+        logger?.info("Finished uninstalling $packageName")
+    }
+
+    /**
+     * Closes the [AdbManager] instance.
+     */
+    override fun close() {
+        logger?.trace("Closed")
+    }
+
+    class RootAdbManager(deviceSerial: String, logger: CliLogger? = null) : AdbManager(deviceSerial, logger) {
+        init {
+            if (!device.hasSu()) throw IllegalArgumentException("Root required on $deviceSerial. Task failed")
+        }
+
+        override fun install(apk: Apk) {
+            logger?.info("Installing by mounting")
+
+            val applyReplacement = getPlaceholderReplacement(
+                apk.packageName ?: throw IllegalArgumentException("Package name is required")
+            )
+
+            device.copyFile(apk.file, PATH_INIT_PUSH)
+
+            device.run("$COMMAND_CREATE_DIR $PATH_INSTALLATION")
+            device.run(COMMAND_PREPARE_MOUNT_APK.applyReplacement())
+
+            device.createFile(PATH_INIT_PUSH, CONTENT_MOUNT_SCRIPT.applyReplacement())
+
+            device.run(COMMAND_INSTALL_MOUNT.applyReplacement())
+            device.run(COMMAND_UMOUNT.applyReplacement()) // Sanity check.
+            device.run(PATH_MOUNT.applyReplacement())
+            device.run(COMMAND_RESTART.applyReplacement())
+
+            super.install(apk)
+        }
+
+        override fun uninstall(packageName: String) {
+            logger?.info("Uninstalling $packageName by unmounting and deleting the package")
+
+            val applyReplacement = getPlaceholderReplacement(packageName)
+
+            device.run(COMMAND_UMOUNT.applyReplacement(packageName))
+            device.run(COMMAND_DELETE.applyReplacement(PATH_PATCHED_APK).applyReplacement())
+            device.run(COMMAND_DELETE.applyReplacement(PATH_MOUNT).applyReplacement())
+
+            super.uninstall(packageName)
+        }
+
+        companion object Utils {
+            private fun getPlaceholderReplacement(with: String): String.() -> String = { replace(PLACEHOLDER, with) }
+            private fun String.applyReplacement(with: String) = replace(PLACEHOLDER, with)
+        }
+    }
+
+    class UserAdbManager(deviceSerial: String, logger: CliLogger? = null) : AdbManager(deviceSerial, logger) {
+        private val packageManager = PackageManager(device)
+
+        override fun install(apk: Apk) {
+            PackageManager(device).install(apk.file)
+
+            super.install(apk)
+        }
+
+        override fun uninstall(packageName: String) {
+            logger?.info("Uninstalling $packageName")
+
+            packageManager.uninstall(Package(packageName))
+
+            super.uninstall(packageName)
+        }
+    }
+
+    /**
+     * Apk file for [AdbManager].
+     *
+     * @param file The [Apk] file.
+     */
+    internal class Apk(val file: File, val packageName: String? = null)
+
+    internal class DeviceNotFoundException(deviceSerial: String?) :
+        Exception(deviceSerial?.let {
+            "The device with the ADB device serial \"$deviceSerial\" can not be found"
+        } ?: "No ADB device found")
+}

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

@@ -2,28 +2,28 @@ package app.revanced.utils.adb
 
 import se.vidstige.jadb.JadbDevice
 import se.vidstige.jadb.RemoteFile
-import se.vidstige.jadb.ShellProcessBuilder
 import java.io.File
+import java.util.concurrent.Callable
+import java.util.concurrent.Executors
 
-internal fun JadbDevice.buildCommand(command: String, su: Boolean = true): ShellProcessBuilder {
-    if (su) {
-        return shellProcessBuilder("su -c \'$command\'")
+// return the input or output stream, depending on which first returns a value
+internal fun JadbDevice.run(command: String, su: Boolean = false) = with(this.startCommand(command, su)) {
+    Executors.newFixedThreadPool(2).let { service ->
+        arrayOf(inputStream, errorStream).map { stream ->
+            Callable { stream.bufferedReader().use { it.readLine() } }
+        }.let { tasks -> service.invokeAny(tasks).also { service.shutdown() } }
     }
-
-    val args = command.split(" ") as ArrayList<String>
-    val cmd = args.removeFirst()
-
-    return shellProcessBuilder(cmd, *args.toTypedArray())
 }
 
-internal fun JadbDevice.run(command: String, su: Boolean = true): Int {
-    return this.buildCommand(command, su).start().waitFor()
-}
+internal fun JadbDevice.hasSu() =
+    this.startCommand("su -h", false).waitFor() == 0
 
-internal fun JadbDevice.copy(targetPath: String, file: File) {
-    push(file, RemoteFile(targetPath))
-}
+internal fun JadbDevice.copyFile(file: File, targetFile: String) =
+    push(file, RemoteFile(targetFile))
 
-internal fun JadbDevice.createFile(targetFile: String, content: String) {
+internal fun JadbDevice.createFile(targetFile: String, content: String) =
     push(content.byteInputStream(), System.currentTimeMillis(), 644, RemoteFile(targetFile))
-}
+
+
+private fun JadbDevice.startCommand(command: String, su: Boolean) =
+    shellProcessBuilder(if (su) "su -c '$command'" else command).start()

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

@@ -1,57 +1,40 @@
 package app.revanced.utils.adb
 
 internal object Constants {
-    // template placeholder to replace a string in commands
     internal const val PLACEHOLDER = "TEMPLATE_PACKAGE_NAME"
 
-    // utility commands
-    private const val COMMAND_CHMOD_MOUNT = "chmod +x"
-    internal const val COMMAND_PID_OF = "pidof -s"
-    internal const val COMMAND_CREATE_DIR = "mkdir -p"
-    internal const val COMMAND_LOGCAT = "logcat -c && logcat | grep AndroidRuntime"
-    internal const val COMMAND_RESTART = "pm resolve-activity --brief $PLACEHOLDER | tail -n 1 | xargs am start -n && kill ${'$'}($COMMAND_PID_OF $PLACEHOLDER)"
-
-    // default mount file name
-    private const val NAME_MOUNT_SCRIPT = "mount_revanced_$PLACEHOLDER.sh"
-
-    // initial directory to push files to via adb push
     internal const val PATH_INIT_PUSH = "/data/local/tmp/revanced.delete"
+    internal const val PATH_INSTALLATION = "/data/adb/revanced/"
+    internal const val PATH_PATCHED_APK = "$PATH_INSTALLATION$PLACEHOLDER.apk"
+    internal const val PATH_MOUNT = "/data/adb/service.d/mount_revanced_$PLACEHOLDER.sh"
 
-    // revanced path
-    internal const val PATH_REVANCED = "/data/adb/revanced/"
-
-    // revanced apk path
-    internal const val PATH_REVANCED_APP = "$PATH_REVANCED$PLACEHOLDER.apk"
-
-    // delete command
     internal const val COMMAND_DELETE = "rm -rf $PLACEHOLDER"
+    internal const val COMMAND_CREATE_DIR = "mkdir -p"
+    internal const val COMMAND_RESTART = "pm resolve-activity --brief $PLACEHOLDER | tail -n 1 | " +
+            "xargs am start -n && kill ${'$'}(pidof -s $PLACEHOLDER)"
 
-    // mount script path
-    internal const val PATH_MOUNT = "/data/adb/service.d/$NAME_MOUNT_SCRIPT"
+    internal const val COMMAND_PREPARE_MOUNT_APK = "base_path=\"$PATH_PATCHED_APK\" && " +
+            "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"
 
-    // move to revanced apk path & set permissions
-    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 =
         "grep $PLACEHOLDER /proc/mounts | while read -r line; do echo ${'$'}line | cut -d \" \" -f 2 | sed 's/apk.*/apk/' | xargs -r umount -l; done"
 
-    // install mount script & set permissions
-    internal const val COMMAND_INSTALL_MOUNT = "mv $PATH_INIT_PUSH $PATH_MOUNT && $COMMAND_CHMOD_MOUNT $PATH_MOUNT"
+    internal const val COMMAND_INSTALL_MOUNT = "mv $PATH_INIT_PUSH $PATH_MOUNT && chmod +x $PATH_MOUNT"
 
-    // mount script
-    internal val CONTENT_MOUNT_SCRIPT =
+    internal const val CONTENT_MOUNT_SCRIPT =
         """
             #!/system/bin/sh
             MAGISKTMP="${'$'}(magisk --path)" || MAGISKTMP=/sbin
             MIRROR="${'$'}MAGISKTMP/.magisk/mirror"
             while [ "${'$'}(getprop sys.boot_completed | tr -d '\r')" != "1" ]; do sleep 1; done
             
-            base_path="$PATH_REVANCED_APP"
+            base_path="$PATH_PATCHED_APK"
             stock_path=${'$'}( pm path $PLACEHOLDER | grep base | sed 's/package://g' )
 
             chcon u:object_r:apk_data_file:s0  ${'$'}base_path
             mount -o bind ${'$'}MIRROR${'$'}base_path ${'$'}stock_path
-        """.trimIndent()
+        """
 }

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

@@ -1,6 +1,6 @@
-package app.revanced.utils.signing.align
+package app.revanced.utils.align
 
-import app.revanced.utils.signing.align.zip.structures.ZipEntry
+import app.revanced.utils.align.zip.structures.ZipEntry
 
 internal object ZipAligner {
     private const val DEFAULT_ALIGNMENT = 4

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

@@ -1,4 +1,4 @@
-package app.revanced.utils.signing.align.zip
+package app.revanced.utils.align.zip
 
 import java.io.DataInput
 import java.io.DataOutput

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

@@ -1,7 +1,7 @@
-package app.revanced.utils.signing.align.zip
+package app.revanced.utils.align.zip
 
-import app.revanced.utils.signing.align.zip.structures.ZipEndRecord
-import app.revanced.utils.signing.align.zip.structures.ZipEntry
+import app.revanced.utils.align.zip.structures.ZipEndRecord
+import app.revanced.utils.align.zip.structures.ZipEntry
 import java.io.Closeable
 import java.io.File
 import java.io.RandomAccessFile
@@ -11,15 +11,15 @@ import java.util.zip.CRC32
 import java.util.zip.Deflater
 
 class ZipFile(file: File) : Closeable {
-    var entries: MutableList<ZipEntry> = mutableListOf()
+    private var entries: MutableList<ZipEntry> = mutableListOf()
 
     private val filePointer: RandomAccessFile = RandomAccessFile(file, "rw")
-    private var CDNeedsRewrite = false
+    private var centralDirectoryNeedsRewrite = false
 
     private val compressionLevel = 5
 
     init {
-        //if file isn't empty try to load entries
+        // If file isn't empty try to load entries.
         if (file.length() > 0) {
             val endRecord = findEndRecord()
 
@@ -29,17 +29,17 @@ class ZipFile(file: File) : Closeable {
             entries = readEntries(endRecord).toMutableList()
         }
 
-        //seek back to start for writing
+        // 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
+        // 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
+            // Possible beginning of signature.
             if (filePointer.readByte() == 0x50.toByte()) {
-                //seek back to get the full int
+                // Seek back to get the full int.
                 filePointer.seek(i)
                 val possibleSignature = filePointer.readUIntLE()
                 if (possibleSignature == ZipEndRecord.ECD_SIGNATURE) {
@@ -76,7 +76,7 @@ class ZipFile(file: File) : Closeable {
     }
 
     private fun writeCD() {
-        val CDStart = filePointer.channel.position().toUInt()
+        val centralDirectoryStartOffset = filePointer.channel.position().toUInt()
 
         entries.forEach {
             filePointer.channel.write(it.toCDE())
@@ -89,8 +89,8 @@ class ZipFile(file: File) : Closeable {
             0u,
             entriesCount,
             entriesCount,
-            filePointer.channel.position().toUInt() - CDStart,
-            CDStart,
+            filePointer.channel.position().toUInt() - centralDirectoryStartOffset,
+            centralDirectoryStartOffset,
             ""
         )
 
@@ -98,7 +98,7 @@ class ZipFile(file: File) : Closeable {
     }
 
     private fun addEntry(entry: ZipEntry, data: ByteBuffer) {
-        CDNeedsRewrite = true
+        centralDirectoryNeedsRewrite = true
 
         entry.localHeaderOffset = filePointer.channel.position().toUInt()
 
@@ -114,8 +114,7 @@ class ZipFile(file: File) : Closeable {
         compressor.finish()
 
         val uncompressedSize = data.size
-        val compressedData =
-            ByteArray(uncompressedSize) //i'm guessing compression won't make the data bigger
+        val compressedData = ByteArray(uncompressedSize) // I'm guessing compression won't make the data bigger.
 
         val compressedDataLength = compressor.deflate(compressedData)
         val compressedBuffer =
@@ -126,7 +125,7 @@ class ZipFile(file: File) : Closeable {
         val crc = CRC32()
         crc.update(data)
 
-        entry.compression = 8u //deflate compression
+        entry.compression = 8u // Deflate compression.
         entry.uncompressedSize = uncompressedSize.toUInt()
         entry.compressedSize = compressedDataLength.toUInt()
         entry.crc32 = crc.value.toUInt()
@@ -136,14 +135,14 @@ class ZipFile(file: File) : Closeable {
 
     private fun addEntryCopyData(entry: ZipEntry, data: ByteBuffer, alignment: Int? = null) {
         alignment?.let {
-            //calculate where data would end up
+            // Calculate where data would end up.
             val dataOffset = filePointer.filePointer + entry.LFHSize
 
             val mod = dataOffset % alignment
 
-            //wrong alignment
+            // Wrong alignment.
             if (mod != 0L) {
-                //add padding at end of extra field
+                // Add padding at end of extra field.
                 entry.localExtraField =
                     entry.localExtraField.copyOf((entry.localExtraField.size + (alignment - mod)).toInt())
             }
@@ -152,7 +151,7 @@ class ZipFile(file: File) : Closeable {
         addEntry(entry, data)
     }
 
-    fun getDataForEntry(entry: ZipEntry): ByteBuffer {
+    private fun getDataForEntry(entry: ZipEntry): ByteBuffer {
         return filePointer.channel.map(
             FileChannel.MapMode.READ_ONLY,
             entry.dataOffset.toLong(),
@@ -160,9 +159,15 @@ class ZipFile(file: File) : Closeable {
         )
     }
 
+    /**
+     * Copies all entries from [file] to this file but skip already existing entries.
+     *
+     * @param file The file to copy entries from.
+     * @param entryAlignment A function that returns the alignment for a given entry.
+     */
     fun copyEntriesFromFileAligned(file: ZipFile, entryAlignment: (entry: ZipEntry) -> Int?) {
         for (entry in file.entries) {
-            if (entries.any { it.fileName == entry.fileName }) continue //don't add duplicates
+            if (entries.any { it.fileName == entry.fileName }) continue // Skip duplicates
 
             val data = file.getDataForEntry(entry)
             addEntryCopyData(entry, data, entryAlignment(entry))
@@ -170,7 +175,7 @@ class ZipFile(file: File) : Closeable {
     }
 
     override fun close() {
-        if (CDNeedsRewrite) writeCD()
+        if (centralDirectoryNeedsRewrite) writeCD()
         filePointer.close()
     }
 }

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

@@ -1,9 +1,9 @@
-package app.revanced.utils.signing.align.zip.structures
+package app.revanced.utils.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 app.revanced.utils.align.zip.putUInt
+import app.revanced.utils.align.zip.putUShort
+import app.revanced.utils.align.zip.readUIntLE
+import app.revanced.utils.align.zip.readUShortLE
 import java.io.DataInput
 import java.nio.ByteBuffer
 import java.nio.ByteOrder

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

@@ -1,6 +1,6 @@
-package app.revanced.utils.signing.align.zip.structures
+package app.revanced.utils.align.zip.structures
 
-import app.revanced.utils.signing.align.zip.*
+import app.revanced.utils.align.zip.*
 import java.io.DataInput
 import java.nio.ByteBuffer
 import java.nio.ByteOrder

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

@@ -1,76 +0,0 @@
-package app.revanced.utils.patcher
-
-import app.revanced.cli.command.MainCommand
-import app.revanced.cli.command.MainCommand.args
-import app.revanced.cli.command.MainCommand.logger
-import app.revanced.cli.command.PatchList
-import app.revanced.patcher.Patcher
-import app.revanced.patcher.data.Context
-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
-
-fun Patcher.addPatchesFiltered(allPatches: PatchList) {
-    val packageName = this.context.packageMetadata.packageName
-    val packageVersion = this.context.packageMetadata.packageVersion
-
-    val includedPatches = mutableListOf<Class<out Patch<Context>>>()
-    allPatches.forEach patchLoop@{ patch ->
-        val compatiblePackages = patch.compatiblePackages
-        val patchName = patch.patchName
-        val args = MainCommand.args.patchArgs?.patchingArgs!!
-
-        val prefix = "Skipping $patchName"
-
-        if (compatiblePackages == null) logger.trace("$patchName: No constraint on packages.")
-        else {
-            if (!compatiblePackages.any { it.name == packageName }) {
-                logger.trace("$prefix: Incompatible with $packageName. This patch is only compatible with ${
-                    compatiblePackages.joinToString(
-                        ", "
-                    ) { it.name }
-                }")
-                return@patchLoop
-            }
-
-            if (!(args.experimental || compatiblePackages.any { it.versions.isEmpty() || it.versions.any { version -> version == packageVersion } })) {
-                val compatibleWith = compatiblePackages.joinToString(";") { _package ->
-                    "${_package.name}: ${_package.versions.joinToString(", ")}"
-                }
-                logger.warn("$prefix: Incompatible with version $packageVersion. This patch is only compatible with $compatibleWith")
-                return@patchLoop
-            }
-        }
-
-        if (args.excludedPatches.contains(patchName)) {
-            logger.info("$prefix: Manually excluded")
-            return@patchLoop
-        } else if ((!patch.include || args.exclusive) && !args.includedPatches.contains(patchName)) {
-            logger.info("$prefix: Excluded by default")
-            return@patchLoop
-        }
-
-        logger.trace("Adding $patchName")
-        includedPatches.add(patch)
-    }
-
-    this.addPatches(includedPatches)
-}
-
-fun Patcher.applyPatchesVerbose() {
-    this.executePatches().forEach { (patch, result) ->
-        if (result.isSuccess) {
-            logger.info("$patch succeeded")
-            return@forEach
-        }
-        logger.error("$patch failed:")
-        result.exceptionOrNull()!!.printStackTrace()
-    }
-}
-
-fun Patcher.mergeFiles() {
-    this.addIntegrations(args.patchArgs?.patchingArgs!!.mergeFiles) { file ->
-        logger.info("Merging $file")
-    }
-}

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

@@ -1,7 +1,6 @@
 package app.revanced.utils.signing
 
-import app.revanced.cli.command.MainCommand.logger
-import app.revanced.cli.signing.SigningOptions
+import app.revanced.cli.command.logger
 import com.android.apksig.ApkSigner
 import org.bouncycastle.asn1.x500.X500Name
 import org.bouncycastle.asn1.x509.SubjectPublicKeyInfo
@@ -18,10 +17,40 @@ import java.security.*
 import java.security.cert.X509Certificate
 import java.util.*
 
-internal class Signer(
+internal class ApkSigner(
     private val signingOptions: SigningOptions
 ) {
+    private val signer: ApkSigner.Builder
     private val passwordCharArray = signingOptions.password.toCharArray()
+
+    init {
+        Security.addProvider(BouncyCastleProvider())
+
+        val keyStore = KeyStore.getInstance("BKS", "BC")
+        val alias = keyStore.let { store ->
+            FileInputStream(File(signingOptions.keyStoreFilePath).also {
+                if (!it.exists()) {
+                    logger.info("Creating keystore at ${it.absolutePath}")
+                    newKeystore(it)
+                } else {
+                    logger.info("Using keystore at ${it.absolutePath}")
+                }
+            }).use { fis -> store.load(fis, null) }
+            store.aliases().nextElement()
+        }
+
+        with(
+            ApkSigner.SignerConfig.Builder(
+                signingOptions.cn,
+                keyStore.getKey(alias, passwordCharArray) as PrivateKey,
+                listOf(keyStore.getCertificate(alias) as X509Certificate)
+            ).build()
+        ) {
+            this@ApkSigner.signer = ApkSigner.Builder(listOf(this))
+            signer.setCreatedBy(signingOptions.cn)
+        }
+    }
+
     private fun newKeystore(out: File) {
         val (publicKey, privateKey) = createKey()
         val privateKS = KeyStore.getInstance("BKS", "BC")
@@ -50,30 +79,12 @@ internal class Signer(
         return JcaX509CertificateConverter().getCertificate(builder.build(signer)) to pair.private
     }
 
-    fun signApk(input: File, output: File) {
-        Security.addProvider(BouncyCastleProvider())
-
-        // TODO: keystore should be saved securely
-        val ks = File(signingOptions.keyStoreFilePath)
-        if (!ks.exists()) newKeystore(ks) else {
-            logger.info("Found existing keystore: ${ks.name}")
-        }
-
-        val keyStore = KeyStore.getInstance("BKS", "BC")
-        FileInputStream(ks).use { fis -> keyStore.load(fis, null) }
-        val alias = keyStore.aliases().nextElement()
-
-        val config = ApkSigner.SignerConfig.Builder(
-            signingOptions.cn,
-            keyStore.getKey(alias, passwordCharArray) as PrivateKey,
-            listOf(keyStore.getCertificate(alias) as X509Certificate)
-        ).build()
-
-        val signer = ApkSigner.Builder(listOf(config))
-        signer.setCreatedBy(signingOptions.cn)
+    fun signApk(input: File, output: File): File {
         signer.setInputApk(input)
         signer.setOutputApk(output)
 
         signer.build().sign()
+
+        return output
     }
 }

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

@@ -1,4 +1,4 @@
-package app.revanced.cli.signing
+package app.revanced.utils.signing
 
 data class SigningOptions(
     val cn: String,

src/main/resources/app/revanced/cli/version.properties

@@ -0,0 +1 @@
+version=${projectVersion}

src/test/kotlin/app/revanced/patcher/options/PatchOptionOptionsTest.kt

@@ -2,7 +2,10 @@ package app.revanced.patcher.options
 
 import app.revanced.patcher.data.BytecodeContext
 import app.revanced.patcher.data.Context
-import app.revanced.patcher.patch.*
+import app.revanced.patcher.patch.BytecodePatch
+import app.revanced.patcher.patch.OptionsContainer
+import app.revanced.patcher.patch.Patch
+import app.revanced.patcher.patch.PatchOption
 import app.revanced.utils.Options
 import app.revanced.utils.Options.setOptions
 import org.junit.jupiter.api.MethodOrderer
@@ -11,8 +14,8 @@ import org.junit.jupiter.api.Test
 import org.junit.jupiter.api.TestMethodOrder
 
 class PatchOptionsTestPatch : BytecodePatch() {
-    override fun execute(context: BytecodeContext): PatchResult {
-        return PatchResultSuccess()
+    override fun execute(context: BytecodeContext) {
+        // Do nothing
     }
 
     companion object : OptionsContainer() {
@@ -32,7 +35,7 @@ class PatchOptionsTestPatch : BytecodePatch() {
 
 @TestMethodOrder(MethodOrderer.OrderAnnotation::class)
 internal object PatchOptionOptionsTest {
-    private var patches = listOf(PatchOptionsTestPatch::class.java as Class<out Patch<Context>>)
+    private var patches = listOf(PatchOptionsTestPatch::class.java as Class<out Patch<Context<*>>>)
 
     @Test
     @Order(1)