Restore ES6 module processing of input

src/com/google/javascript/jscomp/Compiler.java

@@ -1785,6 +1785,11 @@ Node parseInputs() {
         if (!inputsToRewrite.isEmpty()) {
           forceToEs6Modules(inputsToRewrite.values());
         }
+
+        if (options.needsTranspilationFrom(FeatureSet.ES6_MODULES)) {		
+          processEs6Modules(parsePotentialModules(inputs));		
+        }
+
       } else {
         // Use an empty module loader if we're not actually dealing with modules.
         this.moduleLoader = ModuleLoader.EMPTY;
@@ -2031,6 +2036,20 @@ void forceToEs6Modules(Collection<CompilerInput> inputsToProcess) {
     }
   }
 
+  void processEs6Modules(List<CompilerInput> inputsToProcess) {		
+    for (CompilerInput input : inputsToProcess) {		
+      input.setCompiler(this);		
+      Node root = input.getAstRoot(this);		
+      if (root == null) {		
+        continue;		
+      }		
+      if (Es6RewriteModules.isEs6ModuleRoot(root)) {		
+        new Es6RewriteModules(this).processFile(root);		
+      }		
+    }		
+    setFeatureSet(featureSet.without(Feature.MODULES));		
+  }
+
   private List<CompilerInput> parsePotentialModules(List<CompilerInput> inputsToProcess) {
     List<CompilerInput> filteredInputs = new ArrayList<>();
     for (CompilerInput input : inputsToProcess) {

src/com/google/javascript/jscomp/Es6RewriteModules.java

@@ -142,7 +142,7 @@ public void hotSwapScript(Node scriptNode, Node originalRoot) {
   /**
    * Rewrite a single ES6 module file to a global script version.
    */
-  private void processFile(Node root) {
+  public void processFile(Node root) {
     checkArgument(isEs6ModuleRoot(root), root);
     clearState();
     NodeTraversal.traverseEs6(compiler, root, this);