fix: configure git auth for GHES in incremental patch fetch

[Copilot]

push_to_pull_request_branch MCP handler fails with Cannot generate incremental patch: failed to fetch because generate_git_patch.cjs runs git fetch origin via spawnSync without authentication. When the MCP server owns stdin (piped for protocol I/O), git cannot interactively prompt for credentials — failing with fatal: could not read Username for 'https://github.com': No such device or address — and on GHES the auth header configured by actions/checkout targets the enterprise endpoint, not github.com.

Changes

• generate_git_patch.cjs — incremental mode fetch: Before calling git fetch origin, configure http.<serverUrl>/.extraheader using GITHUB_TOKEN and GITHUB_SERVER_URL, matching the pattern already used in dynamic_checkout.cjs. The header is written immediately before the fetch and removed in a finally block immediately after, ensuring the token is never left in .git/config for the duration of the agent session:

constgithubToken=process.env.GITHUB_TOKEN;constgithubServerUrl=process.env.GITHUB_SERVER_URL||"https://github.com";constextraHeaderKey=`http.${githubServerUrl}/.extraheader`;letauthHeaderSet=false;try{if(githubToken){consttokenBase64=Buffer.from(`x-access-token:${githubToken}`).toString("base64");execGitSync(["config","--local",extraHeaderKey,`Authorization: basic ${tokenBase64}`],{ cwd });authHeaderSet=true;}execGitSync(["fetch","origin","--",`${branchName}:refs/remotes/origin/${branchName}`],{ cwd });}catch(fetchError){// ...}finally{if(authHeaderSet){execGitSync(["config","--local","--unset-all",extraHeaderKey],{ cwd });}}

This ensures the fetch uses the correct authenticated endpoint on both github.com and GHES without relying on interactive credential prompts.

• git_patch_integration.test.cjs — auth header cleanup tests: Added two integration tests that verify the security boundary is upheld:
  • Asserts the http.<serverUrl>/.extraheader key is absent from .git/config after a successful incremental fetch.
  • Asserts the key is absent even when the fetch fails (branch does not exist on origin), confirming the finally block runs in all code paths.

Security

The workflow's clean_git_credentials.sh runs before the agent starts to prevent the agent from accessing git credentials. Writing a token to .git/config after that cleanup point and leaving it there for the rest of the session would undermine this security boundary — the agent could read the token from .git/config if it has filesystem access (e.g., Codex sandbox, other MCP tools with file access).

The try/finally pattern guarantees the http.<serverUrl>/.extraheader is removed from .git/config immediately after the fetch completes, regardless of success or failure. JavaScript finally semantics ensure cleanup even when catch contains a return statement.

Original prompt

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This section details on the original issue you should resolve

<issue_title>safeoutputs-push_to_pull_request_branch fails on fetch</issue_title>
<issue_description>The safeoutputs-push_to_pull_request_branch step in the agent job fails with: `Cannot generate incremental patch: failed to fetch ***

Safe Outputs MCP Server Logs:

Safe Outputs MCP Server Log
Start time: Fri Feb 27 13:45:03 UTC 2026
===========================================
...
[2026-02-27T13:46:56.055Z] [safeoutputs] Calling handler for tool: push_to_pull_request_branch
[2026-02-27T13:46:56.060Z] [safeoutputs] Using current branch for push_to_pull_request_branch: article/abcdefgh-634-20230227-b93ea53335bed345
[2026-02-27T13:46:56.060Z] [safeoutputs] Generating incremental patch for push_to_pull_request_branch with branch: article/abcdefgh-634-20230227-b93ea53335bed345
[generate_git_patch] Starting patch generation: mode=incremental, branch=article/abcdefgh-634-20230227-b93ea53335bed345, defaultBranch=main
[generate_git_patch] Environment: cwd=/home/runner/work/my-repo/my-repo, GITHUB_SHA=ec12debf24c77b128445bes895289bd512eec4a8
[generate_git_patch] Strategy 1: Checking if branch 'article/abcdefgh-634-20230227-b93ea53335bed345' exists locally
[debug] Executing git command: git show-ref --verify --quiet refs/heads/article/abcdefgh-634-20230227-b93ea53335bed345
[debug] Git command completed successfully with no output
[generate_git_patch] Strategy 1: Branch 'article/abcdefgh-634-20230227-b93ea53335bed345' exists locally
[generate_git_patch] Strategy 1 (incremental): Fetching origin/article/abcdefgh-634-20230227-b93ea53335bed345
[debug] Executing git command: git fetch origin -- article/abcdefgh-634-20230227-b93ea53335bed345:refs/remotes/origin/article/abcdefgh-634-20230227-b93ea53335bed345
[error] Git command failed: git fetch origin -- article/abcdefgh-634-20230227-b93ea53335bed345:refs/remotes/origin/article/abcdefgh-634-20230227-b93ea53335bed345
[error] Exit status: 128
[error] Stderr: fatal: could not read Username for 'https://github.com': No such device or address
[generate_git_patch] Strategy 1 (incremental): Fetch failed - ERR_SYSTEM: fatal: could not read Username for 'https://github.com': No such device or address
[2026-02-27T13:46:56.185Z] [safeoutputs] Patch generation failed: Cannot generate incremental patch: failed to fetch origin/article/abcdefgh-634-20230227-b93ea53335bed345. This typically happens when the remote branch doesn't exist yet or was force-pushed. Error: ERR_SYSTEM: fatal: could not read Username for 'https://github.com': No such device or address
[2026-02-27T13:46:56.185Z] [safeoutputs] Handler returned for tool: push_to_pull_request_branch
```</issue_description>
## Comments on the Issue (you are @copilot in this section)
<comments>
<comment_new><author>@pelikhan</author><body>
@copilot ensure that we are using the github enterprise endpoint in this handler. </body></comment_new>
</comments>

• Fixessafeoutputs-push_to_pull_request_branch fails on fetch #18703

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[pelikhan]

@copilot do a deep security review

[Copilot]

Security review findings and fixes (d4cff95):

Issue found: token persisted in .git/config for duration of agent session

clean_git_credentials.sh runs before the agent starts as a security measure. The previous commit wrote GITHUB_TOKEN to .git/config via http.<serverUrl>/.extraheader during the agent session without cleanup — meaning the token remained readable from .git/config for the rest of the session (e.g., by Codex in its sandbox, or via other MCP tools with filesystem access).

Fix: Added a try/finally block around the fetch that calls git config --local --unset-all <key> to remove the header immediately after the fetch completes, regardless of success or failure. JavaScript finally runs even when catch contains a return, so cleanup is guaranteed in all code paths:

• Token set → fetch succeeds → finally removes token
• Token set → fetch fails → catch prepares error → finally removes token → return fires
• GITHUB_TOKEN absent → no config write → finally is a no-op

Other findings (no action needed):

• execGitSync debug logging via core.debug only activates when core is defined (GitHub Actions context only); in the MCP server process core is undefined so the token value is never logged. GitHub Actions also masks GITHUB_TOKEN in logs.
• GITHUB_SERVER_URL is set by GitHub Actions infrastructure, not user-controlled input, so there is no header-injection risk.
• --local flag scopes the config write to the specific repo at cwd, not the global git config.

[pelikhan]

@dsyme@lpcox

[Copilot]

Pull request overview

Configures authenticated git fetch for incremental patch generation so push_to_pull_request_branch works in non-interactive environments (and on GHES) where Git cannot prompt for credentials.

Changes:

• Add temporary http.<GITHUB_SERVER_URL>/.extraheader configuration using GITHUB_TOKEN immediately before the incremental git fetch.
• Ensure the extraheader is removed in a finally block after the fetch attempt (success or failure).
• Add explanatory security-focused comments and debug logs around the incremental fetch flow.

Comments suppressed due to low confidence (1)

actions/setup/js/generate_git_patch.cjs:156

• The call to execGitSync with Authorization: basic ${tokenBase64} as an argument will cause the full base64-encoded GITHUB_TOKEN to be emitted in logs via execGitSync's debug logging (core.debug / console.debug in the shim), leaking the token into MCP/server or Actions logs. Anyone with access to these logs could recover and reuse the token outside its intended context, effectively bypassing the protections provided by clean_git_credentials.sh. To fix this, avoid passing the raw authorization header through a logging helper (e.g., use a path that does not log arguments, or ensure execGitSync redacts Authorization values before logging) so that the token never appears in logs.

 execGitSync(["config", "--local", extraHeaderKey, `Authorization: basic ${tokenBase64}`], { cwd });

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[Copilot]

This change adds new behavior in incremental mode (setting/unsetting http.<serverUrl>/.extraheader based on GITHUB_TOKEN). The existing vitest suite for generate_git_patch.cjs doesn’t appear to assert that the auth header is removed on both success and fetch failure. Adding a test that creates a temporary repo and verifies the config key is unset after the incremental fetch path would help prevent regressions, especially for the security boundary described in the comments.

[pelikhan]

@copilot address comments

[Copilot]

@copilot address comments

Addressed in ca376d3:

1. Misleading comment — already fixed in d4cff95 with the reviewer's suggested text (removed the reference to clean_git_credentials.sh as a fallback).

2. Missing auth header cleanup tests — added two new integration tests to git_patch_integration.test.cjs:

   • "should remove auth extraheader from git config after a successful fetch" — sets a fake GITHUB_TOKEN/GITHUB_SERVER_URL, runs incremental mode with a valid remote branch, and asserts the http.*.extraheader key is absent from .git/config afterwards.
   • "should remove auth extraheader from git config even when fetch fails" — same setup but the branch is not pushed, so the fetch fails, and the test still asserts the key is absent.

   Extracted a setTestEnv helper to avoid duplicating the env var save/restore logic.