diff --git a/src/main/kotlin/app/revanced/cli/aligning/Aligning.kt b/src/main/kotlin/app/revanced/cli/aligning/Aligning.kt
index ef6d615d..d67c2ade 100644
--- a/src/main/kotlin/app/revanced/cli/aligning/Aligning.kt
+++ b/src/main/kotlin/app/revanced/cli/aligning/Aligning.kt
@@ -1,12 +1,37 @@
 package app.revanced.cli.aligning
 
 import app.revanced.cli.command.MainCommand.logger
+import app.revanced.patcher.PatcherResult
 import app.revanced.utils.signing.align.ZipAligner
+import app.revanced.utils.signing.align.zip.ZipFile
+import app.revanced.utils.signing.align.zip.structures.ZipEntry
 import java.io.File
 
 object Aligning {
-    fun align(inputFile: File, outputFile: File) {
+    fun align(result: PatcherResult, inputFile: File, outputFile: File) {
         logger.info("Aligning ${inputFile.name} to ${outputFile.name}")
-        ZipAligner.align(inputFile, outputFile)
+
+        if (outputFile.exists()) outputFile.delete()
+
+        ZipFile(outputFile).use { file ->
+            result.dexFiles.forEach {
+                file.addEntryCompressData(
+                    ZipEntry.createWithName(it.name),
+                    it.stream.readBytes()
+                )
+            }
+
+            result.resourceFile?.let {
+                file.copyEntriesFromFileAligned(
+                    ZipFile(it),
+                    ZipAligner::getEntryAlignment
+                )
+            }
+
+            file.copyEntriesFromFileAligned(
+                ZipFile(inputFile),
+                ZipAligner::getEntryAlignment
+            )
+        }
     }
 }
diff --git a/src/main/kotlin/app/revanced/cli/command/MainCommand.kt b/src/main/kotlin/app/revanced/cli/command/MainCommand.kt
index 49f9fb4d..aff17a0f 100644
--- a/src/main/kotlin/app/revanced/cli/command/MainCommand.kt
+++ b/src/main/kotlin/app/revanced/cli/command/MainCommand.kt
@@ -151,16 +151,14 @@ internal object MainCommand : Runnable {
             Adb(outputFile, patcher.context.packageMetadata.packageName, args.deploy!!, !pArgs.mount)
         }
 
-        val patchedFile = File(pArgs.cacheDirectory).resolve("${outputFile.nameWithoutExtension}_raw.apk")
-
         // start the patcher
-        Patcher.start(patcher, patchedFile, allPatches)
+        val result = Patcher.start(patcher, allPatches)
 
         val cacheDirectory = File(pArgs.cacheDirectory)
 
         // align the file
         val alignedFile = cacheDirectory.resolve("${outputFile.nameWithoutExtension}_aligned.apk")
-        Aligning.align(patchedFile, alignedFile)
+        Aligning.align(result, args.inputFile, alignedFile)
 
         // sign the file
         val finalFile = if (!pArgs.mount) {
diff --git a/src/main/kotlin/app/revanced/cli/patcher/Patcher.kt b/src/main/kotlin/app/revanced/cli/patcher/Patcher.kt
index dfe7b3d5..d1e5333b 100644
--- a/src/main/kotlin/app/revanced/cli/patcher/Patcher.kt
+++ b/src/main/kotlin/app/revanced/cli/patcher/Patcher.kt
@@ -1,24 +1,17 @@
 package app.revanced.cli.patcher
 
-import app.revanced.cli.command.MainCommand.args
-import app.revanced.cli.command.MainCommand.logger
+import app.revanced.patcher.PatcherResult
 import app.revanced.patcher.data.Context
 import app.revanced.patcher.patch.Patch
-import app.revanced.utils.filesystem.ZipFileSystemUtils
 import app.revanced.utils.patcher.addPatchesFiltered
 import app.revanced.utils.patcher.applyPatchesVerbose
 import app.revanced.utils.patcher.mergeFiles
-import java.io.File
-import java.nio.file.Files
 
 internal object Patcher {
     internal fun start(
         patcher: app.revanced.patcher.Patcher,
-        output: File,
         allPatches: List<Class<out Patch<Context>>>
-    ) {
-        val inputFile = args.inputFile
-
+    ): PatcherResult {
         // merge files like necessary integrations
         patcher.mergeFiles()
         // add patches, but filter incompatible or excluded patches
@@ -26,28 +19,6 @@ internal object Patcher {
         // apply patches
         patcher.applyPatchesVerbose()
 
-        // write output file
-        if (output.exists()) Files.delete(output.toPath())
-        inputFile.copyTo(output)
-
-        val result = patcher.save()
-        ZipFileSystemUtils(output).use { outputFileSystem ->
-            // replace all dex files
-            result.dexFiles.forEach {
-                logger.info("Writing dex file ${it.name}")
-                outputFileSystem.write(it.name, it.stream.readAllBytes())
-            }
-
-            result.resourceFile?.let {
-                logger.info("Writing resources...")
-
-                ZipFileSystemUtils(it).use { resourceFileSystem ->
-                    val resourceFiles = resourceFileSystem.getFile(File.separator)
-                    outputFileSystem.writePathRecursively(resourceFiles)
-                }
-            }
-
-            result.doNotCompress?.let { outputFileSystem.uncompress(*it.toTypedArray()) }
-        }
+        return patcher.save()
     }
 }
diff --git a/src/main/kotlin/app/revanced/utils/signing/align/ZipAligner.kt b/src/main/kotlin/app/revanced/utils/signing/align/ZipAligner.kt
index 1a348f67..be40ba1b 100644
--- a/src/main/kotlin/app/revanced/utils/signing/align/ZipAligner.kt
+++ b/src/main/kotlin/app/revanced/utils/signing/align/ZipAligner.kt
@@ -1,28 +1,11 @@
 package app.revanced.utils.signing.align
 
-import app.revanced.utils.signing.align.zip.ZipFile
-import java.io.File
+import app.revanced.utils.signing.align.zip.structures.ZipEntry
 
 internal object ZipAligner {
     private const val DEFAULT_ALIGNMENT = 4
     private const val LIBRARY_ALIGNMENT = 4096
 
-    fun align(input: File, output: File) {
-        val inputZip = ZipFile(input)
-        val outputZip = ZipFile(output)
-
-        for (entry in inputZip.entries) {
-            val data = inputZip.getDataForEntry(entry)
-
-            if (entry.compression == 0.toUShort()) {
-                val alignment = if (entry.fileName.endsWith(".so")) LIBRARY_ALIGNMENT else DEFAULT_ALIGNMENT
-
-                outputZip.addEntryAligned(entry, data, alignment)
-            } else {
-                outputZip.addEntry(entry, data)
-            }
-        }
-
-        outputZip.finish()
-    }
+    fun getEntryAlignment(entry: ZipEntry): Int? =
+        if (entry.compression.toUInt() != 0u) null else if (entry.fileName.endsWith(".so")) LIBRARY_ALIGNMENT else DEFAULT_ALIGNMENT
 }
diff --git a/src/main/kotlin/app/revanced/utils/signing/align/zip/ZipFile.kt b/src/main/kotlin/app/revanced/utils/signing/align/zip/ZipFile.kt
index 41c63481..e64cd1a1 100644
--- a/src/main/kotlin/app/revanced/utils/signing/align/zip/ZipFile.kt
+++ b/src/main/kotlin/app/revanced/utils/signing/align/zip/ZipFile.kt
@@ -2,15 +2,21 @@ package app.revanced.utils.signing.align.zip
 
 import app.revanced.utils.signing.align.zip.structures.ZipEndRecord
 import app.revanced.utils.signing.align.zip.structures.ZipEntry
+import java.io.Closeable
 import java.io.File
 import java.io.RandomAccessFile
 import java.nio.ByteBuffer
 import java.nio.channels.FileChannel
+import java.util.zip.CRC32
+import java.util.zip.Deflater
 
-class ZipFile(val file: File) {
+class ZipFile(file: File) : Closeable {
     var entries: MutableList<ZipEntry> = mutableListOf()
 
     private val filePointer: RandomAccessFile = RandomAccessFile(file, "rw")
+    private var CDNeedsRewrite = false
+
+    private val compressionLevel = 5
 
     init {
         //if file isn't empty try to load entries
@@ -53,23 +59,24 @@ class ZipFile(val file: File) {
 
         return buildList(numberOfEntries) {
             for (i in 1..numberOfEntries) {
-                add(ZipEntry.fromCDE(filePointer).also
-                {
-                    //for some reason the local extra field can be different from the central one
-                    it.readLocalExtra(
-                        filePointer.channel.map(
-                            FileChannel.MapMode.READ_ONLY,
-                            it.localHeaderOffset.toLong() + 28,
-                            2
+                add(
+                    ZipEntry.fromCDE(filePointer).also
+                    {
+                        //for some reason the local extra field can be different from the central one
+                        it.readLocalExtra(
+                            filePointer.channel.map(
+                                FileChannel.MapMode.READ_ONLY,
+                                it.localHeaderOffset.toLong() + 28,
+                                2
+                            )
                         )
-                    )
-                })
+                    })
             }
         }
     }
 
-    private fun writeCDE() {
-        val CDEStart = filePointer.channel.position().toUInt()
+    private fun writeCD() {
+        val CDStart = filePointer.channel.position().toUInt()
 
         entries.forEach {
             filePointer.channel.write(it.toCDE())
@@ -82,15 +89,17 @@ class ZipFile(val file: File) {
             0u,
             entriesCount,
             entriesCount,
-            filePointer.channel.position().toUInt() - CDEStart,
-            CDEStart,
+            filePointer.channel.position().toUInt() - CDStart,
+            CDStart,
             ""
         )
 
         filePointer.channel.write(endRecord.toECD())
     }
 
-    fun addEntry(entry: ZipEntry, data: ByteBuffer) {
+    private fun addEntry(entry: ZipEntry, data: ByteBuffer) {
+        CDNeedsRewrite = true
+
         entry.localHeaderOffset = filePointer.channel.position().toUInt()
 
         filePointer.channel.write(entry.toLFH())
@@ -99,17 +108,45 @@ class ZipFile(val file: File) {
         entries.add(entry)
     }
 
-    fun addEntryAligned(entry: ZipEntry, data: ByteBuffer, alignment: Int) {
-        //calculate where data would end up
-        val dataOffset = filePointer.filePointer + entry.LFHSize
+    fun addEntryCompressData(entry: ZipEntry, data: ByteArray) {
+        val compressor = Deflater(compressionLevel, true)
+        compressor.setInput(data)
+        compressor.finish()
+
+        val uncompressedSize = data.size
+        val compressedData =
+            ByteArray(uncompressedSize) //i'm guessing compression won't make the data bigger
+
+        val compressedDataLength = compressor.deflate(compressedData)
+        val compressedBuffer =
+            ByteBuffer.wrap(compressedData.take(compressedDataLength).toByteArray())
 
-        val mod = dataOffset % alignment
+        compressor.end()
+
+        val crc = CRC32()
+        crc.update(data)
+
+        entry.compression = 8u //deflate compression
+        entry.uncompressedSize = uncompressedSize.toUInt()
+        entry.compressedSize = compressedDataLength.toUInt()
+        entry.crc32 = crc.value.toUInt()
+
+        addEntry(entry, compressedBuffer)
+    }
 
-        //wrong alignment
-        if (mod != 0L) {
-            //add padding at end of extra field
-            entry.localExtraField =
-                entry.localExtraField.copyOf((entry.localExtraField.size + (alignment - mod)).toInt())
+    private fun addEntryCopyData(entry: ZipEntry, data: ByteBuffer, alignment: Int? = null) {
+        alignment?.let {
+            //calculate where data would end up
+            val dataOffset = filePointer.filePointer + entry.LFHSize
+
+            val mod = dataOffset % alignment
+
+            //wrong alignment
+            if (mod != 0L) {
+                //add padding at end of extra field
+                entry.localExtraField =
+                    entry.localExtraField.copyOf((entry.localExtraField.size + (alignment - mod)).toInt())
+            }
         }
 
         addEntry(entry, data)
@@ -123,8 +160,17 @@ class ZipFile(val file: File) {
         )
     }
 
-    fun finish() {
-        writeCDE()
+    fun copyEntriesFromFileAligned(file: ZipFile, entryAlignment: (entry: ZipEntry) -> Int?) {
+        for (entry in file.entries) {
+            if (entries.any { it.fileName == entry.fileName }) continue //don't add duplicates
+
+            val data = file.getDataForEntry(entry)
+            addEntryCopyData(entry, data, entryAlignment(entry))
+        }
+    }
+
+    override fun close() {
+        if (CDNeedsRewrite) writeCD()
         filePointer.close()
     }
-}
+}
\ No newline at end of file
diff --git a/src/main/kotlin/app/revanced/utils/signing/align/zip/structures/ZipEntry.kt b/src/main/kotlin/app/revanced/utils/signing/align/zip/structures/ZipEntry.kt
index 480377f6..d99a73d4 100644
--- a/src/main/kotlin/app/revanced/utils/signing/align/zip/structures/ZipEntry.kt
+++ b/src/main/kotlin/app/revanced/utils/signing/align/zip/structures/ZipEntry.kt
@@ -9,12 +9,12 @@ data class ZipEntry(
     val version: UShort,
     val versionNeeded: UShort,
     val flags: UShort,
-    val compression: UShort,
+    var compression: UShort,
     val modificationTime: UShort,
     val modificationDate: UShort,
-    val crc32: UInt,
-    val compressedSize: UInt,
-    val uncompressedSize: UInt,
+    var crc32: UInt,
+    var compressedSize: UInt,
+    var uncompressedSize: UInt,
     val diskNumber: UShort,
     val internalAttributes: UShort,
     val externalAttributes: UInt,
@@ -22,7 +22,7 @@ data class ZipEntry(
     val fileName: String,
     val extraField: ByteArray,
     val fileComment: String,
-    var localExtraField: ByteArray = ByteArray(0), //seperate for alignment
+    var localExtraField: ByteArray = ByteArray(0), //separate for alignment
 ) {
     val LFHSize: Int
         get() = LFH_HEADER_SIZE + fileName.toByteArray(Charsets.UTF_8).size + localExtraField.size
@@ -37,6 +37,27 @@ data class ZipEntry(
         const val LFH_HEADER_SIZE = 30
         const val LFH_SIGNATURE = 0x04034b50u
 
+        fun createWithName(fileName: String): ZipEntry {
+            return ZipEntry(
+                0x1403u, //made by unix, version 20
+                0u,
+                0u,
+                0u,
+                0x0821u, //seems to be static time google uses, no idea
+                0x0221u, //same as above
+                0u,
+                0u,
+                0u,
+                0u,
+                0u,
+                0u,
+                0u,
+                fileName,
+                ByteArray(0),
+                ""
+            )
+        }
+
         fun fromCDE(input: DataInput): ZipEntry {
             val signature = input.readUIntLE()
 
@@ -55,7 +76,7 @@ data class ZipEntry(
             val fileNameLength = input.readUShortLE()
             var fileName = ""
             val extraFieldLength = input.readUShortLE()
-            var extraField = ByteArray(extraFieldLength.toInt())
+            val extraField = ByteArray(extraFieldLength.toInt())
             val fileCommentLength = input.readUShortLE()
             var fileComment = ""
             val diskNumber = input.readUShortLE()
@@ -63,7 +84,8 @@ data class ZipEntry(
             val externalAttributes = input.readUIntLE()
             val localHeaderOffset = input.readUIntLE()
 
-            val variableFieldsLength = fileNameLength.toInt() + extraFieldLength.toInt() + fileCommentLength.toInt()
+            val variableFieldsLength =
+                fileNameLength.toInt() + extraFieldLength.toInt() + fileCommentLength.toInt()
 
             if (variableFieldsLength > 0) {
                 val fileNameBytes = ByteArray(fileNameLength.toInt())
@@ -77,7 +99,8 @@ data class ZipEntry(
                 fileComment = fileCommentBytes.toString(Charsets.UTF_8)
             }
 
-            flags = (flags and 0b1000u.inv().toUShort()) //disable data descriptor flag as they are not used
+            flags = (flags and 0b1000u.inv()
+                .toUShort()) //disable data descriptor flag as they are not used
 
             return ZipEntry(
                 version,
@@ -134,8 +157,9 @@ data class ZipEntry(
         val nameBytes = fileName.toByteArray(Charsets.UTF_8)
         val commentBytes = fileComment.toByteArray(Charsets.UTF_8)
 
-        val buffer = ByteBuffer.allocate(CDE_HEADER_SIZE + nameBytes.size + extraField.size + commentBytes.size)
-            .also { it.order(ByteOrder.LITTLE_ENDIAN) }
+        val buffer =
+            ByteBuffer.allocate(CDE_HEADER_SIZE + nameBytes.size + extraField.size + commentBytes.size)
+                .also { it.order(ByteOrder.LITTLE_ENDIAN) }
 
         buffer.putUInt(CDE_SIGNATURE)
         buffer.putUShort(version)
@@ -162,5 +186,4 @@ data class ZipEntry(
         buffer.flip()
         return buffer
     }
-}
-
+}
\ No newline at end of file