revert: feat: remove extra zipalign step

This reverts commit c8e793e.

src/main/kotlin/app/revanced/cli/aligning/Aligning.kt

@@ -0,0 +1,12 @@
+package app.revanced.cli.aligning
+
+import app.revanced.cli.command.MainCommand.logger
+import app.revanced.utils.signing.align.ZipAligner
+import java.io.File
+
+object Aligning {
+    fun align(inputFile: File, outputFile: File) {
+        logger.info("Aligning ${inputFile.name} to ${outputFile.name}")
+        ZipAligner.align(inputFile, outputFile)
+    }
+}

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

@@ -1,5 +1,6 @@
 package app.revanced.cli.command
 
+import app.revanced.cli.aligning.Aligning
 import app.revanced.cli.logging.impl.DefaultCliLogger
 import app.revanced.cli.patcher.Patcher
 import app.revanced.cli.patcher.logging.impl.PatcherLogger
@@ -160,11 +161,15 @@ internal object MainCommand : Runnable {
 
         val cacheDirectory = File(pArgs.cacheDirectory)
 
+        // align the file
+        val alignedFile = cacheDirectory.resolve("${outputFile.nameWithoutExtension}_aligned.apk")
+        Aligning.align(patchedFile, alignedFile)
+
         // sign the file
         val finalFile = if (!pArgs.mount) {
             val signedOutput = cacheDirectory.resolve("${outputFile.nameWithoutExtension}_signed.apk")
             Signing.sign(
-                patchedFile,
+                alignedFile,
                 signedOutput,
                 SigningOptions(
                     pArgs.cn,
@@ -177,7 +182,7 @@ internal object MainCommand : Runnable {
 
             signedOutput
         } else
-            patchedFile
+            alignedFile
 
         // finally copy to the specified output file
         logger.info("Copying ${finalFile.name} to ${outputFile.name}")

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

@@ -2,12 +2,10 @@ package app.revanced.cli.patcher
 
 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
 import app.revanced.utils.patcher.mergeFiles
-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
 import java.nio.file.Files
 
@@ -25,22 +23,26 @@ internal object Patcher {
 
         // write output file
         if (output.exists()) Files.delete(output.toPath())
+        inputFile.copyTo(output)
 
         val result = patcher.save()
-        ZipFile(output).use { outputFile ->
+        ZipFileSystemUtils(output).use { outputFileSystem ->
             // replace all dex files
             result.dexFiles.forEach {
                 logger.info("Writing dex file ${it.name}")
-                outputFile.addEntryCompressData(ZipEntry.createWithName(it.name), it.dexFileInputStream.readAllBytes())
+                outputFileSystem.write(it.name, it.dexFileInputStream.readAllBytes())
             }
 
             if (!args.disableResourcePatching) {
                 logger.info("Writing resources...")
 
-                outputFile.copyEntriesFromFileAligned(ZipFile(result.resourceFile!!), ZipAligner::getEntryAlignment)
+                ZipFileSystemUtils(result.resourceFile!!).use { resourceFileSystem ->
+                    val resourceFiles = resourceFileSystem.getFile(File.separator)
+                    outputFileSystem.writePathRecursively(resourceFiles)
+                }
             }
 
-            outputFile.copyEntriesFromFileAligned(ZipFile(inputFile), ZipAligner::getEntryAlignment)
+            result.doNotCompress?.let { outputFileSystem.uncompress(*it.toTypedArray()) }
         }
     }
 }

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

@@ -0,0 +1,64 @@
+package app.revanced.utils.filesystem
+
+import java.io.Closeable
+import java.io.File
+import java.nio.file.FileSystems
+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))
+
+    private fun Path.deleteRecursively() {
+        if (!Files.exists(this)) {
+            throw IllegalStateException("File exists in real folder but not in zip file system")
+        }
+
+        if (Files.isDirectory(this)) {
+            Files.list(this).forEach { path ->
+                path.deleteRecursively()
+            }
+        }
+
+        Files.delete(this)
+    }
+
+    internal fun getFile(path: String) = zipFileSystem.getPath(path)
+
+    internal fun writePathRecursively(path: Path) {
+        Files.list(path).use { fileStream ->
+            fileStream.forEach { filePath ->
+                val fileSystemPath = filePath.getRelativePath(path)
+                fileSystemPath.deleteRecursively()
+            }
+        }
+
+        Files.walk(path).use { fileStream ->
+            // don't include build directory
+            // by skipping the root node.
+            fileStream.skip(1).forEach { filePath ->
+                val relativePath = filePath.getRelativePath(path)
+
+                if (Files.isDirectory(filePath)) {
+                    Files.createDirectory(relativePath)
+                    return@forEach
+                }
+
+                Files.copy(filePath, relativePath)
+            }
+        }
+    }
+
+    internal fun write(path: String, content: ByteArray) = Files.write(zipFileSystem.getPath(path), content)
+
+    private fun Path.getRelativePath(path: Path): Path = zipFileSystem.getPath(path.relativize(this).toString())
+
+    // TODO: figure out why the file system is uncompressed by default and how to fix it
+    internal fun uncompress(vararg paths: String) =
+        paths.forEach { Files.setAttribute(zipFileSystem.getPath(it), "zip:method", ZipEntry.STORED) }
+
+    override fun close() = zipFileSystem.close()
+}

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

@@ -1,11 +1,28 @@
 package app.revanced.utils.signing.align
 
-import app.revanced.utils.signing.align.zip.structures.ZipEntry
+import app.revanced.utils.signing.align.zip.ZipFile
+import java.io.File
 
 internal object ZipAligner {
     private const val DEFAULT_ALIGNMENT = 4
     private const val LIBRARY_ALIGNMENT = 4096
 
-    fun getEntryAlignment(entry: ZipEntry): Int? =
-        if (entry.compression.toUInt() != 0u) null else if (entry.fileName.endsWith(".so")) LIBRARY_ALIGNMENT else DEFAULT_ALIGNMENT
+    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()
+    }
 }

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

@@ -2,21 +2,15 @@ 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) : Closeable {
+class ZipFile(val file: File) {
     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
@@ -59,24 +53,23 @@ class ZipFile(val file: File) : Closeable {
 
         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 writeCD() {
-        val CDStart = filePointer.channel.position().toUInt()
+    private fun writeCDE() {
+        val CDEStart = filePointer.channel.position().toUInt()
 
         entries.forEach {
             filePointer.channel.write(it.toCDE())
@@ -89,17 +82,15 @@ class ZipFile(val file: File) : Closeable {
             0u,
             entriesCount,
             entriesCount,
-            filePointer.channel.position().toUInt() - CDStart,
-            CDStart,
+            filePointer.channel.position().toUInt() - CDEStart,
+            CDEStart,
             ""
         )
 
         filePointer.channel.write(endRecord.toECD())
     }
 
-    private fun addEntry(entry: ZipEntry, data: ByteBuffer) {
-        CDNeedsRewrite = true
-
+    fun addEntry(entry: ZipEntry, data: ByteBuffer) {
         entry.localHeaderOffset = filePointer.channel.position().toUInt()
 
         filePointer.channel.write(entry.toLFH())
@@ -108,45 +99,17 @@ class ZipFile(val file: File) : Closeable {
         entries.add(entry)
     }
 
-    fun addEntryCompressData(entry: ZipEntry, data: ByteArray) {
-        val compressor = Deflater(compressionLevel, true)
-        compressor.setInput(data)
-        compressor.finish()
-
-        val uncompressedSize = data.size
-        val compressedData =
-            ByteArray(uncompressedSize) //i'm guessing compression won't make the data bigger
-
-        val compressedDataLength = compressor.deflate(compressedData)
-        val compressedBuffer =
-            ByteBuffer.wrap(compressedData.take(compressedDataLength).toByteArray())
+    fun addEntryAligned(entry: ZipEntry, data: ByteBuffer, alignment: Int) {
+        //calculate where data would end up
+        val dataOffset = filePointer.filePointer + entry.LFHSize
 
-        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)
-    }
+        val mod = dataOffset % alignment
 
-    fun addEntryCopyData(entry: ZipEntry, data: ByteBuffer, alignment: Int? = null) {
-        alignment?.let { alignment ->
-            //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())
-            }
+        //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)
@@ -160,17 +123,8 @@ class ZipFile(val file: File) : Closeable {
         )
     }
 
-    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()
+    fun finish() {
+        writeCDE()
         filePointer.close()
     }
 }

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

@@ -58,8 +58,7 @@ data class ZipEndRecord(
     fun toECD(): ByteBuffer {
         val commentBytes = fileComment.toByteArray(Charsets.UTF_8)
 
-        val buffer = ByteBuffer.allocate(ECD_HEADER_SIZE + commentBytes.size)
-            .also { it.order(ByteOrder.LITTLE_ENDIAN) }
+        val buffer = ByteBuffer.allocate(ECD_HEADER_SIZE + commentBytes.size).also { it.order(ByteOrder.LITTLE_ENDIAN) }
 
         buffer.putUInt(ECD_SIGNATURE)
         buffer.putUShort(diskNumber)