diff --git a/README.md b/README.md
index 40f3e6c..f9bd11e 100644
--- a/README.md
+++ b/README.md
@@ -29,8 +29,8 @@ It can be invoked as a standalone executable Jar-File. Java 17 is required.
 ```
 Usage: jst [-hV] [--in-format=<inputFormat>] [--libraries-list=<librariesList>]
            [--max-queue-depth=<maxQueueDepth>] [--out-format=<outputFormat>]
-           [--classpath=<addToClasspath>]... [--enable-parchment
-           --parchment-mappings=<mappingsPath> [--[no-]parchment-javadoc]
+           [--classpath=<addToClasspath>]... [--ignore-prefix=<ignoredPrefixes>]...
+           [--enable-parchment --parchment-mappings=<mappingsPath> [--[no-]parchment-javadoc]
            [--parchment-conflict-prefix=<conflictPrefix>]] [--enable-accesstransformers
            --access-transformer=<atFiles> [--access-transformer=<atFiles>]...
            [--access-transformer-validation=<validation>]] INPUT OUTPUT
@@ -40,6 +40,9 @@ Usage: jst [-hV] [--in-format=<inputFormat>] [--libraries-list=<librariesList>]
       --classpath=<addToClasspath>
                            Additional classpath entries to use. Is combined with --libraries-list.
   -h, --help               Show this help message and exit.
+      --ignore-prefix=<ignoredPrefixes>
+                           Do not apply transformations to paths that start with any of these
+                             prefixes.
       --in-format=<inputFormat>
                            Specify the format of INPUT explicitly. AUTO (the default) performs
                              auto-detection. Other options are SINGLE_FILE for Java files, ARCHIVE
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 3a41047..613d2e1 100644
--- a/cli/src/main/java/net/neoforged/jst/cli/Main.java
+++ b/cli/src/main/java/net/neoforged/jst/cli/Main.java
@@ -32,6 +32,9 @@ 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 apply transformations to paths that start with any of these prefixes.")
+    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<>();
 
@@ -73,6 +76,9 @@ 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 b3c97c3..c97b113 100644
--- a/cli/src/main/java/net/neoforged/jst/cli/SourceFileProcessor.java
+++ b/cli/src/main/java/net/neoforged/jst/cli/SourceFileProcessor.java
@@ -18,6 +18,7 @@
 import java.nio.file.Path;
 import java.nio.file.attribute.FileTime;
 import java.time.Instant;
+import java.util.ArrayList;
 import java.util.List;
 
 /**
@@ -29,6 +30,8 @@ class SourceFileProcessor implements AutoCloseable {
     private int maxQueueDepth = 50;
     private final Logger logger;
 
+    private final List<String> ignoredPrefixes = new ArrayList<>();
+
     public SourceFileProcessor(Logger logger) throws IOException {
         this.logger = logger;
         ijEnv = new IntelliJEnvironmentImpl(logger);
@@ -90,7 +93,7 @@ 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) {
@@ -101,6 +104,15 @@ 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
@@ -145,6 +157,11 @@ public void addLibrary(Path library) {
         ClasspathSetup.addLibrary(logger, 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 45631e4..e5aa9ca 100644
--- a/parchment/src/main/java/net/neoforged/jst/parchment/GatherReplacementsVisitor.java
+++ b/parchment/src/main/java/net/neoforged/jst/parchment/GatherReplacementsVisitor.java
@@ -61,8 +61,9 @@ 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());
                 }
             }