diff --git a/src/babel/transformation/file/index.js b/src/babel/transformation/file/index.js
index 49cedda07e..5dd1c9f970 100644
--- a/src/babel/transformation/file/index.js
+++ b/src/babel/transformation/file/index.js
@@ -482,32 +482,30 @@ export default class File {
     if (modFormatter.init && this.transformers["es6.modules"].canTransform()) {
       modFormatter.init();
     }
+    this.populateModuleMetadata();
     this.log.debug("End module formatter init");
+  }
 
+  populateModuleMetadata() {
+    var modules = {};
+    this.metadata.modules = modules;
+  }
+
+  transform(dependencyGraph) {
     this.call("pre");
     for (var pass of (this.transformerStack: Array)) {
       pass.transform();
     }
     this.call("post");
+
+    return this.generate();
   }
 
   wrap(code, callback) {
     code = code + "";
 
     try {
-      if (this.shouldIgnore()) {
-        return {
-          metadata: this.metadata,
-          ignored:  true,
-          code:     code,
-          map:      null,
-          ast:      null
-        };
-      }
-
-      callback();
-
-      return this.generate();
+      return callback();
     } catch (err) {
       if (err._babel) {
         throw err;
@@ -540,11 +538,11 @@ export default class File {
     code = (code || "") + "";
     code = this.parseInputSourceMap(code);
     this.code = code;
+  }
 
-    if (parseCode) {
-      this.parseShebang();
-      this.addAst(this.parse(this.code));
-    }
+  parseCode() {
+    this.parseShebang();
+    this.addAst(this.parse(this.code));
   }
 
   shouldIgnore() {
@@ -581,28 +579,37 @@ export default class File {
     }
   }
 
-  generate(): {
-    usedHelpers?: Array<string>;
-    code: string;
-    map?: Object;
-    ast?: Object;
-  } {
-    var opts = this.opts;
-    var ast  = this.ast;
-
+  makeResult({ code, map = null, ast, ignored }) {
     var result = {
-      metadata: this.metadata,
-      code:     "",
-      map:      null,
-      ast:      null
+      metadata: null,
+      ignored:  !!ignored,
+      code:     null,
+      ast:      null,
+      map:      map
     };
 
-    if (this.opts.metadataUsedHelpers) {
+    if (this.opts.code) {
+      result.code = code;
+    }
+
+    if (this.opts.ast) {
+      result.ast = ast;
+    }
+
+    if (this.opts.metadata) {
+      result.metadata = this.metadata;
       result.metadata.usedHelpers = Object.keys(this.usedHelpers);
     }
 
-    if (opts.ast) result.ast = ast;
-    if (!opts.code) return result;
+    return result;
+  }
+
+  generate() {
+    var opts = this.opts;
+    var ast  = this.ast;
+
+    var result = { ast };
+    if (!opts.code) return this.makeResult(result);
 
     this.log.debug("Generation start");
 
@@ -629,6 +636,6 @@ export default class File {
       result.map = null;
     }
 
-    return result;
+    return this.makeResult(result);
   }
 }
diff --git a/src/babel/transformation/file/options.json b/src/babel/transformation/file/options.json
index 564979bf28..d1207b14dd 100644
--- a/src/babel/transformation/file/options.json
+++ b/src/babel/transformation/file/options.json
@@ -139,6 +139,12 @@
     "type": "boolean"
   },
 
+  "metadata": {
+    "hidden": true,
+    "default": true,
+    "type": "boolean"
+  },
+
   "ast": {
     "hidden": true,
     "default": true,
@@ -179,6 +185,7 @@
   },
 
   "metadataUsedHelpers": {
+    "deprecated": "Not required anymore as this is enabled by default",
     "type": "boolean",
     "default": false,
     "hidden": true
diff --git a/src/babel/transformation/modules/_default.js b/src/babel/transformation/modules/_default.js
index 0f2394425f..54dabd1cd1 100644
--- a/src/babel/transformation/modules/_default.js
+++ b/src/babel/transformation/modules/_default.js
@@ -69,44 +69,44 @@ var remapVisitor = {
   }
 };
 
-var importsVisitor = {
-  ImportDeclaration: {
-    enter(node, parent, scope, formatter) {
-      formatter.hasLocalImports = true;
-      extend(formatter.localImports, this.getBindingIdentifiers());
+var metadataVisitor = {
+  ModuleDeclaration(node, parent, scope, formatter) {
+    if (node.source) {
+      node.source.value = formatter.file.resolveModuleSource(node.source.value);
     }
-  }
-};
+  },
 
-var exportsVisitor = {
-  ExportDeclaration: {
-    enter(node, parent, scope, formatter) {
-      formatter.hasLocalExports = true;
+  ImportDeclaration(node, parent, scope, formatter) {
+    formatter.hasLocalImports = true;
+    extend(formatter.localImports, this.getBindingIdentifiers());
+  },
 
-      var declar = this.get("declaration");
-      if (declar.isStatement()) {
-        var bindings = declar.getBindingIdentifiers()
-        for (var name in bindings) {
-          var binding = bindings[name];
-          formatter._addExport(name, binding);
-        }
+  ExportDeclaration(node, parent, scope, formatter) {
+    formatter.hasLocalExports = true;
+
+    var declar = this.get("declaration");
+    if (declar.isStatement()) {
+      var bindings = declar.getBindingIdentifiers()
+      for (var name in bindings) {
+        var binding = bindings[name];
+        formatter._addExport(name, binding);
       }
+    }
 
-      if (this.isExportNamedDeclaration() && node.specifiers) {
-        for (var i = 0; i < node.specifiers.length; i++) {
-          var specifier = node.specifiers[i];
-          var local = specifier.local;
-          if (!local) continue;
+    if (this.isExportNamedDeclaration() && node.specifiers) {
+      for (var i = 0; i < node.specifiers.length; i++) {
+        var specifier = node.specifiers[i];
+        var local = specifier.local;
+        if (!local) continue;
 
-          formatter._addExport(local.name, specifier.exported);
-        }
+        formatter._addExport(local.name, specifier.exported);
       }
+    }
 
-      if (!t.isExportDefaultDeclaration(node)) {
-        var onlyDefault = node.specifiers && node.specifiers.length === 1 && t.isSpecifierDefault(node.specifiers[0]);
-        if (!onlyDefault) {
-          formatter.hasNonDefaultExports = true;
-        }
+    if (!t.isExportDefaultDeclaration(node)) {
+      var onlyDefault = node.specifiers && node.specifiers.length === 1 && t.isSpecifierDefault(node.specifiers[0]);
+      if (!onlyDefault) {
+        formatter.hasNonDefaultExports = true;
       }
     }
   }
@@ -128,8 +128,7 @@ export default class DefaultFormatter {
     this.localExports = object();
     this.localImports = object();
 
-    this.getLocalExports();
-    this.getLocalImports();
+    this.getMetadata();
   }
 
   isModuleType(node, type) {
@@ -145,12 +144,8 @@ export default class DefaultFormatter {
     return (t.isExportDefaultDeclaration(node) || t.isSpecifierDefault(node)) && !this.noInteropRequireExport && !this.hasNonDefaultExports;
   }
 
-  getLocalExports() {
-    this.file.path.traverse(exportsVisitor, this);
-  }
-
-  getLocalImports() {
-    this.file.path.traverse(importsVisitor, this);
+  getMetadata() {
+    this.file.path.traverse(metadataVisitor, this);
   }
 
   remapAssignments() {
diff --git a/src/babel/transformation/transformer-pipeline.js b/src/babel/transformation/transformer-pipeline.js
index 5a4c704b49..d8c43abbd9 100644
--- a/src/babel/transformation/transformer-pipeline.js
+++ b/src/babel/transformation/transformer-pipeline.js
@@ -57,10 +57,21 @@ export default class TransformerPipeline {
     return true;
   }
 
+  pretransform(code: string, opts?: Object) {
+    var file = new File(opts, this);
+    return file.wrap(code, function () {
+      file.addCode(code);
+      file.parseCode(code);
+      return file;
+    });
+  }
+
   transform(code: string, opts?: Object) {
     var file = new File(opts, this);
     return file.wrap(code, function () {
-      file.addCode(code, true);
+      file.addCode(code);
+      file.parseCode(code);
+      return file.transform();
     });
   }
 
@@ -71,6 +82,7 @@ export default class TransformerPipeline {
     return file.wrap(code, function () {
       file.addCode(code);
       file.addAst(ast);
+      return file.transform();
     });
   }