[BUG] Toast notification Allow/Deny buttons are no-ops; permission must still be granted in Code. Very annoying.

Preflight Checklist

• [x] I have searched existing issues and this hasn't been reported yet
• [x] This is a single bug report (please file separate reports for different bugs)
• [x] I am using the latest version of Claude Code

What's Wrong?

When I click "Allow" for actions in the pop-ups thatappear, they do absolute nothing. So it actualy wastes time. I have to close the pop-up, since it obstructs the "Allow" button in Claude, and then click "Allow" inside Claude. This is annoying and wastes time. I use Claude Code in Claude Desktop.

What Should Happen?

When I click "Allow" on the pop-up notification, then the "Allow" message in Code should disappear and it must carry on immediately. Currently the Allow in Code stays there, even if I have already clicked "Allow" on the pop-up. The pop-up also does not offer "Allow Always" so then I am FORCED to close the op-up anyway, and click Allow Always in the Desktop App. The pop-up obstructs the Allow button in Claude Desktop, so I now have to click TWICE for every Allow occurrence.

Error Messages/Logs

Steps to Reproduce

1. Ask Claude to do something that requires permission.
2. Claude Desktop asks "Allow Always" or "Allow Once"
3. The pop-up message appears and covers the "Allow Once" button.
4. Clicking "Allow" on the pop-up does nothing
5. Close the pop-up.
6. Click Allow in the App again.
7. Pop-ups should NOT appear if Claude Desktop is already open and the front most app.
8. They MUST also let the Claude app know that I have clicked Allow, so the Desktop App can carry on.

Claude Model

Opus

Is this a regression?

No, this never worked

Last Working Version

_No response_

Claude Code Version

2.1.96 (Claude Code)

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Windows Terminal

Additional Information

I have only experienced this when using Claude Code in the Claude Desktop.