[MCP][filesystem] Does not work

[WillCodeForCash]

What happened?

After pulling docker images and updating to 0.8.1-rc1, MCP filesystem server is no longer functional - sometimes it shows up as an MCP server with no tools, sometimes it does not show up at all.
I have tried reverting all configs and following the current docs for setting up filesystem mcp.

Version Information

❯ docker images | grep librechat
ghcr.io/danny-avila/librechat-dev latest 54fe94f67053 21 hours ago 2.78GB

❯ git rev-parse HEAD
4a13867

Steps to Reproduce

librechat.yaml:

# For more information, see the Configuration Guide:
# https://www.librechat.ai/docs/configuration/librechat_yaml

# Configuration version (required)
version: 1.3.1

mcpServers:
  filesystem:
    command: npx
    args:
    - -y
    - "@modelcontextprotocol/server-filesystem"
    - /sources/my/folder1
    - /sources/my/folder2
    - /sources/my/folder3

endpoints:
  agents:
    # (optional) Default recursion depth for agents, defaults to 25
    recursionLimit: 50
    # (optional) Max recursion depth for agents, defaults to 25
    maxRecursionLimit: 100

docker-compose.override.yml:

services:
  api:
    volumes:
      - type: bind
        source: ./librechat.yaml
        target: /app/librechat.yaml
      - type: bind
        source: D:/Some/Source/Folder1
        target: /sources/my/folder1
      - type: bind
        source: D:/Some/Source/Folder2
        target: /sources/my/folder2
      - type: bind
        source: D:/Some/Source/Folder3
        target: /sources/my/folder3

Use specified .yml files and run docker compose -f docker-compose.yml -f docker-compose.override.yml up -d, use UI and observe that filesystem MCP server does not work.

What browsers are you seeing the problem on?

No response

Relevant log output

> LibreChat@v0.8.1-rc1 backend
> cross-env NODE_ENV=production node api/server/index.js

2025-11-19 14:40:58 info: Mongo Connection options
2025-11-19 14:40:58 info: {
  "bufferCommands": false
}
2025-11-19 14:41:01 info: Connected to MongoDB
2025-11-19 14:41:01 info: [indexSync] Starting index synchronization check...
2025-11-19 14:41:02 info: [getAppConfig] App configuration not initialized. Initializing AppService...
2025-11-19 14:41:02 info: Custom config file loaded:
2025-11-19 14:41:02 info: {
  "version": "1.3.1",
  "mcpServers": {
    "filesystem": {
      "command": "npx",
      "args": [
        "-y",
        "@modelcontextprotocol/server-filesystem",
        "/sources/my/folder1",
        "/sources/my/folder2",
        "/sources/my/folder3"
      ]
    }
  },
  "endpoints": {
    "agents": {
      "recursionLimit": 50,
      "maxRecursionLimit": 100
    }
  }
}
2025-11-19 14:41:02 warn: Default value for CREDS_KEY is being used.
2025-11-19 14:41:02 warn: Default value for CREDS_IV is being used.
2025-11-19 14:41:02 warn: Default value for JWT_SECRET is being used.
2025-11-19 14:41:02 warn: Default value for JWT_REFRESH_SECRET is being used.
2025-11-19 14:41:02 info: Please replace any default secret values.
2025-11-19 14:41:02 info: ​

    For your convenience, use this tool to generate your own secret values:
    https://www.librechat.ai/toolkit/creds_generator

    ​
2025-11-19 14:41:02 warn: The `CHECK_BALANCE` environment variable is deprecated. Please use the `balance` field in the `librechat.yaml` config file instead.
ore info: https://librechat.ai/docs/configuration/librechat_yaml/object_structure/balance#overview
2025-11-19 14:41:02 info: RAG API is running and reachable at http://rag_api:8000.
2025-11-19 14:41:02 info: Server listening on all interfaces at port 3080. Use http://localhost:3080 to access it
2025-11-19 14:41:02 info: [indexSync] Messages are fully synced: 2724/2724
2025-11-19 14:41:02 info: [indexSync] Conversations are fully synced: 456/456
2025-11-19 14:41:02 warn: [FlowStateManager] Cannot complete flow - flow state not found
2025-11-19 14:41:05 info: [MCP][filesystem] -------------------------------------------------┐
2025-11-19 14:41:05 info: [MCP][filesystem] URL: N/A
2025-11-19 14:41:05 info: [MCP][filesystem] OAuth Required: false
2025-11-19 14:41:05 info: [MCP][filesystem] Capabilities: {"tools":{}}
2025-11-19 14:41:05 info: [MCP][filesystem] Tools: undefined
2025-11-19 14:41:05 info: [MCP][filesystem] Server Instructions: undefined
2025-11-19 14:41:05 info: [MCP][filesystem] Initialized in: 3824ms
2025-11-19 14:41:05 info: [MCP][filesystem] -------------------------------------------------┘
2025-11-19 14:41:05 info: MCP servers initialized successfully. Added 0 MCP tools.
2025-11-19 14:41:05 info: OAuth reconnect manager initialized successfully.
2025-11-19 14:41:11 error: [getMCPTools] [
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      0,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      1,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      2,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      3,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      4,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      5,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      6,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      7,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      8,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      9,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      10,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      11,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  },
  {
    "code": "invalid_literal",
    "expected": "object",
    "path": [
      "tools",
      12,
      "inputSchema",
      "type"
    ],
    "message": "Invalid literal value, expected \"object\""
  }
]

Screenshots

No response

Code of Conduct

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

[danny-avila]

Thanks for the report. I spent a few hours investigating this issue since I use the same MCP server internally. This is a bug in the official filesystem MCP server, not LibreChat.

Root Cause

The filesystem MCP server's latest versions install zod-to-json-schema without locked dependencies. At runtime, this pulls in Zod v4, while the MCP SDK uses Zod v3, causing schema validation errors where the type: "object" field is missing from tool definitions.

Solution

I've patched the issue in a fork by explicitly pinning zod: "^3.23.3" as a dependency, forcing all packages to use compatible Zod v3 versions.

Patched fork: https://github.com/danny-avila/server-filesystem

How to Use

Add this to your Dockerfile before the CMD ["npm", "run", "backend"] line:

WORKDIR /app/mcp_servers
RUN git clone https://github.com/danny-avila/server-filesystem.git
WORKDIR /app/mcp_servers/server-filesystem
RUN npm install
RUN npm run build
WORKDIR /app

Then configure in your librechat.yaml:

mcpServers:
  filesystem:
    command: node
    args:
      - /app/mcp_servers/server-filesystem/dist/index.js
      - /app  # or whatever directory you want accessible

Reporting Upstream

This needs to be reported to the official repo: https://github.com/modelcontextprotocol/servers/issues

If someone wants to open an issue there, please reference that the problem occurs when zod-to-json-schema transitively installs Zod v4 while @modelcontextprotocol/sdk expects v3.

[danny-avila]

You can also build the MCP server wherever and just make the output dist/index.js available to your LibreChat instance.

[WillCodeForCash]

Thank you for the detailed response 😸