revert: feat: remove extra zipalign step

This reverts commit c8e793efab.

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}")