chore(release): 2.21.3-dev.1 [skip ci]

## [2.21.3-dev.1](https://github.com/revanced/revanced-cli/compare/v2.21.2...v2.21.3-dev.1) (2023-06-07)

.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

@@ -1,4 +1,5 @@
 name: Release
+
 on:
   workflow_dispatch:
   push:
@@ -9,6 +10,7 @@ on:
     branches:
       - main
       - dev
+
 jobs:
   release:
     name: Release
@@ -17,24 +19,24 @@ jobs:
       - name: Checkout
         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@v3
         with:
           java-version: '17'
-          distribution: 'temurin'
+          distribution: 'zulu'
           cache: gradle
       - name: Setup Node.js
         uses: actions/setup-node@v3
         with:
-          node-version: "lts/*"
-      - name: Build with Gradle
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        run: ./gradlew build clean
+          node-version: "18"
+          cache: 'npm'
       - 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/
@@ -112,5 +113,10 @@ gradle-app.setting
 
 # # Work around https://youtrack.jetbrains.com/issue/IDEA-116898
 # gradle/wrapper/gradle-wrapper.properties
+
+# Dependency directories
+node_modules/
+
+# ReVanced CLI
 revanced-cache/
-options.toml
+options.toml

.idea/.gitignore

@@ -1,9 +0,0 @@
-# Default ignored files
-/shelf/
-/workspace.xml
-# Editor-based HTTP Client requests
-/httpRequests/
-# Datasource local storage ignored files
-/dataSources/
-/dataSources.local.xml
-/kotlinc.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

@@ -1,14 +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="PWA">
-    <option name="enabled" value="true" />
-    <option name="wasEnabledAtLeastOnce" value="true" />
-  </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

@@ -1,12 +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" />
-  </component>
-</project>

.releaserc

@@ -7,11 +7,13 @@
     }
   ],
   "plugins": [
-    ["@semantic-release/commit-analyzer", {
-      "releaseRules": [
-        {"type": "build", "release": "patch"}
-      ]
-    }],
+    [
+      "@semantic-release/commit-analyzer", {
+        "releaseRules": [
+          { "type": "build", "scope": "revanced-patcher", "release": "patch" }
+        ]
+      }
+    ],
     "@semantic-release/release-notes-generator",
     "@semantic-release/changelog",
     "gradle-semantic-release-plugin",
@@ -31,7 +33,15 @@
           {
             "path": "build/libs/*all.jar"
           }
-        ]
+        ],
+        successComment: false
+      }
+    ],
+    [
+      "@saithodev/semantic-release-backmerge",
+      {
+        backmergeBranches: [{"from": "main", "to": "dev"}],
+        clearWorkspace: true
       }
     ]
   ]

build.gradle.kts

@@ -1,5 +1,5 @@
 plugins {
-    kotlin("jvm") version "1.7.0"
+    kotlin("jvm") version "1.8.10"
     id("com.github.johnrengelman.shadow") version "7.1.2"
 }
 
@@ -23,25 +23,39 @@ repositories {
 }
 
 dependencies {
-    implementation(kotlin("reflect"))
+    implementation("org.jetbrains.kotlin:kotlin-reflect:1.8.20-RC")
 
-    implementation("app.revanced:revanced-patcher:6.0.2")
-    implementation("info.picocli:picocli:4.7.0")
-    implementation("com.android.tools.build:apksig:7.2.1")
-    implementation("com.github.revanced:jadb:master-SNAPSHOT") // updated fork
+    implementation("app.revanced:revanced-patcher:11.0.0")
+    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("cc.ekblad:4koma:1.1.0")
+    implementation("com.fasterxml.jackson.module:jackson-module-kotlin:2.14.+")
+    testImplementation("org.jetbrains.kotlin:kotlin-test:1.8.20-RC")
+}
+
+kotlin {
+    jvmToolchain(11)
 }
 
 tasks {
+    test {
+        useJUnitPlatform()
+        testLogging {
+            events("PASSED", "SKIPPED", "FAILED")
+        }
+    }
     build {
         dependsOn(shadowJar)
     }
     shadowJar {
         manifest {
             attributes("Main-Class" to "app.revanced.cli.main.MainKt")
-            attributes("Implementation-Title" to project.name)
-            attributes("Implementation-Version" to project.version)
+        }
+        minimize {
+            exclude(dependency("org.jetbrains.kotlin:.*"))
+            exclude(dependency("org.bouncycastle:.*"))
+            exclude(dependency("app.revanced:.*"))
         }
     }
     // Dummy task to fix the Gradle semantic-release plugin.

docs/0_prerequisites.md

@@ -0,0 +1,15 @@
+# 💼 Prerequisites
+
+To use ReVanced CLI, you will need to fulfill certain 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
+- 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)
+
+## ⏭️ 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 +1,74 @@
+# 🛠️ Using ReVanced CLI
+
+Learn how to ReVanced CLI.
+
+## ⚡ Setup (optional)
+
+1. Make sure your device is connected
+
+   ```bash
+   adb shell exit
+   ```
+
+   If you plan to use the root variant, check if you have root access
+
+   ```bash
+   adb shell su -c exit
+   ```
+
+2. Copy the ADB device name
+
+   ```bash
+   adb devices
+   ```
+
+## 🔨 ReVanced CLI Usage
+
+- ### 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 without root permissions
+
+  ```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
+
+  ```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
+  ```
+
+> **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.

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 = 2.15.1
+version = 2.21.3-dev.1

gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.4.2-all.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/aligning/Aligning.kt

@@ -1,12 +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(inputFile: File, outputFile: File) {
+    fun align(result: PatcherResult, inputFile: File, outputFile: File) {
         logger.info("Aligning ${inputFile.name} to ${outputFile.name}")
-        ZipAligner.align(inputFile, outputFile)
+
+        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/MainCommand.kt

@@ -7,16 +7,24 @@ 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.OptionsLoader
+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"
@@ -35,13 +43,16 @@ internal object MainCommand : Runnable {
     lateinit var args: Args
 
     class Args {
-        @Option(names = ["-a", "--apk"], description = ["Input file to be patched"], required = true)
+        @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 adb device with given name"])
+        @Option(
+            names = ["-d", "--deploy-on"],
+            description = ["If specified, deploy to device over ADB with given name"]
+        )
         var deploy: String? = null
 
         @ArgGroup(exclusive = false)
@@ -49,11 +60,11 @@ internal object MainCommand : Runnable {
     }
 
     class PatchArgs {
-        @Option(names = ["-b", "--bundles"], description = ["One or more bundles of patches"], required = true)
+        @Option(names = ["-b", "--bundle"], description = ["One or more bundles of patches"], required = true)
         var patchBundles = arrayOf<String>()
 
-        @Option(names = ["--options"], description = ["Configuration file for all patch options"])
-        var options: File = File("options.toml")
+        @Option(names = ["--options"], description = ["Path to patch options JSON file"])
+        var optionsFile: File = File("options.json")
 
         @ArgGroup(exclusive = false)
         var listingArgs: ListingArgs? = null
@@ -63,7 +74,7 @@ internal object MainCommand : Runnable {
     }
 
     class ListingArgs {
-        @Option(names = ["-l", "--list"], description = ["List patches only"], required = true)
+        @Option(names = ["-l", "--list"], description = ["List patches"], required = true)
         var listOnly: Boolean = false
 
         @Option(names = ["--with-versions"], description = ["List patches with compatible versions"])
@@ -71,9 +82,6 @@ internal object MainCommand : Runnable {
 
         @Option(names = ["--with-packages"], description = ["List patches with compatible packages"])
         var withPackages: Boolean = false
-
-        @Option(names = ["--with-descriptions"], description = ["List patches with their descriptions"])
-        var withDescriptions: Boolean = true
     }
 
     class PatchingArgs {
@@ -87,7 +95,7 @@ internal object MainCommand : Runnable {
             names = ["--exclusive"],
             description = ["Only installs the patches you include, not including any patch by default"]
         )
-        var defaultExclude = false
+        var exclusive = false
 
         @Option(names = ["-i", "--include"], description = ["Include patches"])
         var includedPatches = arrayOf<String>()
@@ -134,7 +142,10 @@ internal object MainCommand : Runnable {
             PatchBundle.Jar(bundle).loadPatches()
         }
 
-        OptionsLoader.init(args.patchArgs!!.options, allPatches)
+        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(
@@ -151,16 +162,14 @@ internal object MainCommand : Runnable {
             Adb(outputFile, patcher.context.packageMetadata.packageName, args.deploy!!, !pArgs.mount)
         }
 
-        val patchedFile = File(pArgs.cacheDirectory).resolve("${outputFile.nameWithoutExtension}_raw.apk")
-
         // start the patcher
-        Patcher.start(patcher, patchedFile, allPatches)
+        val result = Patcher.start(patcher, allPatches)
 
         val cacheDirectory = File(pArgs.cacheDirectory)
 
         // align the file
         val alignedFile = cacheDirectory.resolve("${outputFile.nameWithoutExtension}_aligned.apk")
-        Aligning.align(patchedFile, alignedFile)
+        Aligning.align(result, args.inputFile, alignedFile)
 
         // sign the file
         val finalFile = if (!pArgs.mount) {
@@ -222,7 +231,7 @@ internal object MainCommand : Runnable {
         for (patchBundlePath in args.patchArgs?.patchBundles!!) for (patch in PatchBundle.Jar(patchBundlePath)
             .loadPatches()) {
             if (patch.patchName in logged) continue
-            for (compatiblePackage in patch.compatiblePackages!!) {
+            for (compatiblePackage in patch.compatiblePackages ?: continue) {
                 val packageEntryStr = buildString {
                     // Add package if flag is set
                     if (args.patchArgs?.listingArgs?.withPackages == true) {
@@ -230,14 +239,15 @@ internal object MainCommand : Runnable {
                         append(packageName)
                         append("\t")
                     }
+
                     // Add patch name
                     val patchName = patch.patchName.padStart(25)
                     append(patchName)
+
                     // Add description if flag is set.
-                    if (args.patchArgs?.listingArgs?.withDescriptions == true) {
-                        append("\t")
-                        append(patch.description)
-                    }
+                    append("\t")
+                    append(patch.description)
+
                     // Add compatible versions, if flag is set
                     if (args.patchArgs?.listingArgs?.withVersions == true) {
                         val compatibleVersions = compatiblePackage.versions.joinToString(separator = ", ")

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

@@ -1,24 +1,16 @@
 package app.revanced.cli.patcher
 
-import app.revanced.cli.command.MainCommand.args
-import app.revanced.cli.command.MainCommand.logger
-import app.revanced.patcher.data.Context
-import app.revanced.patcher.patch.Patch
-import app.revanced.utils.filesystem.ZipFileSystemUtils
+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
-import java.io.File
-import java.nio.file.Files
 
 internal object Patcher {
     internal fun start(
         patcher: app.revanced.patcher.Patcher,
-        output: File,
-        allPatches: List<Class<out Patch<Context>>>
-    ) {
-        val inputFile = args.inputFile
-
+        allPatches: PatchList
+    ): PatcherResult {
         // merge files like necessary integrations
         patcher.mergeFiles()
         // add patches, but filter incompatible or excluded patches
@@ -26,28 +18,6 @@ internal object Patcher {
         // apply patches
         patcher.applyPatchesVerbose()
 
-        // write output file
-        if (output.exists()) Files.delete(output.toPath())
-        inputFile.copyTo(output)
-
-        val result = patcher.save()
-        ZipFileSystemUtils(output).use { outputFileSystem ->
-            // replace all dex files
-            result.dexFiles.forEach {
-                logger.info("Writing dex file ${it.name}")
-                outputFileSystem.write(it.name, it.stream.readAllBytes())
-            }
-
-            result.resourceFile?.let {
-                logger.info("Writing resources...")
-
-                ZipFileSystemUtils(it).use { resourceFileSystem ->
-                    val resourceFiles = resourceFileSystem.getFile(File.separator)
-                    outputFileSystem.writePathRecursively(resourceFiles)
-                }
-            }
-
-            result.doNotCompress?.let { outputFileSystem.uncompress(*it.toTypedArray()) }
-        }
+        return patcher.save()
     }
 }

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

@@ -0,0 +1,103 @@
+package app.revanced.utils
+
+import app.revanced.cli.command.PatchList
+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 com.fasterxml.jackson.module.kotlin.jacksonObjectMapper
+import java.io.File
+
+
+internal object Options {
+    private var mapper = jacksonObjectMapper()
+
+    /**
+     * Serializes the options for the patches in the list.
+     *
+     * @param patches The list of patches to serialize.
+     * @param prettyPrint Whether to pretty print the JSON.
+     * @return The JSON string containing the options.
+     * @see PatchList
+     */
+    fun serialize(patches: PatchList, prettyPrint: Boolean = false): String = patches
+        .filter { it.options?.any() == true }
+        .map { patch ->
+            PatchOption(
+                patch.patchName,
+                patch.options!!.map { option -> PatchOption.Option(option.key, option.value) }
+            )
+        }.let {
+            if (prettyPrint)
+                mapper.writerWithDefaultPrettyPrinter().writeValueAsString(it)
+            else
+                mapper.writeValueAsString(it)
+        }
+
+    /**
+     * Deserializes the options for the patches in the list.
+     *
+     * @param json The JSON string containing the options.
+     * @return The list of [PatchOption]s.
+     * @see PatchOption
+     * @see PatchList
+     */
+    @Suppress("MemberVisibilityCanBePrivate")
+    fun deserialize(json: String): Array<PatchOption> = mapper.readValue(json, Array<PatchOption>::class.java)
+
+    /**
+     * Sets the options for the patches in the list.
+     *
+     * @param json The JSON string containing the options.
+     * @param logger The logger to use for logging.
+     */
+    fun PatchList.setOptions(json: String, logger: CliLogger? = null) {
+        filter { it.options?.any() == true }.let { patches ->
+            if (patches.isEmpty()) return
+
+            val patchOptions = deserialize(json)
+
+            patches.forEach { patch ->
+                patchOptions.find { option -> option.patchName == patch.patchName }?.let {
+                    it.options.forEach { option ->
+                        try {
+                            patch.options?.set(option.key, option.value)
+                                ?: logger?.warn("${patch.patchName} has no options")
+                        } catch (e: NoSuchOptionException) {
+                            logger?.error(e.message ?: "Unknown error")
+                        }
+                    }
+                }
+            }
+        }
+    }
+
+    /**
+     * Sets the options for the patches in the list.
+     *
+     * @param file The file containing the JSON string containing the options.
+     * @param logger The logger to use for logging.
+     * @see setOptions
+     */
+    fun PatchList.setOptions(file: File, logger: CliLogger? = null) = setOptions(file.readText(), logger)
+
+    /**
+     * Data class for a patch and its [Option]s.
+     *
+     * @property patchName The name of the patch.
+     * @property options The [Option]s for the patch.
+     */
+    internal data class PatchOption(
+        val patchName: String,
+        val options: List<Option>
+    ) {
+
+        /**
+         * Data class for patch option.
+         *
+         * @property key The name of the option.
+         * @property value The value of the option.
+         */
+        internal data class Option(val key: String, val value: Any?)
+    }
+}

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

@@ -1,77 +0,0 @@
-package app.revanced.utils
-
-import app.revanced.cli.command.MainCommand.logger
-import app.revanced.patcher.Patcher
-import app.revanced.patcher.data.Context
-import app.revanced.patcher.extensions.PatchExtensions.options
-import app.revanced.patcher.extensions.PatchExtensions.patchName
-import app.revanced.patcher.patch.Patch
-import cc.ekblad.toml.encodeToString
-import cc.ekblad.toml.model.TomlValue
-import cc.ekblad.toml.serialization.from
-import cc.ekblad.toml.tomlMapper
-import java.io.File
-
-private typealias PatchList = List<Class<out Patch<Context>>>
-private typealias OptionsMap = MutableMap<String, MutableMap<String, Any>>
-
-object OptionsLoader {
-    @JvmStatic
-    private val mapper = tomlMapper {}
-
-    @JvmStatic
-    fun init(file: File, patches: PatchList) {
-        if (!file.exists()) file.createNewFile()
-        val map = mapper.decodeWithDefaults(generateDefaults(patches), TomlValue.from(file.toPath()))
-        readAndSet(map, patches)
-        save(map, file)
-    }
-
-    private fun readAndSet(map: OptionsMap, patches: PatchList) {
-        for ((patchName, options) in map) {
-            val patch = patches.find { it.patchName == patchName } ?: continue
-            val patchOptions = patch.options ?: continue
-            for ((key, value) in options) {
-                if (value == "null") { // backwards compatibility, subject to removal
-                    options.remove(key)
-                    continue
-                }
-                try {
-                    patchOptions[key] = value
-                } catch (e: Exception) {
-                    logger.error("Error while setting option $key for patch $patchName: ${e.message}")
-                    e.printStackTrace()
-                }
-            }
-        }
-    }
-
-    private fun save(map: OptionsMap, file: File) {
-        val toml = mapper.encodeToString(map)
-        file.writeText(
-            """
-                # A list of options for each patch.
-                # This file does not contain all options by default.
-                # Run the CLI with the "--list --with-options" flags to see all available options.
-                # You can also run the CLI with the aforementioned flags and a patch name to see all available options for that patch.
-                # To set an option, add a line with the format "option = value" or set the value if the option already exists.
-                # To reset an option to its default value, delete the line.
-                # To reset all options to their default values, delete this file.
-                # 
-                # This file was generated by ReVanced Patcher version ${Patcher.version}.
-            """.trimIndent() + "\n\n$toml"
-        )
-    }
-
-    private fun generateDefaults(patches: PatchList) = buildMap {
-        for (patch in patches) {
-            val options = patch.options ?: continue
-            if (!options.iterator().hasNext()) continue
-            put(patch.patchName, buildMap {
-                for (option in options) {
-                    put(option.key, option.value ?: continue)
-                }
-            } as MutableMap)
-        }
-    } as MutableMap
-}

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

@@ -17,7 +17,7 @@ internal class Adb(
     private val device: JadbDevice
 
     init {
-        device = JadbConnection().devices.find { it.serial == deviceName }
+        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)

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

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

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

@@ -3,15 +3,15 @@ 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.deprecated
 import app.revanced.patcher.extensions.PatchExtensions.include
 import app.revanced.patcher.extensions.PatchExtensions.patchName
 import app.revanced.patcher.patch.Patch
 
-fun Patcher.addPatchesFiltered(allPatches: List<Class<out Patch<Context>>>) {
+fun Patcher.addPatchesFiltered(allPatches: PatchList) {
     val packageName = this.context.packageMetadata.packageName
     val packageVersion = this.context.packageMetadata.packageVersion
 
@@ -19,29 +19,14 @@ fun Patcher.addPatchesFiltered(allPatches: List<Class<out Patch<Context>>>) {
     allPatches.forEach patchLoop@{ patch ->
         val compatiblePackages = patch.compatiblePackages
         val patchName = patch.patchName
-
-        val prefix = "Skipping $patchName, reason"
-
         val args = MainCommand.args.patchArgs?.patchingArgs!!
 
-        if (args.excludedPatches.contains(patchName)) {
-            logger.info("$prefix: manually excluded")
-            return@patchLoop
-        } else if ((!patch.include || args.defaultExclude) && !args.includedPatches.contains(patchName)) {
-            logger.info("$prefix: excluded by default")
-            return@patchLoop
-        }
+        val prefix = "Skipping $patchName"
 
-        patch.deprecated?.let { (reason, replacement) ->
-            logger.warn("$prefix: deprecated: $reason")
-            if (replacement != null) logger.warn("Either use ${replacement.java.patchName} instead or include it manually")
-            return@patchLoop
-        }
-
-        if (compatiblePackages == null) logger.warn("$prefix: Missing compatibility annotation. Continuing.")
+        if (compatiblePackages == null) logger.trace("$patchName: No constraint on packages.")
         else {
             if (!compatiblePackages.any { it.name == packageName }) {
-                logger.warn("$prefix: incompatible with $packageName. This patch is only compatible with ${
+                logger.trace("$prefix: Incompatible with $packageName. This patch is only compatible with ${
                     compatiblePackages.joinToString(
                         ", "
                     ) { it.name }
@@ -53,11 +38,19 @@ fun Patcher.addPatchesFiltered(allPatches: List<Class<out Patch<Context>>>) {
                 val compatibleWith = compatiblePackages.joinToString(";") { _package ->
                     "${_package.name}: ${_package.versions.joinToString(", ")}"
                 }
-                logger.warn("$prefix: incompatible with version $packageVersion. This patch is only compatible with version $compatibleWith")
+                logger.warn("$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)
     }
@@ -77,7 +70,7 @@ fun Patcher.applyPatchesVerbose() {
 }
 
 fun Patcher.mergeFiles() {
-    this.addFiles(args.patchArgs?.patchingArgs!!.mergeFiles) { file ->
+    this.addIntegrations(args.patchArgs?.patchingArgs!!.mergeFiles) { file ->
         logger.info("Merging $file")
     }
 }

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

@@ -1,28 +1,11 @@
 package app.revanced.utils.signing.align
 
-import app.revanced.utils.signing.align.zip.ZipFile
-import java.io.File
+import app.revanced.utils.signing.align.zip.structures.ZipEntry
 
 internal object ZipAligner {
     private const val DEFAULT_ALIGNMENT = 4
     private const val LIBRARY_ALIGNMENT = 4096
 
-    fun align(input: File, output: File) {
-        val inputZip = ZipFile(input)
-        val outputZip = ZipFile(output)
-
-        for (entry in inputZip.entries) {
-            val data = inputZip.getDataForEntry(entry)
-
-            if (entry.compression == 0.toUShort()) {
-                val alignment = if (entry.fileName.endsWith(".so")) LIBRARY_ALIGNMENT else DEFAULT_ALIGNMENT
-
-                outputZip.addEntryAligned(entry, data, alignment)
-            } else {
-                outputZip.addEntry(entry, data)
-            }
-        }
-
-        outputZip.finish()
-    }
+    fun getEntryAlignment(entry: ZipEntry): Int? =
+        if (entry.compression.toUInt() != 0u) null else if (entry.fileName.endsWith(".so")) LIBRARY_ALIGNMENT else DEFAULT_ALIGNMENT
 }

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

@@ -2,15 +2,21 @@ package app.revanced.utils.signing.align.zip
 
 import app.revanced.utils.signing.align.zip.structures.ZipEndRecord
 import app.revanced.utils.signing.align.zip.structures.ZipEntry
+import java.io.Closeable
 import java.io.File
 import java.io.RandomAccessFile
 import java.nio.ByteBuffer
 import java.nio.channels.FileChannel
+import java.util.zip.CRC32
+import java.util.zip.Deflater
 
-class ZipFile(val file: File) {
+class ZipFile(file: File) : Closeable {
     var entries: MutableList<ZipEntry> = mutableListOf()
 
     private val filePointer: RandomAccessFile = RandomAccessFile(file, "rw")
+    private var CDNeedsRewrite = false
+
+    private val compressionLevel = 5
 
     init {
         //if file isn't empty try to load entries
@@ -53,23 +59,24 @@ class ZipFile(val file: File) {
 
         return buildList(numberOfEntries) {
             for (i in 1..numberOfEntries) {
-                add(ZipEntry.fromCDE(filePointer).also
-                {
-                    //for some reason the local extra field can be different from the central one
-                    it.readLocalExtra(
-                        filePointer.channel.map(
-                            FileChannel.MapMode.READ_ONLY,
-                            it.localHeaderOffset.toLong() + 28,
-                            2
+                add(
+                    ZipEntry.fromCDE(filePointer).also
+                    {
+                        //for some reason the local extra field can be different from the central one
+                        it.readLocalExtra(
+                            filePointer.channel.map(
+                                FileChannel.MapMode.READ_ONLY,
+                                it.localHeaderOffset.toLong() + 28,
+                                2
+                            )
                         )
-                    )
-                })
+                    })
             }
         }
     }
 
-    private fun writeCDE() {
-        val CDEStart = filePointer.channel.position().toUInt()
+    private fun writeCD() {
+        val CDStart = filePointer.channel.position().toUInt()
 
         entries.forEach {
             filePointer.channel.write(it.toCDE())
@@ -82,15 +89,17 @@ class ZipFile(val file: File) {
             0u,
             entriesCount,
             entriesCount,
-            filePointer.channel.position().toUInt() - CDEStart,
-            CDEStart,
+            filePointer.channel.position().toUInt() - CDStart,
+            CDStart,
             ""
         )
 
         filePointer.channel.write(endRecord.toECD())
     }
 
-    fun addEntry(entry: ZipEntry, data: ByteBuffer) {
+    private fun addEntry(entry: ZipEntry, data: ByteBuffer) {
+        CDNeedsRewrite = true
+
         entry.localHeaderOffset = filePointer.channel.position().toUInt()
 
         filePointer.channel.write(entry.toLFH())
@@ -99,17 +108,45 @@ class ZipFile(val file: File) {
         entries.add(entry)
     }
 
-    fun addEntryAligned(entry: ZipEntry, data: ByteBuffer, alignment: Int) {
-        //calculate where data would end up
-        val dataOffset = filePointer.filePointer + entry.LFHSize
+    fun addEntryCompressData(entry: ZipEntry, data: ByteArray) {
+        val compressor = Deflater(compressionLevel, true)
+        compressor.setInput(data)
+        compressor.finish()
 
-        val mod = dataOffset % alignment
+        val uncompressedSize = data.size
+        val compressedData =
+            ByteArray(uncompressedSize) //i'm guessing compression won't make the data bigger
 
-        //wrong alignment
-        if (mod != 0L) {
-            //add padding at end of extra field
-            entry.localExtraField =
-                entry.localExtraField.copyOf((entry.localExtraField.size + (alignment - mod)).toInt())
+        val compressedDataLength = compressor.deflate(compressedData)
+        val compressedBuffer =
+            ByteBuffer.wrap(compressedData.take(compressedDataLength).toByteArray())
+
+        compressor.end()
+
+        val crc = CRC32()
+        crc.update(data)
+
+        entry.compression = 8u //deflate compression
+        entry.uncompressedSize = uncompressedSize.toUInt()
+        entry.compressedSize = compressedDataLength.toUInt()
+        entry.crc32 = crc.value.toUInt()
+
+        addEntry(entry, compressedBuffer)
+    }
+
+    private fun addEntryCopyData(entry: ZipEntry, data: ByteBuffer, alignment: Int? = null) {
+        alignment?.let {
+            //calculate where data would end up
+            val dataOffset = filePointer.filePointer + entry.LFHSize
+
+            val mod = dataOffset % alignment
+
+            //wrong alignment
+            if (mod != 0L) {
+                //add padding at end of extra field
+                entry.localExtraField =
+                    entry.localExtraField.copyOf((entry.localExtraField.size + (alignment - mod)).toInt())
+            }
         }
 
         addEntry(entry, data)
@@ -123,8 +160,17 @@ class ZipFile(val file: File) {
         )
     }
 
-    fun finish() {
-        writeCDE()
+    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
+
+            val data = file.getDataForEntry(entry)
+            addEntryCopyData(entry, data, entryAlignment(entry))
+        }
+    }
+
+    override fun close() {
+        if (CDNeedsRewrite) writeCD()
         filePointer.close()
     }
-}
+}

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

@@ -9,12 +9,12 @@ data class ZipEntry(
     val version: UShort,
     val versionNeeded: UShort,
     val flags: UShort,
-    val compression: UShort,
+    var compression: UShort,
     val modificationTime: UShort,
     val modificationDate: UShort,
-    val crc32: UInt,
-    val compressedSize: UInt,
-    val uncompressedSize: UInt,
+    var crc32: UInt,
+    var compressedSize: UInt,
+    var uncompressedSize: UInt,
     val diskNumber: UShort,
     val internalAttributes: UShort,
     val externalAttributes: UInt,
@@ -22,7 +22,7 @@ data class ZipEntry(
     val fileName: String,
     val extraField: ByteArray,
     val fileComment: String,
-    var localExtraField: ByteArray = ByteArray(0), //seperate for alignment
+    var localExtraField: ByteArray = ByteArray(0), //separate for alignment
 ) {
     val LFHSize: Int
         get() = LFH_HEADER_SIZE + fileName.toByteArray(Charsets.UTF_8).size + localExtraField.size
@@ -37,6 +37,27 @@ data class ZipEntry(
         const val LFH_HEADER_SIZE = 30
         const val LFH_SIGNATURE = 0x04034b50u
 
+        fun createWithName(fileName: String): ZipEntry {
+            return ZipEntry(
+                0x1403u, //made by unix, version 20
+                0u,
+                0u,
+                0u,
+                0x0821u, //seems to be static time google uses, no idea
+                0x0221u, //same as above
+                0u,
+                0u,
+                0u,
+                0u,
+                0u,
+                0u,
+                0u,
+                fileName,
+                ByteArray(0),
+                ""
+            )
+        }
+
         fun fromCDE(input: DataInput): ZipEntry {
             val signature = input.readUIntLE()
 
@@ -55,7 +76,7 @@ data class ZipEntry(
             val fileNameLength = input.readUShortLE()
             var fileName = ""
             val extraFieldLength = input.readUShortLE()
-            var extraField = ByteArray(extraFieldLength.toInt())
+            val extraField = ByteArray(extraFieldLength.toInt())
             val fileCommentLength = input.readUShortLE()
             var fileComment = ""
             val diskNumber = input.readUShortLE()
@@ -63,7 +84,8 @@ data class ZipEntry(
             val externalAttributes = input.readUIntLE()
             val localHeaderOffset = input.readUIntLE()
 
-            val variableFieldsLength = fileNameLength.toInt() + extraFieldLength.toInt() + fileCommentLength.toInt()
+            val variableFieldsLength =
+                fileNameLength.toInt() + extraFieldLength.toInt() + fileCommentLength.toInt()
 
             if (variableFieldsLength > 0) {
                 val fileNameBytes = ByteArray(fileNameLength.toInt())
@@ -77,7 +99,8 @@ data class ZipEntry(
                 fileComment = fileCommentBytes.toString(Charsets.UTF_8)
             }
 
-            flags = (flags and 0b1000u.inv().toUShort()) //disable data descriptor flag as they are not used
+            flags = (flags and 0b1000u.inv()
+                .toUShort()) //disable data descriptor flag as they are not used
 
             return ZipEntry(
                 version,
@@ -134,8 +157,9 @@ data class ZipEntry(
         val nameBytes = fileName.toByteArray(Charsets.UTF_8)
         val commentBytes = fileComment.toByteArray(Charsets.UTF_8)
 
-        val buffer = ByteBuffer.allocate(CDE_HEADER_SIZE + nameBytes.size + extraField.size + commentBytes.size)
-            .also { it.order(ByteOrder.LITTLE_ENDIAN) }
+        val buffer =
+            ByteBuffer.allocate(CDE_HEADER_SIZE + nameBytes.size + extraField.size + commentBytes.size)
+                .also { it.order(ByteOrder.LITTLE_ENDIAN) }
 
         buffer.putUInt(CDE_SIGNATURE)
         buffer.putUShort(version)
@@ -162,5 +186,4 @@ data class ZipEntry(
         buffer.flip()
         return buffer
     }
-}
-
+}

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

@@ -0,0 +1,57 @@
+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.utils.Options
+import app.revanced.utils.Options.setOptions
+import org.junit.jupiter.api.MethodOrderer
+import org.junit.jupiter.api.Order
+import org.junit.jupiter.api.Test
+import org.junit.jupiter.api.TestMethodOrder
+
+class PatchOptionsTestPatch : BytecodePatch() {
+    override fun execute(context: BytecodeContext): PatchResult {
+        return PatchResultSuccess()
+    }
+
+    companion object : OptionsContainer() {
+        var key1 by option(
+            PatchOption.StringOption(
+                "key1", null, "title1", "description1"
+            )
+        )
+
+        var key2 by option(
+            PatchOption.BooleanOption(
+                "key2", true, "title2", "description2"
+            )
+        )
+    }
+}
+
+@TestMethodOrder(MethodOrderer.OrderAnnotation::class)
+internal object PatchOptionOptionsTest {
+    private var patches = listOf(PatchOptionsTestPatch::class.java as Class<out Patch<Context>>)
+
+    @Test
+    @Order(1)
+    fun serializeTest() {
+        assert(SERIALIZED_JSON == Options.serialize(patches))
+    }
+
+    @Test
+    @Order(2)
+    fun loadOptionsTest() {
+        patches.setOptions(CHANGED_JSON)
+
+        assert(PatchOptionsTestPatch.key1 == "test")
+        assert(PatchOptionsTestPatch.key2 == false)
+    }
+
+    private const val SERIALIZED_JSON =
+        "[{\"patchName\":\"PatchOptionsTestPatch\",\"options\":[{\"key\":\"key1\",\"value\":null},{\"key\":\"key2\",\"value\":true}]}]"
+
+    private const val CHANGED_JSON =
+        "[{\"patchName\":\"PatchOptionsTestPatch\",\"options\":[{\"key\":\"key1\",\"value\":\"test\"},{\"key\":\"key2\",\"value\":false}]}]"
+}