fix: invalid header when writing a ZipFile (#169)

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
+            )
+        }
     }
 }

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) {

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()
     }
 }