Unify MCP configuration and separate from conversation history

Environment

• Platform (select one):
• Anthropic API
• Claude CLI version: 1.0.33 (Claude Code)
• Operating System: macOS 15.5 (Darwin 24.5.0)
• Terminal: Apple Terminal

Bug Description

1. The .claude.json file gets filled up with conversation history mixed with MCP

configurations, causing issues

1. MCP configuration format differs between Claude CLI and Claude Desktop app, requiring

separate config files instead of a unified approach

Steps to Reproduce

1. Configure MCP servers in .claude.json for Claude CLI
2. Use Claude CLI for conversations - history gets added to same file
3. Try to use same MCP config with Claude Desktop app
4. Observe that different config format/location is required

Expected Behavior

• MCP configuration should be separate from conversation history
• Single unified mcp.json config file should work for both Claude CLI and Claude Desktop app

Actual Behavior

• Conversation history and MCP config mixed in same .claude.json file causes issues
• Claude CLI and Desktop app require different MCP configuration formats/locations

Additional Context

This creates a poor developer experience requiring users to maintain separate MCP
configurations for CLI vs Desktop, and the mixing of history with config in CLI makes config
management problematic.