[BUG] Global MCP config in ~./claude.json empties routinely

Environment

• Claude CLI version: 1.0.21 (Claude Code)
• Operating System: Ubuntu 24.04.2 LTS (Noble Numbat)
• Terminal: Gnome Terminal

Bug Description

MCP server config prop in ~/.claude.json resetting routinely today, once was after update but it's happening frequently since.

Steps to Reproduce

reopen claude code

Expected Behavior

Claude code launches with normal config.

Actual Behavior

be prompted for spending mode and warned about prompt injection again (?).
mcpServers: {} in ~/.claude.json

note: There is no documentation about .claude.json vs .claude/settings.json that I can find however it will never read an mcp config from settings.json currently.