diff --git a/cli/src/main/java/net/neoforged/jst/cli/SourceFileProcessor.java b/cli/src/main/java/net/neoforged/jst/cli/SourceFileProcessor.java
index e4cbbc6..ee8d1ad 100644
--- a/cli/src/main/java/net/neoforged/jst/cli/SourceFileProcessor.java
+++ b/cli/src/main/java/net/neoforged/jst/cli/SourceFileProcessor.java
@@ -45,7 +45,7 @@ public void process(FileSource source, FileSink sink, List<SourceTransformer> tr
             transformer.beforeRun(context);
         }
 
-        if (sink.isOrdered()) {
+        if (source.isOrdered() && sink.isOrdered()) {
             try (var stream = source.streamEntries()) {
                 stream.forEach(entry -> {
                     try {
@@ -82,7 +82,8 @@ private void processEntry(FileEntry entry, VirtualFile sourceRoot, List<SourceTr
         try (var in = entry.openInputStream()) {
             byte[] content = in.readAllBytes();
             var lastModified = entry.lastModified();
-            if (entry.hasExtension("java")) {
+
+            if (!transformers.isEmpty() && entry.hasExtension("java")) {
                 var orgContent = content;
                 content = transformSource(sourceRoot, entry.relativePath(), transformers, content);
                 if (orgContent != content) {
diff --git a/cli/src/main/java/net/neoforged/jst/cli/io/ArchiveFileSource.java b/cli/src/main/java/net/neoforged/jst/cli/io/ArchiveFileSource.java
index 04c6fa5..1a13e74 100644
--- a/cli/src/main/java/net/neoforged/jst/cli/io/ArchiveFileSource.java
+++ b/cli/src/main/java/net/neoforged/jst/cli/io/ArchiveFileSource.java
@@ -9,7 +9,10 @@
 
 import java.io.IOException;
 import java.nio.file.Path;
+import java.util.Spliterator;
+import java.util.Spliterators;
 import java.util.stream.Stream;
+import java.util.stream.StreamSupport;
 import java.util.zip.ZipFile;
 
 class ArchiveFileSource implements FileSource {
@@ -28,7 +31,13 @@ public VirtualFile createSourceRoot(VirtualFileManager vfsManager) {
 
     @Override
     public Stream<FileEntry> streamEntries() {
-        return zipFile.stream().map(ze -> FileEntries.ofZipEntry(zipFile, ze));
+        var spliterator = Spliterators.spliterator(
+                zipFile.entries().asIterator(),
+                zipFile.size(),
+                Spliterator.IMMUTABLE | Spliterator.ORDERED
+        );
+        return StreamSupport.stream(spliterator, false)
+                .map(ze -> FileEntries.ofZipEntry(zipFile, ze));
     }
 
     @Override
diff --git a/tests/src/test/java/net/neoforged/jst/tests/EmbeddedTest.java b/tests/src/test/java/net/neoforged/jst/tests/EmbeddedTest.java
index 3c2250f..9715e88 100644
--- a/tests/src/test/java/net/neoforged/jst/tests/EmbeddedTest.java
+++ b/tests/src/test/java/net/neoforged/jst/tests/EmbeddedTest.java
@@ -228,6 +228,7 @@ protected final void runTest(String testDirName, String mappingsFilename) throws
         Files.write(librariesFile, List.of("-e=" + junitJarPath));
 
         runTool(
+                "--max-queue-depth=1",
                 "--libraries-list",
                 librariesFile.toString(),
                 "--enable-parchment",