mcpServers config gets corrupted with nested "mcpServers" key in ~/.claude.json

Bug Report: Claude Code corrupts global mcpServers config in ~/.claude.json

Summary

Claude Code 2.1.133 incorrectly creates a nested mcpServers.mcpServers key inside the global mcpServers object when writing ~/.claude.json at session end, causing MCP config parsing errors in subsequent sessions.

Environment

• Claude Code version: 2.1.133
• OS: macOS 13 (Darwin 22.6.0)
• Shell: zsh

Steps to Reproduce

1. Configure a user-level MCP server in ~/.claude.json:

"mcpServers": {
  "PaddleOCR-VL": {
    "command": "uvx",
    "args": ["--from", "paddleocr-mcp", "paddleocr_mcp"],
    "env": { ... }
  }
}

1. Use Claude Code normally in a project that has "mcpServers": {} in its project entry under the projects object.
2. End the session. Claude Code atomically writes ~/.claude.json.
3. Start a new session → /doctor shows:

[Failed to parse] User config (available in all your projects)
Location: /Users/davidyao/.claude.json
 └ [Error] mcpServers.mcpServers: Does not adhere to MCP server configuration schema

Observed Behavior

After session end, ~/.claude.json contains BOTH the correct flat entry AND a nested mcpServers key:

"mcpServers": {
  "PaddleOCR-VL": { ... },
  "mcpServers": {
    "PaddleOCR-VL": { ... }
  }
}

Root Cause Hypothesis

The projects object in ~/.claude.json contains per-project entries that each have their own "mcpServers": {} key. Claude Code's config serializer appears to incorrectly deep-merge a project's mcpServers key INTO the global mcpServers object during serialization, rather than keeping them at separate levels.

Reproducibility

• Reproduced across 4+ sessions
• Backup files in ~/.claude/backups/ also show the corruption
• Debug log confirms two sequential writes to .claude.json at session end, with the second write (larger file size) corrupting the structure

Impact

• MCP servers are unavailable in all projects until the file is manually fixed
• Error message appears every session