[BUG] Claude Code desktop app launches MCP servers with cwd set to $HOME instead of the session's project directory

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?

The Claude Code desktop app (v1.17377.2, Linux) starts stdio MCP servers with cwd=/home/<user> regardless of the project directory opened in the session. It also does not pass roots in the MCP initialize request. This breaks workspace-aware MCP servers like gopls mcp, which rely on cwd or roots to discover go.mod and index the project.

Tools that depend on the workspace root (go_workspace, go_search, go_vulncheck) fail, while tools that accept absolute file paths (go_file_context, go_symbol_references) work fine.

The cwd field in claude_desktop_config.json is also ignored.

What Should Happen?

The desktop app should either:

1. Launch MCP servers with cwd set to the current session's project directory, or
2. Pass the project directory as roots in the MCP initialize request, or
3. Support the cwd field in claude_desktop_config.json

Error Messages/Logs

go_workspace response when launched from wrong cwd:

This is not a Go workspace. To work on Go code, open a directory inside a Go module.

go_vulncheck response:

govulncheck: no go.mod file
govulncheck only works with Go modules. Try navigating to your module directory.

Environment variables captured from inside the MCP server process confirm PWD=/home/<user>:

PWD=/home/<user>
HOME=/home/<user>

Steps to Reproduce

1. Add gopls MCP to ~/.config/Claude/claude_desktop_config.json:

{
  "mcpServers": {
    "gopls": {
      "command": "gopls",
      "args": ["mcp"]
    }
  }
}

1. Open a session in a Go project directory (e.g. /home/user/myproject with go.mod)
2. Call go_workspace → returns "This is not a Go workspace"
3. Call go_search with any query → returns "No symbols found"
4. Call go_vulncheck → fails with "no go.mod file"

Workaround: Use a wrapper script that does cd before launching gopls:

#!/bin/bash
cd "$(dirname "$(readlink -f "$0")")/.."
exec gopls mcp "$@"

Place it in <project>/.claude/gopls-mcp.sh and point the config to it.

Claude Model

Opus

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

1.17377.2.

Platform

Anthropic API

Operating System

Ubuntu/Debian Linux

Terminal/Shell

Other

Additional Information

Claude Code desktop app version: 1.17377.2 (Linux)
gopls version: v0.22.0
Go version: 1.26.4
Verified that gopls works correctly when launched from the project directory (cwd = project root)
Verified that cwd field in claude_desktop_config.json is ignored
Verified that roots in MCP initialize is not sent by the desktop app (env dump shows no project-related variables)
The Claude Code CLI (claude in terminal) does not have this issue — it launches MCP servers from the project directory