`get_file_contents` is not working properly (Path did not point to a file or directory, but resolved git ref)

[nasxisbest]

Describe the bug

It's not able to resolve a file.

Affected version

GitHub MCP Server
Version: v0.10.0
Commit: 45e90ae
Build Date: 2025-08-01T14:36:17Z

Steps to reproduce the behavior

1. Type "Read file X in repo Y"

Expected vs actual behavior

File should be correctly retrieved from the Github.

Logs

⏺ I found the file localenv.config.yaml. Let me read its contents:

⏺ github_twdcgrid - Get file or directory contents (MCP)(owner: "COST", repo: "baymax", path: "localenv.config.yaml")
  ⎿ Path did not point to a file or directory, but resolved git ref to {"Ref":"refs/heads/main","SHA":"b32ec16443d8f6fef6ba16913d33f0abfc3aa02d"} with possible path matches: ["
    localenv.config.yaml"]

  ⎿  Interrupted by user

> supply "Ref":"refs/heads/main"

✻ Thinking…

  The user wants me to supply the ref parameter with "refs/heads/main" when making the request to get the file contents.

⏺ github_twdcgrid - Get file or directory contents (MCP)(owner: "COST", repo: "baymax", path: "localenv.config.yaml", ref: "refs/heads/main")
  ⎿ Path did not point to a file or directory, but resolved git ref to {"Ref":"refs/heads/main","SHA":"b32ec16443d8f6fef6ba16913d33f0abfc3aa02d"} with possible path matches: ["
    localenv.config.yaml"]

  ⎿  Interrupted by user

> supply sha as well

✻ Thinking…

  The user wants me to supply the SHA as well when making the request. Let me use the SHA that was returned in the previous response.

⏺ github_twdcgrid - Get file or directory contents (MCP)(owner: "COST", repo: "baymax", path: "localenv.config.yaml", sha: "b32ec16443d8f6fef6ba16913d33f0abfc3aa02d")
  ⎿ Path did not point to a file or directory, but resolved git ref to {"Ref":"","SHA":"b32ec16443d8f6fef6ba16913d33f0abfc3aa02d"} with possible path matches: ["localenv.config
    .yaml"]

  ⎿  Interrupted by user

> sha and ref

✻ Thinking…

  The user wants me to supply both sha and ref parameters. Let me try that.

⏺ github_twdcgrid - Get file or directory contents (MCP)(owner: "COST", repo: "baymax", path: "localenv.config.yaml", ref: "refs/heads/main", sha:
                                                        "b32ec16443d8f6fef6ba16913d33f0abfc3aa02d")
  ⎿ Path did not point to a file or directory, but resolved git ref to {"Ref":"","SHA":"b32ec16443d8f6fef6ba16913d33f0abfc3aa02d"} with possible path matches: ["localenv.config
    .yaml"]

  ⎿  Interrupted by user

[tommaso-moro]

Hi @nasxisbest , thank you for reporting this. I am struggling to reproduce this behaviour - is this still happening on your end, on the latest release too? And if so, may I ask which model you're using?

[keeganstreet]

Hi @tommaso-moro,

I'm running ghcr.io/github/github-mcp-server:v0.12.1

GitHub Enterprise Server: 3.16.2

I have tried with GPT 4.1, and Claude Sonnet 4, and they have the same error.

Prompt: Use Github MCP and summarise the readme from repo keegan-street/pr-reviewer.

It tries to use the get_file_contents tool with the following arguments:

{
  "owner": "keegan-street",
  "repo": "pr-reviewer",
  "path": "README.md"
}

Output:

Path did not point to a file or directory, but resolved git ref to {"Ref":"refs/heads/main","SHA":"a2ffc6566e61b65ae9e98131f46390ecb3740c8a"} with possible path matches: ["README.md"]

[jamesforwardnwboxed]

Also experiencing this.

[planetf1]

Seeing the same here with roo code.
Using 0.14 container image
Server is GitHub Enterprise Server 3.16.2

[planetf1]

I wonder if this is specific to GHE 3.16.2 (or just GHE)
I tried the same version of the mcp server against public github.com & it was able to retrieve a file just fine.
A bug with GHE?

[jbittner-dimensional]

Also experiencing this with GitHub Enterprise. I'm able to get the contents of a directory, but not files.

[alfredolopezzz]

I am also experiencing this

• github-mcp-server v0.15.0
• GitHub Enterprise Server 3.15.8
• vscode version 1.104

[rubensilvapipedrive]

From my end I also have the issue
It seems to be only for Github enterprise MCPs.

For public repos it seems to fetch readmes just fine.

[alfredolopezzz]

I am also experiencing this

• github-mcp-server v0.15.0
• GitHub Enterprise Server 3.15.8
• vscode version 1.104

I did some troubleshooting and found the following:

when running against our Github Enteprise Server, the GetRawContent call here returns a 406 error.

I then changed the Accept header in the github "raw" client to accept any type (req.Header.Set("Accept", "*/*") ). I was able to get rid of the 406 error but then client is redirected to a url that needs to go through SSO, so I am not able to reach the contents of the file as it just downloads the SSO page.

I wonder if we could just get the contents through the normal Github API endpoint using fileContent.GetContent() here instead of going through the raw github client.

[mgimenoromanadevinta]

Hello

Also experiencing this in GHE 3.15.8, GitHub MCP Server 0.17.1

Is there a planned fix?

Thanks

[tonytrg]

Hey together,

sorry this one got buried. We are aware and we are looking into the problem.
Thank you for surfacing this one.

It has to do with the subdomain-isolation https://docs.github.com/en/enterprise-server@3.17/admin/configuring-settings/hardening-security-for-your-enterprise/enabling-subdomain-isolation#about-subdomain-isolation