chore(release): 1.11.0 [skip ci]

# [1.11.0](https://github.com/revanced/revanced-cli/compare/v1.10.2...v1.11.0) (2022-06-23)

### Features

* improve logging ([df85fa3](df85fa37ef))

.github/workflows/release.yml

@@ -28,8 +28,6 @@ jobs:
         uses: actions/setup-node@v2
         with:
           node-version: "lts/*"
-      - name: Make gradlew executable
-        run: chmod +x gradlew
       - name: Build with Gradle
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

CHANGELOG.md

@@ -1,3 +1,151 @@
+# [1.11.0](https://github.com/revanced/revanced-cli/compare/v1.10.2...v1.11.0) (2022-06-23)
+
+
+### Features
+
+* improve logging ([df85fa3](https://github.com/revanced/revanced-cli/commit/df85fa37ef067681a027e6fe9212c8a065d4981b))
+
+## [1.10.2](https://github.com/revanced/revanced-cli/compare/v1.10.1...v1.10.2) (2022-06-22)
+
+
+### Bug Fixes
+
+* keystore file not found exception ([#57](https://github.com/revanced/revanced-cli/issues/57)) ([5b8537e](https://github.com/revanced/revanced-cli/commit/5b8537e6b7922f1b44058c3a4fc2f56cb4e15e89))
+
+## [1.10.1](https://github.com/revanced/revanced-cli/compare/v1.10.0...v1.10.1) (2022-06-22)
+
+
+### Bug Fixes
+
+* show actual version in CLI ([1dcdbc9](https://github.com/revanced/revanced-cli/commit/1dcdbc9fe9e3ad2fe232ad3baa76d186817532a4))
+
+# [1.10.0](https://github.com/revanced/revanced-cli/compare/v1.9.3...v1.10.0) (2022-06-22)
+
+
+### Bug Fixes
+
+* add callback for addFiles ([87ffaa4](https://github.com/revanced/revanced-cli/commit/87ffaa4bdb25cb85c6ba7195f5d3b13b09a5f912))
+
+
+### Features
+
+* add logging back ([4a23cb6](https://github.com/revanced/revanced-cli/commit/4a23cb69bc385158d47b6ea8d3da54b0566a242c))
+
+## [1.9.3](https://github.com/revanced/revanced-cli/compare/v1.9.2...v1.9.3) (2022-06-22)
+
+
+### Bug Fixes
+
+* use absolute file path for key store ([d335846](https://github.com/revanced/revanced-cli/commit/d335846202b991e130882e9ce0ab268deb2e27ab))
+
+## [1.9.2](https://github.com/revanced/revanced-cli/compare/v1.9.1...v1.9.2) (2022-06-22)
+
+
+### Bug Fixes
+
+* update patcher version ([0df936e](https://github.com/revanced/revanced-cli/commit/0df936e99b01358a88a628af63eebb5ac92cae76))
+
+## [1.9.1](https://github.com/revanced/revanced-cli/compare/v1.9.0...v1.9.1) (2022-06-22)
+
+
+### Bug Fixes
+
+* add back in: option to specify keystore file path ([c94471f](https://github.com/revanced/revanced-cli/commit/c94471f4643e44b2b472ff0d826db0d2743bdc86))
+* remove logger from Signer.kt ([51e091c](https://github.com/revanced/revanced-cli/commit/51e091ce4021418508044029aa5af6aa7d5162a3))
+
+
+### Reverts
+
+* "feat: use of `java.util.logging.Logger`" ([2c8a106](https://github.com/revanced/revanced-cli/commit/2c8a10615192635202ddc137fc02f175c5914d8f))
+
+# [1.9.0](https://github.com/revanced/revanced-cli/compare/v1.8.0...v1.9.0) (2022-06-22)
+
+
+### Features
+
+* migrate logger to `slf4j` ([6c4c192](https://github.com/revanced/revanced-cli/commit/6c4c1924ee9ae75af3449749a6a82b7ae5572129))
+
+# [1.8.0](https://github.com/revanced/revanced-cli/compare/v1.7.1...v1.8.0) (2022-06-22)
+
+
+### Features
+
+* add option to specify keystore file path ([9331594](https://github.com/revanced/revanced-cli/commit/9331594706404df871d170110da753cde5058d02))
+* use of `java.util.logging.Logger` ([07f6bdf](https://github.com/revanced/revanced-cli/commit/07f6bdf33069da4e11fc40090feb726433de703e))
+
+## [1.7.1](https://github.com/revanced/revanced-cli/compare/v1.7.0...v1.7.1) (2022-06-22)
+
+
+### Bug Fixes
+
+* migrate to changes of patcher ([b30c737](https://github.com/revanced/revanced-cli/commit/b30c7375a7ea61184be5dca19062ee74d1f97692))
+* wrong variable inverted ([f694542](https://github.com/revanced/revanced-cli/commit/f694542d64ccb06bfa4d042f26b6b7192d1e912e))
+
+# [1.7.0](https://github.com/revanced/revanced-cli/compare/v1.6.3...v1.7.0) (2022-06-21)
+
+
+### Features
+
+* show description when listing patches ([af32572](https://github.com/revanced/revanced-cli/commit/af32572f29d0f0a45ee5c3e01ba4cf1f91fe2f10))
+
+## [1.6.3](https://github.com/revanced/revanced-cli/compare/v1.6.2...v1.6.3) (2022-06-21)
+
+
+### Bug Fixes
+
+* update patcher version ([80c11fe](https://github.com/revanced/revanced-cli/commit/80c11fef734bdba9026e91f95ee0a4a522cbefab))
+
+## [1.6.2](https://github.com/revanced/revanced-cli/compare/v1.6.1...v1.6.2) (2022-06-21)
+
+
+### Bug Fixes
+
+* CLI not working ([29105ba](https://github.com/revanced/revanced-cli/commit/29105bab3dabd9d16af6b511caef9727f98afd1a))
+* improper use of mount variable ([31853fe](https://github.com/revanced/revanced-cli/commit/31853fe5393af04805857b78a54434e1c51e4c8e))
+
+## [1.6.1](https://github.com/revanced/revanced-cli/compare/v1.6.0...v1.6.1) (2022-06-21)
+
+
+### Bug Fixes
+
+* remove `-e` from `experimental` option ([3829136](https://github.com/revanced/revanced-cli/commit/3829136c49ddce1dc6b01eda04ce013540b213c2))
+
+# [1.6.0](https://github.com/revanced/revanced-cli/compare/v1.5.1...v1.6.0) (2022-06-21)
+
+
+### Features
+
+* rename `debugging` option to `experimental` ([98bd6f3](https://github.com/revanced/revanced-cli/commit/98bd6f3f4b3eb34c445cbd5e3a3196f399f8bb3b))
+* use `install` mode by default ([1a3db77](https://github.com/revanced/revanced-cli/commit/1a3db77c21b5795220fbac1ec36827fc521fface))
+
+## [1.5.1](https://github.com/revanced/revanced-cli/compare/v1.5.0...v1.5.1) (2022-06-21)
+
+
+### Bug Fixes
+
+* update patcher version ([09b9027](https://github.com/revanced/revanced-cli/commit/09b9027e5e28f0483e74b711cf65a7876267a339)), closes [#45](https://github.com/revanced/revanced-cli/issues/45)
+
+# [1.5.0](https://github.com/revanced/revanced-cli/compare/v1.4.5...v1.5.0) (2022-06-20)
+
+
+### Features
+
+* allow listing patches without other parameters ([#42](https://github.com/revanced/revanced-cli/issues/42)) ([b977d70](https://github.com/revanced/revanced-cli/commit/b977d7039f877be242823a4eef0fb8df6550dd05))
+
+## [1.4.5](https://github.com/revanced/revanced-cli/compare/v1.4.4...v1.4.5) (2022-06-20)
+
+
+### Bug Fixes
+
+* update patcher version (fix apktool) ([496f821](https://github.com/revanced/revanced-cli/commit/496f82121879443609667a792cc1e16441ef5c2f))
+
+## [1.4.4](https://github.com/revanced/revanced-cli/compare/v1.4.3...v1.4.4) (2022-06-18)
+
+
+### Bug Fixes
+
+* add execute permission to `./gradlew` file ([#36](https://github.com/revanced/revanced-cli/issues/36)) ([072d9e1](https://github.com/revanced/revanced-cli/commit/072d9e15d7e44b1080923f3afeb194eeb4fe4682))
+
 ## [1.4.3](https://github.com/revanced/revanced-cli/compare/v1.4.2...v1.4.3) (2022-06-18)
 
 

build.gradle.kts

@@ -31,7 +31,8 @@ repositories {
 dependencies {
     implementation(kotlin("stdlib"))
     implementation(kotlin("reflect"))
-    implementation("app.revanced:revanced-patcher:1.2.5")
+
+    implementation("app.revanced:revanced-patcher:1.10.0")
     implementation("info.picocli:picocli:4.6.3")
     implementation("com.android.tools.build:apksig:7.2.1")
     implementation("com.github.revanced:jadb:master-SNAPSHOT") // updated fork

gradle.properties

@@ -1,2 +1,2 @@
 kotlin.code.style = official
-version = 1.4.3
+version = 1.11.0

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

@@ -1,108 +1,146 @@
 package app.revanced.cli.command
 
+import app.revanced.cli.logging.impl.DefaultCliLogger
 import app.revanced.cli.patcher.Patcher
+import app.revanced.cli.patcher.logging.impl.PatcherLogger
 import app.revanced.cli.signing.Signing
+import app.revanced.cli.signing.SigningOptions
 import app.revanced.patcher.PatcherOptions
+import app.revanced.patcher.extensions.PatchExtensions.description
 import app.revanced.patcher.extensions.PatchExtensions.patchName
 import app.revanced.patcher.util.patch.implementation.JarPatchBundle
 import app.revanced.utils.adb.Adb
-import picocli.CommandLine.Command
-import picocli.CommandLine.Option
+import picocli.CommandLine.*
 import java.io.File
 import java.nio.file.Files
 
+private class CLIVersionProvider : IVersionProvider {
+    override fun getVersion() = arrayOf(
+        MainCommand::class.java.`package`.implementationVersion ?: "unknown"
+    )
+}
+
 @Command(
-    name = "ReVanced-CLI", version = ["1.0.0"], mixinStandardHelpOptions = true,
+    name = "ReVanced-CLI",
+    mixinStandardHelpOptions = true,
+    versionProvider = CLIVersionProvider::class
 )
 internal object MainCommand : Runnable {
-    @Option(names = ["-a", "--apk"], description = ["Input file to be patched"], required = true)
-    lateinit var inputFile: File
+    val logger = DefaultCliLogger()
 
-    @Option(names = ["-o", "--out"], description = ["Output file path"], required = true)
-    lateinit var outputPath: String
+    @ArgGroup(exclusive = false, multiplicity = "1")
+    lateinit var args: Args
 
-    @Option(
-        names = ["-i", "--include"],
-        description = ["Which patches to include. If none is specified, all compatible default patches will be included"]
-    )
-    var includedPatches = arrayOf<String>()
+    class Args {
+        @Option(names = ["-b", "--bundles"], description = ["One or more bundles of patches"], required = true)
+        var patchBundles = arrayOf<String>()
 
-    @Option(names = ["-r", "--resource-patcher"], description = ["Disable patching resources"])
-    var disableResourcePatching: Boolean = false
+        @ArgGroup(exclusive = false)
+        var lArgs: ListingArgs? = null
 
-    @Option(names = ["--debugging"], description = ["Disable patch version compatibility"])
-    var debugging: Boolean = false
+        @ArgGroup(exclusive = false)
+        var pArgs: PatchingArgs? = null
+    }
 
-    @Option(names = ["-m", "--merge"], description = ["One or more dex file containers to merge"])
-    var mergeFiles = listOf<File>()
+    class ListingArgs {
+        @Option(names = ["-l", "--list"], description = ["List patches only"], required = true)
+        var listOnly: Boolean = false
+    }
 
-    @Option(names = ["-b", "--bundles"], description = ["One or more bundles of patches"])
-    var patchBundles = arrayOf<String>()
+    class PatchingArgs {
+        @Option(names = ["-a", "--apk"], description = ["Input file to be patched"], required = true)
+        lateinit var inputFile: File
 
-    @Option(names = ["-l", "--list"], description = ["List patches only"])
-    var listOnly: Boolean = false
+        @Option(names = ["-o", "--out"], description = ["Output file path"], required = true)
+        lateinit var outputPath: String
 
-    @Option(names = ["--install"], description = ["If specified, instead of mounting, install"])
-    var install: Boolean = false
+        @Option(names = ["-e", "--exclude"], description = ["Explicitly exclude patches"])
+        var excludedPatches = arrayOf<String>()
 
-    @Option(names = ["--cn"], description = ["Overwrite the default CN for the signed file"])
-    var cn = "ReVanced"
+        @Option(names = ["-r", "--resource-patcher"], description = ["Disable patching resources"])
+        var disableResourcePatching: Boolean = false
 
-    @Option(names = ["-p", "--password"], description = ["Overwrite the default password for the signed file"])
-    var password = "ReVanced"
+        @Option(names = ["--experimental"], description = ["Disable patch version compatibility patch"])
+        var experimental: Boolean = false
 
-    @Option(names = ["-d", "--deploy-on"], description = ["If specified, deploy to adb device with given name"])
-    var deploy: String? = null
+        @Option(names = ["-m", "--merge"], description = ["One or more dex file containers to merge"])
+        var mergeFiles = listOf<File>()
 
-    @Option(names = ["-t", "--temp-dir"], description = ["Temporal resource cache directory"])
-    var cacheDirectory = "revanced-cache"
+        @Option(names = ["--mount"], description = ["If specified, instead of installing, mount"])
+        var mount: Boolean = false
 
-    @Option(
-        names = ["-c", "--clean"],
-        description = ["Clean the temporal resource cache directory. This will be done anyways when running the patcher"]
-    )
-    var clean: Boolean = false
+        @Option(names = ["--cn"], description = ["Overwrite the default CN for the signed file"])
+        var cn = "ReVanced"
+
+        @Option(names = ["--keystore"], description = ["File path to your keystore"])
+        var keystorePath: String? = null
+
+        @Option(names = ["-p", "--password"], description = ["Overwrite the default password for the signed file"])
+        var password = "ReVanced"
+
+        @Option(names = ["-d", "--deploy-on"], description = ["If specified, deploy to adb device with given name"])
+        var deploy: String? = null
+
+        @Option(names = ["-t", "--temp-dir"], description = ["Temporal resource cache directory"])
+        var cacheDirectory = "revanced-cache"
+
+        @Option(
+            names = ["-c", "--clean"],
+            description = ["Clean the temporal resource cache directory. This will be done anyways when running the patcher"]
+        )
+        var clean: Boolean = false
+    }
 
     override fun run() {
-        if (listOnly) {
-            for (patchBundlePath in patchBundles) for (patch in JarPatchBundle(patchBundlePath).loadPatches()) {
-                println("[available] ${patch.patchName}")
+        if (args.lArgs?.listOnly == true) {
+            for (patchBundlePath in args.patchBundles) for (patch in JarPatchBundle(patchBundlePath).loadPatches()) {
+                logger.info("${patch.patchName}: ${patch.description}")
             }
             return
         }
 
-        val patcher = app.revanced.patcher.Patcher(PatcherOptions(inputFile, cacheDirectory, !disableResourcePatching))
+        val args = args.pArgs ?: return
 
-        val outputFile = File(outputPath)
+        val patcher = app.revanced.patcher.Patcher(
+            PatcherOptions(
+                args.inputFile,
+                args.cacheDirectory,
+                !args.disableResourcePatching,
+                logger = PatcherLogger
+            )
+        )
 
-        val adb: Adb? = deploy?.let {
-            Adb(outputFile, patcher.data.packageMetadata.packageName, deploy!!, install)
+        val outputFile = File(args.outputPath)
+
+        val adb: Adb? = args.deploy?.let {
+            Adb(outputFile, patcher.data.packageMetadata.packageName, args.deploy!!, !args.mount)
         }
 
-        val patchedFile = if (install) File(cacheDirectory).resolve("${outputFile.nameWithoutExtension}_raw.apk") else outputFile
+        val patchedFile = if (args.mount) outputFile
+        else File(args.cacheDirectory).resolve("${outputFile.nameWithoutExtension}_raw.apk")
 
         Patcher.start(patcher, patchedFile)
 
-        println("[aligning & signing]")
-
-        if (install) {
+        if (!args.mount) {
             Signing.start(
                 patchedFile,
                 outputFile,
-                cn,
-                password,
+                SigningOptions(
+                    args.cn,
+                    args.password,
+                    args.keystorePath ?: outputFile.absoluteFile.parentFile
+                        .resolve("${outputFile.nameWithoutExtension}.keystore")
+                        .name
+                )
             )
         }
 
-        if (clean) File(cacheDirectory).deleteRecursively()
+        if (args.clean) File(args.cacheDirectory).deleteRecursively()
 
-        adb?.let {
-            println("[deploying]")
-            it.deploy()
-        }
+        adb?.deploy()
 
-        if (clean && deploy != null) Files.delete(outputFile.toPath())
+        if (args.clean && args.deploy != null) Files.delete(outputFile.toPath())
 
-        println("[done]")
+        logger.info("Finished")
     }
 }

src/main/kotlin/app/revanced/cli/logging/CliLogger.kt

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

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

@@ -0,0 +1,20 @@
+package app.revanced.cli.logging.impl
+
+import app.revanced.cli.command.MainCommand
+import app.revanced.cli.logging.CliLogger
+import java.util.logging.Logger
+
+internal class DefaultCliLogger(
+    private val logger: Logger = Logger.getLogger(MainCommand::javaClass.name)
+) : CliLogger {
+    companion object {
+        init {
+            System.setProperty("java.util.logging.SimpleFormatter.format", "%4\$s: %5\$s %n")
+        }
+    }
+
+    override fun error(msg: String) = logger.severe(msg)
+    override fun info(msg: String) = logger.info(msg)
+    override fun trace(msg: String) = logger.finest(msg)
+    override fun warn(msg: String) = logger.warning(msg)
+}

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

@@ -1,9 +1,7 @@
 package app.revanced.cli.patcher
 
-import app.revanced.cli.command.MainCommand.cacheDirectory
-import app.revanced.cli.command.MainCommand.disableResourcePatching
-import app.revanced.cli.command.MainCommand
-import app.revanced.cli.command.MainCommand.includedPatches
+import app.revanced.cli.command.MainCommand.args
+import app.revanced.cli.command.MainCommand.logger
 import app.revanced.utils.filesystem.ZipFileSystemUtils
 import app.revanced.utils.patcher.addPatchesFiltered
 import app.revanced.utils.patcher.applyPatchesVerbose
@@ -13,27 +11,35 @@ import java.nio.file.Files
 
 internal object Patcher {
     internal fun start(patcher: app.revanced.patcher.Patcher, output: File) {
+        val args = args.pArgs!!
+
         // merge files like necessary integrations
         patcher.mergeFiles()
         // add patches, but filter incompatible or excluded patches
-        patcher.addPatchesFiltered(includeFilter = includedPatches.isNotEmpty())
+        patcher.addPatchesFiltered(excludePatches = args.excludedPatches.isNotEmpty())
         // apply patches
         patcher.applyPatchesVerbose()
 
         // write output file
         if (output.exists()) Files.delete(output.toPath())
-        MainCommand.inputFile.copyTo(output)
+        args.inputFile.copyTo(output)
 
-        ZipFileSystemUtils(output).use { fileSystem ->
+        val result = patcher.save()
+        val inputFile = if (!args.disableResourcePatching && result.resourceFile != null) {
+            result.resourceFile
+        } else null
+        ZipFileSystemUtils(inputFile, output).use { fileSystem ->
             // replace all dex files
-            val result = patcher.save()
             result.dexFiles.forEach {
-                fileSystem.write(it.name, it.memoryDataStore.data)
+                logger.info("Writing dex file ${it.name}")
+                fileSystem.write(it.name, it.dexFileInputStream.readAllBytes())
             }
 
-            // write resources
-            if (!disableResourcePatching) {
-                fileSystem.writePathRecursively(File(cacheDirectory).resolve("build").toPath())
+            // inputFile being null implies resource patching being disabled
+            if (inputFile != null) {
+                // write resources
+                logger.info("Writing resources")
+                fileSystem.writeInput()
                 fileSystem.uncompress(*result.doNotCompress!!.toTypedArray())
             }
         }

src/main/kotlin/app/revanced/cli/patcher/logging/impl/PatcherLogger.kt

@@ -0,0 +1,13 @@
+package app.revanced.cli.patcher.logging.impl
+
+import app.revanced.cli.logging.impl.DefaultCliLogger
+import java.util.logging.Logger
+
+internal object PatcherLogger : app.revanced.patcher.logging.Logger{
+    private val logger = DefaultCliLogger(Logger.getLogger(app.revanced.patcher.Patcher::javaClass.name))
+
+    override fun error(msg: String) = logger.error(msg)
+    override fun info(msg: String) = logger.info(msg)
+    override fun warn(msg: String)= logger.warn(msg)
+    override fun trace(msg: String)= logger.trace(msg)
+}

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

@@ -1,25 +1,28 @@
 package app.revanced.cli.signing
 
-import app.revanced.cli.command.MainCommand.cacheDirectory
+import app.revanced.cli.command.MainCommand.args
+import app.revanced.cli.command.MainCommand.logger
 import app.revanced.utils.signing.Signer
 import app.revanced.utils.signing.align.ZipAligner
 import java.io.File
 
 object Signing {
-    fun start(inputFile: File, outputFile: File, cn: String, password: String) {
-        val cacheDirectory = File(cacheDirectory)
+    fun start(inputFile: File, outputFile: File, signingOptions: SigningOptions) {
+        val cacheDirectory = File(args.pArgs!!.cacheDirectory)
         val alignedOutput = cacheDirectory.resolve("${outputFile.nameWithoutExtension}_aligned.apk")
         val signedOutput = cacheDirectory.resolve("${outputFile.nameWithoutExtension}_signed.apk")
 
         // align the inputFile and write to alignedOutput
+        logger.info("Aligning ${inputFile.name}")
         ZipAligner.align(inputFile, alignedOutput)
         // sign the alignedOutput and write to signedOutput
         // the reason is, in case the signer fails
         // it does not damage the output file
-        val keyStore = Signer(cn, password).signApk(alignedOutput, signedOutput)
+        logger.info("Signing ${alignedOutput.name}")
+        Signer(signingOptions).signApk(alignedOutput, signedOutput)
 
-        // afterwards copy over the file and the keystore to the output
+        // afterwards copy over the file to the output
+        logger.info("Copying ${signedOutput.name} to ${outputFile.name}")
         signedOutput.copyTo(outputFile, true)
-        keyStore.copyTo(outputFile.resolveSibling(keyStore.name), true)
     }
 }

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

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

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

@@ -1,5 +1,6 @@
 package app.revanced.utils.adb
 
+import app.revanced.cli.command.MainCommand.logger
 import se.vidstige.jadb.JadbConnection
 import se.vidstige.jadb.JadbDevice
 import se.vidstige.jadb.managers.PackageManager
@@ -20,7 +21,7 @@ internal class Adb(
             ?: throw IllegalArgumentException("No such device with name $deviceName")
 
         if (!modeInstall && device.run("su -h", false) != 0)
-            throw IllegalArgumentException("Root required on $deviceName. Deploying failed.")
+            throw IllegalArgumentException("Root required on $deviceName. Deploying failed")
     }
 
     private fun String.replacePlaceholder(with: String? = null): String {
@@ -29,8 +30,12 @@ internal class Adb(
 
     internal fun deploy() {
         if (modeInstall) {
+            logger.info("Installing without mounting")
+
             PackageManager(device).install(file)
         } else {
+            logger.info("Installing by mounting")
+
             // push patched file
             device.copy(Constants.PATH_INIT_PUSH, file)
 
@@ -91,10 +96,10 @@ internal class Adb(
                 }
                 break
             } catch (e: Exception) {
-                throw RuntimeException("An error occurred while monitoring state of app", e)
+                throw RuntimeException("An error occurred while monitoring the state of app", e)
             }
         }
-        println("App closed, continuing.")
+        logger.info("Stopped logging because the app was closed")
         process.destroy()
         executor.shutdown()
     }

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

@@ -7,12 +7,17 @@ import java.nio.file.Files
 import java.nio.file.Path
 import java.util.zip.ZipEntry
 
-internal class ZipFileSystemUtils(
-    file: File
-) : Closeable {
-    private var zipFileSystem = FileSystems.newFileSystem(file.toPath(), mapOf("noCompression" to true))
+internal class ZipFileSystemUtils(input: File?, output: File) : Closeable {
+    private val inFileSystem = if (input != null) {
+        FileSystems.newFileSystem(input.toPath())
+    } else null
+    private val outFileSystem = FileSystems.newFileSystem(output.toPath(), mapOf("noCompression" to true))
 
     private fun Path.deleteRecursively() {
+        if (!Files.exists(this)) {
+            throw IllegalStateException("File exists in input but not in output, cannot delete")
+        }
+
         if (Files.isDirectory(this)) {
             Files.list(this).forEach { path ->
                 path.deleteRecursively()
@@ -22,19 +27,25 @@ internal class ZipFileSystemUtils(
         Files.delete(this)
     }
 
-    internal fun writePathRecursively(path: Path) {
-        Files.list(path).let { fileStream ->
+    internal fun writeInput() {
+        if (inFileSystem == null) {
+            throw IllegalArgumentException("Input file not set")
+        }
+        val root = inFileSystem.getPath(inFileSystem.separator)
+
+        Files.list(root).close()
+
+        Files.list(root).also { fileStream ->
             fileStream.forEach { filePath ->
-                val fileSystemPath = filePath.getRelativePath(path)
+                val fileSystemPath = filePath.getRelativePath(root)
                 fileSystemPath.deleteRecursively()
             }
-
-            fileStream
         }.close()
 
-        Files.walk(path).let { fileStream ->
+        Files.walk(root).also { fileStream ->
+            // don't include build directory by skipping the root node.
             fileStream.skip(1).forEach { filePath ->
-                val relativePath = filePath.getRelativePath(path)
+                val relativePath = filePath.getRelativePath(root)
 
                 if (Files.isDirectory(filePath)) {
                     Files.createDirectory(relativePath)
@@ -43,17 +54,18 @@ internal class ZipFileSystemUtils(
 
                 Files.copy(filePath, relativePath)
             }
-
-            fileStream
         }.close()
     }
 
-    internal fun write(path: String, content: ByteArray) = Files.write(zipFileSystem.getPath(path), content)
+    internal fun write(path: String, content: ByteArray) = Files.write(outFileSystem.getPath(path), content)
 
-    private fun Path.getRelativePath(path: Path): Path = zipFileSystem.getPath(path.relativize(this).toString())
+    private fun Path.getRelativePath(path: Path): Path = outFileSystem.getPath(path.relativize(this).toString())
 
     internal fun uncompress(vararg paths: String) =
-        paths.forEach { Files.setAttribute(zipFileSystem.getPath(it), "zip:method", ZipEntry.STORED) }
+        paths.forEach { Files.setAttribute(outFileSystem.getPath(it), "zip:method", ZipEntry.STORED) }
 
-    override fun close() = zipFileSystem.close()
+    override fun close() {
+        inFileSystem?.close()
+        outFileSystem.close()
+    }
 }

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

@@ -1,8 +1,8 @@
 package app.revanced.utils.patcher
 
 import app.revanced.cli.command.MainCommand
-import app.revanced.cli.command.MainCommand.debugging
-import app.revanced.cli.command.MainCommand.patchBundles
+import app.revanced.cli.command.MainCommand.args
+import app.revanced.cli.command.MainCommand.logger
 import app.revanced.patcher.Patcher
 import app.revanced.patcher.data.base.Data
 import app.revanced.patcher.extensions.PatchExtensions.compatiblePackages
@@ -12,44 +12,51 @@ import app.revanced.patcher.patch.base.Patch
 import app.revanced.patcher.util.patch.implementation.JarPatchBundle
 
 fun Patcher.addPatchesFiltered(
-    includeFilter: Boolean = false
+    excludePatches: Boolean = false
 ) {
     val packageName = this.data.packageMetadata.packageName
     val packageVersion = this.data.packageMetadata.packageVersion
 
-    patchBundles.forEach { bundle ->
+    args.patchBundles.forEach { bundle ->
         val includedPatches = mutableListOf<Class<out Patch<Data>>>()
         JarPatchBundle(bundle).loadPatches().forEach patch@{ patch ->
             val compatiblePackages = patch.compatiblePackages
             val patchName = patch.patchName
 
-            val prefix = "[skipped] $patchName"
+            val prefix = "Skipping $patchName"
 
-            if (includeFilter) {
-                if (!MainCommand.includedPatches.contains(patchName)) {
-                    println("$prefix: Explicitly excluded.")
-                    return@patch
-                }
+            val args = MainCommand.args.pArgs!!
+
+            if (excludePatches && args.excludedPatches.contains(patchName)) {
+                logger.info("$prefix: Explicitly excluded")
+                return@patch
             } else if (!patch.include) {
-                println("$prefix: Implicitly excluded.")
+                logger.info("$prefix: Explicitly excluded")
                 return@patch
             }
 
-            if (compatiblePackages == null) println("$prefix: Missing compatibility annotation. Continuing.")
+            if (compatiblePackages == null) logger.warn("$prefix: Missing compatibility annotation. Continuing.")
             else {
                 if (!compatiblePackages.any { it.name == packageName }) {
-                    println("$prefix: Incompatible package.")
+                    logger.warn("$prefix: Incompatible with $packageName. This patch is only compatible with ${
+                        compatiblePackages.joinToString(
+                            ", "
+                        ) { it.name }
+                    }")
                     return@patch
                 }
 
-                if (!(debugging || compatiblePackages.any { it.versions.isEmpty() || it.versions.any { version -> version == packageVersion }})) {
-                    println("$prefix: The package version is $packageVersion and is incompatible.")
+                if (!(args.experimental || compatiblePackages.any { it.versions.isEmpty() || it.versions.any { version -> version == packageVersion } })) {
+                    val compatibleWith = compatiblePackages.map { _package ->
+                        "${_package.name}: ${_package.versions.joinToString(", ")}"
+                    }.joinToString(";")
+                    logger.warn("$prefix: Incompatible with version $packageVersion. This patch is only compatible with version $compatibleWith")
                     return@patch
                 }
             }
 
+            logger.trace("Adding $patchName")
             includedPatches.add(patch)
-            println("[added] $patchName")
         }
         this.addPatches(includedPatches)
     }
@@ -58,14 +65,16 @@ fun Patcher.addPatchesFiltered(
 fun Patcher.applyPatchesVerbose() {
     this.applyPatches().forEach { (patch, result) ->
         if (result.isSuccess) {
-            println("[success] $patch")
+            logger.info("$patch succeeded")
             return@forEach
         }
-        println("[error] $patch:")
+        logger.error("$patch failed:")
         result.exceptionOrNull()!!.printStackTrace()
     }
 }
 
 fun Patcher.mergeFiles() {
-    this.addFiles(MainCommand.mergeFiles)
-}
+    this.addFiles(args.pArgs!!.mergeFiles) { file ->
+        logger.info("Merging $file")
+    }
+}

src/main/kotlin/app/revanced/utils/signature/Signature.kt

@@ -1,7 +1,6 @@
 package app.revanced.utils.signature
 
 import app.revanced.patcher.Patcher
-import org.jf.dexlib2.iface.Method
 
 object Signature {
 
@@ -49,7 +48,7 @@ object Signature {
          */
     }
 
-    private fun Method.toStr(): String {
-        return "${this.name}(${this.parameterTypes.joinToString("")})${this.returnType}"
-    }
+    //private fun Method.toStr(): String {
+    //    return "${this.name}(${this.parameterTypes.joinToString("")})${this.returnType}"
+    //}
 }

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

@@ -1,5 +1,7 @@
 package app.revanced.utils.signing
 
+import app.revanced.cli.command.MainCommand.logger
+import app.revanced.cli.signing.SigningOptions
 import com.android.apksig.ApkSigner
 import org.bouncycastle.asn1.x500.X500Name
 import org.bouncycastle.asn1.x509.SubjectPublicKeyInfo
@@ -17,9 +19,9 @@ import java.security.cert.X509Certificate
 import java.util.*
 
 internal class Signer(
-    private val cn: String, password: String
+    private val signingOptions: SigningOptions
 ) {
-    private val passwordCharArray = password.toCharArray()
+    private val passwordCharArray = signingOptions.password.toCharArray()
     private fun newKeystore(out: File) {
         val (publicKey, privateKey) = createKey()
         val privateKS = KeyStore.getInstance("BKS", "BC")
@@ -34,7 +36,7 @@ internal class Signer(
         val pair = gen.generateKeyPair()
         var serialNumber: BigInteger
         do serialNumber = BigInteger.valueOf(SecureRandom().nextLong()) while (serialNumber < BigInteger.ZERO)
-        val x500Name = X500Name("CN=$cn")
+        val x500Name = X500Name("CN=${signingOptions.cn}")
         val builder = X509v3CertificateBuilder(
             x500Name,
             serialNumber,
@@ -48,30 +50,30 @@ internal class Signer(
         return JcaX509CertificateConverter().getCertificate(builder.build(signer)) to pair.private
     }
 
-    fun signApk(input: File, output: File): File {
+    fun signApk(input: File, output: File) {
         Security.addProvider(BouncyCastleProvider())
 
         // TODO: keystore should be saved securely
-        val ks = File(input.parent, "${output.nameWithoutExtension}.keystore")
-        if (!ks.exists()) newKeystore(ks)
+        val ks = File(signingOptions.keyStoreFilePath)
+        if (!ks.exists()) newKeystore(ks) else {
+            logger.info("Found existing keystore: ${ks.nameWithoutExtension}")
+        }
 
         val keyStore = KeyStore.getInstance("BKS", "BC")
         FileInputStream(ks).use { fis -> keyStore.load(fis, null) }
         val alias = keyStore.aliases().nextElement()
 
         val config = ApkSigner.SignerConfig.Builder(
-            cn,
+            signingOptions.cn,
             keyStore.getKey(alias, passwordCharArray) as PrivateKey,
             listOf(keyStore.getCertificate(alias) as X509Certificate)
         ).build()
 
         val signer = ApkSigner.Builder(listOf(config))
-        signer.setCreatedBy(cn)
+        signer.setCreatedBy(signingOptions.cn)
         signer.setInputApk(input)
         signer.setOutputApk(output)
 
         signer.build().sign()
-
-        return ks
     }
 }