[BUG] MCP server configurations in mcpServers (stored per-project in ~/.claude.json) were wiped to {} after a Claude Code update

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?

MCP server configurations in mcpServers (stored per-project in ~/.claude.json) were wiped to {} after a Claude Code update
What happened: MCP server configurations in mcpServers (stored per-project in ~/.claude.json) were wiped to {} after a Claude Code update
When: Around 2026-04-24
Impact: All custom MCP server definitions lost with no backup mechanism and no warning
Feature request angle: Either (a) don't wipe mcpServers on update, or (b) back up ~/.claude.json before any migration

What Should Happen?

#1: Claude should warn before updating itself
#2: It should not wipe out local settings
#3: it should backup local settings.

Error Messages/Logs

Steps to Reproduce

I can't reproduce see description above

Claude Model

Sonnet (default)

Is this a regression?

Yes, this worked in a previous version

Last Working Version

_No response_

Claude Code Version

2.1.77 (Claude Code)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_