Not shutting down correctly on Windows

I have a project that is (mostly) based on the quick start repo, but when I run it on Windows and close the main window, my command prompt leaves me with a stylized "Terminate batch job (Y/N)?" which keeps the process running. Eventually it will shut down on its own but it's not obvious that it will do that since it seems to be waiting for confirmation. This problem was not present when I was using Electron by itself.

This is my `src/main/index.js`:

```javascript
// @ts-check

import { app, BrowserWindow } from 'electron'
import url from 'url'
import path from 'path'

const isDevelopment = process.env.NODE_ENV !== 'production'

let mainWindow

function createMainWindow() {
mainWindow = new BrowserWindow({
width: 800,
height: 550,
autoHideMenuBar: true,
})

const url_ = isDevelopment ?
`http://localhost:${process.env.ELECTRON_WEBPACK_WDS_PORT}` :
url.format({
pathname: path.join(__dirname, 'index.html'),
protocol: 'file:',
slashes: true
})

if (isDevelopment) {
mainWindow.webContents.openDevTools({ mode: "detach" })
}

mainWindow.loadURL(url_)

mainWindow.on('closed', () => {
mainWindow = null
})

mainWindow.webContents.on('devtools-opened', () => {
mainWindow.focus()
setImmediate(() => {
mainWindow.focus()
})
})
}

app.on('window-all-closed', () => {
if (process.platform !== 'darwin') {
app.quit()
}
})

app.on('activate', () => {
if (mainWindow === null) {
createMainWindow()
}
})

app.on('ready', createMainWindow)
```

Reproduce the quick start project on Windows using the provided src/main/index.js and compare its shutdown behavior with Electron by itself. Start by tracing what happens after the window-all-closed and app.quit events; done means closing the main window exits cleanly without leaving a “Terminate batch job (Y/N)?” prompt.

Written by the indexing model from the issue text.