MCP Server Tool Usage Error - Tool f1e_get_pull_request does not have an implementation registered.

[kato-st]

Describe the bug

I have setup the github-mcp-server to run on the downloaded binary version 0.1.1 via the Releases page (Note: not running through Docker) for my Mac OS system with the following VS Code mcp.json (workspace) configuration.

{
  "servers": {
    "github": {
      "command": "/Users/sayvai/mcp/github-mcp-server_Darwin_arm64/github-mcp-server",
      "args": ["stdio"],
      "envFile": "/Users/sayvai/mcp/.env"
    },
}

The GitHub tools (30 tools discovered) are listed from the VS Code command palette, however after running the following chat prompt in Agent mode (using Claude 3.7 Sonnet LLM):

#get_pull_request What was the last pull request opened on this repo?

Copilot attempts to run the tool, but encounters an immediate error in its response output:

Tool f1e_get_pull_request does not have an implementation registered.

Note: My GITHUB_PERSONAL_ACCESS_TOKEN is set in the path that is referenced in envFile property of the mcp.json configuration above.

Also worth noting, is that the prompting with #list_pull_request tool on its own without additional prompt text returns the same error.

However, prompting with the tool #get_me works on its own in a prompt without further prompt text returning my account details.

Am i using the tools incorrectly in VS Code? Or could I improve my MCP Server configuration? 🤔

Affected version

0.1.1

Steps to reproduce the behavior

1. Open VS Code Insiders
2. Select Agent Mode
3. Select Claude 3.7 Sonnet LLM
4. Enter prompt: #get_pull_request What was the last pull request opened on this repo?
5. Expected output: a summary of the last opened pull request in the repo
6. Actual output: Tool f1e_get_pull_request does not have an implementation registered.

Logs

The logs before and after prompt. No further log output observed after entering prompt:

2025-04-08 13:51:11.812 [info] Starting server github
2025-04-08 13:51:11.813 [info] Connection state: Starting
2025-04-08 13:51:11.822 [info] Starting server from LocalProcess extension host
2025-04-08 13:51:11.824 [info] Connection state: Starting
2025-04-08 13:51:11.825 [info] Connection state: Running
2025-04-08 13:51:16.827 [info] Waiting for server to respond to `initialize` request...
2025-04-08 13:51:17.201 [warning] [server stderr] GitHub MCP Server running on stdio
2025-04-08 13:51:17.206 [info] Discovered 30 tools

[Sayvai]

ℹ Tagging myself through personal GitHub account. Please ignore comment.

[SamMorrowDrums]

I have encountered this too, and when it gets in this broken state if makes the tools unusable. I don't yet have a solution.

[pjirsa]

I was getting the same error. I ran MCP: Clear Cached Tools command and that seemed to resolve the issue.