diff --git a/core/src/main/scala/com/eed3si9n/jarjarabrams/Zip.scala b/core/src/main/scala/com/eed3si9n/jarjarabrams/Zip.scala
index 1bc3df5..0e1cf7a 100644
--- a/core/src/main/scala/com/eed3si9n/jarjarabrams/Zip.scala
+++ b/core/src/main/scala/com/eed3si9n/jarjarabrams/Zip.scala
@@ -1,7 +1,7 @@
 package com.eed3si9n.jarjarabrams
 
-import com.eed3si9n.jarjar.util.{ DuplicateJarEntryException, EntryStruct }
-import java.nio.file.{ Files, NoSuchFileException, Path, StandardCopyOption }
+import com.eed3si9n.jarjar.util.{ DuplicateJarEntryException, EntryStruct, IoUtil }
+import java.nio.file.{ Files, NoSuchFileException, Path }
 import java.nio.file.attribute.FileTime
 import java.io.{ ByteArrayOutputStream, FileNotFoundException, InputStream, OutputStream }
 import java.security.MessageDigest
@@ -83,7 +83,7 @@ object Zip {
           }
         }
       }
-      Files.move(tempJar, outputJar, StandardCopyOption.REPLACE_EXISTING)
+      IoUtil.copyZipWithoutEmptyDirectories(tempJar.toFile, outputJar.toFile)
       resetModifiedTime(outputJar)
       outputJar
     }
diff --git a/core/src/test/scala/testpkg/ShaderTest.scala b/core/src/test/scala/testpkg/ShaderTest.scala
index 9247516..3dc345d 100644
--- a/core/src/test/scala/testpkg/ShaderTest.scala
+++ b/core/src/test/scala/testpkg/ShaderTest.scala
@@ -15,7 +15,7 @@ object ShaderTest extends BasicTestSuite {
       Paths.get(byteBuddyJar),
       resetTimestamp = false,
       expectedClass = expectedByteBuddyClass,
-      expectedSha = "673a5b1d7282ec68def6d6e6845c29d96142e4e3b39796484e122cd92f65edee"
+      expectedSha = "42454701a0b53a13af17d015c1785ef5ea342d8c324315ed17d80831cba98be3"
     )
   }
 
@@ -24,7 +24,7 @@ object ShaderTest extends BasicTestSuite {
       Paths.get(byteBuddyJar),
       resetTimestamp = true,
       expectedClass = expectedByteBuddyClass,
-      expectedSha = "33ceee11fb2b5e4d46ebe552025bc17bc4d9391974c55e07d63f9e85d2ec381a"
+      expectedSha = "0db0b1300533c06a934dca1e7016f6dc2d432c66f1927102d6f6b49086dcfddb"
     )
   }
 
diff --git a/jarjar/src/main/java/com/eed3si9n/jarjar/util/IoUtil.java b/jarjar/src/main/java/com/eed3si9n/jarjar/util/IoUtil.java
index 78bc57b..0bfa57c 100644
--- a/jarjar/src/main/java/com/eed3si9n/jarjar/util/IoUtil.java
+++ b/jarjar/src/main/java/com/eed3si9n/jarjar/util/IoUtil.java
@@ -70,7 +70,7 @@ public static void copyZipWithoutEmptyDirectories(File inputFile, File outputFil
                 int index = name.lastIndexOf('/');
                 while (index > 0) {
                     name = name.substring(0, index);
-                    dirsToRetain.add(name);
+                    dirsToRetain.add(name + "/");
                     index = name.lastIndexOf('/');
                 }
             }
diff --git a/jarjar/src/test/java/com/eed3si9n/jarjar/util/IOUtilTest.java b/jarjar/src/test/java/com/eed3si9n/jarjar/util/IOUtilTest.java
new file mode 100644
index 0000000..9c4a2e3
--- /dev/null
+++ b/jarjar/src/test/java/com/eed3si9n/jarjar/util/IOUtilTest.java
@@ -0,0 +1,68 @@
+package com.eed3si9n.jarjar.util;
+
+import org.junit.Assert;
+import org.junit.Test;
+
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.stream.Stream;
+import java.util.zip.ZipEntry;
+import java.util.zip.ZipFile;
+import java.util.zip.ZipOutputStream;
+
+public class IOUtilTest {
+    @Test
+    public void testCopyZipWithoutEmptyDirectories() throws IOException {
+        // create a temporary directory tree with a few empty files and empty directories
+        Path tree = Files.createTempDirectory("tree");
+        Path zips = Files.createTempDirectory("zips");
+
+        // Create a zip with some empty directories
+        Path a = Files.createDirectory(Paths.get(tree.toString(), "a"));
+        Files.createFile(Paths.get(a.toString(), "a.txt"));
+        Files.createDirectory(Paths.get(tree.toString(), "b"));
+        Path c = Files.createDirectory(Paths.get(tree.toString(), "c"));
+        Files.createDirectory(Paths.get(c.toString(), "d"));
+        File inputZipFile = Paths.get(zips.toString(), "input.zip").toFile();
+        zipDirectory(tree, inputZipFile);
+
+        File outputZipFile = Paths.get(zips.toString(), "output.zip").toFile();
+        IoUtil.copyZipWithoutEmptyDirectories(inputZipFile, outputZipFile);
+        try (ZipFile outputZip = new ZipFile(outputZipFile)) {
+            Assert.assertNotNull(outputZip.getEntry("a/a.txt"));
+            Assert.assertNotNull(outputZip.getEntry("a/"));
+            Assert.assertNull(outputZip.getEntry("b/"));
+            Assert.assertNull(outputZip.getEntry("c/"));
+            Assert.assertNull(outputZip.getEntry("c/d/"));
+        }
+    }
+
+    private static void zipDirectory(Path sourceDir, File zipFile) throws IOException {
+        try (ZipOutputStream zipOutputStream = new ZipOutputStream(new FileOutputStream(zipFile));
+             Stream<Path> paths = Files.walk(sourceDir)
+        ) {
+            paths.forEach(path -> {
+                String name = sourceDir.relativize(path).toString();
+                if (Files.isDirectory(path)) {
+                    name = name + "/";
+                }
+                ZipEntry zipEntry = new ZipEntry(name);
+                try {
+                    zipOutputStream.putNextEntry(zipEntry);
+                    if (!Files.isDirectory(path)) {
+                        Files.copy(path, zipOutputStream);
+                    }
+                    zipOutputStream.closeEntry();
+                } catch (IOException e) {
+                    throw new RuntimeIOException(e);
+                }
+            });
+        }
+    }
+
+
+}