[BUG] [MCP] startup and initialization issue, works in UI, still doesn't in CLI

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 #BUG

Bug: Claude Desktop MCP sandbox forces CWD=/, breaking MCP servers that rely on working directory or --repo path arguments

Claude Code version: 2.1.87
OS: macOS (Apple Silicon)
MCP server tested: code-review-graph v2.2.1

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Summary

Claude Desktop spawns all MCP server processes with CWD=/ (filesystem root) via its disclaimer sandbox helper. This silently breaks any MCP server that determines its working context from the process working directory — even when an explicit --repo path argument is passed in the config. The --repo argument is received by the binary but the server still resolves its database path relative to /, resulting in a [Errno 30] Read-only file system: '/.code-review-graph' error on every tool call.

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Steps to Reproduce

1. Install any MCP server that uses CWD or a --repo/--root flag to locate its data directory (e.g. code-review-graph)
2. Register it in ~/Library/Application Support/Claude/claude_desktop_config.json with an explicit --repo /absolute/path argument
3. Launch Claude Desktop and connect to the MCP server
4. Call any tool on the server

Result: Server resolves all paths relative to / instead of the configured repo path
Expected: Server uses the path provided via --repo argument

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Root Cause

Claude Desktop routes all MCP process spawning through /Applications/Claude.app/Contents/Helpers/disclaimer. This helper forces CWD=/ at the OS level before exec-ing the MCP binary. The following errors are visible in ~/Library/Logs/Claude/main.log:

Failed to spawn node (via disclaimer): ...disclaimer exited with code 1: Failed to spawn process: No such file or directory
Failed to spawn python (via disclaimer): ...disclaimer exited with code 1: Failed to spawn process: No such file or directory

The MCP server binary receives the --repo argument correctly but internally falls back to resolving paths from CWD, which is /.

Verified by: Running the server manually in terminal with an identical command works perfectly. The stdio MCP handshake completes cleanly. The failure is exclusively caused by the Desktop sandbox environment.

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Impact

• Affects all MCP servers that use CWD-relative path resolution
• The args config field in claude_desktop_config.json is effectively broken for path-based arguments
• No error is surfaced to Anonymous — the server appears connected but all tool calls fail with cryptic filesystem errors
• Cannot be fixed via config — no combination of args, env, or path settings resolves it

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Workaround

Pass the repo path explicitly on every individual tool call as a parameter (e.g. repo_root="/absolute/path"). This is impractical for production use and requires the caller to know the internals of each MCP server.

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Suggested Fix

The disclaimer sandbox helper should either:

• Preserve the spawning process's CWD when exec-ing MCP servers, or
• Allow an explicit cwd field in claude_desktop_config.json MCP server entries, e.g.:

{
  "mcpServers": {
    "my-server": {
      "command": "/path/to/binary",
      "args": ["serve"],
      "cwd": "/Anonymouss/Anonymous/myproject"
    }
  }
}

The cwd field is already supported by other MCP host implementations (e.g. VS Code's MCP config) and would resolve this class of issue entirely.

What Should Happen?

Result: Server resolves all paths relative to / instead of the configured repo path
Expected: Server uses the path provided via --repo argument

Error Messages/Logs

Failed to spawn node (via disclaimer): ...disclaimer exited with code 1: Failed to spawn process: No such file or directory
Failed to spawn python (via disclaimer): ...disclaimer exited with code 1: Failed to spawn process: No such file or directory

### Impact

- Affects **all MCP servers** that use CWD-relative path resolution
- The `args` config field in `claude_desktop_config.json` is effectively broken for path-based arguments
- No error is surfaced to Anonymous — the server appears connected but all tool calls fail with cryptic filesystem errors
- Cannot be fixed via config — no combination of `args`, `env`, or path settings resolves it

Steps to Reproduce

Steps to Reproduce

1. Install any MCP server that uses CWD or a --repo/--root flag to locate its data directory (e.g. code-review-graph)
2. Register it in ~/Library/Application Support/Claude/claude_desktop_config.json with an explicit --repo /absolute/path argument
3. Launch Claude Desktop and connect to the MCP server
4. Call any tool on the server

Result: Server resolves all paths relative to / instead of the configured repo path
Expected: Server uses the path provided via --repo argument

Claude Model

Not sure / Multiple models

Is this a regression?

I don't know

Last Working Version

_No response_

Claude Code Version

Claude 1.569.0 (49894a)

Platform

Anthropic API

Operating System

macOS

Terminal/Shell

Terminal.app (macOS)

Additional Information

_No response_