[BUG] Toggling "Always allow" for MCP tool in Chatview restarts server

[hannesrudolph]

Type

Bug

Problem / Value

Toggling the "Always allow" checkbox for an MCP tool in Chatview causes the connected MCP server to restart. This disrupts the chat flow and can delay or interrupt work.

Context

• Affects users who approve MCP tools from within Chatview.
• Occurs every time the checkbox is checked or unchecked.
• Visible as a brief disconnect/reconnect of the server in the UI; any in‑flight operation may be affected.

Reproduction

1. Open Chatview and trigger an MCP tool prompt
2. Click the tool’s "Always allow" checkbox
3. Observe server status/connection state
4. Repeat by unchecking
5. Note if it interrupts an in‑progress tool call

Constraints/Preferences

• Changing "Always allow" should not restart the server. Prefer a lightweight update that doesn’t disrupt active sessions. If a restart is unavoidable, defer it until idle or batch the changes.

[roomote]

I'm exploring a potential fix for this issue where toggling the 'Always allow' checkbox for MCP tools causes server restarts. I'll investigate the MCP tool permission handling to prevent unnecessary server disruptions.

[roomote]

I've opened PR #8233 with a fix for this issue: #8233

The fix prevents unnecessary MCP server restarts when toggling the 'Always allow' checkbox by:

• Adding a flag to track programmatic config updates
• Skipping file watcher triggers during these updates
• Distinguishing between minor updates (tool permissions) and major changes that require restarts

This should resolve the disruption to chat flow when approving MCP tools. The PR is currently undergoing CI checks.