MCP tool permissions require session focus in Desktop app, blocking long-running browser agents

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• [x] This is a single feature request (not multiple features)

Problem Statement

When running a long-running agent that uses MCP tools (Claude in Chrome) in the Desktop app, tool permissions only auto-resolve when the session has focus. Switching to a different session or another app causes the agent to block on a permission prompt that surfaces as a non-actionable Windows notification (e.g., "Allow Claude to computer triple_click?"). The session shows a blue pulsing indicator until I switch back, at which point the permission resolves instantly and work resumes. This happens despite having "defaultMode": "bypassPermissions" and "mcp__*" in the allow list.

Proposed Solution

An explicit opt-in for unattended MCP operation — either per-session or per-MCP-server. For example:

A session-level toggle: "Allow MCP tools without focus"
Or a settings.json flag per MCP server: "unattendedAllowed": true
The current focus-gating is a reasonable default. But for long-running autonomous agents, there should be an escape hatch that doesn't require --dangerously-skip-permissions.

Alternative Solutions

Allow Desktop app to open multiple windows on different sessions so the agent session can remain visible while working in another
Have bypass permissions fully bypass MCP permissions regardless of session focus (current behavior seems to gate on focus even with bypass enabled)
Support running MCP-dependent agents from the CLI where there's no focus concept

Priority

High - Significant impact on productivity

Feature Category

CLI commands and flags

Use Case Example

Running a browser-based agent via Claude in Chrome that autonomously navigates websites for ~2 hours. I need to do other work in other Claude sessions or other apps while it runs. Currently I must keep that session visible and focused the entire time.

Additional Context

Related issues:

#5465 — Task subagents fail to inherit MCP permissions
#24433 — "Always allow" for MCP tools does not persist across sessions
#28580 — MCP tools prompt for permission even when authorized