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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/browser/web_contents_preferences.cc
content::WebContents* web_contents,
    const mate::Dictionary& web_preferences)
    : web_contents_(web_contents) {
  v8::Isolate* isolate = web_preferences.isolate();
  mate::Dictionary copied(isolate, web_preferences.GetHandle()->Clone());
  
  copied.Delete("embedder");
  copied.Delete("isGuest");
  copied.Delete("session");
  mate::ConvertFromV8(isolate, copied.GetHandle(), &preference_);
  web_contents->SetUserData(UserDataKey(), base::WrapUnique(this));
  instances_.push_back(this);
  
  SetDefaultBoolIfUndefined(options::kPlugins, false);
  SetDefaultBoolIfUndefined(options::kExperimentalFeatures, false);
  bool node = SetDefaultBoolIfUndefined(options::kNodeIntegration, true);