diff --git a/build.gradle.kts b/build.gradle.kts
index c9b9851..1b22dc1 100644
--- a/build.gradle.kts
+++ b/build.gradle.kts
@@ -24,31 +24,25 @@ val patchesDependency = "app.revanced:revanced-patches:1.0.0-dev.4"
 
 dependencies {
     implementation(kotlin("stdlib"))
-    implementation("org.jetbrains.kotlinx:kotlinx-cli:0.3.4")
-
-    implementation("app.revanced:revanced-patcher:1.0.0-dev.8")
+    implementation("app.revanced:revanced-patcher:+")
     implementation(patchesDependency)
+    implementation("info.picocli:picocli:+")
 
-    implementation("com.google.code.gson:gson:2.9.0")
-    implementation("me.tongfei:progressbar:0.9.3")
+    implementation("me.tongfei:progressbar:+")
     implementation("com.github.li-wjohnson:jadb:master-SNAPSHOT") // using a fork instead.
-    implementation("org.bouncycastle:bcpkix-jdk15on:1.70")
+    implementation("org.bouncycastle:bcpkix-jdk15on:+")
 }
 
-val cliMainClass = "app.revanced.cli.Main"
-
 tasks {
     build {
         dependsOn(shadowJar)
     }
     shadowJar {
         dependencies {
-            // This makes sure we link to the library, but don't include it.
-            // So, a "runtime only" dependency.
             exclude(dependency(patchesDependency))
         }
         manifest {
-            attributes("Main-Class" to cliMainClass)
+            attributes("Main-Class" to "app.revanced.cli.MainKt")
             attributes("Implementation-Title" to project.name)
             attributes("Implementation-Version" to project.version)
         }
diff --git a/src/main/kotlin/app/revanced/cli/Main.kt b/src/main/kotlin/app/revanced/cli/Main.kt
index a598750..f62f798 100644
--- a/src/main/kotlin/app/revanced/cli/Main.kt
+++ b/src/main/kotlin/app/revanced/cli/Main.kt
@@ -1,178 +1,7 @@
 package app.revanced.cli
 
-import app.revanced.cli.runner.AdbRunner
-import app.revanced.cli.utils.PatchLoader
-import app.revanced.cli.utils.Patches
-import app.revanced.cli.utils.Preconditions
-import app.revanced.patcher.Patcher
-import app.revanced.patcher.patch.PatchMetadata
-import app.revanced.patcher.patch.PatchResult
-import kotlinx.cli.ArgParser
-import kotlinx.cli.ArgType
-import kotlinx.cli.default
-import kotlinx.cli.required
-import me.tongfei.progressbar.ProgressBarBuilder
-import me.tongfei.progressbar.ProgressBarStyle
-import java.io.File
-import java.nio.file.Files
+import picocli.CommandLine
 
-private const val CLI_NAME = "ReVanced CLI"
-private val CLI_VERSION = Main::class.java.`package`.implementationVersion ?: "0.0.0-unknown"
-
-class Main {
-    companion object {
-        private fun runCLI(
-            inApk: String,
-            inPatches: String,
-            inIntegrations: String?,
-            inOutput: String,
-            inRunOnAdb: String?,
-            hideResults: Boolean,
-            noLogging: Boolean,
-        ) {
-            val bar = ProgressBarBuilder()
-                .setTaskName("Working..")
-                .setUpdateIntervalMillis(25)
-                .continuousUpdate()
-                .setStyle(ProgressBarStyle.ASCII)
-                .build()
-                .maxHint(1)
-                .setExtraMessage("Initializing")
-            val apk = Preconditions.isFile(inApk)
-            val patchesFile = Preconditions.isFile(inPatches)
-            val output = Preconditions.isDirectory(inOutput)
-            bar.step()
-
-            val patcher = Patcher(apk)
-
-            inIntegrations?.let {
-                bar.reset().maxHint(1)
-                    .extraMessage = "Merging integrations"
-                val integrations = Preconditions.isFile(it)
-                patcher.addFiles(listOf(integrations))
-                bar.step()
-            }
-
-            bar.reset().maxHint(1)
-                .extraMessage = "Loading patches"
-            PatchLoader.injectPatches(patchesFile)
-            val patches = Patches.loadPatches().map { it() }
-            patcher.addPatches(patches)
-            bar.step()
-
-            bar.reset().maxHint(1)
-                .extraMessage = "Resolving signatures"
-            patcher.resolveSignatures()
-            bar.step()
-
-            val szPatches = patches.size.toLong()
-            bar.reset().maxHint(szPatches)
-                .extraMessage = "Applying patches"
-            val results = patcher.applyPatches {
-                bar.step().extraMessage = "Applying $it"
-            }
-
-            bar.reset().maxHint(-1)
-                .extraMessage = "Generating dex files"
-            val dexFiles = patcher.save()
-
-            val szDexFiles = dexFiles.size.toLong()
-            bar.reset().maxHint(szDexFiles)
-                .extraMessage = "Saving dex files"
-            dexFiles.forEach { (dexName, dexData) ->
-                Files.write(File(output, dexName).toPath(), dexData.data)
-                bar.step()
-            }
-            bar.stepTo(szDexFiles)
-
-            bar.close()
-
-            inRunOnAdb?.let { device ->
-                AdbRunner.runApk(
-                    apk,
-                    dexFiles,
-                    output,
-                    device,
-                    noLogging
-                )
-            }
-
-            println("All done!")
-            if (!hideResults) {
-                printResults(results)
-            }
-        }
-
-        private fun printResults(results: Map<PatchMetadata, Result<PatchResult>>) {
-            for ((metadata, result) in results) {
-                if (result.isSuccess) {
-                    println("${metadata.shortName} was applied successfully!")
-                } else {
-                    println("${metadata.shortName} failed to apply! Cause:")
-                    result.exceptionOrNull()!!.printStackTrace()
-                }
-            }
-        }
-
-        @JvmStatic
-        fun main(args: Array<String>) {
-            println("$CLI_NAME version $CLI_VERSION")
-            val parser = ArgParser(CLI_NAME)
-
-            // TODO: add some kind of incremental building, so merging integrations can be skipped.
-            // this can be achieved manually, but doing it automatically is better.
-
-            val apk by parser.option(
-                ArgType.String,
-                fullName = "apk",
-                shortName = "a",
-                description = "APK file"
-            ).required()
-            val patches by parser.option(
-                ArgType.String,
-                fullName = "patches",
-                shortName = "p",
-                description = "Patches JAR file"
-            ).required()
-            val integrations by parser.option(
-                ArgType.String,
-                fullName = "integrations",
-                shortName = "i",
-                description = "Integrations APK file"
-            )
-            val output by parser.option(
-                ArgType.String,
-                fullName = "output",
-                shortName = "o",
-                description = "Output directory"
-            ).required()
-            val runOnAdb by parser.option(
-                ArgType.String,
-                fullName = "run-on",
-                description = "After the CLI is done building, which ADB device should it run on?"
-            )
-            // TODO: package name
-            val hideResults by parser.option(
-                ArgType.Boolean,
-                fullName = "hide-results",
-                description = "Don't print the patch results."
-            ).default(false)
-            val noLogging by parser.option(
-                ArgType.Boolean,
-                fullName = "no-logging",
-                description = "Don't print the output of the application when used in combination with \"run-on\"."
-            ).default(false)
-
-            parser.parse(args)
-            runCLI(
-                apk,
-                patches,
-                integrations,
-                output,
-                runOnAdb,
-                hideResults,
-                noLogging,
-            )
-        }
-    }
+internal fun main(args: Array<String>) {
+    CommandLine(MainCommand).execute(*args)
 }
\ No newline at end of file
diff --git a/src/main/kotlin/app/revanced/cli/MainCommand.kt b/src/main/kotlin/app/revanced/cli/MainCommand.kt
new file mode 100644
index 0000000..29afa52
--- /dev/null
+++ b/src/main/kotlin/app/revanced/cli/MainCommand.kt
@@ -0,0 +1,84 @@
+package app.revanced.cli
+
+import app.revanced.patch.PatchLoader
+import app.revanced.patch.Patches
+import app.revanced.utils.adb.Adb
+import picocli.CommandLine.*
+import java.io.File
+
+@Command(
+    name = "ReVanced-CLI", version = ["1.0.0"], mixinStandardHelpOptions = true
+)
+internal object MainCommand : Runnable {
+    @Parameters(
+        paramLabel = "INCLUDE",
+        description = ["Which patches to include. If none is specified, all compatible patches will be included"]
+    )
+    internal var includedPatches = arrayOf<String>()
+
+    @Option(names = ["-p", "--patches"], description = ["One or more bundles of patches"])
+    internal var patchBundles = arrayOf<File>()
+
+    @Option(names = ["-t", "--temp-dir"], description = ["Temporal resource cache directory"], required = true)
+    internal lateinit var cacheDirectory: String
+
+    @Option(names = ["-r", "--resource-patcher"], description = ["Enable patching resources"])
+    internal var patchResources: Boolean = false
+
+    @Option(
+        names = ["-c", "--clean"],
+        description = ["Clean the temporal resource cache directory. This will be done anyways when running the patcher"]
+    )
+    internal var clean: Boolean = false
+
+    @Option(names = ["-l", "--list"], description = ["List patches only"])
+    internal var listOnly: Boolean = false
+
+    @Option(names = ["-m", "--merge"], description = ["One or more dex file containers to merge"])
+    internal var mergeFiles = listOf<File>()
+
+    @Option(names = ["-a", "--apk"], description = ["Input file to be patched"], required = true)
+    internal lateinit var inputFile: File
+
+    @Option(names = ["-o", "--out"], description = ["Output file path"], required = true)
+    internal lateinit var outputPath: String
+
+    @Option(names = ["-d", "--deploy-on"], description = ["If specified, deploy to adb device with given name"])
+    internal var deploy: String? = null
+
+    override fun run() {
+        if (listOnly) {
+            patchBundles.forEach {
+                PatchLoader.injectPatches(it)
+                Patches.loadPatches().forEach {
+                    println(it().metadata)
+                }
+            }
+            return
+        }
+
+        val patcher = app.revanced.patcher.Patcher(
+            inputFile,
+            cacheDirectory,
+            patchResources
+        )
+
+        Patcher.start(patcher)
+
+        if (clean) {
+            File(cacheDirectory).deleteRecursively()
+        }
+
+        val outputFile = File(outputPath)
+
+        deploy?.let {
+            Adb(
+                outputFile,
+                patcher.packageName,
+                deploy!!
+            ).deploy()
+        }
+
+        if (clean) outputFile.delete()
+    }
+}
\ No newline at end of file
diff --git a/src/main/kotlin/app/revanced/cli/Patcher.kt b/src/main/kotlin/app/revanced/cli/Patcher.kt
new file mode 100644
index 0000000..59a6b78
--- /dev/null
+++ b/src/main/kotlin/app/revanced/cli/Patcher.kt
@@ -0,0 +1,91 @@
+package app.revanced.cli
+
+import app.revanced.patch.PatchLoader
+import app.revanced.patch.Patches
+import app.revanced.patcher.data.base.Data
+import app.revanced.patcher.patch.base.Patch
+import app.revanced.utils.filesystem.FileSystemUtils
+import app.revanced.utils.signing.Signer
+import java.io.File
+
+internal class Patcher {
+    internal companion object {
+        internal fun start(patcher: app.revanced.patcher.Patcher) {
+            // merge files like necessary integrations
+            patcher.addFiles(MainCommand.mergeFiles)
+            // add patches, but filter incompatible or excluded patches
+            patcher.addPatchesFiltered()
+            // apply patches
+            for ((meta, result) in patcher.applyPatches {
+                println("Applying $it.")
+            }) {
+                println("Applied ${meta.name}. The result was $result.")
+            }
+
+            // write output file
+            val outFile = File(MainCommand.outputPath)
+            if (outFile.exists()) outFile.delete()
+            MainCommand.inputFile.copyTo(outFile)
+
+            val zipFileSystem = FileSystemUtils(outFile)
+
+            // replace all dex files
+            for ((name, data) in patcher.save()) {
+                zipFileSystem.replaceFile(name, data.data)
+            }
+
+            if (MainCommand.patchResources) {
+                for (file in File(MainCommand.cacheDirectory).resolve("build/").listFiles().first().listFiles()) {
+                    if (!file.isDirectory) {
+                        zipFileSystem.replaceFile(file.name, file.readBytes())
+                        continue
+                    }
+                    zipFileSystem.replaceDirectory(file)
+                }
+            }
+
+            // finally close the stream
+            zipFileSystem.close()
+
+            // and sign the apk file
+            Signer.signApk(outFile)
+        }
+
+        private fun app.revanced.patcher.Patcher.addPatchesFiltered() {
+            // TODO: get package metadata (outside of this method) for apk file which needs to be patched
+            val packageName = this.packageName
+            val packageVersion = this.packageVersion
+
+            val checkInclude = MainCommand.includedPatches.isNotEmpty()
+
+            MainCommand.patchBundles.forEach { bundle ->
+                PatchLoader.injectPatches(bundle)
+                val includedPatches = mutableListOf<Patch<Data>>()
+                Patches.loadPatches().forEach patch@{
+                    val patch = it()
+
+                    // TODO: filter out incompatible patches with package metadata
+                    val filterOutPatches = true
+                    if (filterOutPatches && !patch.metadata.compatiblePackages.any { packageMetadata ->
+                            packageMetadata.name == packageName && packageMetadata.versions.any {
+                                it == packageVersion
+                            }
+                        }) {
+
+                        println("Skipping ${patch.metadata.name} due to incompatibility with current package $packageName.")
+                        return@patch
+                    }
+
+                    if (checkInclude && !MainCommand.includedPatches.contains(patch.metadata.shortName)) {
+                        return@patch
+                    }
+
+                    println("Adding ${patch.metadata.name}.")
+                    includedPatches.add(patch)
+
+                }
+                this.addPatches(includedPatches)
+            }
+        }
+    }
+}
diff --git a/src/main/kotlin/app/revanced/cli/runner/AdbRunner.kt b/src/main/kotlin/app/revanced/cli/runner/AdbRunner.kt
deleted file mode 100644
index 99e94b9..0000000
--- a/src/main/kotlin/app/revanced/cli/runner/AdbRunner.kt
+++ /dev/null
@@ -1,160 +0,0 @@
-package app.revanced.cli.runner
-
-import app.revanced.cli.utils.DexReplacer
-import app.revanced.cli.utils.Scripts
-import app.revanced.cli.utils.signer.Signer
-import me.tongfei.progressbar.ProgressBar
-import me.tongfei.progressbar.ProgressBarBuilder
-import me.tongfei.progressbar.ProgressBarStyle
-import org.jf.dexlib2.writer.io.MemoryDataStore
-import se.vidstige.jadb.JadbConnection
-import se.vidstige.jadb.JadbDevice
-import se.vidstige.jadb.RemoteFile
-import se.vidstige.jadb.ShellProcessBuilder
-import java.io.File
-import java.util.concurrent.Executors
-
-object AdbRunner {
-    fun runApk(
-        apk: File,
-        dexFiles: Map<String, MemoryDataStore>,
-        outputDir: File,
-        deviceName: String,
-        noLogging: Boolean
-    ) {
-        lateinit var dvc: JadbDevice
-        pbar("Initializing").use { bar ->
-            dvc = JadbConnection().findDevice(deviceName)
-                ?: throw IllegalArgumentException("No such device with name $deviceName")
-            if (!dvc.hasSu())
-                throw IllegalArgumentException("Device $deviceName is not rooted or does not have su")
-            bar.step()
-        }
-
-        lateinit var tmpFile: File // we need this file at the end to clean up.
-        pbar("Generating APK file", 3).use { bar ->
-            bar.step().extraMessage = "Creating APK file"
-            tmpFile = File(outputDir, "revanced.apk")
-            apk.copyTo(tmpFile, true)
-
-            bar.step().extraMessage = "Replacing dex files"
-            DexReplacer.replaceDex(tmpFile, dexFiles)
-
-            bar.step().extraMessage = "Signing APK file"
-            try {
-                Signer.signApk(tmpFile)
-            } catch (e: SecurityException) {
-                throw IllegalStateException(
-                    "A security exception occurred when signing the APK! " +
-                            "If it has anything to with \"cannot authenticate\" then please make sure " +
-                            "you are using Zulu or OpenJDK as they do work when using the adb runner.",
-                    e
-                )
-            }
-        }
-
-        pbar("Running application", 6, false).use { bar ->
-            bar.step().extraMessage = "Pushing mount scripts"
-            dvc.push(Scripts.MOUNT_SCRIPT, RemoteFile(Scripts.SCRIPT_PATH))
-            dvc.cmd(Scripts.CREATE_DIR_COMMAND).assertZero()
-            dvc.cmd(Scripts.MV_MOUNT_COMMAND).assertZero()
-            dvc.cmd(Scripts.CHMOD_MOUNT_COMMAND).assertZero()
-
-            bar.step().extraMessage = "Pushing APK file"
-            dvc.push(tmpFile, RemoteFile(Scripts.APK_PATH))
-
-            bar.step().extraMessage = "Mounting APK file"
-            dvc.cmd(Scripts.STOP_APP_COMMAND).startAndWait()
-            dvc.cmd(Scripts.START_MOUNT_COMMAND).assertZero()
-
-            bar.step().extraMessage = "Starting APK file"
-            dvc.cmd(Scripts.START_APP_COMMAND).assertZero()
-
-            bar.step().setExtraMessage("Debugging APK file").refresh()
-            println("\nWaiting until app is closed.")
-            val executor = Executors.newSingleThreadExecutor()
-            val pipe = if (noLogging) {
-                ProcessBuilder.Redirect.PIPE
-            } else {
-                ProcessBuilder.Redirect.INHERIT
-            }
-            val p = dvc.cmd(Scripts.LOGCAT_COMMAND)
-                .redirectOutput(pipe)
-                .redirectError(pipe)
-                .useExecutor(executor)
-                .start()
-            Thread.sleep(250) // give the app some time to start up.
-            while (true) {
-                try {
-                    while (dvc.cmd(Scripts.PIDOF_APP_COMMAND).startAndWait() == 0) {
-                        Thread.sleep(250)
-                    }
-                    break
-                } catch (e: Exception) {
-                    throw RuntimeException("An error occurred while monitoring state of app", e)
-                }
-            }
-            println("App closed, continuing.")
-            p.destroy()
-            executor.shutdown()
-
-            bar.step().extraMessage = "Unmounting APK file"
-            var exitCode: Int
-            do {
-                exitCode = dvc.cmd(Scripts.UNMOUNT_COMMAND).startAndWait()
-            } while (exitCode != 0)
-        }
-    }
-}
-
-private fun JadbDevice.push(s: String, remoteFile: RemoteFile) =
-    this.push(s.byteInputStream(), System.currentTimeMillis(), 644, remoteFile)
-
-private fun JadbConnection.findDevice(device: String): JadbDevice? {
-    return devices.find { it.serial == device }
-}
-
-private fun JadbDevice.cmd(s: String): ShellProcessBuilder {
-    val args = s.split(" ") as ArrayList<String>
-    val cmd = args.removeFirst()
-    return shellProcessBuilder(cmd, *args.toTypedArray())
-}
-
-private fun JadbDevice.hasSu(): Boolean {
-    return cmd("su -h").startAndWait() == 0
-}
-
-private fun ShellProcessBuilder.startAndWait(): Int {
-    return start().waitFor()
-}
-
-private fun ShellProcessBuilder.assertZero() {
-    if (startAndWait() != 0) {
-        val cmd = getcmd()
-        throw IllegalStateException("ADB returned non-zero status code for command: $cmd")
-    }
-}
-
-private fun pbar(task: String, steps: Long = 1, update: Boolean = true): ProgressBar {
-    val b = ProgressBarBuilder().setTaskName(task)
-    if (update) b
-        .setUpdateIntervalMillis(250)
-        .continuousUpdate()
-    return b
-        .setStyle(ProgressBarStyle.ASCII)
-        .build()
-        .maxHint(steps + 1)
-}
-
-private fun ProgressBar.use(block: (ProgressBar) -> Unit) {
-    block(this)
-    stepTo(max) // step to 100%
-    extraMessage = "" // clear extra message
-    close()
-}
-
-private fun ShellProcessBuilder.getcmd(): String {
-    val f = this::class.java.getDeclaredField("command")
-    f.isAccessible = true
-    return f.get(this) as String
-}
\ No newline at end of file
diff --git a/src/main/kotlin/app/revanced/cli/utils/DexReplacer.kt b/src/main/kotlin/app/revanced/cli/utils/DexReplacer.kt
deleted file mode 100644
index 171aa1f..0000000
--- a/src/main/kotlin/app/revanced/cli/utils/DexReplacer.kt
+++ /dev/null
@@ -1,31 +0,0 @@
-package app.revanced.cli.utils
-
-import lanchon.multidexlib2.BasicDexFileNamer
-import org.jf.dexlib2.writer.io.MemoryDataStore
-import java.io.File
-import java.nio.file.FileSystems
-import java.nio.file.Files
-
-val NAMER = BasicDexFileNamer()
-
-object DexReplacer {
-    fun replaceDex(source: File, dexFiles: Map<String, MemoryDataStore>) {
-        FileSystems.newFileSystem(
-            source.toPath(),
-            null
-        ).use { fs ->
-            // Delete all classes?.dex files
-            Files.walk(fs.rootDirectories.first()).forEach {
-                if (
-                    it.toString().endsWith(".dex") &&
-                    NAMER.isValidName(it.fileName.toString())
-                ) Files.delete(it)
-            }
-            // Write new dex files
-            dexFiles
-                .forEach { (dexName, dexData) ->
-                    Files.write(fs.getPath("/$dexName"), dexData.data)
-                }
-        }
-    }
-}
\ No newline at end of file
diff --git a/src/main/kotlin/app/revanced/cli/utils/Preconditions.kt b/src/main/kotlin/app/revanced/cli/utils/Preconditions.kt
deleted file mode 100644
index ff0da2d..0000000
--- a/src/main/kotlin/app/revanced/cli/utils/Preconditions.kt
+++ /dev/null
@@ -1,24 +0,0 @@
-package app.revanced.cli.utils
-
-import java.io.File
-import java.io.FileNotFoundException
-
-class Preconditions {
-    companion object {
-        fun isFile(path: String): File {
-            val f = File(path)
-            if (!f.exists()) {
-                throw FileNotFoundException(f.toString())
-            }
-            return f
-        }
-
-        fun isDirectory(path: String): File {
-            val f = isFile(path)
-            if (!f.isDirectory) {
-                throw IllegalArgumentException("$f is not a directory")
-            }
-            return f
-        }
-    }
-}
\ No newline at end of file
diff --git a/src/main/kotlin/app/revanced/cli/utils/Scripts.kt b/src/main/kotlin/app/revanced/cli/utils/Scripts.kt
deleted file mode 100644
index 028c10b..0000000
--- a/src/main/kotlin/app/revanced/cli/utils/Scripts.kt
+++ /dev/null
@@ -1,34 +0,0 @@
-package app.revanced.cli.utils
-
-// TODO: make this a class with PACKAGE_NAME as argument, then use that everywhere.
-// make sure to remove the "const" from all the vals, they won't compile obviously.
-object Scripts {
-    private const val PACKAGE_NAME = "com.google.android.youtube"
-    private const val DATA_PATH = "/data/adb/ReVanced"
-    const val APK_PATH = "/sdcard/base.apk"
-    const val SCRIPT_PATH = "/sdcard/mount.sh"
-
-    val MOUNT_SCRIPT =
-        """
-            base_path="$DATA_PATH/base.apk"
-            stock_path=${'$'}{ pm path $PACKAGE_NAME | grep base | sed 's/package://g' }
-            umount -l ${'$'}stock_path
-            rm ${'$'}base_path
-            mv "$APK_PATH"  ${'$'}base_path
-            chmod 644 ${'$'}base_path
-            chown system:system ${'$'}base_path
-            chcon u:object_r:apk_data_file:s0  ${'$'}base_path
-            mount -o bind ${'$'}base_path ${'$'}stock_path
-        """.trimIndent()
-
-    const val PIDOF_APP_COMMAND = "pidof -s $PACKAGE_NAME"
-    private const val PIDOF_APP = "\$($PIDOF_APP_COMMAND)"
-    const val CREATE_DIR_COMMAND = "su -c \"mkdir -p $DATA_PATH/\""
-    const val MV_MOUNT_COMMAND = "su -c \"mv /sdcard/mount.sh $DATA_PATH/\""
-    const val CHMOD_MOUNT_COMMAND = "su -c \"chmod +x $DATA_PATH/mount.sh\""
-    const val START_MOUNT_COMMAND = "su -c $DATA_PATH/mount.sh"
-    const val UNMOUNT_COMMAND = "su -c \"umount -l $(pm path $PACKAGE_NAME | grep base | sed 's/package://g')\""
-    const val LOGCAT_COMMAND = "su -c \"logcat -c && logcat --pid=$PIDOF_APP\""
-    const val STOP_APP_COMMAND = "su -c \"kill $PIDOF_APP\""
-    const val START_APP_COMMAND = "monkey -p $PACKAGE_NAME 1"
-}
\ No newline at end of file
diff --git a/src/main/kotlin/app/revanced/cli/utils/PatchLoader.kt b/src/main/kotlin/app/revanced/patch/PatchLoader.kt
similarity index 84%
rename from src/main/kotlin/app/revanced/cli/utils/PatchLoader.kt
rename to src/main/kotlin/app/revanced/patch/PatchLoader.kt
index 9da9825..74ca2fd 100644
--- a/src/main/kotlin/app/revanced/cli/utils/PatchLoader.kt
+++ b/src/main/kotlin/app/revanced/patch/PatchLoader.kt
@@ -1,12 +1,12 @@
-package app.revanced.cli.utils
+package app.revanced.patch
 
 import java.io.File
 import java.net.URL
 import java.net.URLClassLoader
 
-class PatchLoader {
-    companion object {
-        fun injectPatches(file: File) {
+internal class PatchLoader {
+    internal companion object {
+        internal fun injectPatches(file: File) {
             // This function will fail on Java 9 and above.
             try {
                 val url = file.toURI().toURL()
diff --git a/src/main/kotlin/app/revanced/cli/utils/Patches.kt b/src/main/kotlin/app/revanced/patch/Patches.kt
similarity index 77%
rename from src/main/kotlin/app/revanced/cli/utils/Patches.kt
rename to src/main/kotlin/app/revanced/patch/Patches.kt
index 65af28a..7ba8147 100644
--- a/src/main/kotlin/app/revanced/cli/utils/Patches.kt
+++ b/src/main/kotlin/app/revanced/patch/Patches.kt
@@ -1,15 +1,15 @@
-package app.revanced.cli.utils
+package app.revanced.patch
 
 import app.revanced.patches.Index
 
-class Patches {
-    companion object {
+internal class Patches {
+    internal companion object {
         // You may ask yourself, "why do this?".
         // We do it like this, because we don't want the Index class
         // to be loaded while the dependency hasn't been injected yet.
         // You can see this as "controlled class loading".
         // Whenever this class is loaded (because it is invoked), all the imports
         // will be loaded too. We don't want to do this until we've injected the class.
-        fun loadPatches() = Index.patches
+        internal fun loadPatches() = Index.patches
     }
 }
\ No newline at end of file
diff --git a/src/main/kotlin/app/revanced/utils/adb/Adb.kt b/src/main/kotlin/app/revanced/utils/adb/Adb.kt
new file mode 100644
index 0000000..c03db28
--- /dev/null
+++ b/src/main/kotlin/app/revanced/utils/adb/Adb.kt
@@ -0,0 +1,94 @@
+package app.revanced.utils.adb
+
+import se.vidstige.jadb.JadbConnection
+import se.vidstige.jadb.JadbDevice
+import java.io.File
+import java.util.concurrent.Executors
+
+internal class Adb(
+    private val apk: File,
+    private val packageName: String,
+    deviceName: String,
+    private val logging: Boolean = true
+) {
+    private val device: JadbDevice
+
+    init {
+        device = JadbConnection().devices.find { it.serial == deviceName }
+            ?: throw IllegalArgumentException("No such device with name $deviceName")
+
+        if (device.run("su -h", false) != 0)
+            throw IllegalArgumentException("Root required on $deviceName. Deploying failed.")
+    }
+
+    private fun String.replacePlaceholder(): String {
+        return this.replace(Constants.PLACEHOLDER, packageName)
+    }
+
+    internal fun deploy() {
+        // create revanced path
+        device.run("${Constants.COMMAND_CREATE_DIR} ${Constants.PATH_REVANCED}")
+
+        // push patched file
+        device.copy(Constants.PATH_INIT_PUSH, apk)
+        // install apk
+        device.run(Constants.COMMAND_INSTALL_APK.replacePlaceholder())
+
+        // push mount script
+        device.createFile(
+            Constants.PATH_INIT_PUSH,
+            Constants.CONTENT_MOUNT_SCRIPT.replacePlaceholder()
+        )
+        // install mount script
+        device.run(Constants.COMMAND_INSTALL_MOUNT.replacePlaceholder())
+
+        // push umount script
+        device.createFile(
+            Constants.PATH_INIT_PUSH,
+            Constants.CONTENT_UMOUNT_SCRIPT.replacePlaceholder()
+        )
+        // install mount script
+        device.run(Constants.COMMAND_INSTALL_UMOUNT.replacePlaceholder())
+
+        // unmount the apk for sanity
+        device.run(Constants.PATH_UMOUNT.replacePlaceholder())
+        // mount the apk
+        device.run(Constants.PATH_MOUNT.replacePlaceholder())
+
+        // relaunch app
+        device.run(Constants.COMMAND_RESTART.replacePlaceholder())
+
+        // log the app
+        log()
+    }
+
+    private fun log() {
+        val executor = Executors.newSingleThreadExecutor()
+        val pipe = if (logging) {
+            ProcessBuilder.Redirect.INHERIT
+        } else {
+            ProcessBuilder.Redirect.PIPE
+        }
+
+        val process = device.buildCommand(Constants.COMMAND_LOGCAT.replacePlaceholder())
+            .redirectOutput(pipe)
+            .redirectError(pipe)
+            .useExecutor(executor)
+            .start()
+
+        Thread.sleep(500) // give the app some time to start up.
+        while (true) {
+            try {
+                while (device.run("${Constants.COMMAND_PID_OF} $packageName") == 0) {
+                    Thread.sleep(1000)
+                }
+                break
+            } catch (e: Exception) {
+                throw RuntimeException("An error occurred while monitoring state of app", e)
+            }
+        }
+        println("App closed, continuing.")
+        process.destroy()
+        executor.shutdown()
+    }
+}
\ No newline at end of file
diff --git a/src/main/kotlin/app/revanced/utils/adb/Commands.kt b/src/main/kotlin/app/revanced/utils/adb/Commands.kt
new file mode 100644
index 0000000..1b3af07
--- /dev/null
+++ b/src/main/kotlin/app/revanced/utils/adb/Commands.kt
@@ -0,0 +1,29 @@
+package app.revanced.utils.adb
+
+import se.vidstige.jadb.JadbDevice
+import se.vidstige.jadb.RemoteFile
+import se.vidstige.jadb.ShellProcessBuilder
+import java.io.File
+
+internal fun JadbDevice.buildCommand(command: String, su: Boolean = true): ShellProcessBuilder {
+    if (su) {
+        return shellProcessBuilder("su -c \'$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.copy(targetPath: String, file: File) {
+    push(file, RemoteFile(targetPath))
+}
+
+internal fun JadbDevice.createFile(targetFile: String, content: String) {
+    push(content.byteInputStream(), System.currentTimeMillis(), 644, RemoteFile(targetFile))
+}
\ No newline at end of file
diff --git a/src/main/kotlin/app/revanced/utils/adb/Constants.kt b/src/main/kotlin/app/revanced/utils/adb/Constants.kt
new file mode 100644
index 0000000..32f7bf1
--- /dev/null
+++ b/src/main/kotlin/app/revanced/utils/adb/Constants.kt
@@ -0,0 +1,57 @@
+package app.revanced.utils.adb
+
+internal object Constants {
+    // template placeholder to replace a string in commands
+    internal const val PLACEHOLDER = "TEMPLATE_PACKAGE_NAME"
+
+    // utility commands
+    private const val COMMAND_CHMOD_MOUNT = "chmod +x"
+    internal const val COMMAND_PID_OF = "pidof -s"
+    internal const val COMMAND_CREATE_DIR = "mkdir -p"
+    internal const val COMMAND_LOGCAT = "logcat -c && logcat --pid=$($COMMAND_PID_OF $PLACEHOLDER)"
+    internal const val COMMAND_RESTART = "monkey -p $PLACEHOLDER 1 && kill ${'$'}($COMMAND_PID_OF $PLACEHOLDER)"
+
+    // default mount file name
+    private const val NAME_MOUNT_SCRIPT = "mount_$PLACEHOLDER.sh"
+
+    // initial directory to push files to via adb push
+    internal const val PATH_INIT_PUSH = "/sdcard/revanced.delete"
+
+    // revanced path
+    internal const val PATH_REVANCED = "/data/adb/revanced/"
+
+    // revanced apk path
+    private const val PATH_REVANCED_APP = "$PATH_REVANCED$PLACEHOLDER.apk"
+
+    // (un)mount script paths
+    internal const val PATH_MOUNT = "/data/adb/service.d/$NAME_MOUNT_SCRIPT"
+    internal const val PATH_UMOUNT = "/data/adb/post-fs-data.d/un$NAME_MOUNT_SCRIPT"
+
+    // move to revanced apk path & set permissions
+    internal const val COMMAND_INSTALL_APK =
+        "base_path=\"$PATH_REVANCED_APP\" && mv $PATH_INIT_PUSH ${'$'}base_path && chmod 644 ${'$'}base_path && chown system:system ${'$'}base_path && chcon u:object_r:apk_data_file:s0  ${'$'}base_path"
+
+    // install mount script & set permissions
+    internal const val COMMAND_INSTALL_MOUNT = "mv $PATH_INIT_PUSH $PATH_MOUNT && $COMMAND_CHMOD_MOUNT $PATH_MOUNT"
+
+    // install umount script & set permissions
+    internal const val COMMAND_INSTALL_UMOUNT = "mv $PATH_INIT_PUSH $PATH_UMOUNT && $COMMAND_CHMOD_MOUNT $PATH_UMOUNT"
+
+    // unmount script
+    internal val CONTENT_UMOUNT_SCRIPT =
+        """
+            #!/system/bin/sh
+            while read line; do echo ${'$'}{line} | grep $PLACEHOLDER | awk '{print ${'$'}2}' | xargs umount -l; done< /proc/mounts
+        """.trimIndent()
+
+    // mount script
+    internal val CONTENT_MOUNT_SCRIPT =
+        """
+            #!/system/bin/sh
+            while [ "${'$'}(getprop sys.boot_completed | tr -d '\r')" != "1" ]; do sleep 1; done
+            
+            base_path="$PATH_REVANCED_APP"
+            stock_path=${'$'}{ pm path $PLACEHOLDER | grep base | sed 's/package://g' }
+            mount -o bind ${'$'}base_path ${'$'}stock_path
+        """.trimIndent()
+}
\ No newline at end of file
diff --git a/src/main/kotlin/app/revanced/utils/filesystem/FileSystemUtils.kt b/src/main/kotlin/app/revanced/utils/filesystem/FileSystemUtils.kt
new file mode 100644
index 0000000..10559d8
--- /dev/null
+++ b/src/main/kotlin/app/revanced/utils/filesystem/FileSystemUtils.kt
@@ -0,0 +1,66 @@
+package app.revanced.utils.filesystem
+
+import java.io.Closeable
+import java.io.File
+import java.nio.file.FileSystem
+import java.nio.file.FileSystems
+import java.nio.file.Files
+
+internal class FileSystemUtils(
+    file: File
+) : Closeable {
+    private var fileSystem: FileSystem
+
+    init {
+        fileSystem = FileSystems.newFileSystem(
+            file.toPath(),
+            null
+        )
+    }
+
+    private fun deleteDirectory(dirPath: String) {
+        val files = Files.walk(fileSystem.getPath("$dirPath/"))
+
+        files
+            .sorted(Comparator.reverseOrder())
+            .forEach {
+
+                Files.delete(it)
+            }
+
+        files.close()
+    }
+
+
+    internal fun replaceDirectory(replacement: File) {
+        if (!replacement.isDirectory) throw Exception("${replacement.name} is not a directory.")
+
+        // FIXME: make this delete the directory recursively
+        //deleteDirectory(replacement.name)
+        //val path = Files.createDirectory(fileSystem.getPath(replacement.name))
+
+        val excludeFromPath = replacement.path.removeSuffix(replacement.name)
+        for (path in Files.walk(replacement.toPath())) {
+            val file = path.toFile()
+            if (file.isDirectory) {
+                val relativePath = path.toString().removePrefix(excludeFromPath)
+                val fileSystemPath = fileSystem.getPath(relativePath)
+                if (!Files.exists(fileSystemPath)) Files.createDirectory(fileSystemPath)
+
+                continue
+            }
+
+            replaceFile(path.toString().removePrefix(excludeFromPath), file.readBytes())
+        }
+    }
+
+    internal fun replaceFile(sourceFile: String, content: ByteArray) {
+        val path = fileSystem.getPath(sourceFile)
+        Files.deleteIfExists(path)
+        Files.write(path, content)
+    }
+
+    override fun close() {
+        fileSystem.close()
+    }
+}
\ No newline at end of file
diff --git a/src/main/kotlin/app/revanced/cli/utils/signer/KeySet.kt b/src/main/kotlin/app/revanced/utils/signing/KeySet.kt
similarity index 81%
rename from src/main/kotlin/app/revanced/cli/utils/signer/KeySet.kt
rename to src/main/kotlin/app/revanced/utils/signing/KeySet.kt
index bbe0134..1eb9da8 100644
--- a/src/main/kotlin/app/revanced/cli/utils/signer/KeySet.kt
+++ b/src/main/kotlin/app/revanced/utils/signing/KeySet.kt
@@ -1,4 +1,4 @@
-package app.revanced.cli.utils.signer
+package app.revanced.utils.signing
 
 import java.security.PrivateKey
 import java.security.cert.X509Certificate
diff --git a/src/main/kotlin/app/revanced/cli/utils/signer/Signer.kt b/src/main/kotlin/app/revanced/utils/signing/Signer.kt
similarity index 99%
rename from src/main/kotlin/app/revanced/cli/utils/signer/Signer.kt
rename to src/main/kotlin/app/revanced/utils/signing/Signer.kt
index 936e279..ff56a29 100644
--- a/src/main/kotlin/app/revanced/cli/utils/signer/Signer.kt
+++ b/src/main/kotlin/app/revanced/utils/signing/Signer.kt
@@ -3,7 +3,7 @@
  * Licensed under the Open Software License version 3.0
  */
 
-package app.revanced.cli.utils.signer
+package app.revanced.utils.signing
 
 import org.bouncycastle.asn1.x500.X500Name
 import org.bouncycastle.asn1.x509.SubjectPublicKeyInfo
@@ -41,7 +41,7 @@ val PASSWORD = "revanced".toCharArray() // TODO: make it secure; random password
 /**
  * APK Signer.
  * @author Aliucord authors
- * @author ReVanced Team
+ * @author ReVanced team
  */
 object Signer {
     private fun newKeystore(out: File) {