Old MCP Server config remains somewhere

[manuelachterberg]

What happened?

Hi,

I'm running librechat-dev 0.8.0-rc3.
There is an issue with former configured MCP servers. I used to test a config via Smithery (hosted by Smithery), namely Office-Word-MCP-Server, which has been completely removed. - I searched through all files and the MongoDB. The MCP Server and tool are not named anywhere. Goes without saying I started with a clean cache.

Now if I call any other MCP server tool it gets weird. The LLM seems to only process the agent's system prompt and answers about it, or does a general greeting, or saying "you did not ask a question". It is ignoring the mcp tool, that actually received a good, working response.

Now the LibreChat-API-Log says:

2025-08-27 11:48:21 warn: [MCP][Office-Word-MCP-Server][find_text_in_document] Tool definition not found, cannot create tool. 2025-08-27 11:48:21 warn: [MCP][Office-Word-MCP-Server][convert_to_pdf] Requested tool not found in available tools, re-initializing MCP server. 2025-08-27 11:48:21 info: [MCP][User: 67c8320ee7d4a33c84721e23][Office-Word-MCP-Server] Establishing new connection 2025-08-27 11:48:21 info: [MCP Reinitialize] getUserConnection threw error: MCP error -32600: [MCP][User: 67c8320ee7d4a33c84721e23] Configuration for server "Office-Word-MCP-Server" not found. 2025-08-27 11:48:21 info: [MCP Reinitialize] OAuth state - oauthRequired: false, oauthUrl: null 2025-08-27 11:48:21 error: [MCP Reinitialize] Error initializing MCP server Office-Word-MCP-Server for user: MCP error -32600: [MCP][User: 67c8320ee7d4a33c84721e23] Configuration for server "Office-Word-MCP-Server" not found. 2025-08-27 11:48:21 warn: [MCP][Office-Word-MCP-Server][convert_to_pdf] Tool definition not found, cannot create tool.

I only fixed it by cleansing all occurences of Office-Word-MCP-Server from the MongoDB.

Version Information

ghcr.io/danny-avila/librechat-rag-api-dev-lite latest bb5e7a783224 5 hours ago 1.67GB
ghcr.io/danny-avila/librechat-rag-api-dev-lite 0da78c464c9a 29 hours ago 1.67GB
ghcr.io/danny-avila/librechat-dev-api latest 4aac21e12811 36 hours ago 1.26GB
ghcr.io/danny-avila/librechat-dev-api 9eabad3954ac 2 weeks ago 1.26GB
ghcr.io/danny-avila/librechat-dev latest bd240b2fc036 4 months ago 919MB
ghcr.io/danny-avila/librechat-rag-api-dev latest 30f6b5ee7c61 4 months ago 7.81GB
ghcr.io/danny-avila/librechat-dev 782f80a8c1e4 5 months ago 888MB
ghcr.io/danny-avila/librechat-rag-api-dev 9a0541a57bb1 8 months ago 7.65GB
ghcr.io/danny-avila/librechat-rag-api-dev-lite 095db2c2ff3b 8 months ago 1.29GB

Steps to Reproduce

1. Install a Smithery-hosted MCP-Server using Smithery script.
2. Try running the MCP Server
3. Uninstall MCP Server from config
4. Try to use a different MCP server

What browsers are you seeing the problem on?

Firefox

Relevant log output

-

Screenshots

Code of Conduct

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

[danny-avila]

How are you uninstalling the MCP server? Are you restarting the server after doing so? Are you using an agent?

Are you not able to use any MCP Servers unless you remove reference of the "uninstalled" one?

In any case, you should be able to remove MCP servers from agents after this update: #9237

Will take other edge cases into account.

[manuelachterberg]

How are you uninstalling the MCP server? Are you restarting the server after doing so? Are you using an agent?
Uninstalling: I removed the mcp server's config from librechat.yml, I also tried
npx -y @smithery/cli@latest uninstall @GongRzhe/Office-Word-MCP-Server --client librechat npm warn deprecated [email protected]: Use your platform's native DOMException instead Server @GongRzhe/Office-Word-MCP-Server is not installed for librechat
I am using an agent. Using no agent produced a similar behavior. When I activated MCP it output nothing most of the time.

Are you not able to use any MCP Servers unless you remove reference of the "uninstalled" one?
correct. This led to the unexpected behavior of successfully using the mcp tool but not processing its output, instead outputting a generic greeting or a reaction about the system prompt.

In any case, you should be able to remove MCP servers from agents after this update: #9237
will try again with this update. Thank you!

I'll try more MCP servers and let you know if I run into similar problems again. Thank you for the support. I really appreciate it!

[dustinhealy]

For the smithery-cli command, that has not been properly implemented for LibreChat yet, so the behavior of that function is currently undefined (meaning you should only remove MCPs manually from the yaml as you stated). Will make a PR soon to smithery in order to add support for uninstalling through the script.

[dustinhealy]

Following up, the PR has been opened on the smithery cli repo, so the uninstall command should work once this gets merged in. Thanks for your patience. You can follow along with the PR here: smithery-ai/cli#371

[dustinhealy]

smithery-ai/cli#371 has been merged in so you can now uninstall servers via the command line with smithery

[dustinhealy]

Hi Manuel,

I wasn't able to replicate the errors / behavior you are experiencing following your reproduction steps.

Wasn't able to test with the Microsoft Word server because of an issue on Smithery's side, but I used Desktop-Commander installed via the auto-generated Smithery script, ran a basic command successfully, removed the MCP server (both from the config manually, and through the deletion button in the agent panel on separate test runs to disambiguate the possible failure paths), and then restarted LC and ran a different MCP server in the same conversation and the tool calls worked properly.

Will try to test more pending your answer to Danny's questions, those answers should help make it easier to diagnose what is going on.

[dustinhealy]

Still looking into the source of this behavior but the loss of context can be seen here with the tokenCount field. It looks like the tool call is not being processed properly somewhere along the line and that is reflected by the tokenCount having a much lower value than I would expect for the response. It is good we have isolated this to be occurring only when the first message of the conversation has a tool call, will help me narrow down my search. Do you know if this behavior is still happening when you try in a conversation with any other providers or also with non-agent endpoints?

  ^ Successful response / recognition of tool call ^
  "conversationId": "cd685655-fbdf-471b-a2fd-2d1c59d56e06",
  "createdAt": "2025-09-11T07:53:18.135Z",
  "endpoint": "agents",
  "error": false,
  "expiredAt": null,
  "isCreatedByUser": false,
  "model": "agent_jnwf3WNu7RvOQNZ7hhcpC",
  "parentMessageId": "b586962f-fcfc-4f39-89e4-6ff6d62f258a",
  "sender": "cassiniGPT",
  "text": "",
  "tokenCount": 32991, <-- token count reflects tool response
  "unfinished": false,
  "updatedAt": "2025-09-11T07:53:18.135Z",
  "children": [],
  "depth": 3,
  "siblingIndex": 0
                                    
                                    
                                    

 {
"type": "text",
"text": "Understood! Please tell me your specific question or request. \n\nIf it relates to any technical, factual, or up-to-date information, I'll always:\n- Confirm from verifiable sources,\n- Ask for clarification if something is ambiguous,\n- Offer a web search with prior warning for external queries.\n\nHow can I help you today?"
    }
],
^ Failed Recognition Response ^
"conversationId": "f936a969-c052-44bc-8d54-14394a47bcdd",
"createdAt": "2025-09-11T07:54:28.396Z",
"endpoint": "agents",
"error": false,
"expiredAt": null,
"isCreatedByUser": false,
"model": "agent_jnwf3WNu7RvOQNZ7hhcpC",
"parentMessageId": "67a6f2cc-d3bf-489c-a365-f0d62290fe4f",
"sender": "cassiniGPT",
"text": "",
"tokenCount": 11962, <-- token count does not account for tool response 
"unfinished": false,
"updatedAt": "2025-09-11T07:54:28.396Z",
"children": [
    {

[dustinhealy]

Also, I am not yet able to replicate the behavior using an agent with AzureOpenAI gpt-4o and https://jsonplaceholder.typicode.com for testing.

New_Chat (15).json

[manuelachterberg]

I also tried other OpenAPI Endpoints and cannot replicate the behavior. It seems to be a MS Graph exclusive thing or maybe my schema is problematic. But I cannot imagine how my schema could lead to this behaviour. Would it help to share the schema?

[dustinhealy]

Sure, although at that point if the problem is external to LibreChat and the schema is valid, I am not sure how much further we can take the troubleshooting on our side beyond that

[manuelachterberg]

I haven't tested numerous different APIs yet. I'm not fully convinced this problem is external since I can open the tool call and see a usable response in the json. The API call happens as it should. It doesn't seem to be passed on to the llm afterwards.

[rromanchuk]

omfg, the amount of hours I just spent on this lol

There needs to be a big, like HUGE warning on https://www.librechat.ai/docs/configuration/redis that if you are making to chatlibre.yaml with docker compose, you absolutely are not making changes.

> KEYS libre-chat*
 1) "libre-chat::ROLES:ADMIN"
 2) "libre-chat::CONFIG_STORE:tools:global"
 3) "libre-chat::CONFIG_STORE:MODELS_CONFIG"
 4) "libre-chat::CONFIG_STORE:tools:user:68b26b8281732978650532c1"
 5) "libre-chat::CONFIG_STORE:ENDPOINT_CONFIG"
 6) "libre-chat::CONFIG_STORE:APP_CONFIG"
 7) "libre-chat::CONFIG_STORE:PLUGINS"
 8) "libre-chat::CONFIG_STORE:tools:user:68b65fddec89b542a38cf266"
 9) "libre-chat::STATIC_CONFIG:LIBRECHAT_YAML_CONFIG"
10) "libre-chat::CONFIG_STORE:STARTUP_CONFIG"
11) "libre-chat::ROLES:USER"

[danny-avila]

Sorry this caused a time sink for you. I highly recommended following this part of the guide:
https://www.librechat.ai/docs/configuration/redis#selective-in-memory-caching

I'm debating making STATIC_CONFIG always default unless explicitly configured otherwise.