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

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

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

@nasxisbest

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?

@tommaso-moro

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"]

Also experiencing this.

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

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?

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

I am also experiencing this

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

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.

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.

Hello

Also experiencing this in GHE 3.15.8, GitHub MCP Server 0.17.1

Is there a planned fix?

Thanks

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

Fix PR #1218

closing this one out please reopen if the fix does not work for you

I wonder if the remote server "https://api.githubcopilot.com/mcp" is released with this change? I am still getting the same error "Failed to get file contents. The path does not point to a file or directory, or the file does not exist in the repository." when talking to the remote github mcp. Thanks.

Seems like the issue is not fully fixed
#1285

The fix was specifically regarding raw api + GHES with subdomain isolation.

This seems to be another problem regarding raw api + org related resources.

Update. The 404s should be fixed now. This was a seperate issue to the GHES one. Thanks for reporting it.

Thanks Tony, can you point me to which PR fixed this issue, and do you know if it is released for https://api.githubcopilot.com/mcp/?

…

On Wed, Nov 19, 2025 at 11:03 AM Tony Truong ***@***.***> wrote: *tonytrg* left a comment (github/github-mcp-server#864) <#864 (comment)> Update. The 404s should be fixed now. This was a seperate issue to the GHES one. Thanks for reporting it. — Reply to this email directly, view it on GitHub <#864 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/BZVEOPKKJ7AFP5MKAXQVIJD35SPERAVCNFSM6AAAAACDYAAMB6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTKNJTG43TKNJVGU> . You are receiving this because you commented.Message ID: ***@***.***>

-- Regards, Qingzhou

@seriousamlqz-qz

@seriousamlqz-qz the fix is internally, for our remote deployment of github mcp. This problem should not occur on the local version.

👋 We're actively looking at improving GHES support for the MCP server! If you have thoughts on GHES-specific needs, please share your feedback in this discussion. 🙏

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`get_file_contents` is not working properly (Path did not point to a file or directory, but resolved git ref) #864

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get_file_contents is not working properly (Path did not point to a file or directory, but resolved git ref) #864

Description

Describe the bug

Affected version

Steps to reproduce the behavior

Expected vs actual behavior

Logs

Activity

tommaso-moro commented on Aug 21, 2025

keeganstreet commented on Aug 21, 2025

jamesforwardnwboxed commented on Aug 26, 2025

planetf1 commented on Sep 3, 2025

planetf1 commented on Sep 3, 2025

jbittner-dimensional commented on Sep 16, 2025

alfredolopezzz commented on Sep 19, 2025

rubensilvapipedrive commented on Sep 19, 2025

alfredolopezzz commented on Sep 26, 2025

mgimenoromanadevinta commented on Oct 8, 2025

tonytrg commented on Oct 10, 2025

tonytrg commented on Oct 14, 2025

tonytrg commented on Oct 16, 2025

seriousamlqz-qz commented on Nov 3, 2025

rubensilvapipedrive commented on Nov 6, 2025

tonytrg commented on Nov 10, 2025

tonytrg commented on Nov 19, 2025

seriousamlqz-qz commented on Nov 19, 2025

tonytrg commented on Nov 25, 2025

SamMorrowDrums commented on Nov 25, 2025

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`get_file_contents` is not working properly (Path did not point to a file or directory, but resolved git ref) #864