feat: add DeleteFile tool to delete files from GitHub repositories

[ashwin-ant]

This adds a tool that matches the behavior of this API endpoint. This is needed since the create_or_update_file tool doesn't allow deletion.

[SamMorrowDrums]

Hey, can you look at adding annotations? You can see examples around the codebase?

For this particular one, as well as the tool title with translation I would add:

ReadOnlyHint: false
DestructiveHint: true

https://modelcontextprotocol.io/docs/concepts/tools#tool-definition-structure

[ashwin-ant]

@SamMorrowDrums done! Thanks for the suggestion.

[williammartin]

@ashwin-ant thanks for this PR. I'm a bit confused about the implementation though. It seems like you:

• Get a github ref for the current branch
• Get the commit for that ref
• Create a new TreeEntry without the file
• Create a new commit
• Update the ref

Why not:

• Get a github ref for the current branch
• Get the commit for that ref
• Get the SHA of the filepath in that commit
• Call client.Repositories.DeleteFile which exactly calls the API endpoint you referenced.

Edit: Maybe the TreeEntry approach allows for deletion of a directory where the contents API doesn't?

[williammartin]

@ashwin-ant I just rebased this and added some e2e tests that we can consider refactoring behind (and perhaps, demonstrating that we can't do directory removal with the contents API). You can run them like:

 GOMAXPROCS=1 GITHUB_MCP_SERVER_E2E_TOKEN=<YOUR TOKEN> go test -v -count=1 -run 'Test.*Deletion' --tags e2e ./e2e

Make sure your token has delete_repo scope to avoid debris.

I'll probably collapse them to one test later, but for the moment while we figure this out it makes sense to keep them separate.

[ashwin-ant]

@williammartin Thanks for reviewing! I actually was going with that approach in my first commit here, but ended up switching to this more complicated approach in 4d5f719.

The reason for this is that I discovered the REST file deletion endpoint (and client.Repositories.DeleteFile) don't add commit signing to the deletion commit, unlike how the endpoint backing the create_or_update_files tool does. This appears to be a quirk of the API. The approach here will get commit signing when used with either the github-actions user or as an app, both of which suit an LLM well.

[williammartin]

That's a great explanation and I'd love it if you put that as a comment in the code for all future reviewers!

[williammartin]

➜  github-mcp-server git:(ashwin/deletefile) ✗ GOMAXPROCS=1 GITHUB_MCP_SERVER_E2E_TOKEN=$(gh auth token) go test -v -count=1 -run TestFileDeletion --tags e2e ./e2e

=== RUN   TestFileDeletion
=== PAUSE TestFileDeletion
=== CONT  TestFileDeletion
    e2e_test.go:50: Building Docker image for e2e tests...
    e2e_test.go:124: Starting Stdio MCP client...
    e2e_test.go:385: Getting current user...
    e2e_test.go:413: Creating repository williammartin/github-mcp-server-e2e-TestFileDeletion-1747137948412...
    e2e_test.go:437: Creating branch in williammartin/github-mcp-server-e2e-TestFileDeletion-1747137948412...
    e2e_test.go:454: Creating commit with new file in williammartin/github-mcp-server-e2e-TestFileDeletion-1747137948412...
    e2e_test.go:478: Getting file contents in williammartin/github-mcp-server-e2e-TestFileDeletion-1747137948412...
    e2e_test.go:506: Deleting file in williammartin/github-mcp-server-e2e-TestFileDeletion-1747137948412...
    e2e_test.go:520: Listing commits in williammartin/github-mcp-server-e2e-TestFileDeletion-1747137948412...
    e2e_test.go:554: Getting commit williammartin/github-mcp-server-e2e-TestFileDeletion-1747137948412:76f50ad460c472d7eb9df09bd1c94d5678a99b96...
    e2e_test.go:422: Deleting repository williammartin/github-mcp-server-e2e-TestFileDeletion-1747137948412...
--- PASS: TestFileDeletion (6.65s)
PASS
ok      github.com/github/github-mcp-server/e2e 6.894s

LGTM, thanks.

[williammartin]

Bypassing the last pusher rule because I fixed minor breaking changes from mcp-go bump on main around annotations and some small error handling additions.

[Copilot]

Pull Request Overview

This PR introduces a new delete_file tool that leverages the Git Data API to delete files with commit signing, and adds accompanying tests.

• Registers DeleteFile in the GitHub toolset initialization.
• Implements DeleteFile in repositories.go, creating a deletion commit via trees and references.
• Adds Test_DeleteFile in repositories_test.go for success and branch-not-found scenarios.

Reviewed Changes

Copilot reviewed 4 out of 4 changed files in this pull request and generated 1 comment.

File	Description
pkg/github/tools.go	Register the new DeleteFile tool in server toolsets.
pkg/github/repositories.go	Implement DeleteFile using Git Data API calls.
pkg/github/repositories_test.go	Add unit tests for the DeleteFile tool.

Comments suppressed due to low confidence (1)

pkg/github/repositories_test.go:1532

• The test covers success and branch-not-found paths; consider adding cases for failures in tree creation, commit creation, and reference updates to ensure robust error handling across all stages of the deletion flow.

func Test_DeleteFile(t *testing.T) {