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mcp/filesystem cannot use working directory only on LM Studio

Open mcDandy opened this issue 5 months ago • 4 comments

Describe the bug mcp/filesystem does not start under LM Studio without specified path or with working directory as described in intelij idea integration

To Reproduce Steps to reproduce the behavior:

  1. put the tool in mcp.json
{
  "mcpServers": {
    "filesystem": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-filesystem",
      ]
    }
  }
}
  1. Enable it Expected behavior The tool should be usable.

Logs

2025-07-20 22:12:47 [ERROR]
 [Plugin(mcp/filesystem)] stderr: Usage: mcp-server-filesystem <allowed-directory> [additional-directories...]
2025-07-20 22:12:47 [ERROR]
 [Plugin(mcp/filesystem)] stderr: Error in LM Studio MCP bridge process: _0x4143fb [McpError]: MCP error -32000: Connection closed
    at _0x477d3a._onclose (D:\Program Files\LM Studio\resources\app\.webpack\lib\mcpbridgeworker.js:1:822761)
    at <computed>.onclose (D:\Program Files\LM Studio\resources\app\.webpack\lib\mcpbridgeworker.js:1:821476)
    at ChildProcess.<anonymous> (D:\Program Files\LM Studio\resources\app\.webpack\lib\mcpbridgeworker.js:1:796633)
    at ChildProcess.emit (node:events:519:28)
    at _0x4f9a1e.<computed> [as emit] (D:\Program Files\LM Studio\resources\app\.webpack\lib\mcpbridgeworker.js:1:279636)
    at maybeClose (node:internal/child_process:1105:16)
    at ChildProcess._handle.onexit (node:internal/child_process:305:5) {
  code: -32000,
  data: undefined
}
_0x4143fb [McpError]: MCP error -32000: Connection closed
    at _0x477d3a._onclose (D:\Program Files\LM Studio\resources\app\.webpack\lib\mcpbridgeworker.js:1:822761)
    at <computed>.onclose (D:\Program Files\LM Studio\resources\app\.webpack\lib\mcpbridgeworker.js:1:821476)
    at ChildProcess.<anonymous> (D:\Program Files\LM Studio\resources\app\.webpack\lib\mcpbridgeworker.js:1:796633)
    at ChildProcess.emit (node:events:519:28)
    at _0x4f9a1e.<computed> [as emit] (D:\Program Files\LM Studio\resources\app\.webpack\lib\mcpbridgeworker.js:1:279636)
    at maybeClose (node:internal/child_process:1105:16)
    at ChildProcess._handle.onexit (node:internal/child_process:305:5) {
  code: -32000,
  data: undefined
}

Additional context with "${workspaceFolder}" as standin for working directory shows

2025-07-20 22:27:14 [ERROR]
 [Plugin(mcp/filesystem)] stderr: Error accessing directory ${workspaceFolder}: Error: ENOENT: no such file or directory, stat 'C:\Users\danda\.lmstudio\extensions\plugins\mcp\filesystem\${workspaceFolder}'
    at async Object.stat (node:internal/fs/promises:1032:18)
    at async file:///C:/Users/danda/AppData/Local/npm-cache/_npx/a3241bba59c344f5/node_modules/@modelcontextprotocol/server-filesystem/dist/index.js:48:23
    at async Promise.all (index 0)
    at async file:///C:/Users/danda/AppData/Local/npm-cache/_npx/a3241bba59c344f5/node_modules/@modelcontextprotocol/server-filesystem/dist/index.js:46:1 {
  errno: -4058,
  code: 'ENOENT',
  syscall: 'stat',
  path: 'C:\\Users\\danda\\.lmstudio\\extensions\\plugins\\mcp\\filesystem\\${workspaceFolder}'
}
2025-07-20 22:27:14 [ERROR]
 [Plugin(mcp/filesystem)] stderr: Error in LM Studio MCP bridge process: _0x4143fb [McpError]: MCP error -32000: Connection closed
    at _0x477d3a._onclose (D:\Program Files\LM Studio\resources\app\.webpack\lib\mcpbridgeworker.js:1:822761)
    at <computed>.onclose (D:\Program Files\LM Studio\resources\app\.webpack\lib\mcpbridgeworker.js:1:821476)
    at ChildProcess.<anonymous> (D:\Program Files\LM Studio\resources\app\.webpack\lib\mcpbridgeworker.js:1:796633)
    at ChildProcess.emit (node:events:519:28)
    at _0x4f9a1e.<computed> [as emit] (D:\Program Files\LM Studio\resources\app\.webpack\lib\mcpbridgeworker.js:1:279636)
    at maybeClose (node:internal/child_process:1105:16)
    at ChildProcess._handle.onexit (node:internal/child_process:305:5) {
  code: -32000,
  data: undefined
}
2025-07-20 22:27:14 [ERROR]
 [Plugin(mcp/filesystem)] stderr: _0x4143fb [McpError]: MCP error -32000: Connection closed
    at _0x477d3a._onclose (D:\Program Files\LM Studio\resources\app\.webpack\lib\mcpbridgeworker.js:1:822761)
    at <computed>.onclose (D:\Program Files\LM Studio\resources\app\.webpack\lib\mcpbridgeworker.js:1:821476)
    at ChildProcess.<anonymous> (D:\Program Files\LM Studio\resources\app\.webpack\lib\mcpbridgeworker.js:1:796633)
    at ChildProcess.emit (node:events:519:28)
    at _0x4f9a1e.<computed> [as emit] (D:\Program Files\LM Studio\resources\app\.webpack\lib\mcpbridgeworker.js:1:279636)
    at maybeClose (node:internal/child_process:1105:16)
    at ChildProcess._handle.onexit (node:internal/child_process:305:5) {
  code: -32000,
  data: undefined
}

mcDandy avatar Jul 20 '25 20:07 mcDandy

Putting in working directory manually does not work also. AI tries to read from wrong directory

Thought for 3 minutes 7 seconds

read_multiple_files
({"paths":["index.html","script.js","style.css"]}…})

mcp/filesystem

Arguments

paths:

[
  "index.html",
  "script.js",
  "style.css"
]
Result

[
  {
    "type": "text",
    "text": "index.html: Error - Access denied - path outside allowed directories: C:\\Users\\danda\\.lmstudio\\extensions\\plugins\\mcp\\filesystem\\index.html not in C:\\Users\\danda\\.lmstudio\\working-directories\\1750330141933\n---\nscript.js: Error - Access denied - path outside allowed directories: C:\\Users\\danda\\.lmstudio\\extensions\\plugins\\mcp\\filesystem\\script.js not in C:\\Users\\danda\\.lmstudio\\working-directories\\1750330141933\n---\nstyle.css: Error - Access denied - path outside allowed directories: C:\\Users\\danda\\.lmstudio\\extensions\\plugins\\mcp\\filesystem\\style.css not in C:\\Users\\danda\\.lmstudio\\working-directories\\1750330141933"
  }
]

mcDandy avatar Jul 20 '25 20:07 mcDandy

bump, same issue

aleenprd avatar Aug 06 '25 19:08 aleenprd

@claude could you help investigate this issue?

olaservo avatar Aug 24 '25 03:08 olaservo

Claude finished @olaservo's task —— View job

Analysis Complete - LM Studio MCP Filesystem Integration Issue

I've analyzed the filesystem MCP server code and identified the root cause of the issue.

Investigation Progress
  • [x] Read and analyze the filesystem server source code
  • [x] Investigate directory argument parsing and validation
  • [x] Check for workspace folder placeholder handling
  • [x] Analyze the error messages and determine root cause
  • [x] Provide recommendations for fixing the issue

Root Cause Analysis

The issue occurs because LM Studio doesn't properly handle MCP server directory requirements. Here's what's happening:

  1. Missing Directory Arguments: The filesystem server (index.ts:36-42) requires directory paths as command-line arguments. When no arguments are provided, it shows the usage error seen in the logs.

  2. Literal Placeholder Handling: When LM Studio uses ${workspaceFolder}, it's being passed literally as a string instead of being resolved to the actual workspace path. The server tries to access C:\Users\danda\.lmstudio\extensions\plugins\mcp\filesystem\${workspaceFolder} instead of the intended workspace directory.

  3. Server Working Directory Issue: The filesystem server runs from its own directory (C:\Users\danda\.lmstudio\extensions\plugins\mcp\filesystem\) rather than the intended workspace, causing path resolution problems.

Technical Details

The server has two methods for specifying allowed directories:

  • Command-line arguments (what LM Studio should use)
  • MCP Roots protocol (dynamic, client-driven)

LM Studio appears to be launching the server without proper directory arguments and without implementing the MCP Roots protocol to provide workspace directories dynamically.

Recommended Solutions

For LM Studio Users:

{
  "mcpServers": {
    "filesystem": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-filesystem",
        "C:\\Users\\danda\\your-actual-workspace-path"
      ]
    }
  }
}

For LM Studio Developers:

  1. Implement MCP Roots protocol - This would allow dynamic workspace directory management
  2. Fix placeholder resolution - ${workspaceFolder} should resolve to actual paths before server launch
  3. Set proper working directory - Launch the MCP server with the workspace as the working directory

The filesystem server code itself is working correctly - this is a client integration issue that needs to be addressed in LM Studio's MCP implementation.

claude[bot] avatar Aug 24 '25 03:08 claude[bot]