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* Electron version: 2.0.0-beta.7
* Operating system: Windows 10 x64

### Expected behavior

<!-- What do you think should happen? -->
When `webPreferences.nativeWindowOpen` is set to true, BrowserWindows opened by `window.open`'s memory will be released after be closed.

### Actual behavior

<!-- What actually happens? -->
The memory is not released and caused memory leak

### How to reproduce
- Clone https://github.com/KochiyaOcean/electron-bugs/tree/native-open-memory-leak
- Run `electron . ` in the cloned repo
- Memory usage of electron process will be increasing in task manager

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atom/renderer/atom_renderer_client.cc
content::RenderFrame* render_frame) {
  
  v8::HandleScope handle_scope(v8::Isolate::GetCurrent());
  node::Environment* env = GetEnvironment(render_frame);
  if (env)
    mate::EmitEvent(env->isolate(), env->process_object(), "document-start");
}
void AtomRendererClient::RunScriptsAtDocumentEnd(
    content::RenderFrame* render_frame) {
  
  v8::HandleScope handle_scope(v8::Isolate::GetCurrent());
  node::Environment* env = GetEnvironment(render_frame);
  if (env)
    mate::EmitEvent(env->isolate(), env->process_object(), "document-end");
}
void AtomRendererClient::DidCreateScriptContext(
    v8::Handle<v8::Context> context,
    content::RenderFrame* render_frame) {
  RendererClientBase::DidCreateScriptContext(context, render_frame);
  
  
  if (!render_frame->IsMainFrame() && !IsDevToolsExtension(render_frame))
    return;