Inconsistent MCP Server Configuration Across Terminal Sessions

Bug Description

Summary
Project-level MCP configurations (.mcp.json) don't load consistently across different Claude Code sessions, even when launched from the same directory.

Expected Behavior

According to the MCP management interface, project configs should be "shared via .mcp.json" - meaning all Claude Code sessions in the same project directory should load the same MCP servers.

Actual Behavior

• Session A (iTerm2): All 4 MCP servers connect (filesystem, linear, playwright, supabase)
• Session B (VSCode terminal): Only some/none connect, despite same directory and same .mcp.json file
• Both sessions show identical config file paths in /mcp interface

Reproduction Steps

1. Create .mcp.json with multiple MCP servers in project directory
2. Launch first Claude Code session in iTerm2 - MCP servers connect successfully
3. Launch second Claude Code session in VSCode terminal from same directory
4. Run /mcp in both - different connection status despite same config
5. Attempting /mcp reconnection in broken session doesn't fix it

Additional Context

Project has both user-level (~/.claude.json) and project-level (.mcp.json) configs
MCP servers include remote (Linear via mcp-remote) and local servers
Terminal environment difference may be relevant to the initialization issue

Impact

Inconsistent developer experience - can't rely on MCP tools being available across sessions, forcing users to stick to one "working" session.

Environment Info

• Platform: darwin
• Terminal: iTerm.app
• Version: 1.0.84
• Feedback ID: 07492ce8-c11c-4deb-9d42-3ed32b2f4815