chore(release): 2.20.0-dev.1 [skip ci]

# [2.20.0-dev.1](https://github.com/revanced/revanced-cli/compare/v2.19.0...v2.20.0-dev.1) (2023-01-01)

### Bug Fixes

* do not list compatible packages if patches do not define them ([31e4a41](31e4a41dd2))

### Features

* remove option `--with-descriptions` ([07a423b](07a423b19e))

.github/ISSUE_TEMPLATE/bug-issue.yml

@@ -59,3 +59,15 @@ body:
       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/feature-issue.yml

@@ -43,4 +43,16 @@ body:
       label: Additional context
       description: Add additional context here.
     validations:
-      required: false
+      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/workflows/pull_request.yml

@@ -0,0 +1,24 @@
+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:
+    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

@@ -15,26 +15,23 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           fetch-depth: 0
       - name: Setup JDK
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v3
         with:
           java-version: '17'
-          distribution: 'adopt'
+          distribution: 'zulu'
           cache: gradle
       - name: Setup Node.js
-        uses: actions/setup-node@v2
+        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: "latest"
+          cache: 'npm'
       - name: Setup semantic-release
-        run: npm install -g semantic-release @semantic-release/git @semantic-release/changelog gradle-semantic-release-plugin -D
-      - name: Release
+        run: npm install semantic-release @saithodev/semantic-release-backmerge @semantic-release/git @semantic-release/changelog gradle-semantic-release-plugin -D
+      - name: Create release
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         run: npx semantic-release

.gitignore

@@ -111,4 +111,11 @@ 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

@@ -6,3 +6,6 @@
 # Datasource local storage ignored files
 /dataSources/
 /dataSources.local.xml
+/kotlinc.xml
+/vcs.xml
+/codeStyles

.idea/misc.xml

@@ -4,6 +4,10 @@
   <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>

.idea/vcs.xml

@@ -8,7 +8,5 @@
   </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

@@ -7,11 +7,7 @@
     }
   ],
   "plugins": [
-    ["@semantic-release/commit-analyzer", {
-      "releaseRules": [
-        {"type": "build", "release": "patch"}
-      ]
-    }],
+    "@semantic-release/commit-analyzer",
     "@semantic-release/release-notes-generator",
     "@semantic-release/changelog",
     "gradle-semantic-release-plugin",
@@ -31,7 +27,15 @@
           {
             "path": "build/libs/*all.jar"
           }
-        ]
+        ],
+        successComment: false
+      }
+    ],
+    [
+      "@saithodev/semantic-release-backmerge",
+      {
+        branches: [{from: "main", to: "dev"}],
+        clearWorkspace: true
       }
     ]
   ]

CHANGELOG.md

@@ -1,3 +1,237 @@
+# [2.20.0-dev.1](https://github.com/revanced/revanced-cli/compare/v2.19.0...v2.20.0-dev.1) (2023-01-01)
+
+
+### Bug Fixes
+
+* do not list compatible packages if patches do not define them ([31e4a41](https://github.com/revanced/revanced-cli/commit/31e4a41dd20f5fa62f840cd8e3b92fe0814eda87))
+
+
+### Features
+
+* remove option `--with-descriptions` ([07a423b](https://github.com/revanced/revanced-cli/commit/07a423b19ec72e9f020aeb0222f4ced571036dbe))
+
+# [2.19.0](https://github.com/revanced/revanced-cli/compare/v2.18.2...v2.19.0) (2022-12-31)
+
+
+### Features
+
+* improve description of options ([#185](https://github.com/revanced/revanced-cli/issues/185)) ([b69e784](https://github.com/revanced/revanced-cli/commit/b69e784785f7f262f83b35c4f241c90036169fc7))
+
+# [2.19.0-dev.1](https://github.com/revanced/revanced-cli/compare/v2.18.2...v2.19.0-dev.1) (2022-12-31)
+
+
+### Features
+
+* improve description of options ([#185](https://github.com/revanced/revanced-cli/issues/185)) ([b69e784](https://github.com/revanced/revanced-cli/commit/b69e784785f7f262f83b35c4f241c90036169fc7))
+
+## [2.18.2](https://github.com/revanced/revanced-cli/compare/v2.18.1...v2.18.2) (2022-12-16)
+
+
+### Bug Fixes
+
+* exclude patcher dependency from minimizing ([d5794b9](https://github.com/revanced/revanced-cli/commit/d5794b94ca19c9287190a3b863c97a089893cc07))
+
+## [2.18.2-dev.1](https://github.com/revanced/revanced-cli/compare/v2.18.1...v2.18.2-dev.1) (2022-12-16)
+
+
+### Bug Fixes
+
+* exclude patcher dependency from minimizing ([d5794b9](https://github.com/revanced/revanced-cli/commit/d5794b94ca19c9287190a3b863c97a089893cc07))
+
+## [2.18.1](https://github.com/revanced/revanced-cli/compare/v2.18.0...v2.18.1) (2022-12-15)
+
+
+### Bug Fixes
+
+* don't log when package is incompatible and `exclusive` option is used ([ad81a1b](https://github.com/revanced/revanced-cli/commit/ad81a1b656586226f8b7b8d1123c52b0f3f2e6f7))
+
+## [2.18.1-dev.1](https://github.com/revanced/revanced-cli/compare/v2.18.0...v2.18.1-dev.1) (2022-12-15)
+
+
+### Bug Fixes
+
+* don't log when package is incompatible and `exclusive` option is used ([ad81a1b](https://github.com/revanced/revanced-cli/commit/ad81a1b656586226f8b7b8d1123c52b0f3f2e6f7))
+
+# [2.18.0](https://github.com/revanced/revanced-cli/compare/v2.17.0...v2.18.0) (2022-12-15)
+
+
+### Bug Fixes
+
+* start with uppercase in log message ([ae91b0d](https://github.com/revanced/revanced-cli/commit/ae91b0d597b107a152e1b630b8c16a795a7ca3b3))
+* use correct prefix in log message ([1a67cd8](https://github.com/revanced/revanced-cli/commit/1a67cd81da5ed7f259b6dbaeb66a7eef4a113034))
+
+
+### Features
+
+* simplify log message ([74d73ca](https://github.com/revanced/revanced-cli/commit/74d73ca3a7ba2f5da872fe9a241629e1c143cd4e))
+
+# [2.18.0](https://github.com/revanced/revanced-cli/compare/v2.17.0...v2.18.0) (2022-12-15)
+
+
+### Bug Fixes
+
+* start with uppercase in log message ([ae91b0d](https://github.com/revanced/revanced-cli/commit/ae91b0d597b107a152e1b630b8c16a795a7ca3b3))
+* use correct prefix in log message ([1a67cd8](https://github.com/revanced/revanced-cli/commit/1a67cd81da5ed7f259b6dbaeb66a7eef4a113034))
+
+
+### Features
+
+* simplify log message ([74d73ca](https://github.com/revanced/revanced-cli/commit/74d73ca3a7ba2f5da872fe9a241629e1c143cd4e))
+
+# [2.18.0-dev.1](https://github.com/revanced/revanced-cli/compare/v2.17.1-dev.2...v2.18.0-dev.1) (2022-12-15)
+
+
+### Bug Fixes
+
+* start with uppercase in log message ([ae91b0d](https://github.com/revanced/revanced-cli/commit/ae91b0d597b107a152e1b630b8c16a795a7ca3b3))
+* use correct prefix in log message ([1a67cd8](https://github.com/revanced/revanced-cli/commit/1a67cd81da5ed7f259b6dbaeb66a7eef4a113034))
+
+
+### Features
+
+* simplify log message ([74d73ca](https://github.com/revanced/revanced-cli/commit/74d73ca3a7ba2f5da872fe9a241629e1c143cd4e))
+
+## [2.17.1-dev.2](https://github.com/revanced/revanced-cli/compare/v2.17.1-dev.1...v2.17.1-dev.2) (2022-12-15)
+
+## [2.17.1-dev.1](https://github.com/revanced/revanced-cli/compare/v2.17.0...v2.17.1-dev.1) (2022-12-15)
+
+# [2.17.0](https://github.com/revanced/revanced-cli/compare/v2.16.1...v2.17.0) (2022-12-14)
+
+
+### Bug Fixes
+
+* invalid header when writing a `ZipFile` ([#169](https://github.com/revanced/revanced-cli/issues/169)) ([6e703eb](https://github.com/revanced/revanced-cli/commit/6e703eb8e8d7da0e52266c4965f37bc8aafb409c))
+
+
+### Features
+
+* improve missing compatibility annotation tracing log ([2c7eb72](https://github.com/revanced/revanced-cli/commit/2c7eb7274c713dfbcb53c5f3b6a9205c751914fa))
+* trace logs when compatibility annotation is missing ([#166](https://github.com/revanced/revanced-cli/issues/166)) ([c590bf5](https://github.com/revanced/revanced-cli/commit/c590bf559c4d2d2667c2af0c0da23d4706fcd4b7))
+
+# [2.17.0-dev.3](https://github.com/revanced/revanced-cli/compare/v2.17.0-dev.2...v2.17.0-dev.3) (2022-12-14)
+
+
+### Features
+
+* improve missing compatibility annotation tracing log ([2c7eb72](https://github.com/revanced/revanced-cli/commit/2c7eb7274c713dfbcb53c5f3b6a9205c751914fa))
+
+# [2.17.0-dev.2](https://github.com/revanced/revanced-cli/compare/v2.17.0-dev.1...v2.17.0-dev.2) (2022-12-14)
+
+
+### Bug Fixes
+
+* invalid header when writing a `ZipFile` ([#169](https://github.com/revanced/revanced-cli/issues/169)) ([6e703eb](https://github.com/revanced/revanced-cli/commit/6e703eb8e8d7da0e52266c4965f37bc8aafb409c))
+
+# [2.17.0-dev.1](https://github.com/revanced/revanced-cli/compare/v2.16.1...v2.17.0-dev.1) (2022-12-11)
+
+
+### Features
+
+* trace logs when compatibility annotation is missing ([#166](https://github.com/revanced/revanced-cli/issues/166)) ([c590bf5](https://github.com/revanced/revanced-cli/commit/c590bf559c4d2d2667c2af0c0da23d4706fcd4b7))
+
+## [2.16.1](https://github.com/revanced/revanced-cli/compare/v2.16.0...v2.16.1) (2022-11-22)
+
+# [2.16.0](https://github.com/revanced/revanced-cli/compare/v2.15.1...v2.16.0) (2022-11-20)
+
+
+### Features
+
+* do not warn on incompatible packages ([39e377b](https://github.com/revanced/revanced-cli/commit/39e377bc485e2892422e9712d30e6ff665856ac1))
+
+## [2.15.1](https://github.com/revanced/revanced-cli/compare/v2.15.0...v2.15.1) (2022-11-18)
+
+# [2.15.0](https://github.com/revanced/revanced-cli/compare/v2.14.0...v2.15.0) (2022-10-31)
+
+
+### Bug Fixes
+
+* **gitignore:** ignore `options.toml` ([#158](https://github.com/revanced/revanced-cli/issues/158)) ([7be9af0](https://github.com/revanced/revanced-cli/commit/7be9af0942de2a834b9e57403d46263b65f1a422))
+
+
+### Features
+
+* use `am` instead of `monkey` to launch the app ([#159](https://github.com/revanced/revanced-cli/issues/159)) ([6a35cf7](https://github.com/revanced/revanced-cli/commit/6a35cf7ea46a4474120626ce03d28490cc96bf07))
+
+# [2.14.0](https://github.com/revanced/revanced-cli/compare/v2.13.0...v2.14.0) (2022-10-05)
+
+
+### Bug Fixes
+
+* escape quotation mark in string ([6e21d81](https://github.com/revanced/revanced-cli/commit/6e21d81964e8160e06ffda7051dd484e4aaaa432))
+
+
+### Features
+
+* handle unmounting deleted files ([#148](https://github.com/revanced/revanced-cli/issues/148)) ([3a733e5](https://github.com/revanced/revanced-cli/commit/3a733e513717799ca0e32327e5b8be043680c556))
+* unmount all occurrences in `/proc/mounts` ([#131](https://github.com/revanced/revanced-cli/issues/131)) ([4f4e1f9](https://github.com/revanced/revanced-cli/commit/4f4e1f9834bf28d9be2efd4fd7bae19951b85258))
+
+# [2.13.0](https://github.com/revanced/revanced-cli/compare/v2.12.0...v2.13.0) (2022-10-01)
+
+
+### Features
+
+* check, if input file exists ([b6dff6d](https://github.com/revanced/revanced-cli/commit/b6dff6d832de4a513a6d86b0a59b2458eddd23c2))
+
+# [2.12.0](https://github.com/revanced/revanced-cli/compare/v2.11.2...v2.12.0) (2022-09-26)
+
+
+### Features
+
+* remove unused option `-r` ([467d838](https://github.com/revanced/revanced-cli/commit/467d8387e646c88d24a30406a5b2e84065ef4d54))
+
+## [2.11.2](https://github.com/revanced/revanced-cli/compare/v2.11.1...v2.11.2) (2022-09-23)
+
+## [2.11.1](https://github.com/revanced/revanced-cli/compare/v2.11.0...v2.11.1) (2022-09-21)
+
+# [2.11.0](https://github.com/revanced/revanced-cli/compare/v2.10.2...v2.11.0) (2022-09-20)
+
+
+### Features
+
+* section `acknowledgements` for issue templates ([0e3ecc3](https://github.com/revanced/revanced-cli/commit/0e3ecc3a51540b71072ae0be0eb94d115a5b1f92))
+
+## [2.10.2](https://github.com/revanced/revanced-cli/compare/v2.10.1...v2.10.2) (2022-09-18)
+
+## [2.10.1](https://github.com/revanced/revanced-cli/compare/v2.10.0...v2.10.1) (2022-09-09)
+
+# [2.10.0](https://github.com/revanced/revanced-cli/compare/v2.9.10...v2.10.0) (2022-09-08)
+
+
+### Features
+
+* Patch Options CLI implementation ([#132](https://github.com/revanced/revanced-cli/issues/132)) ([3f5345a](https://github.com/revanced/revanced-cli/commit/3f5345af6e45bfb6c91d52fc089ab18d81fdc998))
+
+## [2.9.10](https://github.com/revanced/revanced-cli/compare/v2.9.9...v2.9.10) (2022-09-08)
+
+
+### Bug Fixes
+
+* don't print same patch multiple times ([f4b0469](https://github.com/revanced/revanced-cli/commit/f4b04698d8c1717824e86f91da5e01c5021612da))
+
+## [2.9.9](https://github.com/revanced/revanced-cli/compare/v2.9.8...v2.9.9) (2022-09-08)
+
+## [2.9.8](https://github.com/revanced/revanced-cli/compare/v2.9.7...v2.9.8) (2022-09-08)
+
+
+### Bug Fixes
+
+* broken deprecation message ([e3e74ac](https://github.com/revanced/revanced-cli/commit/e3e74ac0e9a844f9d717a499bca09e575dd90435))
+
+## [2.9.7](https://github.com/revanced/revanced-cli/compare/v2.9.6...v2.9.7) (2022-09-08)
+
+## [2.9.6](https://github.com/revanced/revanced-cli/compare/v2.9.5...v2.9.6) (2022-09-07)
+
+## [2.9.5](https://github.com/revanced/revanced-cli/compare/v2.9.4...v2.9.5) (2022-09-01)
+
+
+### Bug Fixes
+
+* mount bind revanced.apk from magisk's mirror ([372470c](https://github.com/revanced/revanced-cli/commit/372470c77b82e8601ca523e87a2cfd44f79d0e31))
+
+## [2.9.4](https://github.com/revanced/revanced-cli/compare/v2.9.3...v2.9.4) (2022-08-31)
+
+## [2.9.3](https://github.com/revanced/revanced-cli/compare/v2.9.2...v2.9.3) (2022-08-14)
+
 ## [2.9.2](https://github.com/revanced/revanced-cli/compare/v2.9.1...v2.9.2) (2022-08-07)
 
 ## [2.9.1](https://github.com/revanced/revanced-cli/compare/v2.9.0...v2.9.1) (2022-08-04)

build.gradle.kts

@@ -23,14 +23,14 @@ repositories {
 }
 
 dependencies {
-    implementation(kotlin("stdlib"))
     implementation(kotlin("reflect"))
 
-    implementation("app.revanced:revanced-patcher:3.3.2")
-    implementation("info.picocli:picocli:4.6.3")
-    implementation("com.android.tools.build:apksig:7.2.1")
+    implementation("app.revanced:revanced-patcher:6.3.2")
+    implementation("info.picocli:picocli:4.7.0")
     implementation("com.github.revanced:jadb:master-SNAPSHOT") // updated fork
+    implementation("com.android.tools.build:apksig:7.2.1")
     implementation("org.bouncycastle:bcpkix-jdk15on:1.70")
+    implementation("cc.ekblad:4koma:1.1.0")
 }
 
 tasks {
@@ -40,8 +40,11 @@ tasks {
     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.

gradle.properties

@@ -1,2 +1,2 @@
 kotlin.code.style = official
-version = 2.9.2
+version = 2.20.0-dev.1

package.json

@@ -0,0 +1,8 @@
+{
+  "devDependencies": {
+    "@semantic-release/changelog": "^6.0.2",
+    "@semantic-release/git": "^10.0.1",
+    "gradle-semantic-release-plugin": "^1.7.4",
+    "semantic-release": "^19.0.5"
+  }
+}

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

@@ -10,7 +10,8 @@ import app.revanced.patcher.PatcherOptions
 import app.revanced.patcher.extensions.PatchExtensions.compatiblePackages
 import app.revanced.patcher.extensions.PatchExtensions.description
 import app.revanced.patcher.extensions.PatchExtensions.patchName
-import app.revanced.patcher.util.patch.impl.JarPatchBundle
+import app.revanced.patcher.util.patch.PatchBundle
+import app.revanced.utils.OptionsLoader
 import app.revanced.utils.adb.Adb
 import picocli.CommandLine.*
 import java.io.File
@@ -48,9 +49,12 @@ 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")
+
         @ArgGroup(exclusive = false)
         var listingArgs: ListingArgs? = null
 
@@ -59,7 +63,7 @@ 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"])
@@ -67,9 +71,6 @@ 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 {
@@ -83,14 +84,11 @@ 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>()
 
-        @Option(names = ["-r", "--resource-patcher"], description = ["Disable patching resources"])
-        var disableResourcePatching: Boolean = false
-
         @Option(names = ["--experimental"], description = ["Disable patch version compatibility patch"])
         var experimental: Boolean = false
 
@@ -123,26 +121,22 @@ internal object MainCommand : Runnable {
     }
 
     override fun run() {
-        if (args.patchArgs?.listingArgs?.listOnly == true) {
-            printListOfPatches()
-            return
-        }
-
-        if (args.uninstall) {
-            uninstall()
-            return
-        }
+        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
 
-        // the file to write to
-        val outputFile = File(pArgs.outputPath)
+        val allPatches = args.patchArgs!!.patchBundles.flatMap { bundle ->
+            PatchBundle.Jar(bundle).loadPatches()
+        }
+
+        OptionsLoader.init(args.patchArgs!!.options, allPatches)
 
         val patcher = app.revanced.patcher.Patcher(
             PatcherOptions(
-                args.inputFile,
+                args.inputFile.also { if (!it.exists()) return logger.error("Input file ${args.inputFile} does not exist.") },
                 pArgs.cacheDirectory,
-                !pArgs.disableResourcePatching,
                 pArgs.aaptPath,
                 pArgs.cacheDirectory,
                 PatcherLogger
@@ -151,19 +145,17 @@ internal object MainCommand : Runnable {
 
         // prepare adb
         val adb: Adb? = args.deploy?.let {
-            Adb(outputFile, patcher.data.packageMetadata.packageName, args.deploy!!, !pArgs.mount)
+            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)
+        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) {
@@ -209,26 +201,23 @@ internal object MainCommand : Runnable {
     }
 
     private fun uninstall() {
-        // temporarily get package name using Patcher method
-        // fix: abstract options in patcher
-        val patcher = app.revanced.patcher.Patcher(
-            PatcherOptions(
-                args.inputFile,
-                "uninstaller-cache",
+        val adb: Adb? = args.deploy?.let {
+            Adb(
+                File("placeholder_file"),
+                app.revanced.patcher.Patcher(PatcherOptions(args.inputFile, "")).context.packageMetadata.packageName,
+                args.deploy!!,
                 false
             )
-        )
-        File("uninstaller-cache").deleteRecursively()
-
-        val adb: Adb? = args.deploy?.let {
-            Adb(File("placeholder_file"), patcher.data.packageMetadata.packageName, args.deploy!!, false)
         }
         adb?.uninstall()
     }
 
     private fun printListOfPatches() {
-        for (patchBundlePath in args.patchArgs?.patchBundles!!) for (patch in JarPatchBundle(patchBundlePath).loadPatches()) {
-            for (compatiblePackage in patch.compatiblePackages!!) {
+        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) {
@@ -236,22 +225,24 @@ 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 = ", ")
                         append("\t")
                         append(compatibleVersions)
                     }
-
                 }
+
+                logged.add(patch.patchName)
                 logger.info(packageEntryStr)
             }
         }

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

@@ -1,48 +1,24 @@
 package app.revanced.cli.patcher
 
-import app.revanced.cli.command.MainCommand.args
-import app.revanced.cli.command.MainCommand.logger
-import app.revanced.utils.filesystem.ZipFileSystemUtils
+import app.revanced.patcher.PatcherResult
+import app.revanced.patcher.data.Context
+import app.revanced.patcher.patch.Patch
 import app.revanced.utils.patcher.addPatchesFiltered
 import app.revanced.utils.patcher.applyPatchesVerbose
 import app.revanced.utils.patcher.mergeFiles
-import java.io.File
-import java.nio.file.Files
 
 internal object Patcher {
-    internal fun start(patcher: app.revanced.patcher.Patcher, output: File) {
-        val inputFile = args.inputFile
-        val args = args.patchArgs?.patchingArgs!!
-
+    internal fun start(
+        patcher: app.revanced.patcher.Patcher,
+        allPatches: List<Class<out Patch<Context>>>
+    ): PatcherResult {
         // merge files like necessary integrations
         patcher.mergeFiles()
         // add patches, but filter incompatible or excluded patches
-        patcher.addPatchesFiltered()
+        patcher.addPatchesFiltered(allPatches)
         // 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())
-            }
-
-            if (!args.disableResourcePatching) {
-                logger.info("Writing resources...")
-
-                ZipFileSystemUtils(result.resourceFile!!).use { resourceFileSystem ->
-                    val resourceFiles = resourceFileSystem.getFile(File.separator)
-                    outputFileSystem.writePathRecursively(resourceFiles)
-                }
-            }
-
-            result.doNotCompress?.let { outputFileSystem.uncompress(*it.toTypedArray()) }
-        }
+        return patcher.save()
     }
 }

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

@@ -0,0 +1,77 @@
+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/Constants.kt

@@ -9,7 +9,7 @@ internal object Constants {
     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 = "monkey -p $PLACEHOLDER 1 && kill ${'$'}($COMMAND_PID_OF $PLACEHOLDER)"
+    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"
@@ -35,7 +35,7 @@ internal object Constants {
 
     // unmount command
     internal const val COMMAND_UMOUNT =
-        "stock_path=${'$'}( pm path $PLACEHOLDER | grep base | sed 's/package://g' ) && umount -l ${'$'}stock_path"
+        "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 $PATH_MOUNT"
@@ -44,12 +44,14 @@ internal object Constants {
     internal val CONTENT_MOUNT_SCRIPT =
         """
             #!/system/bin/sh
+            MAGISKTMP="${'$'}(magisk --path)" || MAGISKTMP=/sbin
+            MIRROR="${'$'}MAGISKTMP/.magisk/mirror"
             while [ "${'$'}(getprop sys.boot_completed | tr -d '\r')" != "1" ]; do sleep 1; done
             
             base_path="$PATH_REVANCED_APP"
             stock_path=${'$'}( pm path $PLACEHOLDER | grep base | sed 's/package://g' )
 
             chcon u:object_r:apk_data_file:s0  ${'$'}base_path
-            mount -o bind ${'$'}base_path ${'$'}stock_path
+            mount -o bind ${'$'}MIRROR${'$'}base_path ${'$'}stock_path
         """.trimIndent()
 }

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

@@ -4,64 +4,61 @@ import app.revanced.cli.command.MainCommand
 import app.revanced.cli.command.MainCommand.args
 import app.revanced.cli.command.MainCommand.logger
 import app.revanced.patcher.Patcher
-import app.revanced.patcher.data.Data
+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
-import app.revanced.patcher.util.patch.impl.JarPatchBundle
 
-fun Patcher.addPatchesFiltered() {
-    val packageName = this.data.packageMetadata.packageName
-    val packageVersion = this.data.packageMetadata.packageVersion
+fun Patcher.addPatchesFiltered(allPatches: List<Class<out Patch<Context>>>) {
+    val packageName = this.context.packageMetadata.packageName
+    val packageVersion = this.context.packageMetadata.packageVersion
 
-    args.patchArgs?.patchBundles!!.forEach { bundle ->
-        val includedPatches = mutableListOf<Class<out Patch<Data>>>()
-        JarPatchBundle(bundle).loadPatches().forEach patch@{ patch ->
-            val compatiblePackages = patch.compatiblePackages
-            val patchName = patch.patchName
+    val 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"
+        val prefix = "Skipping $patchName"
 
-            val args = MainCommand.args.patchArgs?.patchingArgs!!
-
-            if (args.excludedPatches.contains(patchName)) {
-                logger.info("$prefix: Explicitly excluded")
-                return@patch
-            } else if ((!patch.include || args.defaultExclude) && !args.includedPatches.contains(patchName)) {
-                logger.info("$prefix: Not explicitly included")
-                return@patch
+        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 (compatiblePackages == null) logger.warn("$prefix: Missing compatibility annotation. Continuing.")
-            else {
-                if (!compatiblePackages.any { it.name == packageName }) {
-                    logger.warn("$prefix: Incompatible with $packageName. This patch is only compatible with ${
-                        compatiblePackages.joinToString(
-                            ", "
-                        ) { it.name }
-                    }")
-                    return@patch
-                }
-
-                if (!(args.experimental || compatiblePackages.any { it.versions.isEmpty() || it.versions.any { version -> version == packageVersion } })) {
-                    val compatibleWith = compatiblePackages.map { _package ->
-                        "${_package.name}: ${_package.versions.joinToString(", ")}"
-                    }.joinToString(";")
-                    logger.warn("$prefix: Incompatible with version $packageVersion. This patch is only compatible with version $compatibleWith")
-                    return@patch
+            if (!(args.experimental || compatiblePackages.any { it.versions.isEmpty() || it.versions.any { version -> version == packageVersion } })) {
+                val compatibleWith = compatiblePackages.joinToString(";") { _package ->
+                    "${_package.name}: ${_package.versions.joinToString(", ")}"
                 }
+                logger.warn("$prefix: Incompatible with version $packageVersion. This patch is only compatible with version $compatibleWith")
+                return@patchLoop
             }
-
-            logger.trace("Adding $patchName")
-            includedPatches.add(patch)
         }
-        this.addPatches(includedPatches)
+
+        if (args.excludedPatches.contains(patchName)) {
+            logger.info("$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.applyPatches().forEach { (patch, result) ->
+    this.executePatches().forEach { (patch, result) ->
         if (result.isSuccess) {
             logger.info("$patch succeeded")
             return@forEach

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

@@ -1,10 +1,6 @@
 package app.revanced.utils.signing.align.zip.structures
 
-import app.revanced.utils.signing.align.zip.getUShort
-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.signing.align.zip.*
 import java.io.DataInput
 import java.nio.ByteBuffer
 import java.nio.ByteOrder
@@ -13,12 +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,
@@ -26,7 +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
@@ -41,6 +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()
 
@@ -59,7 +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()
@@ -67,7 +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())
@@ -81,7 +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,
@@ -138,8 +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)
@@ -166,5 +186,4 @@ data class ZipEntry(
         buffer.flip()
         return buffer
     }
-}
-
+}