[BUG] "Yes, don't ask again" for Bash commands does not persist in desktop app

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?

Description

When I click "Yes, don't ask again" on a Bash command permission prompt,
the approval is not persisted. The confirmation prompt appears again on the next execution of the same command.

Steps to Reproduce

1. Open Claude Code desktop app
2. Ask Claude to run a Bash command that writes to a file

(e.g., echo "test" >> memo.txt)

1. When the permission prompt appears, click "Yes, don't ask again"
2. Ask Claude to run the same command again
3. The permission prompt appears again

Expected Behavior

According to the documentation, Bash command approvals should be persisted
permanently per project directory and command.

Actual Behavior

The permission prompt appears every time, even after selecting "don't ask again".

Environment

• Client: Claude Code Desktop App
• OS: macOS (Darwin 25.3.0)
• Permission mode: Default

What Should Happen?

After selecting "Yes, don't ask again" for a Bash command,
the same command should be automatically approved in future executions
without showing the permission prompt again.

Error Messages/Logs

Steps to Reproduce

1. Open Claude Code desktop app
2. Ask Claude to run a Bash command that writes to a file

(e.g., echo "test" >> memo.txt)

1. When the permission prompt appears, click "Yes, don't ask again"
2. Ask Claude to run the same command again
3. The permission prompt appears again

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.104

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_