--- old/src/java.base/share/classes/jdk/internal/module/ModulePatcher.java	2017-02-07 13:13:46.264125853 +0000
+++ new/src/java.base/share/classes/jdk/internal/module/ModulePatcher.java	2017-02-07 13:13:46.095114247 +0000
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2015, 2016, Oracle and/or its affiliates. All rights reserved.
+ * Copyright (c) 2015, 2017, Oracle and/or its affiliates. All rights reserved.
  * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
  *
  * This code is free software; you can redistribute it and/or modify it
@@ -31,6 +31,7 @@
 import java.io.InputStream;
 import java.io.UncheckedIOException;
 import java.lang.module.ModuleDescriptor;
+import java.lang.module.ModuleDescriptor.Builder;
 import java.lang.module.ModuleReader;
 import java.lang.module.ModuleReference;
 import java.net.MalformedURLException;
@@ -54,6 +55,7 @@
 import java.util.stream.Stream;
 
 import jdk.internal.loader.Resource;
+import jdk.internal.loader.ResourceHelper;
 import jdk.internal.misc.JavaLangModuleAccess;
 import jdk.internal.misc.SharedSecrets;
 import sun.net.www.ParseUtil;
@@ -108,8 +110,11 @@
         if (paths == null)
             return mref;
 
-        // scan the JAR file or directory tree to get the set of packages
+        // Scan the JAR file or directory tree to get the set of packages.
+        // For automatic modules then packages that do not contain class files
+        // must be ignored.
         Set<String> packages = new HashSet<>();
+        boolean isAutomatic = descriptor.isAutomatic();
         try {
             for (Path file : paths) {
                 if (Files.isRegularFile(file)) {
@@ -118,8 +123,10 @@
                     // is not supported by the boot class loader
                     try (JarFile jf = new JarFile(file.toFile())) {
                         jf.stream()
+                          .filter(e -> !e.isDirectory()
+                                  && (!isAutomatic || e.getName().endsWith(".class")))
                           .map(e -> toPackageName(file, e))
-                          .filter(Checks::isJavaIdentifier)
+                          .filter(Checks::isPackageName)
                           .forEach(packages::add);
                     }
 
@@ -129,8 +136,10 @@
                     Path top = file;
                     Files.find(top, Integer.MAX_VALUE,
                                ((path, attrs) -> attrs.isRegularFile()))
+                            .filter(path -> !isAutomatic
+                                    || path.toString().endsWith(".class"))
                             .map(path -> toPackageName(top, path))
-                            .filter(Checks::isJavaIdentifier)
+                            .filter(Checks::isPackageName)
                             .forEach(packages::add);
 
                 }
@@ -141,10 +150,30 @@
         }
 
         // if there are new packages then we need a new ModuleDescriptor
-        Set<String> original = descriptor.packages();
-        packages.addAll(original);
-        if (packages.size() > original.size()) {
-            descriptor = JLMA.newModuleDescriptor(descriptor, packages);
+        packages.removeAll(descriptor.packages());
+        if (!packages.isEmpty()) {
+            Builder builder = JLMA.newModuleBuilder(descriptor.name(),
+                                                    /*strict*/ false,
+                                                    descriptor.modifiers());
+            if (!descriptor.isAutomatic()) {
+                descriptor.requires().forEach(builder::requires);
+                descriptor.exports().forEach(builder::exports);
+                descriptor.opens().forEach(builder::opens);
+                descriptor.uses().forEach(builder::uses);
+            }
+            descriptor.provides().forEach(builder::provides);
+
+            descriptor.version().ifPresent(builder::version);
+            descriptor.mainClass().ifPresent(builder::mainClass);
+            descriptor.osName().ifPresent(builder::osName);
+            descriptor.osArch().ifPresent(builder::osArch);
+            descriptor.osVersion().ifPresent(builder::osVersion);
+
+            // original + new packages
+            builder.packages(descriptor.packages());
+            builder.packages(packages);
+
+            descriptor = builder.build();
         }
 
         // return a module reference to the patched module
@@ -471,23 +500,14 @@
 
         @Override
         public Resource find(String name) throws IOException {
-            Path file = Paths.get(name.replace('/', File.separatorChar));
-            if (file.getRoot() == null) {
-                file = dir.resolve(file);
-            } else {
-                // drop the root component so that the resource is
-                // located relative to the module directory
-                int n = file.getNameCount();
-                if (n == 0)
-                    return null;
-                file = dir.resolve(file.subpath(0, n));
-            }
-
-            if (Files.isRegularFile(file)) {
-                return newResource(name, dir, file);
-            } else {
-                return null;
+            Path path = ResourceHelper.toFilePath(name);
+            if (path != null) {
+                Path file = dir.resolve(path);
+                if (Files.isRegularFile(file)) {
+                    return newResource(name, dir, file);
+                }
             }
+            return null;
         }
 
         private Resource newResource(String name, Path top, Path file) {