Write a chrome extension that can read my email, open the reply field and copy an AI generated reply to my clipboard. For each files, write a full code with a features attached. Do not write a simple sample, but a real complete and professional code. Firstly, write a comprehensive and detailed manifest.json.
Here is a basic manifest.json for your Chrome Extension:
```javascript
{
  "manifest_version": 2,

  "name": "AI Reply",
  "description": "A Chrome Extension that reads emails and generates replies based on user input.",
  "browser_action": {
    "default_icon": "icon.png",
    "default_popup": "index.html"
  },
  "permissions": [
    "activeTab",
    "clipboardRead"
  ]
}
```
This manifest specifies that the extension will have two main actions - browser action popup (which opens in active tab) and content script which runs in background. The permissions are set so that only users who accept the extension's prompt when installing it would be able to use this feature.