diff --git a/local-cli/generator/index.js b/local-cli/generator/index.js
index 1879fa35f6..5e11dec0b9 100644
--- a/local-cli/generator/index.js
+++ b/local-cli/generator/index.js
@@ -2,6 +2,7 @@
 
 var path = require('path');
 var yeoman = require('yeoman-generator');
+var utils = require('../generator-utils');
 
 module.exports = yeoman.generators.NamedBase.extend({
   constructor: function() {
@@ -33,10 +34,12 @@ module.exports = yeoman.generators.NamedBase.extend({
   },
 
   configuring: function() {
-    this.fs.copy(
-      this.templatePath('_flowconfig'),
-      this.destinationPath('.flowconfig')
+    utils.copyAndReplace(
+      this.templatePath('../../../.flowconfig'),
+      this.destinationPath('.flowconfig'),
+      { 'Libraries\/react-native\/react-native-interface.js' : 'node_modules/react-native/Libraries/react-native/react-native-interface.js' }
     );
+
     this.fs.copy(
       this.templatePath('_gitignore'),
       this.destinationPath('.gitignore')
diff --git a/local-cli/generator/templates/_flowconfig b/local-cli/generator/templates/_flowconfig
deleted file mode 100644
index 48f0ba0d41..0000000000
--- a/local-cli/generator/templates/_flowconfig
+++ /dev/null
@@ -1,48 +0,0 @@
-[ignore]
-
-# We fork some components by platform.
-.*/*.web.js
-.*/*.android.js
-
-# Some modules have their own node_modules with overlap
-.*/node_modules/node-haste/.*
-
-# Ignore react-tools where there are overlaps, but don't ignore anything that
-# react-native relies on
-.*/node_modules/react-tools/src/React.js
-.*/node_modules/react-tools/src/renderers/shared/event/EventPropagators.js
-.*/node_modules/react-tools/src/renderers/shared/event/eventPlugins/ResponderEventPlugin.js
-.*/node_modules/react-tools/src/shared/vendor/core/ExecutionEnvironment.js
-
-# Ignore commoner tests
-.*/node_modules/commoner/test/.*
-
-# See https://github.com/facebook/flow/issues/442
-.*/react-tools/node_modules/commoner/lib/reader.js
-
-# Ignore jest
-.*/react-native/node_modules/jest-cli/.*
-
-[include]
-
-[libs]
-node_modules/react-native/Libraries/react-native/react-native-interface.js
-
-[options]
-module.system=haste
-
-munge_underscores=true
-
-module.name_mapper='^image![a-zA-Z0-9$_-]+$' -> 'GlobalImageStub'
-module.name_mapper='^[./a-zA-Z0-9$_-]+\.png$' -> 'RelativeImageStub'
-
-suppress_type=$FlowIssue
-suppress_type=$FlowFixMe
-suppress_type=$FixMe
-
-suppress_comment=\\(.\\|\n\\)*\\$FlowFixMe\\($\\|[^(]\\|(\\(>=0\\.\\(1[0-6]\\|[0-9]\\).[0-9]\\)? *\\(site=[a-z,_]*react_native[a-z,_]*\\)?)\\)
-suppress_comment=\\(.\\|\n\\)*\\$FlowIssue\\((\\(>=0\\.\\(1[0-6]\\|[0-9]\\).[0-9]\\)? *\\(site=[a-z,_]*react_native[a-z,_]*\\)?)\\)? #[0-9]+
-suppress_comment=\\(.\\|\n\\)*\\$FlowFixedInNextDeploy
-
-[version]
-0.16.0