diff --git a/modules/@angular/compiler_cli/integrationtest.sh b/modules/@angular/compiler_cli/integrationtest.sh
index a1a889f3a0..86c88c6224 100755
--- a/modules/@angular/compiler_cli/integrationtest.sh
+++ b/modules/@angular/compiler_cli/integrationtest.sh
@@ -5,5 +5,7 @@ set -e -o pipefail
 cd $(dirname $0)
 cd $(pwd)/../../..
 export NODE_PATH=$NODE_PATH:$(pwd)/dist/all:$(pwd)/dist/tools
-node dist/all/@angular/compiler_cli/src/main -p modules/@angular/compiler_cli/integrationtest
-node dist/tools/cjs-jasmine -- @angular/compiler_cli/integrationtest/**/*_spec.js
+readonly TESTDIR="modules/@angular/compiler_cli/integrationtest"
+rm $TESTDIR/src/*.{ngfactory,css.shim}.ts
+node dist/all/@angular/compiler_cli/src/main -p $TESTDIR
+node dist/tools/cjs-jasmine -- $TESTDIR/**/*_spec.js
diff --git a/modules/@angular/compiler_cli/integrationtest/tsconfig.json b/modules/@angular/compiler_cli/integrationtest/tsconfig.json
index 07d017a174..5a4f51baae 100644
--- a/modules/@angular/compiler_cli/integrationtest/tsconfig.json
+++ b/modules/@angular/compiler_cli/integrationtest/tsconfig.json
@@ -14,10 +14,15 @@
         "outDir": "../../../../dist/all/@angular/compiler_cli/integrationtest",
         "rootDir": "",
         "declaration": true,
-
+        "lib": ["es6", "dom"],
         "baseUrl": ".",
         "paths": {
           "@angular/*": ["../../../../dist/all/@angular/*"]
         }
-    }
+    },
+
+    "files": [
+      "src/bootstrap.ts",
+      "typings.d.ts"
+    ]
 }
diff --git a/modules/@angular/compiler_cli/integrationtest/typings.d.ts b/modules/@angular/compiler_cli/integrationtest/typings.d.ts
index b233a0dc0c..b99e33358e 100644
--- a/modules/@angular/compiler_cli/integrationtest/typings.d.ts
+++ b/modules/@angular/compiler_cli/integrationtest/typings.d.ts
@@ -1,4 +1,2 @@
-/// <reference path="../../typings/es6-collections/es6-collections.d.ts" />
-/// <reference path="../../typings/es6-promise/es6-promise.d.ts" />
 /// <reference path="../../typings/node/node.d.ts" />
 /// <reference path="../../typings/jasmine/jasmine.d.ts" />
diff --git a/modules/@angular/compiler_cli/src/codegen.ts b/modules/@angular/compiler_cli/src/codegen.ts
index be4f8152e2..546e473882 100644
--- a/modules/@angular/compiler_cli/src/codegen.ts
+++ b/modules/@angular/compiler_cli/src/codegen.ts
@@ -155,8 +155,10 @@ export class CodeGenerator {
               return Promise.all(stylesheetPromises);
             })
             .catch((e) => { console.error(e.stack); });
-    return Promise.all(
-        this.program.getRootFileNames().filter(f => !GENERATED_FILES.test(f)).map(generateOneFile));
+    return Promise.all(this.program.getSourceFiles()
+                           .map(sf => sf.fileName)
+                           .filter(f => !GENERATED_FILES.test(f))
+                           .map(generateOneFile));
   }
 
   static create(ngOptions: AngularCompilerOptions, program: ts.Program, options: ts.CompilerOptions,