diff --git a/docs/1_usage.md b/docs/1_usage.md
index 31ee72a3..68911ad3 100644
--- a/docs/1_usage.md
+++ b/docs/1_usage.md
@@ -13,10 +13,12 @@ java -jar revanced-cli.jar -h
 ## 📃 List patches
 
 ```bash
-java -jar revanced-cli.jar list-patches --with-descriptions --with-packages --with-versions --with-options --with-universal-patches revanced-patches.rvp
+java -jar revanced-cli.jar list-patches --with-packages --with-versions --with-options revanced-patches.rvp
 ```
 
-## 💉 Patch an app with the default list of patches
+## 💉 Patch an app
+
+To patch an app using the default list of patches, use the `patch` command:
 
 ```bash
 java -jar revanced-cli.jar patch -b revanced-patches.rvp input.apk
@@ -28,22 +30,37 @@ You can also use multiple patch bundles:
 java -jar revanced-cli.jar patch -b revanced-patches.rvp -b another-patches.rvp input.apk
 ```
 
-To manually include or exclude patches, use the options `-i` and `-e`.
-Keep in mind the name of the patch must be an exact match.
-You can also use the options `--ii` and `--ie` to include or exclude patches by their index
-if two patches have the same name.
-To know the indices of patches, use the option `--with-indices` when listing patches:
+To change the default set of used patches, use the option `-i` or `-e` to use or disuse specific patches.
+You can use the `list-patches` command to see which patches are used by default.
+
+To only use specific patches, you can use the option `--exclusive` combined with `-i`.
+Remember that the options `-i` and `-e` match the patch's name exactly. Here is an example:
 
 ```bash
-java -jar revanced-cli.jar list-patches --with-indices revanced-patches.rvp
+java -jar revanced-cli.jar patch -b revanced-patches.rvp --exclusive -i "Patch name" -i "Another patch name" input.apk
 ```
 
-Then you can use the indices to include or exclude patches:
+You can also use the options `--ii` and `--ie` to use or disuse patches by their index.
+This is useful, if two patches happen to have the same name.
+To know the indices of patches, use the command `list-patches`:
+
+```bash
+java -jar revanced-cli.jar list-patches revanced-patches.rvp
+```
+
+Then you can use the indices to use or disuse patches:
 
 ```bash
 java -jar revanced-cli.jar patch -b revanced-patches.rvp --ii 123 --ie 456 input.apk
 ```
 
+You can combine the option `-i`, `-e`, `--ii`, `--ie` and `--exclusive`. Here is an example:
+
+```bash
+java -jar revanced-cli.jar patch -b revanced-patches.rvp --exclusive -i "Patch name" --ii 123 input.apk
+```
+
+
 > [!TIP]
 > You can use the option `-d` to automatically install the patched app after patching.
 > Make sure ADB is working:
@@ -62,7 +79,52 @@ java -jar revanced-cli.jar patch -b revanced-patches.rvp --ii 123 --ie 456 input
 > adb install input.apk
 > ```
 
-## 📦 Install an app manually
+Patches can have options you can set using the option `--set-options`.
+To know the options of a patch, use the option `--with-options` when listing patches:
+
+```bash
+java -jar revanced-cli.jar list-patches --with-options revanced-patches.rvp
+```
+
+Each patch can have multiple options. You can set them using the option `--set-options`.
+For example, to set the options for the patch with the name `Patch name`
+with the key `key1` and `key2` to `value1` and `value2` respectively, use the following command:
+
+```bash
+java -jar revanced-cli.jar patch -b revanced-patches.rvp --set-options "Patch name" -Okey1=value1 -Okey2=value2 input.apk
+```
+
+If you want to set a value to `null`, you can omit the value:
+
+```bash
+java -jar revanced-cli.jar patch -b revanced-patches.rvp --set-options "Patch name" -Okey1 input.apk
+```
+
+> [!WARNING]
+> The values of options are typed. If you set a value with the wrong type, the patching process will fail.
+> The type of the option value can be seen when listing patches with the option `--with-options`.
+> 
+> Example values:
+>
+> String: `string`  
+> Boolean: `true`, `false`  
+> Integer: `123`  
+> Double: `1.0`  
+> Float: `1.0f`  
+> Long: `1234567890`, `1L`  
+> List: `item1,item2,item3`  
+>
+> In addition to that, you can escape quotes (`\"`, `\'`) and commas (`\,`) to treat values as string literals:
+> 
+> Integer as string: `\'123\'`  
+> List with an integer, an integer as a string and a string with a comma: `123,\'123\',str\,ing`
+>
+> Example command with escaped quotes:
+> 
+> ```bash
+> java -jar revanced-cli.jar -b revanced-patches.rvp --set-options "Patch name" -OstringKey=\'1\' input.apk
+> ```
+## 📦 Install an app manually 
 
 ```bash
 java -jar revanced-cli.jar utility install -a input.apk
diff --git a/src/main/kotlin/app/revanced/cli/command/ListCompatibleVersions.kt b/src/main/kotlin/app/revanced/cli/command/ListCompatibleVersions.kt
index 31f5cfa4..9816fcf2 100644
--- a/src/main/kotlin/app/revanced/cli/command/ListCompatibleVersions.kt
+++ b/src/main/kotlin/app/revanced/cli/command/ListCompatibleVersions.kt
@@ -1,8 +1,8 @@
 package app.revanced.cli.command
 
 import app.revanced.library.PackageName
-import app.revanced.library.PatchUtils
 import app.revanced.library.VersionMap
+import app.revanced.library.mostCommonCompatibleVersions
 import app.revanced.patcher.patch.loadPatchesFromJar
 import picocli.CommandLine
 import java.io.File
@@ -12,7 +12,7 @@ import java.util.logging.Logger
     name = "list-versions",
     description = [
         "List the most common compatible versions of apps that are compatible " +
-                "with the patches in the supplied patch bundles.",
+            "with the patches in the supplied patch bundles.",
     ],
 )
 internal class ListCompatibleVersions : Runnable {
@@ -58,8 +58,7 @@ internal class ListCompatibleVersions : Runnable {
 
         val patches = loadPatchesFromJar(patchBundles)
 
-        PatchUtils.getMostCommonCompatibleVersions(
-            patches,
+        patches.mostCommonCompatibleVersions(
             packageNames,
             countUnusedPatches,
         ).entries.joinToString("\n", transform = ::buildString).let(logger::info)
diff --git a/src/main/kotlin/app/revanced/cli/command/ListPatchesCommand.kt b/src/main/kotlin/app/revanced/cli/command/ListPatchesCommand.kt
index d3c66a10..079d8c0d 100644
--- a/src/main/kotlin/app/revanced/cli/command/ListPatchesCommand.kt
+++ b/src/main/kotlin/app/revanced/cli/command/ListPatchesCommand.kt
@@ -95,9 +95,11 @@ internal object ListPatchesCommand : Runnable {
                 } ?: append("Key: $key")
 
                 values?.let { values ->
-                    appendLine("\nValid values:")
+                    appendLine("\nPossible values:")
                     append(values.map { "${it.value} (${it.key})" }.joinToString("\n").prependIndent("\t"))
                 }
+
+                append("\nType: $type")
             }
 
         fun IndexedValue<Patch<*>>.buildString() =
diff --git a/src/main/kotlin/app/revanced/cli/command/MainCommand.kt b/src/main/kotlin/app/revanced/cli/command/MainCommand.kt
index 4d33a4de..5ceeef15 100644
--- a/src/main/kotlin/app/revanced/cli/command/MainCommand.kt
+++ b/src/main/kotlin/app/revanced/cli/command/MainCommand.kt
@@ -34,7 +34,6 @@ private object CLIVersionProvider : IVersionProvider {
     versionProvider = CLIVersionProvider::class,
     subcommands = [
         PatchCommand::class,
-        OptionsCommand::class,
         ListPatchesCommand::class,
         ListCompatibleVersions::class,
         UtilityCommand::class,
diff --git a/src/main/kotlin/app/revanced/cli/command/OptionsCommand.kt b/src/main/kotlin/app/revanced/cli/command/OptionsCommand.kt
index dbc1ada3..e69de29b 100644
--- a/src/main/kotlin/app/revanced/cli/command/OptionsCommand.kt
+++ b/src/main/kotlin/app/revanced/cli/command/OptionsCommand.kt
@@ -1,62 +0,0 @@
-package app.revanced.cli.command
-
-import app.revanced.library.Options
-import app.revanced.library.Options.setOptions
-import app.revanced.patcher.patch.loadPatchesFromJar
-import picocli.CommandLine
-import picocli.CommandLine.Help.Visibility.ALWAYS
-import java.io.File
-import java.util.logging.Logger
-
-@CommandLine.Command(
-    name = "options",
-    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..*",
-    )
-    private lateinit var patchBundles: Set<File>
-
-    @CommandLine.Option(
-        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,
-    )
-    private var overwrite: Boolean = false
-
-    @CommandLine.Option(
-        names = ["-u", "--update"],
-        description = ["Update existing options by adding missing and removing non-existent options."],
-        showDefaultValue = ALWAYS,
-    )
-    private var update: Boolean = false
-
-    override fun run() =
-        try {
-            loadPatchesFromJar(patchBundles).let { patches ->
-                val exists = filePath.exists()
-                if (!exists || overwrite) {
-                    if (exists && update) patches.setOptions(filePath)
-
-                    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")
-        }
-
-    class OptionsFileAlreadyExistsException : Exception()
-}
diff --git a/src/main/kotlin/app/revanced/cli/command/PatchCommand.kt b/src/main/kotlin/app/revanced/cli/command/PatchCommand.kt
index 69f24f16..2cade1da 100644
--- a/src/main/kotlin/app/revanced/cli/command/PatchCommand.kt
+++ b/src/main/kotlin/app/revanced/cli/command/PatchCommand.kt
@@ -2,21 +2,22 @@ package app.revanced.cli.command
 
 import app.revanced.library.ApkUtils
 import app.revanced.library.ApkUtils.applyTo
-import app.revanced.library.Options
-import app.revanced.library.Options.setOptions
 import app.revanced.library.installation.installer.*
+import app.revanced.library.setOptions
 import app.revanced.patcher.Patcher
 import app.revanced.patcher.PatcherConfig
 import app.revanced.patcher.patch.Patch
 import app.revanced.patcher.patch.loadPatchesFromJar
 import kotlinx.coroutines.runBlocking
 import picocli.CommandLine
+import picocli.CommandLine.ArgGroup
 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
+import java.util.*
 import java.util.logging.Logger
 
 @CommandLine.Command(
@@ -27,7 +28,7 @@ internal object PatchCommand : Runnable {
     private val logger = Logger.getLogger(PatchCommand::class.java.name)
 
     @Spec
-    lateinit var spec: CommandSpec // injected by picocli
+    lateinit var spec: CommandSpec
 
     private lateinit var apk: File
 
@@ -35,15 +36,15 @@ internal object PatchCommand : Runnable {
 
     @CommandLine.Option(
         names = ["-i", "--include"],
-        description = ["List of patches to include."],
+        description = ["List of patches to include by name."],
     )
     private var includedPatches = hashSetOf<String>()
 
     @CommandLine.Option(
         names = ["--ii"],
-        description = ["List of patches to include by their index in relation to the supplied patch bundles."],
+        description = ["List of patches to include by their index in the combined list of all supplied patch bundles."],
     )
-    private var includedPatchesByIndex = arrayOf<Int>()
+    private var includedPatchesByIndex = setOf<Int>()
 
     @CommandLine.Option(
         names = ["-e", "--exclude"],
@@ -53,15 +54,29 @@ internal object PatchCommand : Runnable {
 
     @CommandLine.Option(
         names = ["--ei"],
-        description = ["List of patches to exclude by their index in relation to the supplied patch bundles."],
+        description = ["List of patches to exclude by their index in the combined list of all supplied patch bundles."],
     )
-    private var excludedPatchesByIndex = arrayOf<Int>()
-
-    @CommandLine.Option(
-        names = ["--options"],
-        description = ["Path to patch options JSON file."],
-    )
-    private var optionsFile: File? = null
+    private var excludedPatchesByIndex = setOf<Int>()
+
+    @ArgGroup(exclusive = false, multiplicity = "0..*", heading = "Options:%n")
+    private lateinit var options: Set<Option>
+
+    private class Option {
+        @CommandLine.Option(
+            names = ["--set-options"],
+            description = ["The name of the patch to set the options of."],
+            required = true,
+        )
+        lateinit var patch: String
+
+        @CommandLine.Option(
+            names = ["-O", "--options"],
+            description = ["The option values keyed by the option keys."],
+            mapFallbackValue = CommandLine.Option.NULL_VALUE,
+            converter = [OptionKeyConverter::class, OptionValueConverter::class],
+        )
+        lateinit var options: Map<String, Any?>
+    }
 
     @CommandLine.Option(
         names = ["--exclusive"],
@@ -154,13 +169,6 @@ internal object PatchCommand : Runnable {
     )
     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",
@@ -176,15 +184,6 @@ internal object PatchCommand : Runnable {
         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: Set<File>) {
-        logger.warning("The --merge option is not used anymore.")
-    }
-
     @CommandLine.Option(
         names = ["-b", "--patch-bundle"],
         description = ["One or more bundles of patches."],
@@ -226,11 +225,6 @@ internal object PatchCommand : Runnable {
                 "${outputFilePath.nameWithoutExtension}-temporary-files",
             )
 
-        val optionsFile =
-            optionsFile ?: outputFilePath.parentFile.resolve(
-                "${outputFilePath.nameWithoutExtension}-options.json",
-            )
-
         val keystoreFilePath =
             keystoreFilePath ?: outputFilePath.parentFile
                 .resolve("${outputFilePath.nameWithoutExtension}.keystore")
@@ -243,21 +237,10 @@ internal object PatchCommand : Runnable {
 
         val patches = loadPatchesFromJar(patchBundles)
 
-        // 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
 
         val patcherTemporaryFilesPath = temporaryFilesPath.resolve("patcher")
+
         val (packageName, patcherResult) = Patcher(
             PatcherConfig(
                 apk,
@@ -267,16 +250,10 @@ internal object PatchCommand : Runnable {
                 true,
             ),
         ).use { patcher ->
-            val filteredPatches =
-                patcher.filterPatchSelection(patches).also { patches ->
-                    logger.info("Setting patch options")
-
-                    if (optionsFile.exists()) {
-                        patches.setOptions(optionsFile)
-                    } else {
-                        Options.serialize(patches, prettyPrint = true).let(optionsFile::writeText)
-                    }
-                }
+            val filteredPatches = patcher.filterPatchSelection(patches)
+
+            logger.info("Setting patch options")
+            filteredPatches.setOptions(options.associate { it.patch to it.options })
 
             patcher += filteredPatches
 
@@ -421,3 +398,66 @@ internal object PatchCommand : Runnable {
         logger.info(result)
     }
 }
+
+class OptionKeyConverter : CommandLine.ITypeConverter<String> {
+    override fun convert(value: String): String = value
+}
+
+class OptionValueConverter : CommandLine.ITypeConverter<Any?> {
+    override fun convert(value: String?): Any? {
+        value ?: return null
+
+        // Check if the value starts with '[' and ends with ']'
+        if (value.startsWith("[") && value.endsWith("]")) {
+            val innerValue = value.substring(1, value.length - 1)
+
+            val list = buildList {
+                var escaped = false
+                var insideEscape = false
+
+                buildString {
+                    for (char in innerValue) {
+                        if (escaped) {
+                            append(char)
+                            escaped = false
+                        } else if (char == '\\') {
+                            escaped = true
+                        } else if (char == '[' && !insideEscape) {
+                            insideEscape = true
+                            append(char)
+                        } else if (char == ']' && insideEscape) {
+                            insideEscape = false
+                            append(char)
+                        } else if (char == ',' && !insideEscape) {
+                            add(toString())
+                            setLength(0)
+                        } else {
+                            append(char)
+                        }
+                    }
+                    add(toString()) // Add the last element
+                }
+            }
+
+            if (list.size > 1) {
+                return list.map(::convert)
+            }
+
+            return list
+        }
+
+        return when {
+            value.startsWith("\"") && value.endsWith("\"") -> value.substring(1, value.length - 1)
+            value.startsWith("'") && value.endsWith("'") -> value.substring(1, value.length - 1)
+            value.endsWith("f") -> value.dropLast(1).toFloatOrNull() ?: value
+            value.endsWith("L") -> value.dropLast(1).toLongOrNull() ?: value
+            value.equals("true", ignoreCase = true) -> true
+            value.equals("false", ignoreCase = true) -> false
+            value.toIntOrNull() != null -> value.toInt()
+            value.toLongOrNull() != null -> value.toLong()
+            value.toDoubleOrNull() != null -> value.toDouble()
+            value.toFloatOrNull() != null -> value.toFloat()
+            else -> value
+        }
+    }
+}
diff --git a/src/test/kotlin/app/revanced/cli/command/OptionValueConverterTest.kt b/src/test/kotlin/app/revanced/cli/command/OptionValueConverterTest.kt
new file mode 100644
index 00000000..a0d880f0
--- /dev/null
+++ b/src/test/kotlin/app/revanced/cli/command/OptionValueConverterTest.kt
@@ -0,0 +1,68 @@
+package app.revanced.cli.command
+
+import kotlin.test.Test
+
+class OptionValueConverterTest {
+    @Test
+    fun `converts to string`() {
+        "string" convertsTo "string" because "Strings should remain the same"
+    }
+
+    @Test
+    fun `converts to boolean`() {
+        "true" convertsTo true because "true should convert to a boolean true"
+        "True" convertsTo true because "Casing should not matter"
+        "\"true\"" convertsTo "true" because "Escaped booleans should be converted to strings"
+        "\'True\'" convertsTo "True" because "Casing in escaped booleans should not matter"
+        "tr ue" convertsTo "tr ue" because "Malformed booleans should be converted to strings"
+    }
+
+    @Test
+    fun `converts to numbers`() {
+        "1" convertsTo 1 because "Integers should convert to integers"
+        "1.0" convertsTo 1.0 because "Doubles should convert to doubles"
+        "1.0f" convertsTo 1.0f because "The suffix f should convert to a float"
+        Long.MAX_VALUE.toString() convertsTo Long.MAX_VALUE because "Values that are too large for an integer should convert to longs"
+        "1L" convertsTo 1L because "The suffix L should convert to a long"
+    }
+
+    @Test
+    fun `converts escaped numbers to string`() {
+        "\"1\"" convertsTo "1" because "Escaped numbers should convert to strings"
+        "\"1.0\"" convertsTo "1.0" because "Escaped doubles should convert to strings"
+        "\"1L\"" convertsTo "1L" because "Escaped longs should convert to strings"
+        "\'1\'" convertsTo "1" because "Single quotes should not be treated as escape symbols"
+        "\'.0\'" convertsTo ".0" because "Single quotes should not be treated as escape symbols"
+        "\'1L\'" convertsTo "1L" because "Single quotes should not be treated as escape symbols"
+    }
+
+    @Test
+    fun `trims escape symbols once`() {
+        "\"\"\"1\"\"\"" convertsTo "\"\"1\"\"" because "The escape symbols should be trimmed once"
+        "\'\'\'1\'\'\'" convertsTo "''1''" because "Single quotes should not be treated as escape symbols"
+    }
+
+    @Test
+    fun `converts lists`() {
+        "1,2" convertsTo "1,2" because "Lists without square brackets should not be converted to lists"
+        "[1,2" convertsTo "[1,2" because "Invalid lists should not be converted to lists"
+        "\\[1,2]" convertsTo "[1,2]" because "Lists with escaped square brackets should not be converted to lists"
+        "\\[1,2\\]" convertsTo "[1,2\\]" because "Escaping the closing square bracket should be treated as a normal character"
+
+        "[]" convertsTo listOf<String>() because "Empty untyped lists should convert to empty lists of strings"
+        "int[]" convertsTo listOf<Int>() because "Empty typed lists should convert to lists of the specified type"
+        "int[][]" convertsTo listOf<List<Int>>() because "Nested typed lists should convert to nested lists of the specified type"
+
+        "[1,2,3]" convertsTo listOf(1, 2, 3) because "Lists of integers should convert to lists of integers"
+        "[[1,2],[3,4]]" convertsTo listOf(listOf(1, 2), listOf(3, 4)) because "Nested lists should convert to nested lists"
+        "[1\\,2]" convertsTo listOf("1,2") because "Values in lists should not be split by escaped commas"
+        "[1\\\\,2]" convertsTo listOf("1\\", "2") because "Values in lists should not be split by escaped escape symbols"
+        "[[1\\,2]]" convertsTo listOf(listOf("1,2")) because "Values in nested lists should not be split by escaped commas"
+        "[.1,.2f,,true,FALSE]" convertsTo listOf(.1, .2f, "", true, false) because "Values in lists should be converted to the correct type"
+    }
+
+    private val convert = OptionValueConverter()::convert
+
+    private infix fun String.convertsTo(to: Any) = convert(this) to to
+    private infix fun Pair<Any?, Any>.because(reason: String) = assert(this.first == this.second) { reason }
+}