Fixing MCP Filesystem: Server Disconnected (Node via mise)

Introduction

If you’re using Claude Desktop and trying to enable filesystem access, you might run into this annoying error:

MCP filesystem: Server disconnected

In my case, I was using mise to manage my Node.js setup — and that ended up being the root of the problem. Claude couldn’t find the right node or npx binary because GUI apps don’t inherit the shell’s $PATH.

Here’s exactly how I got it working.

What Was Going Wrong

Claude tries to run the filesystem plugin via npx. But since my Node was installed through mise, the npx command wasn’t available to Claude, even though it worked fine in the terminal.

I also made the mistake of adding --yes to the plugin args — which made things worse, because the plugin tried to treat that as a folder.

Step-by-Step Fix

1. Make sure Node.js is installed via `mise`

This is what I ran to install and set Node globally:

mise install node@lts
mise use -g node@lts

To double-check that Node is working and see where it’s coming from:

which node

Mine showed something like:

/Users/oz/.local/share/mise/installs/node/22.11.0/bin/node

If that’s what you see, you’re good.

2. Create a wrapper script for `npx`

Claude Desktop can’t see your shell environment, so we need to help it out a bit.

Create a script like this:

mkdir -p ~/bin/scripts
nano ~/bin/scripts/npx-for-claude

And paste this in:

#!/usr/bin/env bash

export PATH="/Users/oz/.local/share/mise/installs/node/22.11.0/bin:$PATH"
exec npx "$@"

Give it permission to run:

chmod +x ~/bin/scripts/npx-for-claude

This script makes sure the right version of npx runs, even if Claude can’t see your terminal’s setup.

3. Tell Claude to use your script

Open your Claude config file:

~/Library/Application Support/Claude/claude_desktop_config.json

Update the filesystem section to look like this:

{
  "mcpServers": {
    "filesystem": {
      "command": "/Users/oz/bin/scripts/npx-for-claude",
      "args": [
        "@modelcontextprotocol/server-filesystem",
        "/Users/oz/Desktop",
        "/Users/oz/Downloads"
      ]
    }
  }
}

Make sure to replace /Users/oz/ with your actual username if it’s different.

Also important: don’t include --yes here — I tried that at first and it broke everything. The plugin interpreted it as a folder name and crashed.

4. Run it once manually (optional)

To avoid Claude prompting you to install the plugin the first time, I just ran this myself once:

~/bin/scripts/npx-for-claude @modelcontextprotocol/server-filesystem /Users/oz/Desktop

That installed the plugin and made it easier to debug since I could see any errors directly.

5. Restart Claude Desktop

Once the config is set and the plugin is installed, quit Claude and open it again.

Then go to:

Settings → Developer → Filesystem

You should see:

filesystem: ✅ connected

It finally worked 🎉

Troubleshooting Tips

If you still get errors, here’s what helped me debug:

Make sure the script path is correct and executable

Add a simple debug log to the script:

echo "[Claude MCP] Running..." >> /tmp/claude.log
exec npx "$@" >> /tmp/claude.log 2>&1

Check the Claude logs (Settings → Open Logs Folder)
Remove any bad flags like --yes from the config

References

Final Thoughts

This took longer than I expected to figure out, but once I realized Claude didn’t inherit my terminal’s environment, everything clicked. If you're using a Node version manager like mise, that little wrapper script is all you need to get filesystem access working again.

Hope this saves someone a few hours of debugging.