chore(release): 4.1.0-dev.3 [skip ci]

# [4.1.0-dev.3](https://github.com/ReVanced/revanced-cli/compare/v4.1.0-dev.2...v4.1.0-dev.3) (2023-11-03)

.github/ISSUE_TEMPLATE/bug-issue.yml

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

.github/ISSUE_TEMPLATE/bug-report.yml

@@ -0,0 +1,49 @@
+name: 🐞 Bug report
+description: Report a bug or an issue.
+title: 'bug: '
+labels: ['Bug report']
+body:
+  - type: markdown
+    attributes:
+      value: |
+        # ReVanced CLI bug report
+
+        Please check for existing bug reports
+        [here](https://github.com/ReVanced/revanced-cli/labels/Bug%20report)
+        before creating a new one.
+
+  - type: textarea
+    attributes:
+      label: Bug description
+      description: |
+        - Describe your bug in detail
+        - Add steps to reproduce the bug if possible (Step 1. ... Step 2. ...)
+        - Add images and videos if possible
+        - List used patches if applicable
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Error logs
+      description: Exceptions can be captured by running `logcat | grep AndroidRuntime` in a shell.
+      render: shell
+  - type: textarea
+    attributes:
+      label: Solution
+      description: If applicable, add a possible solution to the bug.
+  - type: textarea
+    attributes:
+      label: Additional context
+      description: Add additional context here.
+  - type: checkboxes
+    id: acknowledgements
+    attributes:
+      label: Acknowledgements
+      description: Your issue will be closed if you don't follow the checklist below.
+      options:
+        - label: This request is not a duplicate of an existing issue.
+          required: true
+        - label: I have chosen an appropriate title.
+          required: true
+        - label: All requested information has been provided properly.
+          required: true

.github/ISSUE_TEMPLATE/config.yml

@@ -1,8 +1,5 @@
 blank_issues_enabled: false
 contact_links:
-  - name: 📃 Documentation
-    url: https://github.com/revanced/revanced-documentation/
-    about: Don't know how or where to start? Check out our documentation!
   - name: 🗨 Discussions
     url: https://github.com/revanced/revanced-suggestions/discussions
-    about: Got something you think should change or be added? Search for or start a new discussion!
+    about: Have something unspecific to ReVanced CLI in mind? Search for or start a new discussion!

.github/ISSUE_TEMPLATE/feature-issue.yml

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

.github/ISSUE_TEMPLATE/feature-request.yml

@@ -0,0 +1,45 @@
+name: ⭐ Feature request
+description: Create a detailed request for a new feature.
+title: 'feat: '
+labels: ['Feature request']
+body:
+  - type: markdown
+    attributes:
+      value: |
+        # ReVanced CLI feature request
+
+        Please check for existing feature requests
+        [here](https://github.com/ReVanced/revanced-cli/labels/Feature%20request)
+        before creating a new one.
+
+  - type: textarea
+    attributes:
+      label: Feature description
+      description: |
+        - Describe your feature in detail
+        - Add images, videos, links, examples, references, etc. if possible
+        - Add the target application name in case you request a new patch
+  - type: textarea
+    attributes:
+      label: Motivation
+      description: |
+        A strong motivation is necessary for a feature request to be considered.
+        
+        - Why should this feature be implemented? 
+        - What is the explicit use case?
+        - What are the benefits?
+        - What makes this feature important?
+    validations:
+      required: true
+  - type: checkboxes
+    id: acknowledgements
+    attributes:
+      label: Acknowledgements
+      description: Your issue will be closed if you don't follow the checklist below.
+      options:
+        - label: This request is not a duplicate of an existing issue.
+          required: true
+        - label: I have chosen an appropriate title.
+          required: true
+        - label: All requested information has been provided properly.
+          required: true

.github/workflows/pull_request.yml

@@ -1,4 +1,4 @@
-name: PR to main
+name: Open a PR to main
 
 on:
   push:
@@ -7,7 +7,7 @@ on:
   workflow_dispatch:
 
 env:
-  MESSAGE: merge branch `${{ github.head_ref || github.ref_name }}` to `main`
+  MESSAGE: Merge branch `${{ github.head_ref || github.ref_name }}` to `main`
 
 jobs:
   pull-request:
@@ -15,7 +15,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
       - name: Open pull request
         uses: repo-sync/pull-request@v2
         with:

.github/workflows/release.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           # Make sure the release step uses its own credentials:
           # https://github.com/cycjimmy/semantic-release-action#private-packages

CHANGELOG.md

@@ -1,3 +1,183 @@
+# [4.1.0-dev.3](https://github.com/ReVanced/revanced-cli/compare/v4.1.0-dev.2...v4.1.0-dev.3) (2023-11-03)
+
+# [4.1.0-dev.2](https://github.com/ReVanced/revanced-cli/compare/v4.1.0-dev.1...v4.1.0-dev.2) (2023-11-03)
+
+
+### Features
+
+* Include or exclude patches by their index in relation to supplied patch bundles ([b2055ce](https://github.com/ReVanced/revanced-cli/commit/b2055ce07df3ab9a9f3f73ab17d8c2cf02f2ae62))
+
+
+### Performance Improvements
+
+* Use a `HashSet` to check for included and excluded patches ([616d14f](https://github.com/ReVanced/revanced-cli/commit/616d14f0097c1ee7ba6dc07be417590f6418e8e5))
+
+# [4.1.0-dev.1](https://github.com/ReVanced/revanced-cli/compare/v4.0.3-dev.2...v4.1.0-dev.1) (2023-11-03)
+
+
+### Features
+
+* List patches which are compatible with any app ([#297](https://github.com/ReVanced/revanced-cli/issues/297)) ([0139dfe](https://github.com/ReVanced/revanced-cli/commit/0139dfe0bfa06a13f56dc03e7718aaf644029614))
+
+## [4.0.3-dev.2](https://github.com/ReVanced/revanced-cli/compare/v4.0.3-dev.1...v4.0.3-dev.2) (2023-10-30)
+
+## [4.0.3-dev.1](https://github.com/ReVanced/revanced-cli/compare/v4.0.2...v4.0.3-dev.1) (2023-10-23)
+
+## [4.0.2](https://github.com/ReVanced/revanced-cli/compare/v4.0.1...v4.0.2) (2023-10-12)
+
+
+### Bug Fixes
+
+* Move file to output even when mounting ([59dfc98](https://github.com/ReVanced/revanced-cli/commit/59dfc988e351374eb718923d19bd9bdd94e8d3c0))
+* Use punctuation in option descriptions ([da4469f](https://github.com/ReVanced/revanced-cli/commit/da4469f402c26ad95898404236b0acf0202907e2))
+
+
+### Performance Improvements
+
+* Use multiple threads for writing dex files ([28648a1](https://github.com/ReVanced/revanced-cli/commit/28648a1c53520eef8c799504ff61a35947f878b8))
+
+## [4.0.2-dev.3](https://github.com/ReVanced/revanced-cli/compare/v4.0.2-dev.2...v4.0.2-dev.3) (2023-10-10)
+
+
+### Bug Fixes
+
+* Move file to output even when mounting ([59dfc98](https://github.com/ReVanced/revanced-cli/commit/59dfc988e351374eb718923d19bd9bdd94e8d3c0))
+
+## [4.0.2-dev.2](https://github.com/ReVanced/revanced-cli/compare/v4.0.2-dev.1...v4.0.2-dev.2) (2023-10-10)
+
+
+### Performance Improvements
+
+* Use multiple threads for writing dex files ([28648a1](https://github.com/ReVanced/revanced-cli/commit/28648a1c53520eef8c799504ff61a35947f878b8))
+
+## [4.0.2-dev.1](https://github.com/ReVanced/revanced-cli/compare/v4.0.1...v4.0.2-dev.1) (2023-10-08)
+
+
+### Bug Fixes
+
+* Use punctuation in option descriptions ([da4469f](https://github.com/ReVanced/revanced-cli/commit/da4469f402c26ad95898404236b0acf0202907e2))
+
+## [4.0.1](https://github.com/ReVanced/revanced-cli/compare/v4.0.0...v4.0.1) (2023-10-08)
+
+
+### Bug Fixes
+
+* Correct warning message ([ba573f7](https://github.com/ReVanced/revanced-cli/commit/ba573f73d0e310fdeb8be2831fd40a7188473fff))
+
+## [4.0.1-dev.1](https://github.com/ReVanced/revanced-cli/compare/v4.0.0...v4.0.1-dev.1) (2023-10-07)
+
+
+### Bug Fixes
+
+* Correct warning message ([e4e339d](https://github.com/ReVanced/revanced-cli/commit/e4e339dff40542d6265de59496545c859312cf11))
+
+# [4.0.0](https://github.com/ReVanced/revanced-cli/compare/v3.1.1...v4.0.0) (2023-10-04)
+
+
+### Bug Fixes
+
+* Check, if mounting is possible ([3e13fb5](https://github.com/ReVanced/revanced-cli/commit/3e13fb5d56eb2a90c2a4a1ddfc05852b1f70add5))
+* Delete temporal files if it exists ([a022feb](https://github.com/ReVanced/revanced-cli/commit/a022febd0c70807ddc3fa9948207a2a70d5191da))
+* Do not sign if mounting ([578e16b](https://github.com/ReVanced/revanced-cli/commit/578e16b099fddfd2bb56accb225d04dfcd409b0c))
+* Filter logs correctly ([43fc20d](https://github.com/ReVanced/revanced-cli/commit/43fc20d90e0a694b231b17bb7d9ecfa22bb5d9a0))
+* Log correct options command ([#262](https://github.com/ReVanced/revanced-cli/issues/262)) ([96c196d](https://github.com/ReVanced/revanced-cli/commit/96c196dcb14e37ad91b751af61ee8382547c1ca3))
+* Log logs with levels over warning to error output stream ([075f6ad](https://github.com/ReVanced/revanced-cli/commit/075f6ad56528a667dca1f0bed704cf7e5381026f))
+* Only open files for reading and writing if writeable ([3846f72](https://github.com/ReVanced/revanced-cli/commit/3846f721ca015ab39a7e4b8d3f3d61163a6f1650))
+* Only set options for filtered patches ([64d9127](https://github.com/ReVanced/revanced-cli/commit/64d9127291ea9a8abe21a0e82721721495094472))
+
+
+### Features
+
+* Add function to get the most common compatible version ([77d9173](https://github.com/ReVanced/revanced-cli/commit/77d91735ffbbd6e733f08176f535bfd39ece0c29))
+* Add option to filter patches to be listed by package name ([50c0f98](https://github.com/ReVanced/revanced-cli/commit/50c0f98ce5927e07839437a2e550aa85f5a7e62d))
+* Add option to warn about patches not being found in supplied patch bundles ([e46d855](https://github.com/ReVanced/revanced-cli/commit/e46d85564320f46c6faa54b2d3fa7fca3fa60019))
+* Add ReVanced Library subproject ([#265](https://github.com/ReVanced/revanced-cli/issues/265)) ([157278c](https://github.com/ReVanced/revanced-cli/commit/157278c9ba25f0f786c5fe58e3e23f6890107118))
+* Do not format patch names ([80a8d88](https://github.com/ReVanced/revanced-cli/commit/80a8d88406b2b04d13dca4fb0d7d7d62e1910317))
+* Extend signing API ([592dc1c](https://github.com/ReVanced/revanced-cli/commit/592dc1c64ae4078e73bb71eba11380b301c79dea))
+* Improve option descriptions ([d5ea5a0](https://github.com/ReVanced/revanced-cli/commit/d5ea5a0ab1cc015730063e5be94ee18bd88cc906))
+* Log stacktrace in new line ([c67e3c7](https://github.com/ReVanced/revanced-cli/commit/c67e3c70c7eaa514cde1bebe775a2216bc4a6074))
+* Use ReVanced Library in ReVanced CLI ([7794327](https://github.com/ReVanced/revanced-cli/commit/7794327a11e8a0e0f28176cd45fad797b924c45f))
+* Word log message better ([6942b22](https://github.com/ReVanced/revanced-cli/commit/6942b22a68de5e991987ea89882915917aec93a3))
+
+
+### Performance Improvements
+
+* Do not check, if the options file exists twice ([e3c5550](https://github.com/ReVanced/revanced-cli/commit/e3c55507cf52e697b9ce9d59decc1cbe4cfe5b43))
+
+
+### BREAKING CHANGES
+
+* This changes many signatures of existing APIs and adds new functions for signing
+* This changes the log handler signature
+
+# [4.0.0-dev.5](https://github.com/ReVanced/revanced-cli/compare/v4.0.0-dev.4...v4.0.0-dev.5) (2023-10-04)
+
+
+### Bug Fixes
+
+* Only set options for filtered patches ([64d9127](https://github.com/ReVanced/revanced-cli/commit/64d9127291ea9a8abe21a0e82721721495094472))
+
+
+### Performance Improvements
+
+* Do not check, if the options file exists twice ([e3c5550](https://github.com/ReVanced/revanced-cli/commit/e3c55507cf52e697b9ce9d59decc1cbe4cfe5b43))
+
+# [4.0.0-dev.4](https://github.com/ReVanced/revanced-cli/compare/v4.0.0-dev.3...v4.0.0-dev.4) (2023-10-01)
+
+# [4.0.0-dev.3](https://github.com/ReVanced/revanced-cli/compare/v4.0.0-dev.2...v4.0.0-dev.3) (2023-09-27)
+
+# [4.0.0-dev.2](https://github.com/ReVanced/revanced-cli/compare/v4.0.0-dev.1...v4.0.0-dev.2) (2023-09-24)
+
+
+### Features
+
+* Improve option descriptions ([d5ea5a0](https://github.com/ReVanced/revanced-cli/commit/d5ea5a0ab1cc015730063e5be94ee18bd88cc906))
+
+# [4.0.0-dev.1](https://github.com/ReVanced/revanced-cli/compare/v3.1.2-dev.1...v4.0.0-dev.1) (2023-09-23)
+
+
+### Bug Fixes
+
+* Check, if mounting is possible ([3e13fb5](https://github.com/ReVanced/revanced-cli/commit/3e13fb5d56eb2a90c2a4a1ddfc05852b1f70add5))
+* Delete temporal files if it exists ([a022feb](https://github.com/ReVanced/revanced-cli/commit/a022febd0c70807ddc3fa9948207a2a70d5191da))
+* Do not sign if mounting ([578e16b](https://github.com/ReVanced/revanced-cli/commit/578e16b099fddfd2bb56accb225d04dfcd409b0c))
+* Filter logs correctly ([43fc20d](https://github.com/ReVanced/revanced-cli/commit/43fc20d90e0a694b231b17bb7d9ecfa22bb5d9a0))
+* Log logs with levels over warning to error output stream ([075f6ad](https://github.com/ReVanced/revanced-cli/commit/075f6ad56528a667dca1f0bed704cf7e5381026f))
+* Only open files for reading and writing if writeable ([3846f72](https://github.com/ReVanced/revanced-cli/commit/3846f721ca015ab39a7e4b8d3f3d61163a6f1650))
+
+
+### Features
+
+* Add function to get the most common compatible version ([77d9173](https://github.com/ReVanced/revanced-cli/commit/77d91735ffbbd6e733f08176f535bfd39ece0c29))
+* Add option to filter patches to be listed by package name ([50c0f98](https://github.com/ReVanced/revanced-cli/commit/50c0f98ce5927e07839437a2e550aa85f5a7e62d))
+* Add option to warn about patches not being found in supplied patch bundles ([e46d855](https://github.com/ReVanced/revanced-cli/commit/e46d85564320f46c6faa54b2d3fa7fca3fa60019))
+* Add ReVanced Library subproject ([#265](https://github.com/ReVanced/revanced-cli/issues/265)) ([157278c](https://github.com/ReVanced/revanced-cli/commit/157278c9ba25f0f786c5fe58e3e23f6890107118))
+* Do not format patch names ([80a8d88](https://github.com/ReVanced/revanced-cli/commit/80a8d88406b2b04d13dca4fb0d7d7d62e1910317))
+* Extend signing API ([592dc1c](https://github.com/ReVanced/revanced-cli/commit/592dc1c64ae4078e73bb71eba11380b301c79dea))
+* Log stacktrace in new line ([c67e3c7](https://github.com/ReVanced/revanced-cli/commit/c67e3c70c7eaa514cde1bebe775a2216bc4a6074))
+* Use ReVanced Library in ReVanced CLI ([7794327](https://github.com/ReVanced/revanced-cli/commit/7794327a11e8a0e0f28176cd45fad797b924c45f))
+* Word log message better ([6942b22](https://github.com/ReVanced/revanced-cli/commit/6942b22a68de5e991987ea89882915917aec93a3))
+
+
+### BREAKING CHANGES
+
+* This changes many signatures of existing APIs and adds new functions for signing
+* This changes the log handler signature
+
+# [3.2.0-dev.1](https://github.com/ReVanced/revanced-cli/compare/v3.1.2-dev.1...v3.2.0-dev.1) (2023-09-20)
+
+
+### Features
+
+* Log stacktrace in new line ([c67e3c7](https://github.com/ReVanced/revanced-cli/commit/c67e3c70c7eaa514cde1bebe775a2216bc4a6074))
+
+## [3.1.2-dev.1](https://github.com/ReVanced/revanced-cli/compare/v3.1.1...v3.1.2-dev.1) (2023-09-12)
+
+
+### Bug Fixes
+
+* Log correct options command ([#262](https://github.com/ReVanced/revanced-cli/issues/262)) ([96c196d](https://github.com/ReVanced/revanced-cli/commit/96c196dcb14e37ad91b751af61ee8382547c1ca3))
+
 ## [3.1.1](https://github.com/ReVanced/revanced-cli/compare/v3.1.0...v3.1.1) (2023-09-09)
 
 

CONTRIBUTING.md

@@ -0,0 +1,79 @@
+<p align="center">
+  <picture>
+    <source
+      width="256px"
+      media="(prefers-color-scheme: dark)"
+      srcset="assets/revanced-headline/revanced-headline-vertical-dark.svg"
+    >
+    <img 
+      src="assets/revanced-headline/revanced-headline-vertical-light.svg"
+    >
+  </picture>
+  <br>
+  <a href="https://revanced.app/">
+       <img height="24px" src="assets/revanced-logo/revanced-logo-round.svg" />
+   </a>&nbsp;&nbsp;&nbsp;
+   <a href="https://github.com/revanced">
+       <picture>
+           <source height="24px" media="(prefers-color-scheme: dark)" srcset="https://i.ibb.co/dMMmCrW/Git-Hub-Mark.png" />
+           <img height="24px" src="https://i.ibb.co/9wV3HGF/Git-Hub-Mark-Light.png" />
+       </picture>
+   </a>&nbsp;&nbsp;&nbsp;
+   <a href="http://revanced.app/discord">
+       <img height="24px" src="https://user-images.githubusercontent.com/13122796/178032563-d4e084b7-244e-4358-af50-26bde6dd4996.png" />
+   </a>&nbsp;&nbsp;&nbsp;
+   <a href="https://reddit.com/r/revancedapp">
+       <img height="24px" src="https://user-images.githubusercontent.com/13122796/178032351-9d9d5619-8ef7-470a-9eec-2744ece54553.png" />
+   </a>&nbsp;&nbsp;&nbsp;
+   <a href="https://t.me/app_revanced">
+       <img height="24px" src="https://user-images.githubusercontent.com/13122796/178032213-faf25ab8-0bc3-4a94-a730-b524c96df124.png" />
+   </a>&nbsp;&nbsp;&nbsp;
+   <a href="https://twitter.com/revancedapp">
+       <img height="24px" src="https://user-images.githubusercontent.com/13122796/178032018-6da37214-7474-4641-a1da-7af7db3a31cd.png" />
+   </a>&nbsp;&nbsp;&nbsp;
+   <a href="https://www.youtube.com/@ReVanced">
+       <img height="24px" src="https://user-images.githubusercontent.com/13122796/178032714-c51c7492-0666-44ac-99c2-f003a695ab50.png" />
+   </a>&nbsp;&nbsp;&nbsp;
+   <br>
+   <br>
+   Continuing the legacy of Vanced
+</p>
+
+# 👋 Contribution guidelines
+
+This document describes how to contribute to ReVanced CLI.
+
+## 📖 Resources to help you get started
+
+* The [documentation](/docs) explains how to use ReVanced CLI
+* [Our backlog](https://github.com/orgs/ReVanced/projects/12) is where we keep track of what we're working on
+* [Issues](https://github.com/ReVanced/revanced-cli/issues) are where we keep track of bugs and feature requests
+
+## 🙏 Submitting a feature request
+
+Features can be requested by opening an issue using the
+[Feature request issue template](https://github.com/ReVanced/revanced-cli/issues/new?assignees=&labels=Feature+request&projects=&template=feature-request.yml&title=feat%3A+).
+
+> **Note**
+> Requests can be accepted or rejected at the discretion of maintainers of ReVanced CLI.
+> Good motivation has to be provided for a request to be accepted.
+
+## 🐞 Submitting a bug report
+
+If you encounter a bug while using ReVanced CLI, open an issue using the
+[Bug report issue template](https://github.com/ReVanced/revanced-cli/issues/new?assignees=&labels=Bug+report&projects=&template=bug-report.yml&title=bug%3A+).
+
+## 📝 How to contribute
+
+1. Before contributing, it is recommended to open an issue to discuss your change
+   with the maintainers of ReVanced CLI. This will help you determine whether your change is acceptable
+   and whether it is worth your time to implement it
+2. Development happens on the `dev` branch. Fork the repository and create your branch from `dev`
+3. Commit your changes.
+4. Submit a pull request to the `dev` branch of the repository and reference issues
+   that your pull request closes in the description of your pull request
+5. Our team will review your pull request and provide feedback. Once your pull request is approved,
+   it will be merged into the `dev` branch and will be included in the next release of ReVanced CLI
+
+❤️ Thank you for considering contributing to ReVanced CLI,
+ReVanced

README.md

@@ -1,3 +1,78 @@
+<p align="center">
+  <picture>
+    <source
+      width="256px"
+      media="(prefers-color-scheme: dark)"
+      srcset="assets/revanced-headline/revanced-headline-vertical-dark.svg"
+    >
+    <img 
+      src="assets/revanced-headline/revanced-headline-vertical-light.svg"
+    >
+  </picture>
+  <br>
+  <a href="https://revanced.app/">
+       <img height="24px" src="assets/revanced-logo/revanced-logo-round.svg" />
+   </a>&nbsp;&nbsp;&nbsp;
+   <a href="https://github.com/revanced">
+       <picture>
+           <source height="24px" media="(prefers-color-scheme: dark)" srcset="https://i.ibb.co/dMMmCrW/Git-Hub-Mark.png" />
+           <img height="24px" src="https://i.ibb.co/9wV3HGF/Git-Hub-Mark-Light.png" />
+       </picture>
+   </a>&nbsp;&nbsp;&nbsp;
+   <a href="http://revanced.app/discord">
+       <img height="24px" src="https://user-images.githubusercontent.com/13122796/178032563-d4e084b7-244e-4358-af50-26bde6dd4996.png" />
+   </a>&nbsp;&nbsp;&nbsp;
+   <a href="https://reddit.com/r/revancedapp">
+       <img height="24px" src="https://user-images.githubusercontent.com/13122796/178032351-9d9d5619-8ef7-470a-9eec-2744ece54553.png" />
+   </a>&nbsp;&nbsp;&nbsp;
+   <a href="https://t.me/app_revanced">
+       <img height="24px" src="https://user-images.githubusercontent.com/13122796/178032213-faf25ab8-0bc3-4a94-a730-b524c96df124.png" />
+   </a>&nbsp;&nbsp;&nbsp;
+   <a href="https://x.com/revancedapp">
+      <picture>
+         <source media="(prefers-color-scheme: dark)" srcset="https://user-images.githubusercontent.com/93124920/270180600-7c1b38bf-889b-4d68-bd5e-b9d86f91421a.png">
+         <img height="24px" src="https://user-images.githubusercontent.com/93124920/270108715-d80743fa-b330-4809-b1e6-79fbdc60d09c.png" />
+       <picture/>
+   </a>&nbsp;&nbsp;&nbsp;
+   <a href="https://www.youtube.com/@ReVanced">
+       <img height="24px" src="https://user-images.githubusercontent.com/13122796/178032714-c51c7492-0666-44ac-99c2-f003a695ab50.png" />
+   </a>
+   <br>
+   <br>
+   Continuing the legacy of Vanced
+</p>
+
+
 # 💻 ReVanced CLI
 
+![GitHub Workflow Status (with event)](https://img.shields.io/github/actions/workflow/status/ReVanced/revanced-cli/release.yml)
+![GPLv3 License](https://img.shields.io/badge/License-GPL%20v3-yellow.svg)
+
 Command line application to use ReVanced.
+
+## ❓ About
+
+ReVanced CLI is a command line application to patch apps using ReVanced.
+ReVanced CLI also comes with commands to uninstall or install patched apps and list patches from supplied patch bundles.
+
+## 🚀 Download
+
+You can download the most recent version of ReVanced CLI from 
+[here](https://github.com/ReVanced/revanced-cli/releases/latest). Learn how to use ReVanced CLI by following the [documentation](/docs).
+
+## 📚 Everything else
+
+### 📙 Contributing
+
+Thank you for considering contributing to ReVanced CLI.
+You can find the contribution guidelines [here](CONTRIBUTING.md).
+
+### 🛠️ Building
+
+In order to build ReVanced CLI, you can follow the [documentation](/docs).
+
+## 📜 Licence
+
+ReVanced CLI is licensed under the GPLv3 licence. Please see the [licence file](LICENSE) for more information.
+[tl;dr](https://www.tldrlegal.com/license/gnu-general-public-license-v3-gpl-3) you may copy, distribute and modify ReVanced CLI as long as you track changes/dates in source files.
+Any modifications to ReVanced CLI must also be made available under the GPL along with build & install instructions.

assets/revanced-logo/revanced-logo-round.svg

@@ -0,0 +1 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?><!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd"><svg width="100%" height="100%" viewBox="0 0 800 800" version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" xml:space="preserve" xmlns:serif="http://www.serif.com/" style="fill-rule:evenodd;clip-rule:evenodd;stroke-linejoin:round;stroke-miterlimit:2;"><g id="Logo"><g id="Ring"><circle id="Ring-Background" serif:id="Ring Background" cx="400" cy="400" r="400" style="fill:#1b1b1b;"/><path id="Ring1" serif:id="Ring" d="M400,0c220.766,0 400,179.234 400,400c-0,220.766 -179.234,400 -400,400c-220.766,-0 -400,-179.234 -400,-400c0,-220.766 179.234,-400 400,-400Zm-0,36c200.897,-0 364,163.103 364,364c0,200.897 -163.103,364 -364,364c-200.897,0 -364,-163.103 -364,-364c-0,-200.897 163.103,-364 364,-364Z" style="fill:url(#_Linear1);"/></g><g id="Shape"><path id="V-Shape" serif:id="V Shape" d="M538.74,269.872c1.481,-3.382 1.157,-7.283 -0.863,-10.373c-2.021,-3.091 -5.464,-4.954 -9.156,-4.954c-5.148,0 -10.435,0 -14.165,0c-3.1,0 -5.907,1.834 -7.153,4.672c-12.468,28.396 -78.273,178.273 -100.25,228.328c-1.246,2.838 -4.053,4.671 -7.154,4.671c-3.1,0 -5.907,-1.833 -7.153,-4.671c-21.977,-50.055 -87.782,-199.932 -100.25,-228.328c-1.246,-2.838 -4.053,-4.672 -7.153,-4.672c-3.73,0 -9.017,0 -14.164,0c-3.693,0 -7.135,1.863 -9.156,4.954c-2.02,3.09 -2.344,6.991 -0.863,10.373c23.557,53.766 101.872,232.519 117.871,269.034c1.743,3.979 5.674,6.549 10.018,6.549c6.293,-0 15.408,-0 21.701,-0c4.344,-0 8.275,-2.57 10.018,-6.549c15.999,-36.515 94.315,-215.268 117.872,-269.034Z" style="fill:#fff;"/><path id="Diamond" d="M408.119,395.312c-1.675,2.901 -4.77,4.688 -8.119,4.688c-3.349,-0 -6.444,-1.787 -8.119,-4.688c-16.997,-29.44 -56.156,-97.264 -73.153,-126.704c-1.675,-2.901 -1.675,-6.474 0,-9.375c1.675,-2.901 4.77,-4.688 8.119,-4.688c33.995,0 112.311,0 146.306,0c3.349,0 6.444,1.787 8.119,4.688c1.675,2.901 1.675,6.474 -0,9.375c-16.997,29.44 -56.156,97.264 -73.153,126.704Z" style="fill:url(#_Linear2);"/></g></g><defs><linearGradient id="_Linear1" x1="0" y1="0" x2="1" y2="0" gradientUnits="userSpaceOnUse" gradientTransform="matrix(4.89859e-14,800,-800,4.89859e-14,400.001,3.31681e-10)"><stop offset="0" style="stop-color:#f04e98;stop-opacity:1"/><stop offset="0.5" style="stop-color:#5f65d4;stop-opacity:1"/><stop offset="1" style="stop-color:#4e98f0;stop-opacity:1"/></linearGradient><linearGradient id="_Linear2" x1="0" y1="0" x2="1" y2="0" gradientUnits="userSpaceOnUse" gradientTransform="matrix(1.77155e-14,289.317,-282.535,1.73003e-14,400,254.545)"><stop offset="0" style="stop-color:#f04e98;stop-opacity:1"/><stop offset="0.5" style="stop-color:#5f65d4;stop-opacity:1"/><stop offset="1" style="stop-color:#4e98f0;stop-opacity:1"/></linearGradient></defs></svg>

build.gradle.kts

@@ -1,19 +1,23 @@
 plugins {
-    kotlin("jvm") version "1.8.20"
+    kotlin("jvm") version "1.9.10"
     alias(libs.plugins.shadow)
 }
 
 group = "app.revanced"
 
+repositories {
+    mavenCentral()
+    mavenLocal()
+    google()
+    maven { url = uri("https://jitpack.io") }
+}
+
 dependencies {
     implementation(libs.revanced.patcher)
-    implementation(libs.kotlin.reflect)
+    implementation(libs.revanced.library)
     implementation(libs.kotlinx.coroutines.core)
     implementation(libs.picocli)
-    implementation(libs.jadb) // Updated fork
-    implementation(libs.apksig)
-    implementation(libs.bcpkix.jdk15on)
-    implementation(libs.jackson.module.kotlin)
+
     testImplementation(libs.kotlin.test)
 }
 
@@ -46,12 +50,21 @@ tasks {
         dependsOn(shadowJar)
     }
 
-    // Dummy task to fix the Gradle semantic-release plugin.
-    // Remove this if you forked it to support building only.
-    // Tracking issue: https://github.com/KengoTODA/gradle-semantic-release-plugin/issues/435
+    /*
+    Dummy task to hack gradle-semantic-release-plugin to release this project.
+
+    Explanation:
+    SemVer is a standard for versioning libraries.
+    For that reason the semantic-release plugin uses the "publish" task to publish libraries.
+    However, this subproject is not a library, and the "publish" task is not available for this subproject.
+    Because semantic-release is not designed to handle this case, we need to hack it.
+
+    RE: https://github.com/KengoTODA/gradle-semantic-release-plugin/issues/435
+     */
+
     register<DefaultTask>("publish") {
-        group = "publish"
-        description = "Dummy task"
+        group = "publishing"
+        description = "Dummy task to hack gradle-semantic-release-plugin to release ReVanced CLI"
         dependsOn(build)
     }
 }

docs/0_prerequisites.md

@@ -1,14 +1,12 @@
 # 💼 Prerequisites
 
-To use ReVanced CLI, you will need to fulfil specific requirements.
+To use ReVanced CLI, you will need to fulfill specific requirements.
 
 ## 🤝 Requirements
 
 - Java SDK 11 (Azul Zulu JDK or OpenJDK)
 - [Android Debug Bridge (adb)](https://developer.android.com/studio/command-line/adb) if you want to install the patched APK file on your device
 - An ABI other than ARMv7 such as x86 or x86-64 (or a custom AAPT binary that supports ARMv7)
-- ReVanced Patches
-- ReVanced Integrations, if the patches require it
 
 ## ⏭️ Whats next
 

docs/1_usage.md

@@ -2,36 +2,17 @@
 
 Learn how to ReVanced CLI.
 
-## ⚡ Setup ADB
+## 🔨 Usage
 
-1. Ensure that ADB is working
+ReVanced CLI is divided into the following fundamental commands:
 
-   ```bash
-   adb shell exit
-   ```
-
-   Optionally, you can install the patched APK file on your device by mounting it on top of the original APK file. 
-   You will need root permissions for this. Check if you have root permissions by running the following command:
-
-   ```bash
-   adb shell su -c exit
-   ```
-
-2. Get your device's serial
-
-   ```bash
-   adb devices
-   ```
-
-## 🔨 Using ReVanced CLI
-
-- ### ⚙️ Show all available options for ReVanced CLI
+- ### 🚀 Show all available options for ReVanced CLI
 
   ```bash
   java -jar revanced-cli.jar -h
   ```
 
-- ### 📃 List patches from supplied patch bundles
+- ### 📃 List patches
 
   ```bash
   java -jar revanced-cli.jar list-patches \
@@ -41,65 +22,110 @@ Learn how to ReVanced CLI.
    revanced-patches.jar [<patch-bundle> ...]
   ```
 
-- ### ⚙️ Generate options from patches using ReVanced CLI
+- ### ⚙️ Generate options
 
   This will generate an `options.json` file for the patches from a list of supplied patch bundles.
   The file can be supplied to ReVanced CLI later on.
  
-- ```bash
+  ```bash
   java -jar revanced-cli.jar options \
    --path options.json \
    --overwrite \
    revanced-patches.jar [<patch-bundle> ...]
   ```
 
-  > **Note**: A default `options.json` file will be automatically generated, if it does not exist 
+  > [!NOTE]  
+  > A default `options.json` file will be automatically created, if it does not exist 
   without any need for intervention when using the `patch` command.
 
-- ### 💉 Use ReVanced CLI to patch an APK file but install without root permissions
+- ### 💉 Patch an app
 
-  This will install the patched APK file regularly on your device.
+  You can patch apps by supplying patch bundles and the app to patch.
+  After patching, ReVanced CLI can install the patched app on your device using two methods:
 
-  ```bash
-  java -jar revanced-cli.jar patch \
-   --patch-bundle revanced-patches.jar \
-   --out output.apk \
-   --device-serial <device-serial> \
-   input.apk
-  ```
+  > [!NOTE]  
+  > For ReVanced CLI to be able to install the patched app on your device, make sure ADB is working:
+  >
+  > ```bash
+  > adb shell exit
+  > ```
+  >
+  > To get your device's serial, run the following command:
+  >
+  > ```bash
+  > adb devices
+  > ```
+  >
+  > If you want to mount the patched app on top of the un-patched app, make sure you have root permissions:
+  >
+  > ```bash
+  > adb shell su -c exit
+  > ```
+  >
 
-- ### 👾 Use ReVanced CLI to patch an APK file but install with root permissions
+  > [!WARNING]  
+  > Some patches may require integrations
+  > such as [ReVanced Integrations](https://github.com/revanced/revanced-integrations).
+  > Supply them with the option `--merge`. ReVanced Patcher will automatically determine if they are necessary.
 
-  This will install the patched APK file on your device by mounting it on top of the original APK file.
+  - #### 👾 Patch an app and install it on your device regularly
 
-  ```bash
-  adb install input.apk
-  java -jar revanced-cli.jar patch \
-   --patch-bundle revanced-patches.jar \
-   --include some-other-patch \
-   --exclude some-patch \
-   --out patched-output.apk \
-   --device-serial <device-serial> \
-   --mount \
-   input.apk
-  ```
+    ```bash
+    java -jar revanced-cli.jar patch \
+     --patch-bundle revanced-patches.jar \
+     --out patched-app.apk \
+     --device-serial <device-serial> \
+     input.apk
+    ```
 
-  > **Note**: Some patches may require integrations
-  such as [ReVanced Integrations](https://github.com/revanced/revanced-integrations). 
-  Supply them with the option `--merge`. If any patches accepted by ReVanced Patcher require ReVanced Integrations, 
-  they will be merged into the APK file automatically.
+  - #### 👾 Patch an app and mount it on top of the un-patched app with root permissions
+  
+    > [!IMPORTANT]  
+    > Ensure sure the same app you are patching and mounting over is installed on your device:
+    > 
+    > ```bash
+    > adb install app.apk
+    > ```
+
+    > [!NOTE]  
+    > You can use the option `--ii` to include or `--ie` to exclude
+    > patches by their index in relation to supplied patch bundles,
+    > similarly to the option `--include` and `--exclude`.
+    > 
+    > This is useful in case two patches have the same name, and you need to include or exclude one of them.  
+    > The index of a patch is calculated by the position of the patch in the list of patches
+    > from patch bundles supplied using the option `--patch-bundle`.
+    > 
+    > You can list all patches with their indices using the command `list-patches`.
+    > 
+    > Keep in mind, that the indices can change based on the order of the patch bundles supplied,
+    > as well if the patch bundles are updated, because patches can be added or removed.
+
+    ```bash
+    java -jar revanced-cli.jar patch \
+     --patch-bundle revanced-patches.jar \
+     --include "Some patch" \
+     --ii 123 \
+     --exclude "Some other patch" \
+     --out patched-app.apk \
+     --device-serial <device-serial> \
+     --mount \
+     app.apk
+    ```
+
+- ### 🗑️ Uninstall an app
 
-- ### 🗑️ Uninstall a patched APK file
   ```bash
   java -jar revanced-cli.jar utility uninstall \
    --package-name <package-name> \
    <device-serial>
   ```
 
-  > **Note**: You can unmount an APK file
-  with the option `--unmount`.
+  > [!NOTE]  
+  > You can unmount an APK file
+  by adding the option `--unmount`.
 
-- ### ️ ⚙️ Manually install an APK file
+- ### ️ 📦 Install an app
 
   ```bash
   java -jar revanced-cli.jar utility install \
@@ -107,5 +133,6 @@ Learn how to ReVanced CLI.
    <device-serial>
   ```
 
-  > **Note**: You can mount an APK file 
-  by supplying the package name of the app to mount the supplied APK file to over the option `--mount`.
+  > [!NOTE]  
+  > You can mount an APK file 
+  > by supplying the package name of the app to mount the supplied APK file to over the option `--mount`.

gradle.properties

@@ -1,4 +1,4 @@
 org.gradle.parallel = true
 org.gradle.caching = true
 kotlin.code.style = official
-version = 3.1.1
+version = 4.1.0-dev.3

gradle/libs.versions.toml

@@ -1,25 +1,17 @@
 [versions]
 shadow = "8.1.1"
-apksig = "8.1.1"
-bcpkix-jdk15on = "1.70"
-jackson-module-kotlin = "2.14.3"
-jadb = "2531a28109"
-kotlin-reflect = "1.9.0"
 kotlin-test = "1.8.20-RC"
-kotlinx-coroutines-core = "1.7.1"
+kotlinx-coroutines-core = "1.7.3"
 picocli = "4.7.3"
-revanced-patcher = "14.2.1"
+revanced-patcher = "19.0.0"
+revanced-library = "1.2.0"
 
 [libraries]
-apksig = { module = "com.android.tools.build:apksig", version.ref = "apksig" }
-bcpkix-jdk15on = { module = "org.bouncycastle:bcpkix-jdk15on", version.ref = "bcpkix-jdk15on" }
-jackson-module-kotlin = { module = "com.fasterxml.jackson.module:jackson-module-kotlin", version.ref = "jackson-module-kotlin" }
-jadb = { module = "com.github.revanced:jadb", version.ref = "jadb" }
-kotlin-reflect = { module = "org.jetbrains.kotlin:kotlin-reflect", version.ref = "kotlin-reflect" }
 kotlin-test = { module = "org.jetbrains.kotlin:kotlin-test", version.ref = "kotlin-test" }
 kotlinx-coroutines-core = { module = "org.jetbrains.kotlinx:kotlinx-coroutines-core", version.ref = "kotlinx-coroutines-core" }
 picocli = { module = "info.picocli:picocli", version.ref = "picocli" }
 revanced-patcher = { module = "app.revanced:revanced-patcher", version.ref = "revanced-patcher" }
+revanced-library = { module = "app.revanced:revanced-library", version.ref = "revanced-library" }
 
 [plugins]
-shadow = { id = "com.github.johnrengelman.shadow", version.ref = "shadow" }
+shadow = { id = "com.github.johnrengelman.shadow", version.ref = "shadow" }

settings.gradle.kts

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

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

@@ -1,91 +1,123 @@
 package app.revanced.cli.command
 
 import app.revanced.patcher.PatchBundleLoader
-import app.revanced.patcher.annotation.Package
-import app.revanced.patcher.extensions.PatchExtensions.compatiblePackages
-import app.revanced.patcher.extensions.PatchExtensions.description
-import app.revanced.patcher.extensions.PatchExtensions.options
-import app.revanced.patcher.extensions.PatchExtensions.patchName
-import app.revanced.patcher.patch.PatchClass
-import app.revanced.patcher.patch.PatchOption
+import app.revanced.patcher.patch.Patch
+import app.revanced.patcher.patch.options.PatchOption
 import picocli.CommandLine.*
 import picocli.CommandLine.Help.Visibility.ALWAYS
 import java.io.File
 import java.util.logging.Logger
 
 
-@Command(name = "list-patches", description = ["List patches from supplied patch bundles"])
+@Command(name = "list-patches", description = ["List patches from supplied patch bundles."])
 internal object ListPatchesCommand : Runnable {
     private val logger = Logger.getLogger(ListPatchesCommand::class.java.name)
 
     @Parameters(
-        description = ["Paths to patch bundles"], arity = "1..*"
+        description = ["Paths to patch bundles."], arity = "1..*"
     )
     private lateinit var patchBundles: Array<File>
 
     @Option(
-        names = ["-d", "--with-descriptions"], description = ["List their descriptions"], showDefaultValue = ALWAYS
+        names = ["-d", "--with-descriptions"], description = ["List their descriptions."], showDefaultValue = ALWAYS
     )
     private var withDescriptions: Boolean = true
 
     @Option(
         names = ["-p", "--with-packages"],
-        description = ["List the packages the patches are compatible with"],
+        description = ["List the packages the patches are compatible with."],
         showDefaultValue = ALWAYS
     )
     private var withPackages: Boolean = false
 
     @Option(
         names = ["-v", "--with-versions"],
-        description = ["List the versions of the apps the patches are compatible with"],
+        description = ["List the versions of the apps the patches are compatible with."],
         showDefaultValue = ALWAYS
     )
     private var withVersions: Boolean = false
 
     @Option(
-        names = ["-o", "--with-options"], description = ["List the options of the patches"], showDefaultValue = ALWAYS
+        names = ["-o", "--with-options"], description = ["List the options of the patches."], showDefaultValue = ALWAYS
     )
     private var withOptions: Boolean = false
 
+    @Option(
+        names = ["-u", "--with-universal-patches"],
+        description = ["List patches which are compatible with any app."],
+        showDefaultValue = ALWAYS
+    )
+    private var withUniversalPatches: Boolean = true
+
+    @Option(
+        names = ["-i", "--index"],
+        description = ["List the index of of each patch in relation to the supplied patch bundles."],
+        showDefaultValue = ALWAYS
+    )
+    private var withIndex: Boolean = true
+
+    @Option(
+        names = ["-f", "--filter-package-name"], description = ["Filter patches by package name."]
+    )
+    private var packageName: String? = null
+
     override fun run() {
-        fun Package.buildString() = buildString {
-            if (withVersions && versions.isNotEmpty()) {
+        fun Patch.CompatiblePackage.buildString() = buildString {
+            if (withVersions && versions != null) {
                 appendLine("Package name: $name")
                 appendLine("Compatible versions:")
-                append(versions.joinToString("\n") { version -> version }.prependIndent("\t"))
+                append(versions!!.joinToString("\n") { version -> version }.prependIndent("\t"))
             } else append("Package name: $name")
         }
 
         fun PatchOption<*>.buildString() = buildString {
             appendLine("Title: $title")
-            appendLine("Description: $description")
-
-            value?.let {
+            description?.let { appendLine("Description: $it") }
+            default?.let {
                 appendLine("Key: $key")
-                append("Value: $it")
+                append("Default: $it")
             } ?: append("Key: $key")
-        }
 
-        fun PatchClass.buildString() = buildString {
-            append("Name: $patchName")
-
-            if (withDescriptions) append("\nDescription: $description")
-
-            if (withOptions && options != null) {
-                appendLine("\nOptions:")
-                append(
-                    options!!.joinToString("\n\n") { option -> option.buildString() }.prependIndent("\t")
-                )
-            }
-
-            if (withPackages && compatiblePackages != null) {
-                appendLine("\nCompatible packages:")
-                append(
-                    compatiblePackages!!.joinToString("\n") { it.buildString() }.prependIndent("\t")
-                )
+            values?.let { values ->
+                appendLine("\nValid values:")
+                append(values.map { "${it.value} (${it.key})" }.joinToString("\n").prependIndent("\t"))
             }
         }
 
-        logger.info(PatchBundleLoader.Jar(*patchBundles).joinToString("\n\n") { it.buildString() })
+        fun IndexedValue<Patch<*>>.buildString() = let { (index, patch) ->
+            buildString {
+                if (withIndex) appendLine("Index: $index")
+
+                append("Name: ${patch.name}")
+
+                if (withDescriptions) append("\nDescription: ${patch.description}")
+
+                if (withOptions && patch.options.isNotEmpty()) {
+                    appendLine("\nOptions:")
+                    append(
+                        patch.options.values.joinToString("\n\n") { option ->
+                            option.buildString()
+                        }.prependIndent("\t")
+                    )
+                }
+
+                if (withPackages && patch.compatiblePackages != null) {
+                    appendLine("\nCompatible packages:")
+                    append(patch.compatiblePackages!!.joinToString("\n") {
+                        it.buildString()
+                    }.prependIndent("\t"))
+                }
+            }
+        }
+
+        fun Patch<*>.filterCompatiblePackages(name: String) = compatiblePackages?.any { it.name == name }
+            ?: withUniversalPatches
+
+        val patches = PatchBundleLoader.Jar(*patchBundles).withIndex().toList()
+
+        val filtered =
+            packageName?.let { patches.filter { (_, patch) -> patch.filterCompatiblePackages(it) } } ?: patches
+
+        if (filtered.isNotEmpty()) logger.info(filtered.joinToString("\n\n") { it.buildString() })
     }
 }

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

@@ -1,60 +1,32 @@
 package app.revanced.cli.command
 
 import app.revanced.cli.command.utility.UtilityCommand
-import app.revanced.patcher.patch.PatchClass
+import app.revanced.library.logging.Logger
 import picocli.CommandLine
 import picocli.CommandLine.Command
 import picocli.CommandLine.IVersionProvider
 import java.util.*
-import java.util.logging.*
 
 
 fun main(args: Array<String>) {
-    System.setProperty("java.util.logging.SimpleFormatter.format", "%4\$s: %5\$s %n")
-    Logger.getLogger("").apply {
-        handlers.forEach {
-            it.close()
-            removeHandler(it)
-        }
-
-        object : Handler() {
-            override fun publish(record: LogRecord) = formatter.format(record).toByteArray().let {
-                if (record.level.intValue() > Level.INFO.intValue())
-                    System.err.write(it)
-                else
-                    System.out.write(it)
-            }
-
-            override fun flush() {
-                System.out.flush()
-                System.err.flush()
-            }
-
-            override fun close() = flush()
-        }.also {
-            it.level = Level.ALL
-            it.formatter = SimpleFormatter()
-        }.let(::addHandler)
-    }
-
+    Logger.setDefault()
     CommandLine(MainCommand).execute(*args)
 }
 
-internal typealias PatchList = List<PatchClass>
-
 private object CLIVersionProvider : IVersionProvider {
-    override fun getVersion(): Array<String> {
-        Properties().apply {
-            load(MainCommand::class.java.getResourceAsStream("/app/revanced/cli/version.properties"))
-        }.let {
-            return arrayOf("ReVanced CLI v${it.getProperty("version")}")
-        }
-    }
+    override fun getVersion() = arrayOf(
+        MainCommand::class.java.getResourceAsStream(
+            "/app/revanced/cli/version.properties"
+        )?.use { stream ->
+            Properties().apply { load(stream) }.let {
+                "ReVanced CLI v${it.getProperty("version")}"
+            }
+        } ?: "ReVanced CLI")
 }
 
 @Command(
     name = "revanced-cli",
-    description = ["Command line application to use ReVanced"],
+    description = ["Command line application to use ReVanced."],
     mixinStandardHelpOptions = true,
     versionProvider = CLIVersionProvider::class,
     subcommands = [

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

@@ -1,8 +1,8 @@
 package app.revanced.cli.command
 
+import app.revanced.library.Options
+import app.revanced.library.Options.setOptions
 import app.revanced.patcher.PatchBundleLoader
-import app.revanced.utils.Options
-import app.revanced.utils.Options.setOptions
 import picocli.CommandLine
 import picocli.CommandLine.Help.Visibility.ALWAYS
 import java.io.File
@@ -10,37 +10,45 @@ import java.util.logging.Logger
 
 @CommandLine.Command(
     name = "options",
-    description = ["Generate options file from patches"],
+    description = ["Generate options file from patches."],
 )
 internal object OptionsCommand : Runnable {
     private val logger = Logger.getLogger(OptionsCommand::class.java.name)
 
     @CommandLine.Parameters(
-        description = ["Paths to patch bundles"], arity = "1..*"
+        description = ["Paths to patch bundles."], arity = "1..*"
     )
     private lateinit var patchBundles: Array<File>
 
     @CommandLine.Option(
-        names = ["-p", "--path"], description = ["Path to patch options JSON file"], showDefaultValue = ALWAYS
+        names = ["-p", "--path"], description = ["Path to patch options JSON file."], showDefaultValue = ALWAYS
     )
     private var filePath: File = File("options.json")
 
     @CommandLine.Option(
-        names = ["-o", "--overwrite"], description = ["Overwrite existing options file"], showDefaultValue = ALWAYS
+        names = ["-o", "--overwrite"], description = ["Overwrite existing options file."], showDefaultValue = ALWAYS
     )
     private var overwrite: Boolean = false
 
     @CommandLine.Option(
         names = ["-u", "--update"],
-        description = ["Update existing options by adding missing and removing non-existent options"],
+        description = ["Update existing options by adding missing and removing non-existent options."],
         showDefaultValue = ALWAYS
     )
     private var update: Boolean = false
 
-    override fun run() = if (!filePath.exists() || overwrite) with(PatchBundleLoader.Jar(*patchBundles)) {
-        if (update && filePath.exists()) setOptions(filePath)
+    override fun run() = try {
+        PatchBundleLoader.Jar(*patchBundles).let { patches ->
+            val exists = filePath.exists()
+            if (!exists || overwrite) {
+                if (exists && update) patches.setOptions(filePath)
 
-        Options.serialize(this, prettyPrint = true).let(filePath::writeText)
+                Options.serialize(patches, prettyPrint = true).let(filePath::writeText)
+            } else throw OptionsFileAlreadyExistsException()
+        }
+    } catch (ex: OptionsFileAlreadyExistsException) {
+        logger.severe("Options file already exists, use --overwrite to override it")
     }
-    else logger.severe("Options file already exists, use --override to override it")
+
+    class OptionsFileAlreadyExistsException : Exception()
 }

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

@@ -1,23 +1,18 @@
 package app.revanced.cli.command
 
+import app.revanced.library.ApkUtils
+import app.revanced.library.Options
+import app.revanced.library.Options.setOptions
+import app.revanced.library.adb.AdbManager
 import app.revanced.patcher.PatchBundleLoader
+import app.revanced.patcher.PatchSet
 import app.revanced.patcher.Patcher
 import app.revanced.patcher.PatcherOptions
-import app.revanced.patcher.PatcherResult
-import app.revanced.patcher.extensions.PatchExtensions.compatiblePackages
-import app.revanced.patcher.extensions.PatchExtensions.include
-import app.revanced.patcher.extensions.PatchExtensions.patchName
-import app.revanced.utils.Options
-import app.revanced.utils.Options.setOptions
-import app.revanced.utils.adb.AdbManager
-import app.revanced.utils.align.ZipAligner
-import app.revanced.utils.align.zip.ZipFile
-import app.revanced.utils.align.zip.structures.ZipEntry
-import app.revanced.utils.signing.ApkSigner
-import app.revanced.utils.signing.SigningOptions
 import kotlinx.coroutines.runBlocking
 import picocli.CommandLine
 import picocli.CommandLine.Help.Visibility.ALWAYS
+import picocli.CommandLine.Model.CommandSpec
+import picocli.CommandLine.Spec
 import java.io.File
 import java.io.PrintWriter
 import java.io.StringWriter
@@ -25,322 +20,323 @@ import java.util.logging.Logger
 
 
 @CommandLine.Command(
-    name = "patch", description = ["Patch an APK file"]
+    name = "patch", description = ["Patch an APK file."]
 )
 internal object PatchCommand : Runnable {
     private val logger = Logger.getLogger(PatchCommand::class.java.name)
 
-    @CommandLine.Parameters(
-        description = ["APK file to be patched"], arity = "1..1"
-    )
+    @Spec
+    lateinit var spec: CommandSpec // injected by picocli
+
     private lateinit var apk: File
 
-    @CommandLine.Option(
-        names = ["-b", "--patch-bundle"], description = ["One or more bundles of patches"], required = true
-    )
+    private var integrations = listOf<File>()
+
     private var patchBundles = emptyList<File>()
 
     @CommandLine.Option(
-        names = ["-m", "--merge"], description = ["One or more DEX files or containers to merge into the APK"]
+        names = ["-i", "--include"], description = ["List of patches to include."]
     )
-    private var integrations = listOf<File>()
+    private var includedPatches = hashSetOf<String>()
 
     @CommandLine.Option(
-        names = ["-i", "--include"], description = ["List of patches to include"]
+        names = ["--ii"],
+        description = ["List of patches to include by their index in relation to the supplied patch bundles."]
     )
-    private var includedPatches = arrayOf<String>()
+    private var includedPatchesByIndex = arrayOf<Int>()
 
     @CommandLine.Option(
-        names = ["-e", "--exclude"], description = ["List of patches to exclude"]
+        names = ["-e", "--exclude"], description = ["List of patches to exclude."]
     )
-    private var excludedPatches = arrayOf<String>()
+    private var excludedPatches = hashSetOf<String>()
 
     @CommandLine.Option(
-        names = ["--options"], description = ["Path to patch options JSON file"], showDefaultValue = ALWAYS
+        names = ["--ei"],
+        description = ["List of patches to exclude by their index in relation to the supplied patch bundles."]
+    )
+    private var excludedPatchesByIndex = arrayOf<Int>()
+
+    @CommandLine.Option(
+        names = ["--options"], description = ["Path to patch options JSON file."], showDefaultValue = ALWAYS
     )
     private var optionsFile: File = File("options.json")
 
     @CommandLine.Option(
         names = ["--exclusive"],
-        description = ["Only include patches that are explicitly specified to be included"],
+        description = ["Only include patches that are explicitly specified to be included."],
         showDefaultValue = ALWAYS
     )
     private var exclusive = false
 
     @CommandLine.Option(
         names = ["-f","--force"],
-        description = ["Force inclusion of patches that are incompatible with the supplied APK file's version"],
+        description = ["Bypass compatibility checks for the supplied APK's version."],
         showDefaultValue = ALWAYS
     )
     private var force: Boolean = false
 
     @CommandLine.Option(
-        names = ["-o", "--out"], description = ["Path to save the patched APK file to"], required = true
+        names = ["-o", "--out"], description = ["Path to save the patched APK file to."], required = true
     )
     private lateinit var outputFilePath: File
 
     @CommandLine.Option(
-        names = ["-d", "--device-serial"], description = ["ADB device serial to install to"], showDefaultValue = ALWAYS
+        names = ["-d", "--device-serial"], description = ["ADB device serial to install to."], showDefaultValue = ALWAYS
     )
     private var deviceSerial: String? = null
 
     @CommandLine.Option(
-        names = ["--mount"], description = ["Install by mounting the patched APK file"], showDefaultValue = ALWAYS
+        names = ["--mount"], description = ["Install by mounting the patched APK file."], showDefaultValue = ALWAYS
     )
     private var mount: Boolean = false
 
     @CommandLine.Option(
-        names = ["--common-name"],
-        description = ["The common name of the signer of the patched APK file"],
+        names = ["--keystore"], description = ["Path to the keystore to sign the patched APK file with."],
+    )
+    private var keystoreFilePath: File? = null
+
+    // key store password
+    @CommandLine.Option(
+        names = ["--keystore-password"],
+        description = ["The password of the keystore to sign the patched APK file with."],
+    )
+    private var keyStorePassword: String? = null // Empty password by default
+
+    @CommandLine.Option(
+        names = ["--alias"], description = ["The alias of the key from the keystore to sign the patched APK file with."],
         showDefaultValue = ALWAYS
-
     )
-    private var commonName = "ReVanced"
+    private var alias = "ReVanced Key"
 
     @CommandLine.Option(
-        names = ["--keystore"], description = ["Path to the keystore to sign the patched APK file with"]
+        names = ["--keystore-entry-password"],
+        description = ["The password of the entry from the keystore for the key to sign the patched APK file with."]
     )
-    private var keystorePath: String? = null
+    private var password = "" // Empty password by default
 
     @CommandLine.Option(
-        names = ["--password"], description = ["The password of the keystore to sign the patched APK file with"]
+        names = ["--signer"], description = ["The name of the signer to sign the patched APK file with."],
+        showDefaultValue = ALWAYS
     )
-    private var password = "ReVanced"
+    private var signer = "ReVanced"
 
     @CommandLine.Option(
         names = ["-r", "--resource-cache"],
-        description = ["Path to temporary resource cache directory"],
+        description = ["Path to temporary resource cache directory."],
         showDefaultValue = ALWAYS
     )
-    private var resourceCachePath = File("revanced-resource-cache")
+    private var resourceCachePath = File("revanced-resource-cache.")
 
-    @CommandLine.Option(
-        names = ["--custom-aapt2-binary"], description = ["Path to a custom AAPT binary to compile resources with"]
-    )
-    private var aaptBinaryPath = File("")
+    private var aaptBinaryPath: File? = null
 
     @CommandLine.Option(
         names = ["-p", "--purge"],
-        description = ["Purge the temporary resource cache directory after patching"],
+        description = ["Purge the temporary resource cache directory after patching."],
         showDefaultValue = ALWAYS
     )
     private var purge: Boolean = false
 
+    @CommandLine.Option(
+        names = ["-w", "--warn"],
+        description = ["Warn if a patch can not be found in the supplied patch bundles."],
+        showDefaultValue = ALWAYS
+    )
+    private var warn: Boolean = false
+
+    @CommandLine.Parameters(
+        description = ["APK file to be patched."], arity = "1..1"
+    )
+    @Suppress("unused")
+    private fun setApk(apk: File) {
+        if (!apk.exists()) throw CommandLine.ParameterException(
+            spec.commandLine(),
+            "APK file ${apk.name} does not exist"
+        )
+        this.apk = apk
+    }
+
+    @CommandLine.Option(
+        names = ["-m", "--merge"], description = ["One or more DEX files or containers to merge into the APK."]
+    )
+    @Suppress("unused")
+    private fun setIntegrations(integrations: Array<File>) {
+        integrations.firstOrNull { !it.exists() }?.let {
+            throw CommandLine.ParameterException(spec.commandLine(), "Integrations file ${it.name} does not exist.")
+        }
+        this.integrations += integrations
+    }
+
+    @CommandLine.Option(
+        names = ["-b", "--patch-bundle"], description = ["One or more bundles of patches."], required = true
+    )
+    @Suppress("unused")
+    private fun setPatchBundles(patchBundles: Array<File>) {
+        patchBundles.firstOrNull { !it.exists() }?.let {
+            throw CommandLine.ParameterException(spec.commandLine(), "Patch bundle ${it.name} does not exist")
+        }
+        this.patchBundles = patchBundles.toList()
+    }
+
+    @CommandLine.Option(
+        names = ["--custom-aapt2-binary"], description = ["Path to a custom AAPT binary to compile resources with."]
+    )
+    @Suppress("unused")
+    private fun setAaptBinaryPath(aaptBinaryPath: File) {
+        if (!aaptBinaryPath.exists()) throw CommandLine.ParameterException(
+            spec.commandLine(),
+            "AAPT binary ${aaptBinaryPath.name} does not exist"
+        )
+        this.aaptBinaryPath = aaptBinaryPath
+    }
+
     override fun run() {
-        // region Prepare
-
-        if (!apk.exists()) {
-            logger.severe("APK file ${apk.name} does not exist")
-            return
-        }
-
-        integrations.filter { !it.exists() }.let {
-            if (it.isEmpty()) return@let
-
-            it.forEach { integration ->
-                logger.severe("Integration file ${integration.name} does not exist")
-            }
-            return
-        }
-
-        val adbManager = deviceSerial?.let { serial ->
-            if (mount) AdbManager.RootAdbManager(serial)
-            else AdbManager.UserAdbManager(serial)
-        }
-
-        // endregion
+        val adbManager = deviceSerial?.let { serial -> AdbManager.getAdbManager(serial, mount) }
 
         // region Load patches
 
         logger.info("Loading patches")
 
         val patches = PatchBundleLoader.Jar(*patchBundles.toTypedArray())
-        val integrations = integrations
 
-        logger.info("Setting patch options")
-
-        optionsFile.let {
-            if (it.exists()) patches.setOptions(it)
-            else Options.serialize(patches, prettyPrint = true).let(it::writeText)
+        // Warn if a patch can not be found in the supplied patch bundles.
+        if (warn) patches.map { it.name }.toHashSet().let { availableNames ->
+            (includedPatches + excludedPatches).filter { name ->
+                !availableNames.contains(name)
+            }
+        }.let { unknownPatches ->
+            if (unknownPatches.isEmpty()) return@let
+            logger.warning("Unknown input of patches:\n${unknownPatches.joinToString("\n")}")
         }
 
         // endregion
 
-        // region Patch
-
-        val patcher = Patcher(
+        Patcher(
             PatcherOptions(
                 apk,
                 resourceCachePath,
-                aaptBinaryPath.path,
+                aaptBinaryPath?.path,
                 resourceCachePath.absolutePath,
+                true
             )
-        )
+        ).use { patcher ->
+            val filteredPatches = patcher.filterPatchSelection(patches).also { patches ->
+                logger.info("Setting patch options")
 
-        val result = patcher.apply {
-            acceptIntegrations(integrations)
-            acceptPatches(filterPatchSelection(patches))
-
-            // Execute patches.
-            runBlocking {
-                apply(false).collect { patchResult ->
-                    patchResult.exception?.let {
-                        StringWriter().use { writer ->
-                            it.printStackTrace(PrintWriter(writer))
-                            logger.severe("${patchResult.patchName} failed: $writer")
-                        }
-                    } ?: logger.info("${patchResult.patchName} succeeded")
-                }
+                if (optionsFile.exists()) patches.setOptions(optionsFile)
+                else Options.serialize(patches, prettyPrint = true).let(optionsFile::writeText)
             }
-        }.get()
 
-        patcher.close()
+            // region Patch
 
-        // endregion
+            val patcherResult = patcher.apply {
+                acceptIntegrations(integrations)
+                acceptPatches(filteredPatches.toList())
 
-        // region Finish
+                // Execute patches.
+                runBlocking {
+                    apply(false).collect { patchResult ->
+                        patchResult.exception?.let {
+                            StringWriter().use { writer ->
+                                it.printStackTrace(PrintWriter(writer))
+                                logger.severe("${patchResult.patch.name} failed:\n$writer")
+                            }
+                        } ?: logger.info("${patchResult.patch.name} succeeded")
+                    }
+                }
+            }.get()
 
-        val alignAndSignedFile = sign(
-            apk.newAlignedFile(
-                result, resourceCachePath.resolve("${outputFilePath.nameWithoutExtension}_aligned.apk")
+            // endregion
+
+            // region Save
+
+            val alignedFile = resourceCachePath.resolve(apk.name).apply {
+                ApkUtils.copyAligned(apk, this, patcherResult)
+            }
+
+            val keystoreFilePath = keystoreFilePath ?: outputFilePath.absoluteFile.parentFile
+                .resolve("${outputFilePath.nameWithoutExtension}.keystore")
+
+            if (!mount) ApkUtils.sign(
+                alignedFile,
+                outputFilePath,
+                ApkUtils.SigningOptions(
+                    keystoreFilePath,
+                    keyStorePassword,
+                    alias,
+                    password,
+                    signer
+                )
             )
-        )
+            else alignedFile.renameTo(outputFilePath)
 
-        logger.info("Copying to ${outputFilePath.name}")
-        alignAndSignedFile.copyTo(outputFilePath, overwrite = true)
+            // endregion
 
-        adbManager?.install(AdbManager.Apk(outputFilePath, patcher.context.packageMetadata.packageName))
+            // region Install
+
+            adbManager?.install(AdbManager.Apk(outputFilePath, patcher.context.packageMetadata.packageName))
+
+            // endregion
+        }
 
         if (purge) {
             logger.info("Purging temporary files")
             purge(resourceCachePath)
         }
-
-        // endregion
     }
 
 
     /**
      * Filter the patches to be added to the patcher. The filter is based on the following:
-     * - [includedPatches] (explicitly included)
-     * - [excludedPatches] (explicitly excluded)
-     * - [exclusive] (only include patches that are explicitly included)
-     * - [force] (ignore patches incompatibility to versions)
-     * - Package name and version of the input APK file (if [force] is false)
      *
      * @param patches The patches to filter.
      * @return The filtered patches.
      */
-    private fun Patcher.filterPatchSelection(patches: PatchList) = buildList {
-        // TODO: Remove this eventually because
-        //  patches named "patch-name" and "patch name" will conflict.
-        fun String.format() = lowercase().replace(" ", "-")
-
-        val formattedExcludedPatches = excludedPatches.map { it.format() }
-        val formattedIncludedPatches = includedPatches.map { it.format() }
-
+    private fun Patcher.filterPatchSelection(patches: PatchSet): PatchSet = buildSet {
         val packageName = context.packageMetadata.packageName
         val packageVersion = context.packageMetadata.packageVersion
 
-        patches.forEach patch@{ patch ->
-            val formattedPatchName = patch.patchName.format()
+        patches.withIndex().forEach patch@{ (i, patch) ->
+            val patchName = patch.name!!
 
-            val explicitlyExcluded = formattedExcludedPatches.contains(formattedPatchName)
-            if (explicitlyExcluded) return@patch logger.info("Excluding ${patch.patchName}")
+            val explicitlyExcluded = excludedPatches.contains(patchName) || excludedPatchesByIndex.contains(i)
+            if (explicitlyExcluded) return@patch logger.info("Excluding $patchName")
 
             // Make sure the patch is compatible with the supplied APK files package name and version.
             patch.compatiblePackages?.let { packages ->
                 packages.singleOrNull { it.name == packageName }?.let { `package` ->
-                    val matchesVersion = force || `package`.versions.let {
-                        it.isEmpty() || it.any { version -> version == packageVersion }
-                    }
+                    val matchesVersion = force || `package`.versions?.let {
+                        it.any { version -> version == packageVersion }
+                    } ?: true
 
                     if (!matchesVersion) return@patch logger.warning(
-                        "${patch.patchName} is incompatible with version $packageVersion. "
+                        "$patchName is incompatible with version $packageVersion. "
                                 + "This patch is only compatible with version "
                                 + packages.joinToString(";") { pkg ->
-                            "${pkg.name}: ${pkg.versions.joinToString(", ")}"
+                            pkg.versions!!.joinToString(", ")
                         }
                     )
-                } ?: return@patch logger.fine("${patch.patchName} is incompatible with $packageName. "
+                } ?: return@patch logger.fine(
+                    "$patchName is incompatible with $packageName. "
                         + "This patch is only compatible with "
                         + packages.joinToString(", ") { `package` -> `package`.name })
 
                 return@let
-            } ?: logger.fine("$formattedPatchName: No constraint on packages.")
+            } ?: logger.fine("$patchName has no constraint on packages.")
 
-            // If the patch is implicitly included, it will be only included if [exclusive] is false.
-            val implicitlyIncluded = !exclusive && patch.include
-            // If the patch is explicitly included, it will be included even if [exclusive] is false.
-            val explicitlyIncluded = formattedIncludedPatches.contains(formattedPatchName)
+            // If the patch is implicitly used, it will be only included if [exclusive] is false.
+            val implicitlyIncluded = !exclusive && patch.use
+            // If the patch is explicitly used, it will be included even if [exclusive] is false.
+            val explicitlyIncluded = includedPatches.contains(patchName) || includedPatchesByIndex.contains(i)
 
             val included = implicitlyIncluded || explicitlyIncluded
-            if (!included) return@patch logger.info("${patch.patchName} excluded by default") // Case 1.
+            if (!included) return@patch logger.info("$patchName excluded") // Case 1.
 
-            logger.fine("Adding $formattedPatchName")
+            logger.fine("Adding $patchName")
 
             add(patch)
         }
     }
 
-    /**
-     * Create a new aligned APK file.
-     *
-     * @param result The result of the patching process.
-     * @param outputFile The file to save the aligned APK to.
-     */
-    private fun File.newAlignedFile(
-        result: PatcherResult, outputFile: File
-    ): File {
-        logger.info("Aligning $name")
-
-        if (outputFile.exists()) outputFile.delete()
-
-        ZipFile(outputFile).use { file ->
-            result.dexFiles.forEach {
-                file.addEntryCompressData(
-                    ZipEntry.createWithName(it.name), it.stream.readBytes()
-                )
-            }
-
-            result.resourceFile?.let {
-                file.copyEntriesFromFileAligned(
-                    ZipFile(it), ZipAligner::getEntryAlignment
-                )
-            }
-
-            // TODO: Do not compress result.doNotCompress
-
-            file.copyEntriesFromFileAligned(
-                ZipFile(this), ZipAligner::getEntryAlignment
-            )
-        }
-
-        return outputFile
-    }
-
-    /**
-     * Sign the APK file.
-     *
-     * @param inputFile The APK file to sign.
-     * @return The signed APK file. If [mount] is true, the input file will be returned.
-     */
-    private fun sign(inputFile: File) = if (mount) inputFile
-    else {
-        logger.info("Signing ${inputFile.name}")
-
-        val keyStoreFilePath = keystorePath
-            ?: outputFilePath.absoluteFile.parentFile.resolve("${outputFilePath.nameWithoutExtension}.keystore").canonicalPath
-
-        val options = SigningOptions(
-            commonName, password, keyStoreFilePath
-        )
-
-        ApkSigner(options).signApk(
-                inputFile, resourceCachePath.resolve("${outputFilePath.nameWithoutExtension}_signed.apk")
-            )
-    }
-
     private fun purge(resourceCachePath: File) {
         val result = if (resourceCachePath.deleteRecursively()) "Purged resource cache directory"
         else "Failed to purge resource cache directory"

src/main/kotlin/app/revanced/cli/command/utility/InstallCommand.kt

@@ -1,6 +1,6 @@
 package app.revanced.cli.command.utility
 
-import app.revanced.utils.adb.AdbManager
+import app.revanced.library.adb.AdbManager
 import picocli.CommandLine.*
 import java.io.File
 import java.util.logging.Logger
@@ -28,15 +28,11 @@ internal object InstallCommand : Runnable {
     )
     private var packageName: String? = null
 
-    override fun run() = try {
-        deviceSerials.forEach { deviceSerial ->
-            if (packageName != null) {
-                AdbManager.RootAdbManager(deviceSerial)
-            } else {
-                AdbManager.UserAdbManager(deviceSerial)
-            }.install(AdbManager.Apk(apk, packageName))
+    override fun run() = deviceSerials.forEach { deviceSerial ->
+        try {
+            AdbManager.getAdbManager(deviceSerial, packageName != null).install(AdbManager.Apk(apk, packageName))
+        } catch (e: AdbManager.DeviceNotFoundException) {
+            logger.severe(e.toString())
         }
-    } catch (e: AdbManager.DeviceNotFoundException) {
-        logger.severe(e.toString())
     }
 }

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

@@ -1,6 +1,6 @@
 package app.revanced.cli.command.utility
 
-import app.revanced.utils.adb.AdbManager
+import app.revanced.library.adb.AdbManager
 import picocli.CommandLine.*
 import picocli.CommandLine.Help.Visibility.ALWAYS
 import java.util.logging.Logger
@@ -26,15 +26,11 @@ internal object UninstallCommand : Runnable {
     )
     private var unmount: Boolean = false
 
-    override fun run() = try {
-        deviceSerials.forEach { deviceSerial ->
-            if (unmount) {
-                AdbManager.RootAdbManager(deviceSerial)
-            } else {
-                AdbManager.UserAdbManager(deviceSerial)
-            }.uninstall(packageName)
+    override fun run() = deviceSerials.forEach { deviceSerial ->
+        try {
+            AdbManager.getAdbManager(deviceSerial, unmount).uninstall(packageName)
+        } catch (e: AdbManager.DeviceNotFoundException) {
+            logger.severe(e.toString())
         }
-    } catch (e: AdbManager.DeviceNotFoundException) {
-        logger.severe(e.toString())
     }
 }

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

@@ -1,110 +0,0 @@
-package app.revanced.utils
-
-import app.revanced.cli.command.PatchList
-import app.revanced.patcher.extensions.PatchExtensions.options
-import app.revanced.patcher.extensions.PatchExtensions.patchName
-import app.revanced.patcher.patch.NoSuchOptionException
-import app.revanced.utils.Options.PatchOption.Option
-import com.fasterxml.jackson.module.kotlin.jacksonObjectMapper
-import java.io.File
-import java.util.logging.Logger
-
-
-internal object Options {
-    private val logger = Logger.getLogger(Options::class.java.name)
-
-    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 -> Option(option.key, option.value) }
-            )
-        }
-        // See https://github.com/revanced/revanced-patches/pull/2434/commits/60e550550b7641705e81aa72acfc4faaebb225e7.
-        .distinctBy { it.patchName }
-        .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.
-     */
-    fun PatchList.setOptions(json: String) {
-        filter { it.options?.any() == true }.let { patches ->
-            if (patches.isEmpty()) return
-
-            val patchOptions = deserialize(json)
-
-            patches.forEach patch@{ patch ->
-                patchOptions.find { option -> option.patchName == patch.patchName }?.let {
-                    it.options.forEach { option ->
-                        try {
-                            patch.options?.set(option.key, option.value)
-                                ?: run{
-                                    logger.warning("${patch.patchName} has no options")
-                                    return@patch
-                                }
-                        } catch (e: NoSuchOptionException) {
-                            logger.info(e.toString())
-                        }
-                    }
-                }
-            }
-        }
-    }
-
-    /**
-     * Sets the options for the patches in the list.
-     *
-     * @param file The file containing the JSON string containing the options.
-     * @see setOptions
-     */
-    fun PatchList.setOptions(file: File) = setOptions(file.readText())
-
-    /**
-     * 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/adb/AdbManager.kt

@@ -1,140 +0,0 @@
-package app.revanced.utils.adb
-
-import app.revanced.utils.adb.AdbManager.Apk
-import app.revanced.utils.adb.Constants.CREATE_DIR
-import app.revanced.utils.adb.Constants.DELETE
-import app.revanced.utils.adb.Constants.INSTALLATION_PATH
-import app.revanced.utils.adb.Constants.INSTALL_MOUNT
-import app.revanced.utils.adb.Constants.INSTALL_PATCHED_APK
-import app.revanced.utils.adb.Constants.MOUNT_PATH
-import app.revanced.utils.adb.Constants.MOUNT_SCRIPT
-import app.revanced.utils.adb.Constants.PATCHED_APK_PATH
-import app.revanced.utils.adb.Constants.PLACEHOLDER
-import app.revanced.utils.adb.Constants.RESTART
-import app.revanced.utils.adb.Constants.TMP_PATH
-import app.revanced.utils.adb.Constants.UMOUNT
-import se.vidstige.jadb.JadbConnection
-import se.vidstige.jadb.managers.Package
-import se.vidstige.jadb.managers.PackageManager
-import java.io.Closeable
-import java.io.File
-import java.util.logging.Logger
-
-/**
- * Adb manager. Used to install and uninstall [Apk] files.
- *
- * @param deviceSerial The serial of the device.
- */
-internal sealed class AdbManager(deviceSerial: String? = null) : Closeable {
-    protected val logger: Logger = Logger.getLogger(AdbManager::class.java.name)
-
-    protected val device = JadbConnection().devices.find { device -> device.serial == deviceSerial }
-        ?: throw DeviceNotFoundException(deviceSerial)
-
-    init {
-        logger.fine("Established connection to $deviceSerial")
-    }
-
-    /**
-     * Installs the [Apk] file.
-     *
-     * @param apk The [Apk] file.
-     */
-    open fun install(apk: Apk) {
-        logger.info("Finished installing ${apk.file.name}")
-    }
-
-    /**
-     * Uninstalls the package.
-     *
-     * @param packageName The package name.
-     */
-    open fun uninstall(packageName: String) {
-        logger.info("Finished uninstalling $packageName")
-    }
-
-    /**
-     * Closes the [AdbManager] instance.
-     */
-    override fun close() {
-        logger.fine("Closed")
-    }
-
-    class RootAdbManager(deviceSerial: String) : AdbManager(deviceSerial) {
-        init {
-            if (!device.hasSu()) throw IllegalArgumentException("Root required on $deviceSerial. Task failed")
-        }
-
-        override fun install(apk: Apk) {
-            logger.info("Installing by mounting")
-
-            val applyReplacement = getPlaceholderReplacement(
-                apk.packageName ?: throw IllegalArgumentException("Package name is required")
-            )
-
-            device.push(apk.file, TMP_PATH)
-
-            device.run("$CREATE_DIR $INSTALLATION_PATH")
-            device.run(INSTALL_PATCHED_APK.applyReplacement())
-
-            device.createFile(TMP_PATH, MOUNT_SCRIPT.applyReplacement())
-
-            device.run(INSTALL_MOUNT.applyReplacement())
-            device.run(UMOUNT.applyReplacement()) // Sanity check.
-            device.run(MOUNT_PATH.applyReplacement())
-            device.run(RESTART.applyReplacement())
-            device.run(DELETE.applyReplacement(TMP_PATH).applyReplacement())
-
-            super.install(apk)
-        }
-
-        override fun uninstall(packageName: String) {
-            logger.info("Uninstalling $packageName by unmounting")
-
-            val applyReplacement = getPlaceholderReplacement(packageName)
-
-            device.run(UMOUNT.applyReplacement(packageName))
-            device.run(DELETE.applyReplacement(PATCHED_APK_PATH).applyReplacement())
-            device.run(DELETE.applyReplacement(MOUNT_PATH).applyReplacement())
-            device.run(DELETE.applyReplacement(TMP_PATH).applyReplacement())
-
-            super.uninstall(packageName)
-        }
-
-        companion object Utils {
-            private fun getPlaceholderReplacement(with: String): String.() -> String = { replace(PLACEHOLDER, with) }
-            private fun String.applyReplacement(with: String) = replace(PLACEHOLDER, with)
-        }
-    }
-
-    class UserAdbManager(deviceSerial: String) : AdbManager(deviceSerial) {
-        private val packageManager = PackageManager(device)
-
-        override fun install(apk: Apk) {
-            PackageManager(device).install(apk.file)
-
-            super.install(apk)
-        }
-
-        override fun uninstall(packageName: String) {
-            logger.info("Uninstalling $packageName")
-
-            packageManager.uninstall(Package(packageName))
-
-            super.uninstall(packageName)
-        }
-    }
-
-    /**
-     * Apk file for [AdbManager].
-     *
-     * @param file The [Apk] file.
-     * @param packageName The package name of the [Apk] file.
-     */
-    internal class Apk(val file: File, val packageName: String? = null)
-
-    internal class DeviceNotFoundException(deviceSerial: String?) :
-        Exception(deviceSerial?.let {
-            "The device with the ADB device serial \"$deviceSerial\" can not be found"
-        } ?: "No ADB device found")
-}

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

@@ -1,33 +0,0 @@
-package app.revanced.utils.adb
-
-import se.vidstige.jadb.JadbDevice
-import se.vidstige.jadb.RemoteFile
-import se.vidstige.jadb.ShellProcessBuilder
-import java.io.File
-
-
-internal fun JadbDevice.buildCommand(command: String, su: Boolean = true): ShellProcessBuilder {
-    if (su) return shellProcessBuilder("su -c \'$command\'")
-
-    val args = command.split(" ") as ArrayList<String>
-    val cmd = args.removeFirst()
-
-    return shellProcessBuilder(cmd, *args.toTypedArray())
-}
-
-internal fun JadbDevice.run(command: String, su: Boolean = true): Int {
-    return this.buildCommand(command, su).start().waitFor()
-}
-
-internal fun JadbDevice.hasSu() =
-    this.startCommand("su -h", false).waitFor() == 0
-
-internal fun JadbDevice.push(file: File, targetFilePath: String) =
-    push(file, RemoteFile(targetFilePath))
-
-internal fun JadbDevice.createFile(targetFile: String, content: String) =
-    push(content.byteInputStream(), System.currentTimeMillis(), 644, RemoteFile(targetFile))
-
-
-private fun JadbDevice.startCommand(command: String, su: Boolean) =
-    shellProcessBuilder(if (su) "su -c '$command'" else command).start()

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

@@ -1,40 +0,0 @@
-package app.revanced.utils.adb
-
-internal object Constants {
-    internal const val PLACEHOLDER = "PLACEHOLDER"
-
-    internal const val TMP_PATH = "/data/local/tmp/revanced.tmp"
-    internal const val INSTALLATION_PATH = "/data/adb/revanced/"
-    internal const val PATCHED_APK_PATH = "$INSTALLATION_PATH$PLACEHOLDER.apk"
-    internal const val MOUNT_PATH = "/data/adb/service.d/mount_revanced_$PLACEHOLDER.sh"
-
-    internal const val DELETE = "rm -rf $PLACEHOLDER"
-    internal const val CREATE_DIR = "mkdir -p"
-    internal const val RESTART = "pm resolve-activity --brief $PLACEHOLDER | tail -n 1 | " +
-            "xargs am start -n && kill ${'$'}(pidof -s $PLACEHOLDER)"
-
-    internal const val INSTALL_PATCHED_APK = "base_path=\"$PATCHED_APK_PATH\" && " +
-            "mv $TMP_PATH ${'$'}base_path && " +
-            "chmod 644 ${'$'}base_path && " +
-            "chown system:system ${'$'}base_path && " +
-            "chcon u:object_r:apk_data_file:s0  ${'$'}base_path"
-
-    internal const val UMOUNT =
-        "grep $PLACEHOLDER /proc/mounts | while read -r line; do echo ${'$'}line | cut -d \" \" -f 2 | sed 's/apk.*/apk/' | xargs -r umount -l; done"
-
-    internal const val INSTALL_MOUNT = "mv $TMP_PATH $MOUNT_PATH && chmod +x $MOUNT_PATH"
-
-    internal val MOUNT_SCRIPT =
-        """
-            #!/system/bin/sh
-            MAGISKTMP="${'$'}(magisk --path)" || MAGISKTMP=/sbin
-            MIRROR="${'$'}MAGISKTMP/.magisk/mirror"
-            while [ "${'$'}(getprop sys.boot_completed | tr -d '\r')" != "1" ]; do sleep 1; done
-            
-            base_path="$PATCHED_APK_PATH"
-            stock_path=${'$'}( pm path $PLACEHOLDER | grep base | sed 's/package://g' )
-
-            chcon u:object_r:apk_data_file:s0  ${'$'}base_path
-            mount -o bind ${'$'}MIRROR${'$'}base_path ${'$'}stock_path
-        """.trimIndent()
-}

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

@@ -1,11 +0,0 @@
-package app.revanced.utils.align
-
-import app.revanced.utils.align.zip.structures.ZipEntry
-
-internal object ZipAligner {
-    private const val DEFAULT_ALIGNMENT = 4
-    private const val LIBRARY_ALIGNMENT = 4096
-
-    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/align/zip/Extensions.kt

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

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

@@ -1,181 +0,0 @@
-package app.revanced.utils.align.zip
-
-import app.revanced.utils.align.zip.structures.ZipEndRecord
-import app.revanced.utils.align.zip.structures.ZipEntry
-import java.io.Closeable
-import java.io.File
-import java.io.RandomAccessFile
-import java.nio.ByteBuffer
-import java.nio.channels.FileChannel
-import java.util.zip.CRC32
-import java.util.zip.Deflater
-
-class ZipFile(file: File) : Closeable {
-    private var entries: MutableList<ZipEntry> = mutableListOf()
-
-    private val filePointer: RandomAccessFile = RandomAccessFile(file, "rw")
-    private var centralDirectoryNeedsRewrite = false
-
-    private val compressionLevel = 5
-
-    init {
-        // If file isn't empty try to load entries.
-        if (file.length() > 0) {
-            val endRecord = findEndRecord()
-
-            if (endRecord.diskNumber > 0u || endRecord.totalEntries != endRecord.diskEntries)
-                throw IllegalArgumentException("Multi-file archives are not supported")
-
-            entries = readEntries(endRecord).toMutableList()
-        }
-
-        // Seek back to start for writing.
-        filePointer.seek(0)
-    }
-
-    private fun findEndRecord(): ZipEndRecord {
-        // Look from end to start since end record is at the end.
-        for (i in filePointer.length() - 1 downTo 0) {
-            filePointer.seek(i)
-            // Possible beginning of signature.
-            if (filePointer.readByte() == 0x50.toByte()) {
-                // Seek back to get the full int.
-                filePointer.seek(i)
-                val possibleSignature = filePointer.readUIntLE()
-                if (possibleSignature == ZipEndRecord.ECD_SIGNATURE) {
-                    filePointer.seek(i)
-                    return ZipEndRecord.fromECD(filePointer)
-                }
-            }
-        }
-
-        throw Exception("Couldn't find end record")
-    }
-
-    private fun readEntries(endRecord: ZipEndRecord): List<ZipEntry> {
-        filePointer.seek(endRecord.centralDirectoryStartOffset.toLong())
-
-        val numberOfEntries = endRecord.diskEntries.toInt()
-
-        return buildList(numberOfEntries) {
-            for (i in 1..numberOfEntries) {
-                add(
-                    ZipEntry.fromCDE(filePointer).also
-                    {
-                        //for some reason the local extra field can be different from the central one
-                        it.readLocalExtra(
-                            filePointer.channel.map(
-                                FileChannel.MapMode.READ_ONLY,
-                                it.localHeaderOffset.toLong() + 28,
-                                2
-                            )
-                        )
-                    })
-            }
-        }
-    }
-
-    private fun writeCD() {
-        val centralDirectoryStartOffset = filePointer.channel.position().toUInt()
-
-        entries.forEach {
-            filePointer.channel.write(it.toCDE())
-        }
-
-        val entriesCount = entries.size.toUShort()
-
-        val endRecord = ZipEndRecord(
-            0u,
-            0u,
-            entriesCount,
-            entriesCount,
-            filePointer.channel.position().toUInt() - centralDirectoryStartOffset,
-            centralDirectoryStartOffset,
-            ""
-        )
-
-        filePointer.channel.write(endRecord.toECD())
-    }
-
-    private fun addEntry(entry: ZipEntry, data: ByteBuffer) {
-        centralDirectoryNeedsRewrite = true
-
-        entry.localHeaderOffset = filePointer.channel.position().toUInt()
-
-        filePointer.channel.write(entry.toLFH())
-        filePointer.channel.write(data)
-
-        entries.add(entry)
-    }
-
-    fun addEntryCompressData(entry: ZipEntry, data: ByteArray) {
-        val compressor = Deflater(compressionLevel, true)
-        compressor.setInput(data)
-        compressor.finish()
-
-        val uncompressedSize = data.size
-        val compressedData = ByteArray(uncompressedSize) // I'm guessing compression won't make the data bigger.
-
-        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)
-    }
-
-    private fun getDataForEntry(entry: ZipEntry): ByteBuffer {
-        return filePointer.channel.map(
-            FileChannel.MapMode.READ_ONLY,
-            entry.dataOffset.toLong(),
-            entry.compressedSize.toLong()
-        )
-    }
-
-    /**
-     * Copies all entries from [file] to this file but skip already existing entries.
-     *
-     * @param file The file to copy entries from.
-     * @param entryAlignment A function that returns the alignment for a given entry.
-     */
-    fun copyEntriesFromFileAligned(file: ZipFile, entryAlignment: (entry: ZipEntry) -> Int?) {
-        for (entry in file.entries) {
-            if (entries.any { it.fileName == entry.fileName }) continue // Skip duplicates
-
-            val data = file.getDataForEntry(entry)
-            addEntryCopyData(entry, data, entryAlignment(entry))
-        }
-    }
-
-    override fun close() {
-        if (centralDirectoryNeedsRewrite) writeCD()
-        filePointer.close()
-    }
-}

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

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

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

@@ -1,189 +0,0 @@
-package app.revanced.utils.align.zip.structures
-
-import app.revanced.utils.align.zip.*
-import java.io.DataInput
-import java.nio.ByteBuffer
-import java.nio.ByteOrder
-
-data class ZipEntry(
-    val version: UShort,
-    val versionNeeded: UShort,
-    val flags: UShort,
-    var compression: UShort,
-    val modificationTime: UShort,
-    val modificationDate: UShort,
-    var crc32: UInt,
-    var compressedSize: UInt,
-    var uncompressedSize: UInt,
-    val diskNumber: UShort,
-    val internalAttributes: UShort,
-    val externalAttributes: UInt,
-    var localHeaderOffset: UInt,
-    val fileName: String,
-    val extraField: ByteArray,
-    val fileComment: String,
-    var localExtraField: ByteArray = ByteArray(0), //separate for alignment
-) {
-    val LFHSize: Int
-        get() = LFH_HEADER_SIZE + fileName.toByteArray(Charsets.UTF_8).size + localExtraField.size
-
-    val dataOffset: UInt
-        get() = localHeaderOffset + LFHSize.toUInt()
-
-    companion object {
-        const val CDE_HEADER_SIZE = 46
-        const val CDE_SIGNATURE = 0x02014b50u
-
-        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()
-
-            if (signature != CDE_SIGNATURE)
-                throw IllegalArgumentException("Input doesn't start with central directory entry signature")
-
-            val version = input.readUShortLE()
-            val versionNeeded = input.readUShortLE()
-            var flags = input.readUShortLE()
-            val compression = input.readUShortLE()
-            val modificationTime = input.readUShortLE()
-            val modificationDate = input.readUShortLE()
-            val crc32 = input.readUIntLE()
-            val compressedSize = input.readUIntLE()
-            val uncompressedSize = input.readUIntLE()
-            val fileNameLength = input.readUShortLE()
-            var fileName = ""
-            val extraFieldLength = input.readUShortLE()
-            val extraField = ByteArray(extraFieldLength.toInt())
-            val fileCommentLength = input.readUShortLE()
-            var fileComment = ""
-            val diskNumber = input.readUShortLE()
-            val internalAttributes = input.readUShortLE()
-            val externalAttributes = input.readUIntLE()
-            val localHeaderOffset = input.readUIntLE()
-
-            val variableFieldsLength =
-                fileNameLength.toInt() + extraFieldLength.toInt() + fileCommentLength.toInt()
-
-            if (variableFieldsLength > 0) {
-                val fileNameBytes = ByteArray(fileNameLength.toInt())
-                input.readFully(fileNameBytes)
-                fileName = fileNameBytes.toString(Charsets.UTF_8)
-
-                input.readFully(extraField)
-
-                val fileCommentBytes = ByteArray(fileCommentLength.toInt())
-                input.readFully(fileCommentBytes)
-                fileComment = fileCommentBytes.toString(Charsets.UTF_8)
-            }
-
-            flags = (flags and 0b1000u.inv()
-                .toUShort()) //disable data descriptor flag as they are not used
-
-            return ZipEntry(
-                version,
-                versionNeeded,
-                flags,
-                compression,
-                modificationTime,
-                modificationDate,
-                crc32,
-                compressedSize,
-                uncompressedSize,
-                diskNumber,
-                internalAttributes,
-                externalAttributes,
-                localHeaderOffset,
-                fileName,
-                extraField,
-                fileComment,
-            )
-        }
-    }
-
-    fun readLocalExtra(buffer: ByteBuffer) {
-        buffer.order(ByteOrder.LITTLE_ENDIAN)
-        localExtraField = ByteArray(buffer.getUShort().toInt())
-    }
-
-    fun toLFH(): ByteBuffer {
-        val nameBytes = fileName.toByteArray(Charsets.UTF_8)
-
-        val buffer = ByteBuffer.allocate(LFH_HEADER_SIZE + nameBytes.size + localExtraField.size)
-            .also { it.order(ByteOrder.LITTLE_ENDIAN) }
-
-        buffer.putUInt(LFH_SIGNATURE)
-        buffer.putUShort(versionNeeded)
-        buffer.putUShort(flags)
-        buffer.putUShort(compression)
-        buffer.putUShort(modificationTime)
-        buffer.putUShort(modificationDate)
-        buffer.putUInt(crc32)
-        buffer.putUInt(compressedSize)
-        buffer.putUInt(uncompressedSize)
-        buffer.putUShort(nameBytes.size.toUShort())
-        buffer.putUShort(localExtraField.size.toUShort())
-
-        buffer.put(nameBytes)
-        buffer.put(localExtraField)
-
-        buffer.flip()
-        return buffer
-    }
-
-    fun toCDE(): ByteBuffer {
-        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) }
-
-        buffer.putUInt(CDE_SIGNATURE)
-        buffer.putUShort(version)
-        buffer.putUShort(versionNeeded)
-        buffer.putUShort(flags)
-        buffer.putUShort(compression)
-        buffer.putUShort(modificationTime)
-        buffer.putUShort(modificationDate)
-        buffer.putUInt(crc32)
-        buffer.putUInt(compressedSize)
-        buffer.putUInt(uncompressedSize)
-        buffer.putUShort(nameBytes.size.toUShort())
-        buffer.putUShort(extraField.size.toUShort())
-        buffer.putUShort(commentBytes.size.toUShort())
-        buffer.putUShort(diskNumber)
-        buffer.putUShort(internalAttributes)
-        buffer.putUInt(externalAttributes)
-        buffer.putUInt(localHeaderOffset)
-
-        buffer.put(nameBytes)
-        buffer.put(extraField)
-        buffer.put(commentBytes)
-
-        buffer.flip()
-        return buffer
-    }
-}

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

@@ -1,92 +0,0 @@
-package app.revanced.utils.signing
-
-import com.android.apksig.ApkSigner
-import org.bouncycastle.asn1.x500.X500Name
-import org.bouncycastle.asn1.x509.SubjectPublicKeyInfo
-import org.bouncycastle.cert.X509v3CertificateBuilder
-import org.bouncycastle.cert.jcajce.JcaX509CertificateConverter
-import org.bouncycastle.jce.provider.BouncyCastleProvider
-import org.bouncycastle.operator.ContentSigner
-import org.bouncycastle.operator.jcajce.JcaContentSignerBuilder
-import java.io.File
-import java.io.FileInputStream
-import java.io.FileOutputStream
-import java.math.BigInteger
-import java.security.*
-import java.security.cert.X509Certificate
-import java.util.*
-import java.util.logging.Logger
-
-internal class ApkSigner(
-    private val signingOptions: SigningOptions
-) {
-    private val logger = Logger.getLogger(ApkSigner::class.java.name)
-
-    private val signer: ApkSigner.Builder
-    private val passwordCharArray = signingOptions.password.toCharArray()
-
-    init {
-        Security.addProvider(BouncyCastleProvider())
-
-        val keyStore = KeyStore.getInstance("BKS", "BC")
-        val alias = keyStore.let { store ->
-            FileInputStream(File(signingOptions.keyStoreFilePath).also {
-                if (!it.exists()) {
-                    logger.info("Creating keystore at ${it.absolutePath}")
-                    newKeystore(it)
-                } else {
-                    logger.info("Using keystore at ${it.absolutePath}")
-                }
-            }).use { fis -> store.load(fis, null) }
-            store.aliases().nextElement()
-        }
-
-        with(
-            ApkSigner.SignerConfig.Builder(
-                signingOptions.cn,
-                keyStore.getKey(alias, passwordCharArray) as PrivateKey,
-                listOf(keyStore.getCertificate(alias) as X509Certificate)
-            ).build()
-        ) {
-            this@ApkSigner.signer = ApkSigner.Builder(listOf(this))
-            signer.setCreatedBy(signingOptions.cn)
-        }
-    }
-
-    private fun newKeystore(out: File) {
-        val (publicKey, privateKey) = createKey()
-        val privateKS = KeyStore.getInstance("BKS", "BC")
-        privateKS.load(null, passwordCharArray)
-        privateKS.setKeyEntry("alias", privateKey, passwordCharArray, arrayOf(publicKey))
-        privateKS.store(FileOutputStream(out), passwordCharArray)
-    }
-
-    private fun createKey(): Pair<X509Certificate, PrivateKey> {
-        val gen = KeyPairGenerator.getInstance("RSA")
-        gen.initialize(2048)
-        val pair = gen.generateKeyPair()
-        var serialNumber: BigInteger
-        do serialNumber = BigInteger.valueOf(SecureRandom().nextLong()) while (serialNumber < BigInteger.ZERO)
-        val x500Name = X500Name("CN=${signingOptions.cn}")
-        val builder = X509v3CertificateBuilder(
-            x500Name,
-            serialNumber,
-            Date(System.currentTimeMillis() - 1000L * 60L * 60L * 24L * 30L),
-            Date(System.currentTimeMillis() + 1000L * 60L * 60L * 24L * 366L * 30L),
-            Locale.ENGLISH,
-            x500Name,
-            SubjectPublicKeyInfo.getInstance(pair.public.encoded)
-        )
-        val signer: ContentSigner = JcaContentSignerBuilder("SHA256withRSA").build(pair.private)
-        return JcaX509CertificateConverter().getCertificate(builder.build(signer)) to pair.private
-    }
-
-    fun signApk(input: File, output: File): File {
-        signer.setInputApk(input)
-        signer.setOutputApk(output)
-
-        signer.build().sign()
-
-        return output
-    }
-}

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

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

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

@@ -1,60 +0,0 @@
-package app.revanced.patcher.options
-
-import app.revanced.patcher.data.BytecodeContext
-import app.revanced.patcher.data.Context
-import app.revanced.patcher.patch.BytecodePatch
-import app.revanced.patcher.patch.OptionsContainer
-import app.revanced.patcher.patch.Patch
-import app.revanced.patcher.patch.PatchOption
-import app.revanced.utils.Options
-import app.revanced.utils.Options.setOptions
-import org.junit.jupiter.api.MethodOrderer
-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) {
-        // Do nothing
-    }
-
-    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}]}]"
-}