Atom Electron 9 CLI disconnects after running commands and never exits 

<details>
<summary>Prerequisites</summary>

### Prerequisites

* [x] Put an X between the brackets on this line if you have done all of the following:
    * Reproduced the problem in Safe Mode: <https://flight-manual.atom.io/hacking-atom/sections/debugging/#using-safe-mode>
    * Followed all applicable steps in the debugging guide: <https://flight-manual.atom.io/hacking-atom/sections/debugging/>
    * Checked the FAQs on the message board for common solutions: <https://discuss.atom.io/c/faq>
    * Checked that your issue isn't already filed: <https://github.com/issues?utf8=✓&q=is%3Aissue+user%3Aatom>
    * Checked that there is not already an Atom package that provides the described functionality: <https://atom.io/packages>

</details>

### Description

Running CLI commands using Atom Electron 9 doesn't work like previous versions. For example, running `atom --version` it first exists, and then prints to the shell:

```ps1
aminy@LAPTOP-DHBEBJRL  ~\Documents\GitHub\JavaScript\atom-dev                                                [22:06]
❯ ./atom-dev --version

aminy@LAPTOP-DHBEBJRL  ~\Documents\GitHub\JavaScript\atom-dev                                                [22:06]
❯
Atom    : 1.57.0-dev-9887b306
Electron: 9.4.4
Chrome  : 83.0.4103.122
Node    : 12.14.1

```
![image](https://user-images.githubusercontent.com/16418197/110734433-711eac80-81ed-11eb-8916-e5d45d70466e.png)


Also, no matter how much you wait, it never exits, and stopping with CTRL+C creates this mess:

![image](https://user-images.githubusercontent.com/16418197/110734446-7a0f7e00-81ed-11eb-8579-36e6fc26badd.png)


If you run `atom --test spec` a lot of additional errors are issued to the command line which shouldn't for the end-users (we should suppress these warnings somehow): 

```ps1
aminy@LAPTOP-DHBEBJRL  ~\Documents\GitHub\JavaScript\@atom-ide-community\atom-ide-outline   master ↓2      [22:11]
❯ C:/Users/aminy/Documents/GitHub/JavaScript/atom-dev/atom-dev.exe --test spec
aminy@LAPTOP-DHBEBJRL  ~\Documents\GitHub\JavaScript\@atom-ide-community\atom-ide-outline
  master ↓2                                                                                                 [22:11]
❯ (node:18520) Electron: Loading non-context-aware native module in renderer: '\\?\C:\Users\aminy\Documents\GitHub\JavaScript\atom-dev\resources\app.asar.unpacked\node_modules\pathwatcher\build\Release\pathwatcher.node'. This is deprecated, see https://github.com/electron/electron/issues/18397.
(node:18520) Electron: Loading non-context-aware native module in renderer: '\\?\C:\Users\aminy\Documents\GitHub\JavaScript\atom-dev\resources\app.asar.unpacked\node_modules\oniguruma\build\Release\onig_scanner.node'. This is deprecated, see https://github.com/electron/electron/issues/18397.
(node:18520) Electron: Loading non-context-aware native module in renderer: '\\?\C:\Users\aminy\Documents\GitHub\JavaScript\atom-dev\resources\app.asar.unpacked\node_modules\superstring\build\Release\superstring.node'. This is deprecated, see https://github.com/electron/electron/issues/18397.
(node:18520) Electron: Loading non-context-aware native module in renderer: '\\?\C:\Users\aminy\Documents\GitHub\JavaScript\atom-dev\resources\app.asar.unpacked\node_modules\tree-sitter\build\Release\tree_sitter_runtime_binding.node'. This is deprecated, see https://github.com/electron/electron/issues/18397.
(node:18520) Electron: Loading non-context-aware native module in renderer: '\\?\C:\Users\aminy\Documents\GitHub\JavaScript\atom-dev\resources\app.asar.unpacked\node_modules\@atom\nsfw\build\Release\nsfw.node'. This is deprecated, see https://github.com/electron/electron/issues/18397.
(node:18520) Electron: Loading non-context-aware native module in renderer: '\\?\C:\Users\aminy\Documents\GitHub\JavaScript\atom-dev\resources\app.asar.unpacked\node_modules\git-utils\build\Release\git.node'. This is deprecated, see https://github.com/electron/electron/issues/18397.
(node:18520) Electron: Loading non-context-aware native module in renderer: '\\?\C:\Users\aminy\Documents\GitHub\JavaScript\atom-dev\resources\app.asar.unpacked\node_modules\scrollbar-style\build\Release\scrollbar-style-observer.node'. This is deprecated, see https://github.com/electron/electron/issues/18397.
.........


9 specs, 0 failures
Finished in 2.454 seconds
```

If you force-exit `atom --test spec` after finishing, it will not actually exit, but it prints this. The only way is to close the terminal
```ps1
[process exited with code 3762504530]
```

### Steps to Reproduce

1. Run cli commands using Atom-dev such as `atom --version` or `atom --test spec`


**Expected behavior:**

CLI command should stay connected and exit with 0 code afterward.

**Actual behavior:**

CLI disconnects and never exits.


**Reproduces how often:**

Always

### Versions

```
Atom    : 1.57.0-dev-9887b306
Electron: 9.4.4
Chrome  : 83.0.4103.122
Node    : 12.14.1
```


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Atom Electron 9 CLI disconnects after running commands and never exits #22024

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Atom Electron 9 CLI disconnects after running commands and never exits #22024

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