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 613d2e1..2415666 100644
--- a/cli/src/main/java/net/neoforged/jst/cli/Main.java
+++ b/cli/src/main/java/net/neoforged/jst/cli/Main.java
@@ -35,6 +35,9 @@ public class Main implements Callable<Integer> {
     @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 = "--hidden-prefix", description = "Do not process or emit paths that start with any of these prefixes.")
+    List<String> hiddenPrefixes = 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<>();
 
@@ -79,6 +82,10 @@ public Integer call() throws Exception {
             for (String ignoredPrefix : ignoredPrefixes) {
                 processor.addIgnoredPrefix(ignoredPrefix);
             }
+            for (String hiddenPrefix : hiddenPrefixes) {
+                processor.addIgnoredPrefix(hiddenPrefix);
+                processor.addHiddenPrefix(hiddenPrefix);
+            }
 
             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 5e7dd06..a20fc92 100644
--- a/cli/src/main/java/net/neoforged/jst/cli/SourceFileProcessor.java
+++ b/cli/src/main/java/net/neoforged/jst/cli/SourceFileProcessor.java
@@ -34,6 +34,7 @@ class SourceFileProcessor implements AutoCloseable {
     private final Logger logger;
 
     private final List<String> ignoredPrefixes = new ArrayList<>();
+    private final List<String> hiddenPrefixes = new ArrayList<>();
 
     public SourceFileProcessor(Logger logger) throws IOException {
         this.logger = logger;
@@ -114,13 +115,21 @@ private boolean processEntry(FileEntry entry, VirtualFile sourceRoot, List<Sourc
                     lastModified = FileTime.from(Instant.now());
                 }
             }
-            sink.putFile(entry.relativePath(), lastModified, content);
+            if (!isHidden(entry.relativePath())) sink.putFile(entry.relativePath(), lastModified, content);
         }
         return true;
     }
 
     private boolean isIgnored(String relativePath) {
-        for (String ignoredPrefix : ignoredPrefixes) {
+        return isRelativePathIn(relativePath, this.ignoredPrefixes);
+    }
+
+    private boolean isHidden(String relativePath) {
+        return isRelativePathIn(relativePath, this.hiddenPrefixes);
+    }
+
+    private boolean isRelativePathIn(String relativePath, List<String> prefixes) {
+        for (String ignoredPrefix : prefixes) {
             if (relativePath.startsWith(ignoredPrefix)) {
                 return true;
             }
@@ -187,6 +196,12 @@ public void addIgnoredPrefix(String ignoredPrefix) {
         this.ignoredPrefixes.add(ignoredPrefix);
     }
 
+    public void addHiddenPrefix(String hiddenPrefix) {
+        System.out.println("Not reading entries starting with " + hiddenPrefix);
+        this.ignoredPrefixes.add(hiddenPrefix);
+        this.hiddenPrefixes.add(hiddenPrefix);
+    }
+
     @Override
     public void close() throws IOException {
         ijEnv.close();