[BUG] Desktop app: "Bypass permissions mode" still shows permission dialogs for Edit/Bash actions

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?

aIn the Claude Code desktop app (Windows 11), when "Bypass permissions mode" is enabled (yellow banner at top confirms it), the app still shows "Allow Claude to Edit/Run?" permission dialogs for every Edit and Bash action.

Steps to reproduce:

1. Open Claude Code desktop app on Windows 11
2. 2. Toggle permissions mode to "Bypass permissions mode" using Shift+Tab (yellow banner appears at top: "Bypass permissions mode: Claude can take actions without asking")
3. 3. Also have ~/.claude/settings.json with broad permissions: "allow": ["Read", "Edit", "Write", "Glob", "Grep", "Bash(*)"]
4. 4. Start a new conversation and ask Claude to edit a file or run a bash command
5. 5. Permission dialog still appears asking "Allow Claude to Edit/Run?"

Additional context:

• The yellow banner at top clearly says "Bypass permissions mode: Claude can take actions without asking, including modifying or deleting files"
• - This happens in every new conversation, not just carryover from a previous mode
• - - The dialog shows "Allow once (Enter)" and "Always allow for session (Ctrl+Enter)" buttons — but these should not appear at all in Bypass mode
• - - - settings.json has Edit, Write, Read, and Bash(*) in the allow list

What Should Happen?

aWhen "Bypass permissions mode" is active, all Edit and Bash actions should execute immediately without showing any permission dialog. The yellow anner already confirms the mode is active — the behavior should match.

Error Messages/Logs

Steps to Reproduce

a1. Open Claude Code desktop app on Windows 11

1. Press Shift+Tab until "Bypass permissions mode" appears (yellow banner at top confirms it)
2. 3. Have ~/.claude/settings.json with: "allow": ["Read", "Edit", "Write", "Glob", "Grep", "Bash(*)"]
3. 4. Start a new conversation
4. 5. Ask Claude to edit a Python file (e.g., "add a comment to normalizer.py")
5. 6. Permission dialog appears: "Allow Claude to Edit ...?" with "Allow once" and "Always allow for session" buttons
6. 7. This happens on every new conversation, not just once

Claude Model

None

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

Desktop app (latest as of 2026-04-14)

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

Non-interactive/CI environment

Additional Information

_No response_