MCP Filesystem server fails to initialize when launched via npx due to stdio connection issues

[SamirSaidani]

What happened?

When launching the MCP Filesystem server using npx inside Docker on a remote server, not locally, the server starts but LibreChat fails to connect, resulting in connection timeouts or premature closures (MCP error -32000: Connection closed). Running the server directly with node and the same arguments works reliably. Locally weirdly enough it works out of the box...

Version Information

ghcr.io/danny-avila/librechat-dev-api latest 5de54fbf6745 2 days ago 1.13GB
ghcr.io/danny-avila/librechat-dev latest 69836bf6d276 2 weeks ago 1.04GB
ghcr.io/danny-avila/librechat-api latest 1b83ccf384fe 5 weeks ago 1.09GB
ghcr.io/danny-avila/librechat latest 17cfdb1df083 5 weeks ago 1.02GB
ghcr.io/danny-avila/librechat-rag-api-dev-lite latest e7da8e6aca0f 5 weeks ago 1.31GB

Steps to Reproduce

Steps to reproduce:

Install a vanilla librechat docker instance on a remote server, with mcpserver filesystem enable inside librechat.yaml :

mcpServers:
 filesystem:
     type: stdio
     command: npx
     args:
       - -y
       - "@modelcontextprotocol/server-filesystem"
       - /home/user/LibreChat
 filesystem2:
    type: stdio
    command: node
    args:
      - /root/.npm/_npx/a3241bba59c344f5/node_modules/@modelcontextprotocol/server-filesystem/dist/index.js
      - /home/user/LibreChat

Result:
error: [MCP][filesystem] Connection failed: Connection timeout
error: [MCP][filesystem] Connection failed: MCP error -32000: Connection closed
error: [MCP][filesystem] Connection failed: MCP error -32000: Connection closed
info: [MCP][filesystem] ✗ Failed

But for the second filesytem2 it works

What browsers are you seeing the problem on?

No response

Relevant log output

2025-06-14 12:57:54 info: [MCP] Initializing app-level servers
LibreChat         | [DEBUG] MCP started with args: [
LibreChat         |   '/usr/local/bin/node',
LibreChat         |   '/root/.npm/_npx/a3241bba59c344f5/node_modules/@modelcontextprotocol/server-filesystem/dist/index.js',
LibreChat         |   '/home/user/LibreChat'
LibreChat         | ]
LibreChat         | [DEBUG] ENV: {
LibreChat         |   HOME: '/root',
LibreChat         |   PATH: '/app/node_modules/.bin:/node_modules/.bin:/usr/local/lib/node_modules/npm/node_modules/@npmcli/run-script/lib/node-gyp-bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin'
LibreChat         | }
LibreChat         | Secure MCP Filesystem Server running on stdio
LibreChat         | Allowed directories: [ '/home/user/LibreChat' ]
LibreChat         | 2025-06-14 12:57:56 info: [MCP][filesystem2] Capabilities: {"tools":{}}
LibreChat         | 2025-06-14 12:57:56 info: [MCP][filesystem2] Available tools: read_file, read_multiple_files, write_file, edit_file, create_directory, list_directory, directory_tree, move_file, search_files, get_file_info, list_allowed_directories
chat-mongodb      | {"t":{"$date":"2025-06-14T12:58:04.602+00:00"},"s":"I",  "c":"NETWORK",  "id":22943,   "ctx":"listener","msg":"Connection accepted","attr":{"remote":"172.18.0.6:58938","uuid":{"uuid":{"$uuid":"105de933-b812-4a5c-bfb5-82d48d1f08ab"}},"connectionId":12,"connectionCount":12}}
chat-mongodb      | {"t":{"$date":"2025-06-14T12:58:04.618+00:00"},"s":"I",  "c":"NETWORK",  "id":51800,   "ctx":"conn12","msg":"client metadata","attr":{"remote":"172.18.0.6:58938","client":"conn12","negotiatedCompressors":[],"doc":{"driver":{"name":"nodejs|Mongoose","version":"6.14.2|8.12.1"},"platform":"Node.js v20.19.2, LE","os":{"name":"linux","architecture":"x64","version":"6.8.0-60-generic","type":"Linux"},"env":{"container":{"runtime":"docker"}}}}}
LibreChat         | 2025-06-14 12:58:05 error: [MCP][filesystem] Connection failed: Connection timeout
LibreChat         | [DEBUG] MCP started with args: [
LibreChat         |   '/usr/local/bin/node',
LibreChat         |   '/root/.npm/_npx/a3241bba59c344f5/node_modules/.bin/mcp-server-filesystem',
LibreChat         |   '/home/user/LibreChat'
LibreChat         | ]
LibreChat         | [DEBUG] ENV: {
LibreChat         |   npm_config_user_agent: 'npm/10.8.2 node/v20.19.2 linux x64 workspaces/false',
LibreChat         |   npm_node_execpath: '/usr/local/bin/node',
LibreChat         |   npm_config_noproxy: '',
LibreChat         |   SHLVL: '1',
LibreChat         |   HOME: '/root',
LibreChat         |   npm_package_json: '/app/package.json',
LibreChat         |   npm_config_userconfig: '/root/.npmrc',
LibreChat         |   npm_config_local_prefix: '/app',
LibreChat         |   npm_config_yes: 'true',
LibreChat         |   COLOR: '0',
LibreChat         |   npm_config_prefix: '/usr/local',
LibreChat         |   npm_config_npm_version: '10.8.2',
LibreChat         |   npm_config_cache: '/root/.npm',
LibreChat         |   npm_config_node_gyp: '/usr/local/lib/node_modules/npm/node_modules/node-gyp/bin/node-gyp.js',
LibreChat         |   PATH: '/root/.npm/_npx/a3241bba59c344f5/node_modules/.bin:/app/node_modules/.bin:/node_modules/.bin:/usr/local/lib/node_modules/npm/node_modules/@npmcli/run-script/lib/node-gyp-bin:/app/node_modules/.bin:/node_modules/.bin:/usr/local/lib/node_modules/npm/node_modules/@npmcli/run-script/lib/node-gyp-bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin',
LibreChat         |   NODE: '/usr/local/bin/node',
LibreChat         |   npm_package_name: 'LibreChat',
LibreChat         |   npm_lifecycle_script: 'mcp-server-filesystem',
LibreChat         |   npm_package_version: 'v0.7.8',
LibreChat         |   npm_lifecycle_event: 'npx',
LibreChat         |   npm_config_globalconfig: '/usr/local/etc/npmrc',
LibreChat         |   npm_config_init_module: '/root/.npm-init.js',
LibreChat         |   npm_execpath: '/usr/local/lib/node_modules/npm/bin/npm-cli.js',
LibreChat         |   PWD: '/app',
LibreChat         |   npm_config_global_prefix: '/usr/local',
LibreChat         |   npm_command: 'exec',
LibreChat         |   INIT_CWD: '/app',
LibreChat         |   EDITOR: 'vi'
LibreChat         | }
LibreChat         | Secure MCP Filesystem Server running on stdio
LibreChat         | Allowed directories: [ '/home/user/LibreChat' ]
LibreChat         | 2025-06-14 12:58:07 error: [MCP][filesystem] Connection failed: MCP error -32000: Connection closed

Screenshots

No response

Code of Conduct

• I agree to follow this project's Code of Conduct

[danny-avila]

Within docker, it can run reliably, but it needs a volume mounted for the host-level file directory you wish to give it access to:

LibreChat         | 2025-06-14 14:08:37 info: [MCP] Initializing app-level servers
LibreChat         | Secure MCP Filesystem Server running on stdio
LibreChat         | Allowed directories: [ '/app/obsidian' ]
LibreChat         | 2025-06-14 14:08:40 info: [MCP][filesystem] Instructions not included (serverInstructions not configured)
LibreChat         | 2025-06-14 14:08:40 info: [MCP][filesystem] Capabilities: {"tools":{}}
LibreChat         | 2025-06-14 14:08:40 info: [MCP][filesystem] Available tools: read_file, read_multiple_files, write_file, edit_file, create_directory, list_directory, directory_tree, move_file, search_files, get_file_info, list_allowed_directories
LibreChat         | 2025-06-14 14:08:40 info: [MCP] Initialized 1/1 app-level server(s)
LibreChat         | 2025-06-14 14:08:40 info: [MCP][filesystem] ✓ Initialized
LibreChat         | 2025-06-14 14:08:40 info: [MCP] All app-level servers initialized successfully

Example librechat.yaml:

  filesystem:
    type: stdio
    command: npx
    args:
      - -y
      - "@modelcontextprotocol/server-filesystem"
      - /app/obsidian

and making use of docker-compose.override.yml:

services:
  api:
    volumes:
      - /mnt/c/Users/danny/Documents/obsidian:/app/obsidian

[danny-avila]

if you wanted it to have access to the files within the docker app, which is equivalent to pointing to the LibreChat project files, you could simply use:

  filesystem:
    type: stdio
    command: npx
    args:
      - -y
      - "@modelcontextprotocol/server-filesystem"
      - /app

LibreChat         | 2025-06-14 14:12:21 info: [MCP] Initializing app-level servers
LibreChat         | Secure MCP Filesystem Server running on stdio
LibreChat         | Allowed directories: [ '/app' ]

[SamirSaidani]

Within docker, it can run reliably, but it needs a volume mounted for the host-level file directory you wish to give it access to:
Example librechat.yaml:

  filesystem:
    type: stdio
    command: npx
    args:
      - -y
      - "@modelcontextprotocol/server-filesystem"
      - /app/obsidian

and making use of docker-compose.override.yml:

services:
  api:
    volumes:
      - /mnt/c/Users/danny/Documents/obsidian:/app/obsidian

Thanks for your quick answer!
Sure I've already done the job on my librechat.yaml and binded /home/user/LibreChat (docker) with. ./shared (remote server) on the docker-compose override, otherwise filesystem2 mcp server wouldn't work (see the log and my librechat.yaml ).

services:
  api:
  volumes:
    - type: bind
       source:  ./shared
       target: /home/user/LibreChat

If you look at librechat.yaml, you can see two different mcp server config for server-filesystem :

• filesystem using npx, KO
• filesystem2 using node, OK

I've added filesystem2 to be sure that the problem comes from npx.

I'm using a VPS server, and there's something wrong with npx. Executing the mcp server on the server directly with node instead of npx works perfectly though, as you can see on the logs and the filesystem2 config in librechat.yaml.

I followed
https://www.youtube.com/live/ip4v7Ijdzf8

I've added some debug logs on the filesystem mcp server source code to help track the problem : echo ARGS and ENV.

As I said, I've done the exact same thing locally on my Linux desktop and the whole setup works without any problem. Reproducing the same step on my vps server makes the error I've shown.

[SamirSaidani]

Ok, found the problem, I'm answering to myself : npx works fine, but the default init timeout is too short to handle the initialization.

Adding initTimeout with more time makes the mcp server work properly :

filesystem:
     type: stdio
     command: npx
     args:
       - -y
       - "@modelcontextprotocol/server-filesystem"
       - /home/user/LibreChat
     initTimeout: 300000