revert: feat: remove extra zipalign step

This reverts commit c8e793efab.

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()) }
         }
     }
 }