[BUG] Desktop app ignores bypassPermissions for ccd_session_mgmt tools despite explicit allow list entries; CLI does not prompt

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?

Environment

• Claude Code desktop app (Windows 11)
• Global settings: "defaultMode": "bypassPermissions"
• Project settings: mcp__ccd_session_mgmt__search_session_transcripts explicitly listed in allow array

Behavior
In the desktop app, ccd_session_mgmt tools (e.g. search_session_transcripts) show a modal:

"This tool requires explicit approval regardless of permission mode."

The allow list entry and bypassPermissions setting are both ignored.

Expected behavior
Same behavior as the CLI — no prompt. The CLI with identical settings does not show this dialog for these tools.

Reproduction

1. Set defaultMode: "bypassPermissions" in global settings.json
2. Add mcp__ccd_session_mgmt__search_session_transcripts to project settings.json allow array
3. CLI: no prompt ✓
4. Desktop app: approval dialog appears mid-task, interrupting automated workflows ✗

Impact
Users running automated/agentic workflows in the desktop app are interrupted by approval dialogs on read-only session lookups. The CLI correctly honors the permission settings. The desktop app diverges from the CLI contract for the same configuration, creating a reliability gap for power users.

Request
ccd_session_mgmt read-only tools should respect bypassPermissions and explicit allow list entries in the desktop app, consistent with CLI behavior.

What Should Happen?

Environment

• Claude Code desktop app (Windows 11)
• Global settings: "defaultMode": "bypassPermissions"
• Project settings: mcp__ccd_session_mgmt__search_session_transcripts explicitly listed in allow array

Behavior
In the desktop app, ccd_session_mgmt tools (e.g. search_session_transcripts) show a modal:

"This tool requires explicit approval regardless of permission mode."

The allow list entry and bypassPermissions setting are both ignored.

Expected behavior
Same behavior as the CLI — no prompt. The CLI with identical settings does not show this dialog for these tools.

Reproduction

1. Set defaultMode: "bypassPermissions" in global settings.json
2. Add mcp__ccd_session_mgmt__search_session_transcripts to project settings.json allow array
3. CLI: no prompt ✓
4. Desktop app: approval dialog appears mid-task, interrupting automated workflows ✗

Impact
Users running automated/agentic workflows in the desktop app are interrupted by approval dialogs on read-only session lookups. The CLI correctly honors the permission settings. The desktop app diverges from the CLI contract for the same configuration, creating a reliability gap for power users.

Request
ccd_session_mgmt read-only tools should respect bypassPermissions and explicit allow list entries in the desktop app, consistent with CLI behavior.

Error Messages/Logs

Steps to Reproduce

1. Set "defaultMode": "bypassPermissions" in global ~/.claude/settings.json
2. Add "mcp__ccd_session_mgmt__search_session_transcripts" to the allow array in project .claude/settings.json
3. Open the same project in the CLI (claude in terminal) — trigger a task that calls search_session_transcripts. No approval prompt appears. ✓
4. Open the same project in the desktop app — trigger the same task. Approval dialog appears with message: "This tool requires explicit approval regardless of permission mode." ✗

Both sessions use identical settings files. The CLI respects the permission configuration; the desktop app does not.

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

CLI version: 2.1.206 (Claude Code) Desktop app version: check Help → About in the app Model: claude-sonnet-4-6 OS: Windows 11 Pro 10.0.26200

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_