chore(release): 2.21.5-dev.2 [skip ci]

## [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)

.github/ISSUE_TEMPLATE/bug-issue.yml

@@ -0,0 +1,73 @@
+name: 🐞 Bug report
+description: Report a very clearly broken issue.
+title: 'bug: <title>'
+labels: [bug]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        # ReVanced bug report
+
+        Important to note that your issue may have already been reported before. Please check for existing issues [here](https://github.com/revanced/revanced-cli/labels/bug).
+
+  - type: dropdown
+    attributes:
+      label: Type
+      options:
+        - Error while running the CLI
+        - Error at runtime
+        - Cosmetic
+        - Other
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Bug description
+      description: How did you find the bug? Any additional details that might help?
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Steps to reproduce
+      description: Add the steps to reproduce this bug including your environment.
+      placeholder: Step 1. Download some files. Step 2. ...
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Relevant log output
+      description: Please copy and paste any relevant log output. This will be automatically formatted into code, so no need for backticks.
+      render: shell
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Screenshots or videos
+      description: Add screenshots or videos that show the bug here.
+      placeholder: Drag and drop the screenshots/videos into this box.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Solution
+      description: If applicable, add a possible solution.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Additional context
+      description: Add additional context here.
+    validations:
+      required: false
+  - type: checkboxes
+    id: acknowledgements
+    attributes:
+      label: Acknowledgements
+      description: Your issue will be closed if you haven't done these steps.
+      options:
+        - label: I have searched the existing issues and this is a new and no duplicate or related to another open issue.
+          required: true
+        - label: I have written a short but informative title.
+          required: true
+        - label: I filled out all of the requested information in this issue properly.
+          required: true

.github/ISSUE_TEMPLATE/config.yml

@@ -0,0 +1,8 @@
+blank_issues_enabled: false
+contact_links:
+  - name: 📃 Documentation
+    url: https://github.com/revanced/revanced-documentation/
+    about: Don't know how or where to start? Check out our documentation!
+  - name: 🗨 Discussions
+    url: https://github.com/revanced/revanced-suggestions/discussions
+    about: Got something you think should change or be added? Search for or start a new discussion!

.github/ISSUE_TEMPLATE/feature-issue.yml

@@ -0,0 +1,58 @@
+name: ⭐ Feature request
+description: Create a detailed feature request.
+title: 'feat: <title>'
+labels: [feature-request]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        # ReVanced feature request
+        
+        Do not submit requests for patches here. Please submit them [here](https://github.com/orgs/revanced/discussions/categories/patches) instead.
+        Important to note that your feature request may have already been made before. Please check for existing feature requests [here](https://github.com/revanced/revanced-cli/labels/feature-request).
+
+  - type: dropdown
+    attributes:
+      label: Type
+      options:
+        - Functionality
+        - Cosmetic
+        - Other
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Issue
+      description: What is the current problem. Why does it require a feature request?
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Feature
+      description: Describe your feature in detail. How does it solve the issue?
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Motivation
+      description: Why should your feature should be considered?
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Additional context
+      description: Add additional context here.
+    validations:
+      required: false
+  - type: checkboxes
+    id: acknowledgements
+    attributes:
+      label: Acknowledgements
+      description: Your issue will be closed if you haven't done these steps.
+      options:
+        - label: I have searched the existing issues and this is a new and no duplicate or related to another open issue.
+          required: true
+        - label: I have written a short but informative title.
+          required: true
+        - label: I filled out all of the requested information in this issue properly.
+          required: true

.github/config.yml

@@ -0,0 +1,2 @@
+firstPRMergeComment: >
+  Thank you for contributing to ReVanced. Join us on [Discord](https://revanced.app/discord) if you want to receive a contributor role.

.github/workflows/pull_request.yml

@@ -0,0 +1,25 @@
+name: PR to main
+
+on:
+  push:
+    branches:
+      - dev
+  workflow_dispatch:
+
+env:
+  MESSAGE: merge branch `${{ github.head_ref || github.ref_name }}` to `main`
+
+jobs:
+  pull-request:
+    name: Open pull request
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+      - name: Open pull request
+        uses: repo-sync/pull-request@v2
+        with:
+          destination_branch: 'main'
+          pr_title: 'chore: ${{ env.MESSAGE }}'
+          pr_body: 'This pull request will ${{ env.MESSAGE }}.'
+          pr_draft: true

.github/workflows/release.yml

@@ -1,5 +1,7 @@
 name: Release
+
 on:
+  workflow_dispatch:
   push:
     branches:
       - main
@@ -8,34 +10,36 @@ on:
     branches:
       - main
       - dev
+
 jobs:
   release:
     name: Release
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
+          # Make sure the release step uses its own credentials:
+          # https://github.com/cycjimmy/semantic-release-action#private-packages
+          persist-credentials: false
           fetch-depth: 0
-      - name: Setup JDK
-        uses: actions/setup-java@v2
+      - name: Cache
+        uses: actions/cache@v3
         with:
-          java-version: '17'
-          distribution: 'adopt'
-          cache: gradle
-      - name: Setup Node.js
-        uses: actions/setup-node@v2
-        with:
-          node-version: "lts/*"
-      - name: Make gradlew executable
-        run: chmod +x gradlew
+          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 build
+        run: ./gradlew clean --no-daemon
       - name: Setup semantic-release
-        run: npm install -g semantic-release @semantic-release/git @semantic-release/changelog gradle-semantic-release-plugin -D
+        run: npm install
       - name: Release
         env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: npx semantic-release
+          GITHUB_TOKEN: ${{ secrets.REPOSITORY_PUSH_ACCESS }}
+        run: npm exec semantic-release

.github/workflows/update-documentation.yml

@@ -0,0 +1,19 @@
+name: Update documentation
+
+on:
+  push:
+    paths:
+      - docs/**
+
+jobs:
+  trigger:
+    runs-on: ubuntu-latest
+    name: Dispatch event to documentation repository
+    if: github.ref == 'refs/heads/main'
+    steps:
+      - uses: peter-evans/repository-dispatch@v2
+        with:
+          token: ${{ secrets.DOCUMENTATION_REPO_ACCESS_TOKEN  }}
+          repository: revanced/revanced-documentation
+          event-type: update-documentation
+          client-payload: '{"repo": "${{ github.event.repository.name }}", "ref": "${{ github.ref }}"}'

.gitignore

@@ -74,6 +74,7 @@ cmake-build-*/
 
 # IntelliJ
 out/
+.idea
 
 # mpeltonen/sbt-idea plugin
 .idea_modules/
@@ -111,4 +112,11 @@ gradle-app.setting
 .gradletasknamecache
 
 # # Work around https://youtrack.jetbrains.com/issue/IDEA-116898
-# gradle/wrapper/gradle-wrapper.properties
+# gradle/wrapper/gradle-wrapper.properties
+
+# Dependency directories
+node_modules/
+
+# ReVanced CLI
+revanced-cache/
+options.toml

.idea/.gitignore

@@ -1,8 +0,0 @@
-# Default ignored files
-/shelf/
-/workspace.xml
-# Editor-based HTTP Client requests
-/httpRequests/
-# Datasource local storage ignored files
-/dataSources/
-/dataSources.local.xml

.idea/discord.xml

@@ -1,7 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="DiscordProjectSettings">
-    <option name="show" value="PROJECT_FILES" />
-    <option name="description" value="" />
-  </component>
-</project>

.idea/git_toolbox_prj.xml

@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="GitToolBoxProjectSettings">
-    <option name="commitMessageIssueKeyValidationOverride">
-      <BoolValueOverride>
-        <option name="enabled" value="true" />
-      </BoolValueOverride>
-    </option>
-    <option name="commitMessageValidationEnabledOverride">
-      <BoolValueOverride>
-        <option name="enabled" value="true" />
-      </BoolValueOverride>
-    </option>
-  </component>
-</project>

.idea/misc.xml

@@ -1,10 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="ExternalStorageConfigurationManager" enabled="true" />
-  <component name="FrameworkDetectionExcludesConfiguration">
-    <file type="web" url="file://$PROJECT_DIR$" />
-  </component>
-  <component name="ProjectRootManager" version="2" languageLevel="JDK_17" default="true" project-jdk-name="azul-17" project-jdk-type="JavaSDK">
-    <output url="file://$PROJECT_DIR$/out" />
-  </component>
-</project>

.idea/vcs.xml

@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project version="4">
-  <component name="CommitMessageInspectionProfile">
-    <profile version="1.0">
-      <inspection_tool class="CommitFormat" enabled="true" level="WARNING" enabled_by_default="true" />
-      <inspection_tool class="CommitNamingConvention" enabled="true" level="WARNING" enabled_by_default="true" />
-    </profile>
-  </component>
-  <component name="VcsDirectoryMappings">
-    <mapping directory="$PROJECT_DIR$" vcs="Git" />
-    <mapping directory="$PROJECT_DIR$/../revanced-patcher" vcs="Git" />
-    <mapping directory="$PROJECT_DIR$/../revanced-patches" vcs="Git" />
-  </component>
-</project>

.releaserc

@@ -7,7 +7,13 @@
     }
   ],
   "plugins": [
-    "@semantic-release/commit-analyzer",
+    [
+      "@semantic-release/commit-analyzer", {
+        "releaseRules": [
+          { "type": "build", "scope": "revanced-patcher", "release": "patch" }
+        ]
+      }
+    ],
     "@semantic-release/release-notes-generator",
     "@semantic-release/changelog",
     "gradle-semantic-release-plugin",
@@ -20,6 +26,23 @@
         ]
       }
     ],
-    "@semantic-release/github"
+    [
+      "@semantic-release/github",
+      {
+        "assets": [
+          {
+            "path": "build/libs/*all.jar"
+          }
+        ],
+        successComment: false
+      }
+    ],
+    [
+      "@saithodev/semantic-release-backmerge",
+      {
+        backmergeBranches: [{"from": "main", "to": "dev"}],
+        clearWorkspace: true
+      }
+    ]
   ]
-}
+}

build.gradle.kts

@@ -1,71 +1,69 @@
 plugins {
-    kotlin("jvm") version "1.6.21"
+    kotlin("jvm") version "1.8.10"
     id("com.github.johnrengelman.shadow") version "7.1.2"
-    java
-    `maven-publish`
 }
 
 group = "app.revanced"
 
+val githubUsername: String = project.findProperty("gpr.user") as? String ?: System.getenv("GITHUB_ACTOR")
+val githubPassword: String = project.findProperty("gpr.key") as? String ?: System.getenv("GITHUB_TOKEN")
+
 repositories {
     mavenCentral()
     mavenLocal()
     maven {
-        url = uri("https://maven.pkg.github.com/revanced/multidexlib2")
+        url = uri("https://maven.pkg.github.com/revanced/revanced-patcher")
         credentials {
-            username = project.findProperty("gpr.user") as String? ?: System.getenv("GITHUB_ACTOR") // DO NOT CHANGE!
-            password = project.findProperty("gpr.key") as String? ?: System.getenv("GITHUB_TOKEN") // DO NOT CHANGE!
+            username = githubUsername
+            password = githubPassword
         }
     }
-    maven {
-        url = uri("https://jitpack.io")
-    }
+    maven { url = uri("https://jitpack.io") }
+    google()
 }
 
 dependencies {
-    implementation("org.jetbrains.kotlin:kotlin-stdlib:1.6.21")
-    implementation("app.revanced:revanced-patcher:+")
-    implementation("app.revanced:revanced-patches:+")
+    implementation("org.jetbrains.kotlin:kotlin-reflect:1.8.20-RC")
 
-    implementation("info.picocli:picocli:4.6.3")
-
-    implementation("com.github.li-wjohnson:jadb:master-SNAPSHOT") // using a fork instead.
+    implementation("app.revanced:revanced-patcher:11.0.3")
+    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("org.jetbrains.kotlin:kotlin-reflect:1.6.21")
+    implementation("com.fasterxml.jackson.module:jackson-module-kotlin:2.14.+")
+    testImplementation("org.jetbrains.kotlin:kotlin-test:1.8.20-RC")
 }
 
-java {
-    withSourcesJar()
-    withJavadocJar()
+kotlin {
+    jvmToolchain(11)
 }
 
 tasks {
+    test {
+        useJUnitPlatform()
+        testLogging {
+            events("PASSED", "SKIPPED", "FAILED")
+        }
+    }
     build {
         dependsOn(shadowJar)
     }
     shadowJar {
         manifest {
-            attributes("Main-Class" to "app.revanced.cli.MainKt")
-            attributes("Implementation-Title" to project.name)
-            attributes("Implementation-Version" to project.version)
+            attributes("Main-Class" to "app.revanced.cli.main.MainKt")
         }
+        minimize {
+            exclude(dependency("org.jetbrains.kotlin:.*"))
+            exclude(dependency("org.bouncycastle:.*"))
+            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)
     }
 }
-
-publishing {
-    repositories {
-        maven {
-            name = "GitHubPackages"
-            url = uri("https://maven.pkg.github.com/revanced/revanced-cli")
-            credentials {
-                username = System.getenv("GITHUB_ACTOR")
-                password = System.getenv("GITHUB_TOKEN")
-            }
-        }
-    }
-    publications {
-        register<MavenPublication>("gpr") {
-            from(components["java"])
-        }
-    }
-}

docs/0_prerequisites.md

@@ -0,0 +1,15 @@
+# 💼 Prerequisites
+
+To use ReVanced CLI, you will need to fulfill certain requirements.
+
+## 🤝 Requirements
+
+- Java SDK 11 (Azul JDK or OpenJDK)
+- [Android Debug Bridge (adb)](https://developer.android.com/studio/command-line/adb) if you want to deploy 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)
+
+## ⏭️ Whats next
+
+The next section will show, how to use [ReVanced CLI](https://github.com/revanced/revanced-cli).
+
+Continue: [🛠️ Using ReVanced CLI](1_usage.md)

docs/1_usage.md

@@ -0,0 +1,76 @@
+# 🛠️ Using ReVanced CLI
+
+Learn how to ReVanced CLI.
+
+## ⚡ Setup ADB
+
+1. Ensure that ADB is working
+
+   ```bash
+   adb shell exit
+   ```
+
+   If you want to deploy the patched APK file on your device by mounting it on top of the original APK file, you will need root access. This is optional.
+
+   ```bash
+   adb shell su -c exit
+   ```
+
+2. Get the name of your device
+
+   ```bash
+   adb devices
+   ```
+
+## 🔨 Using ReVanced CLI
+
+- ### ⚙️ Show all available options for ReVanced CLI
+
+  ```bash
+  java -jar revanced-cli.jar -h
+  ```
+
+- ### 📃 List all available patches from supplied patch bundles
+
+  ```bash
+  java -jar revanced-cli.jar
+   -b revanced-patches.jar \
+   -l
+  ```
+
+- ### 💉 Use ReVanced CLI to patch an APK file but deploy without root permissions
+
+  This will deploy the patched APK file on your device by installing it.
+
+  ```bash
+  java -jar revanced-cli.jar \
+   -a input.apk \
+   -o patched-output.apk \
+   -b revanced-patches.jar \
+   -d device-name
+  ```
+
+- ### 👾 Use ReVanced CLI to patch an APK file but deploy with root permissions
+
+  This will deploy 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 \
+   -a input.apk \
+   -o patched-output.apk \
+   -b revanced-patches.jar \
+   -e vanced-microg-support \
+   -d device-name \
+   --mount
+  ```
+
+  > **Note**: Some patches from [ReVanced Patches](https://github.com/revanced/revanced-patches) also require [ReVanced Integrations](https://github.com/revanced/revanced-integrations). Supply them with the option `-m`. ReVanced Patcher will merge ReVanced Integrations automatically, depending on if the supplied patches require them.
+
+- ### ⚙️ Supply options to patches using ReVanced CLI
+
+  Some patches provide options. Currently, ReVanced CLI will generate and consume an `options.json` file at the location that is specified in `-o`. If the option is not specified, the options file will be generated in the current working directory.
+  
+  The options file contains all options from supplied patch bundles.
+
+  > **Note**: The `options.json` file will be generated at the first time you use ReVanced CLI to patch an APK file for now. This will be changed in the future.

docs/README.md

@@ -0,0 +1,8 @@
+# 💻 Documentation and guides of ReVanced CLI
+
+This documentation explains how to use [ReVanced CLI](https://github.com/revanced/revanced-cli).
+
+## 📖 Table of contents
+
+1. [💼 Prerequisites](0_prerequisites.md)
+2. [🛠️ Using ReVanced CLI](1_usage.md)

gradle.properties

@@ -1,2 +1,2 @@
 kotlin.code.style = official
-version = 1.1.3
+version = 2.21.5-dev.2

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.1.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.1.1-all.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

package.json

@@ -0,0 +1,9 @@
+{
+  "devDependencies": {
+    "@saithodev/semantic-release-backmerge": "^3.1.0",
+    "@semantic-release/changelog": "^6.0.2",
+    "@semantic-release/git": "^10.0.1",
+    "gradle-semantic-release-plugin": "^1.7.6",
+    "semantic-release": "^20.1.0"
+  }
+}

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

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

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

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

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

@@ -0,0 +1,37 @@
+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/logging/CliLogger.kt

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

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

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

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

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

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

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