diff --git a/cli/src/main/java/net/neoforged/jst/cli/Main.java b/cli/src/main/java/net/neoforged/jst/cli/Main.java
index cef1d0c..c54c54b 100644
--- a/cli/src/main/java/net/neoforged/jst/cli/Main.java
+++ b/cli/src/main/java/net/neoforged/jst/cli/Main.java
@@ -31,6 +31,9 @@ public class Main implements Callable<Integer> {
     @CommandLine.Option(names = "--libraries-list", description = "Specifies a file that contains a path to an archive or directory to add to the classpath on each line.")
     Path librariesList;
 
+    @CommandLine.Option(names = "--ignore-prefix", description = "Do not transforms entry whose path start with this prefix.")
+    List<String> ignoredPrefixes = new ArrayList<>();
+
     @CommandLine.Option(names = "--classpath", description = "Additional classpath entries to use. Is combined with --libraries-list.", converter = ClasspathConverter.class)
     List<Path> addToClasspath = new ArrayList<>();
 
@@ -69,6 +72,9 @@ public Integer call() throws Exception {
             for (Path path : addToClasspath) {
                 processor.addLibrary(path);
             }
+            for (String ignoredPrefix : ignoredPrefixes) {
+                processor.addIgnoredPrefix(ignoredPrefix);
+            }
 
             processor.setMaxQueueDepth(maxQueueDepth);
 
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 1d338f4..e0f43fd 100644
--- a/cli/src/main/java/net/neoforged/jst/cli/SourceFileProcessor.java
+++ b/cli/src/main/java/net/neoforged/jst/cli/SourceFileProcessor.java
@@ -17,6 +17,7 @@
 import java.nio.file.Path;
 import java.nio.file.attribute.FileTime;
 import java.time.Instant;
+import java.util.ArrayList;
 import java.util.List;
 
 /**
@@ -27,6 +28,8 @@ class SourceFileProcessor implements AutoCloseable {
     private final IntelliJEnvironmentImpl ijEnv = new IntelliJEnvironmentImpl();
     private int maxQueueDepth = 50;
 
+    private final List<String> ignoredPrefixes = new ArrayList<>();
+
     public SourceFileProcessor() throws IOException {
         ijEnv.addCurrentJdkToClassPath();
     }
@@ -83,7 +86,7 @@ private void processEntry(FileEntry entry, VirtualFile sourceRoot, List<SourceTr
             byte[] content = in.readAllBytes();
             var lastModified = entry.lastModified();
 
-            if (!transformers.isEmpty() && entry.hasExtension("java")) {
+            if (!isIgnored(entry.relativePath()) && !transformers.isEmpty() && entry.hasExtension("java")) {
                 var orgContent = content;
                 content = transformSource(sourceRoot, entry.relativePath(), transformers, content);
                 if (orgContent != content) {
@@ -94,6 +97,15 @@ private void processEntry(FileEntry entry, VirtualFile sourceRoot, List<SourceTr
         }
     }
 
+    private boolean isIgnored(String relativePath) {
+        for (String ignoredPrefix : ignoredPrefixes) {
+            if (relativePath.startsWith(ignoredPrefix)) {
+                return true;
+            }
+        }
+        return false;
+    }
+
     byte[] transformSource(VirtualFile contentRoot, String path, List<SourceTransformer> transformers, byte[] originalContentBytes) {
         // Instead of parsing the content we actually read from the file, we read the virtual file that is
         // visible to IntelliJ from adding the source jar. The reasoning is that IntelliJ will cache this internally
@@ -138,6 +150,11 @@ public void addLibrary(Path library) {
         ClasspathSetup.addLibrary(library, ijEnv);
     }
 
+    public void addIgnoredPrefix(String ignoredPrefix) {
+        System.out.println("Not transforming entries starting with " + ignoredPrefix);
+        this.ignoredPrefixes.add(ignoredPrefix);
+    }
+
     @Override
     public void close() throws IOException {
         ijEnv.close();
diff --git a/parchment/src/main/java/net/neoforged/jst/parchment/GatherReplacementsVisitor.java b/parchment/src/main/java/net/neoforged/jst/parchment/GatherReplacementsVisitor.java
index db5d351..3e71ce0 100644
--- a/parchment/src/main/java/net/neoforged/jst/parchment/GatherReplacementsVisitor.java
+++ b/parchment/src/main/java/net/neoforged/jst/parchment/GatherReplacementsVisitor.java
@@ -54,8 +54,9 @@ public void visitElement(@NotNull PsiElement element) {
                 if (foundClass == null) {
                     throw new IllegalStateException("Failed to find how class " + psiClass.getQualifiedName() + " was loaded while processing it");
                 } else if (foundClass != psiClass) {
-                    throw new IllegalStateException("Class " + psiClass + " was loaded from two different sources: " +
-                            psiClass.getContainingFile() + " and " + foundClass.getContainingFile());
+                    throw new IllegalStateException("Class " + psiClass.getQualifiedName() + " was loaded from two different sources: " +
+                                                    psiClass.getContainingFile().getVirtualFile().getPath() + " and " +
+                                                    foundClass.getContainingFile().getVirtualFile().getPath());
                 }
             }