[BUG] Can't configure MCP servers so they persist sessions

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 servers configured during a session (using mcp-add) do not persist when starting a new Claude Code session. Users must reconfigure servers every time they open a new session.

Actual Behavior:

• mcp-add adds servers to the current session only
• Starting a new Claude Code session shows no configured servers
• ListMcpResourcesTool returns empty array in new sessions
• Users must reconfigure servers every session

Expected Files:

• Configuration should persist in .claude/ directory or similar persistent location
• Should be readable/editable by users if needed
• Tried adding mcpServers to ~/.claude/mcp.json ~/.claude/.mcp.json ~/.claude/session.json

Impact:
This makes it impractical to use MCP servers regularly, as users must reconfigure them every session.

What Should Happen?

• MCP server configurations should be saved to a configuration file (e.g., .claude/mcp.json or similar)
• When starting a new session, previously configured servers should be automatically loaded
• Users should be able to maintain a consistent set of available tools across multiple sessions

Error Messages/Logs

Steps to Reproduce

1. Start a Claude Code session
2. Use mcp-add to configure one or more MCP servers
3. Close the session
4. Start a new Claude Code session
5. Observe: Previously configured servers are no longer available

Claude Model

Other

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

2.0.45 (Claude Code)

Platform

Anthropic API

Operating System

Windows

Terminal/Shell

VS Code integrated terminal

Additional Information

Using Haiku 4.5, Windows-11, VSCode, Git Bash