feat: defer remote branch creation until first commit (#244)

* feat: defer remote branch creation until first commit

- For commit signing: branches are created remotely by github-file-ops-server on first commit
- For non-signing: branches are created locally with 'git checkout -b' and pushed when needed
- Consolidated duplicate branch creation logic in github-file-ops-server into a shared helper function
- Claude is unaware of these implementation details and simply sees it's on the correct branch
- No branch links are shown in initial comments since branches don't exist remotely yet

* fix: prevent broken branch links in final comment update

- Check if branch exists remotely before adding branch link
- Only add branch links for branches that actually exist on GitHub
- Add test coverage for non-existent remote branches
- Fixes issue where users would see broken branch links for local-only branches

* fix: don't show branch name in comment header when branch doesn't exist remotely

- Only pass branchName to updateCommentBody when branchLink exists
- Prevents showing branch names for branches that only exist locally
- Add test to verify branch name is not shown when branch doesn't exist

* tmp

.github/workflows/issue-triage.yml

@@ -32,7 +32,7 @@ jobs:
                   "--rm",
                   "-e",
                   "GITHUB_PERSONAL_ACCESS_TOKEN",
-                  "ghcr.io/github/github-mcp-server:sha-6d69797"
+                  "ghcr.io/github/github-mcp-server:sha-721fd3e"
                 ],
                 "env": {
                   "GITHUB_PERSONAL_ACCESS_TOKEN": "${{ secrets.GITHUB_TOKEN }}"

FAQ.md

@@ -51,14 +51,29 @@ allowed_tools: "Bash(git rebase:*)" # Use with caution
 
 Claude doesn't create PRs by default. Instead, it pushes commits to a branch and provides a link to a pre-filled PR submission page. This approach ensures your repository's branch protection rules are still adhered to and gives you final control over PR creation.
 
-### Why can't Claude run my tests or see CI results?
+### Can Claude see my GitHub Actions CI results?
 
-Claude cannot access GitHub Actions logs, test results, or other CI/CD outputs by default. It only has access to the repository files. If you need Claude to see test results, you can either:
+Yes! Claude can access GitHub Actions workflow runs, job logs, and test results on the PR where it's tagged. To enable this:
 
-1. Instruct Claude to run tests before making commits
+1. Add `actions: read` permission to your workflow:
-2. Copy and paste CI results into a comment for Claude to analyze
 
-This limitation exists for security reasons but may be reconsidered in the future based on user feedback.
+   ```yaml
+   permissions:
+     contents: write
+     pull-requests: write
+     issues: write
+     actions: read
+   ```
+
+2. Configure the action with additional permissions:
+   ```yaml
+   - uses: anthropics/claude-code-action@beta
+     with:
+       additional_permissions: |
+         actions: read
+   ```
+
+Claude will then be able to analyze CI failures and help debug workflow issues. For running tests locally before commits, you can still instruct Claude to do so in your request.
 
 ### Why does Claude only update one comment instead of creating new ones?
 

README.md

@@ -30,7 +30,9 @@ This command will guide you through setting up the GitHub app and required secre
 **Requirements**: You must be a repository admin to complete these steps.
 
 1. Install the Claude GitHub app to your repository: https://github.com/apps/claude
-2. Add `ANTHROPIC_API_KEY` to your repository secrets ([Learn how to use secrets in GitHub Actions](https://docs.github.com/en/actions/security-for-github-actions/security-guides/using-secrets-in-github-actions))
+2. Add authentication to your repository secrets ([Learn how to use secrets in GitHub Actions](https://docs.github.com/en/actions/security-for-github-actions/security-guides/using-secrets-in-github-actions)):
+   - Either `ANTHROPIC_API_KEY` for API key authentication
+   - Or `CLAUDE_CODE_OAUTH_TOKEN` for OAuth token authentication (Pro and Max users can generate this by running `claude setup-token` locally)
 3. Copy the workflow file from [`examples/claude.yml`](./examples/claude.yml) into your repository's `.github/workflows/`
 
 ## 📚 FAQ
@@ -60,6 +62,8 @@ jobs:
       - uses: anthropics/claude-code-action@beta
         with:
           anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}
+          # Or use OAuth token instead:
+          # claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
           github_token: ${{ secrets.GITHUB_TOKEN }}
           # Optional: add custom trigger phrase (default: @claude)
           # trigger_phrase: "/claude"
@@ -81,30 +85,31 @@ jobs:
 
 ## Inputs
 
-| Input                    | Description                                                                                                          | Required | Default   |
+| Input                     | Description                                                                                                          | Required | Default   |
-| ------------------------ | -------------------------------------------------------------------------------------------------------------------- | -------- | --------- |
+| ------------------------- | -------------------------------------------------------------------------------------------------------------------- | -------- | --------- |
-| `anthropic_api_key`      | Anthropic API key (required for direct API, not needed for Bedrock/Vertex)                                           | No\*     | -         |
+| `anthropic_api_key`       | Anthropic API key (required for direct API, not needed for Bedrock/Vertex)                                           | No\*     | -         |
-| `direct_prompt`          | Direct prompt for Claude to execute automatically without needing a trigger (for automated workflows)                | No       | -         |
+| `claude_code_oauth_token` | Claude Code OAuth token (alternative to anthropic_api_key)                                                           | No\*     | -         |
-| `base_branch`            | The base branch to use for creating new branches (e.g., 'main', 'develop')                                           | No       | -         |
+| `direct_prompt`           | Direct prompt for Claude to execute automatically without needing a trigger (for automated workflows)                | No       | -         |
-| `max_turns`              | Maximum number of conversation turns Claude can take (limits back-and-forth exchanges)                               | No       | -         |
+| `base_branch`             | The base branch to use for creating new branches (e.g., 'main', 'develop')                                           | No       | -         |
-| `timeout_minutes`        | Timeout in minutes for execution                                                                                     | No       | `30`      |
+| `max_turns`               | Maximum number of conversation turns Claude can take (limits back-and-forth exchanges)                               | No       | -         |
-| `use_sticky_comment`     | Use just one comment to deliver PR comments (only applies for pull_request event workflows)                          | No       | `false`   |
+| `timeout_minutes`         | Timeout in minutes for execution                                                                                     | No       | `30`      |
-| `github_token`           | GitHub token for Claude to operate with. **Only include this if you're connecting a custom GitHub app of your own!** | No       | -         |
+| `use_sticky_comment`      | Use just one comment to deliver PR comments (only applies for pull_request event workflows)                          | No       | `false`   |
-| `model`                  | Model to use (provider-specific format required for Bedrock/Vertex)                                                  | No       | -         |
+| `github_token`            | GitHub token for Claude to operate with. **Only include this if you're connecting a custom GitHub app of your own!** | No       | -         |
-| `fallback_model`         | Enable automatic fallback to specified model when primary model is unavailable                                       | No       | -         |
+| `model`                   | Model to use (provider-specific format required for Bedrock/Vertex)                                                  | No       | -         |
-| `anthropic_model`        | **DEPRECATED**: Use `model` instead. Kept for backward compatibility.                                                | No       | -         |
+| `fallback_model`          | Enable automatic fallback to specified model when primary model is unavailable                                       | No       | -         |
-| `use_bedrock`            | Use Amazon Bedrock with OIDC authentication instead of direct Anthropic API                                          | No       | `false`   |
+| `anthropic_model`         | **DEPRECATED**: Use `model` instead. Kept for backward compatibility.                                                | No       | -         |
-| `use_vertex`             | Use Google Vertex AI with OIDC authentication instead of direct Anthropic API                                        | No       | `false`   |
+| `use_bedrock`             | Use Amazon Bedrock with OIDC authentication instead of direct Anthropic API                                          | No       | `false`   |
-| `allowed_tools`          | Additional tools for Claude to use (the base GitHub tools will always be included)                                   | No       | ""        |
+| `use_vertex`              | Use Google Vertex AI with OIDC authentication instead of direct Anthropic API                                        | No       | `false`   |
-| `disallowed_tools`       | Tools that Claude should never use                                                                                   | No       | ""        |
+| `allowed_tools`           | Additional tools for Claude to use (the base GitHub tools will always be included)                                   | No       | ""        |
-| `custom_instructions`    | Additional custom instructions to include in the prompt for Claude                                                   | No       | ""        |
+| `disallowed_tools`        | Tools that Claude should never use                                                                                   | No       | ""        |
-| `mcp_config`             | Additional MCP configuration (JSON string) that merges with the built-in GitHub MCP servers                          | No       | ""        |
+| `custom_instructions`     | Additional custom instructions to include in the prompt for Claude                                                   | No       | ""        |
-| `assignee_trigger`       | The assignee username that triggers the action (e.g. @claude). Only used for issue assignment                        | No       | -         |
+| `mcp_config`              | Additional MCP configuration (JSON string) that merges with the built-in GitHub MCP servers                          | No       | ""        |
-| `label_trigger`          | The label name that triggers the action when applied to an issue (e.g. "claude")                                     | No       | -         |
+| `assignee_trigger`        | The assignee username that triggers the action (e.g. @claude). Only used for issue assignment                        | No       | -         |
-| `trigger_phrase`         | The trigger phrase to look for in comments, issue/PR bodies, and issue titles                                        | No       | `@claude` |
+| `label_trigger`           | The label name that triggers the action when applied to an issue (e.g. "claude")                                     | No       | -         |
-| `branch_prefix`          | The prefix to use for Claude branches (defaults to 'claude/', use 'claude-' for dash format)                         | No       | `claude/` |
+| `trigger_phrase`          | The trigger phrase to look for in comments, issue/PR bodies, and issue titles                                        | No       | `@claude` |
-| `claude_env`             | Custom environment variables to pass to Claude Code execution (YAML format)                                          | No       | ""        |
+| `branch_prefix`           | The prefix to use for Claude branches (defaults to 'claude/', use 'claude-' for dash format)                         | No       | `claude/` |
-| `additional_permissions` | Additional permissions to enable. Currently supports 'actions: read' for viewing workflow results                    | No       | ""        |
+| `claude_env`              | Custom environment variables to pass to Claude Code execution (YAML format)                                          | No       | ""        |
+| `additional_permissions`  | Additional permissions to enable. Currently supports 'actions: read' for viewing workflow results                    | No       | ""        |
 
 \*Required when using direct Anthropic API (default and when not using Bedrock or Vertex)
 
@@ -330,6 +335,7 @@ This action is built on top of [`anthropics/claude-code-base-action`](https://gi
   - When triggered on an **issue**: Always creates a new branch for the work
   - When triggered on an **open PR**: Always pushes directly to the existing PR branch
   - When triggered on a **closed PR**: Creates a new branch since the original is no longer active
+- **View GitHub Actions Results**: Can access workflow runs, job logs, and test results on the PR where it's tagged when `actions: read` permission is configured (see [Additional Permissions for CI/CD Integration](#additional-permissions-for-cicd-integration))
 
 ### What Claude Cannot Do
 
@@ -338,7 +344,6 @@ This action is built on top of [`anthropics/claude-code-base-action`](https://gi
 - **Post Multiple Comments**: Claude only acts by updating its initial comment
 - **Execute Commands Outside Its Context**: Claude only has access to the repository and PR/issue context it's triggered in
 - **Run Arbitrary Bash Commands**: By default, Claude cannot execute Bash commands unless explicitly allowed using the `allowed_tools` configuration
-- **View CI/CD Results**: Cannot access CI systems, test results, or build logs unless an additional tool or MCP server is configured
 - **Perform Branch Operations**: Cannot merge branches, rebase, or perform other git operations beyond pushing commits
 
 ## Advanced Configuration
@@ -604,18 +609,21 @@ The [Claude Code GitHub app](https://github.com/apps/claude) requires these perm
 
 All commits made by Claude through this action are automatically signed with commit signatures. This ensures the authenticity and integrity of commits, providing a verifiable trail of changes made by the action.
 
-### ⚠️ ANTHROPIC_API_KEY Protection
+### ⚠️ Authentication Protection
 
-**CRITICAL: Never hardcode your Anthropic API key in workflow files!**
+**CRITICAL: Never hardcode your Anthropic API key or OAuth token in workflow files!**
 
-Your ANTHROPIC_API_KEY must always be stored in GitHub secrets to prevent unauthorized access:
+Your authentication credentials must always be stored in GitHub secrets to prevent unauthorized access:
 
 ```yaml
 # CORRECT ✅
 anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}
+# OR
+claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
 
 # NEVER DO THIS ❌
 anthropic_api_key: "sk-ant-api03-..." # Exposed and vulnerable!
+claude_code_oauth_token: "oauth_token_..." # Exposed and vulnerable!
 ```
 
 ### Setting Up GitHub Secrets
@@ -623,17 +631,18 @@ anthropic_api_key: "sk-ant-api03-..." # Exposed and vulnerable!
 1. Go to your repository's Settings
 2. Click on "Secrets and variables" → "Actions"
 3. Click "New repository secret"
-4. Name: `ANTHROPIC_API_KEY`
+4. For authentication, choose one:
-5. Value: Your Anthropic API key (starting with `sk-ant-`)
+   - API Key: Name: `ANTHROPIC_API_KEY`, Value: Your Anthropic API key (starting with `sk-ant-`)
-6. Click "Add secret"
+   - OAuth Token: Name: `CLAUDE_CODE_OAUTH_TOKEN`, Value: Your Claude Code OAuth token (Pro and Max users can generate this by running `claude setup-token` locally)
+5. Click "Add secret"
 
-### Best Practices for ANTHROPIC_API_KEY
+### Best Practices for Authentication
 
-1. ✅ Always use `${{ secrets.ANTHROPIC_API_KEY }}` in workflows
+1. ✅ Always use `${{ secrets.ANTHROPIC_API_KEY }}` or `${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}` in workflows
-2. ✅ Never commit API keys to version control
+2. ✅ Never commit API keys or tokens to version control
-3. ✅ Regularly rotate your API keys
+3. ✅ Regularly rotate your API keys and tokens
 4. ✅ Use environment secrets for organization-wide access
-5. ❌ Never share API keys in pull requests or issues
+5. ❌ Never share API keys or tokens in pull requests or issues
 6. ❌ Avoid logging workflow variables that might contain keys
 
 ## Security Best Practices

action.yml

@@ -65,6 +65,9 @@ inputs:
   anthropic_api_key:
     description: "Anthropic API key (required for direct API, not needed for Bedrock/Vertex)"
     required: false
+  claude_code_oauth_token:
+    description: "Claude Code OAuth token (alternative to anthropic_api_key)"
+    required: false
   github_token:
     description: "GitHub token with repo and pull request permissions (optional if using GitHub App)"
     required: false
@@ -89,6 +92,10 @@ inputs:
     description: "Use just one comment to deliver issue/PR comments"
     required: false
     default: "false"
+  use_commit_signing:
+    description: "Enable commit signing using GitHub's commit signature verification. When false, Claude uses standard git commands"
+    required: false
+    default: "false"
 
 outputs:
   execution_file:
@@ -130,11 +137,12 @@ runs:
         USE_STICKY_COMMENT: ${{ inputs.use_sticky_comment }}
         ACTIONS_TOKEN: ${{ github.token }}
         ADDITIONAL_PERMISSIONS: ${{ inputs.additional_permissions }}
+        USE_COMMIT_SIGNING: ${{ inputs.use_commit_signing }}
 
     - name: Run Claude Code
       id: claude-code
       if: steps.prepare.outputs.contains_trigger == 'true'
-      uses: anthropics/claude-code-base-action@a835717b36becf75584224421f4094aae288cad7 # v0.0.31
+      uses: anthropics/claude-code-base-action@0f7a229cb06f840f77f49df0b711ee0060868c2c # v0.0.33
       with:
         prompt_file: ${{ runner.temp }}/claude-prompts/claude-prompt.txt
         allowed_tools: ${{ env.ALLOWED_TOOLS }}
@@ -147,11 +155,13 @@ runs:
         use_bedrock: ${{ inputs.use_bedrock }}
         use_vertex: ${{ inputs.use_vertex }}
         anthropic_api_key: ${{ inputs.anthropic_api_key }}
+        claude_code_oauth_token: ${{ inputs.claude_code_oauth_token }}
         claude_env: ${{ inputs.claude_env }}
       env:
         # Model configuration
         ANTHROPIC_MODEL: ${{ inputs.model || inputs.anthropic_model }}
         GITHUB_TOKEN: ${{ steps.prepare.outputs.GITHUB_TOKEN }}
+        NODE_VERSION: ${{ env.NODE_VERSION }}
 
         # Provider configuration
         ANTHROPIC_BASE_URL: ${{ env.ANTHROPIC_BASE_URL }}
@@ -196,6 +206,7 @@ runs:
         PREPARE_SUCCESS: ${{ steps.prepare.outcome == 'success' }}
         PREPARE_ERROR: ${{ steps.prepare.outputs.prepare_error || '' }}
         USE_STICKY_COMMENT: ${{ inputs.use_sticky_comment }}
+        USE_COMMIT_SIGNING: ${{ inputs.use_commit_signing }}
 
     - name: Display Claude Code Report
       if: steps.prepare.outputs.contains_trigger == 'true' && steps.claude-code.outputs.execution_file != ''

examples/claude.yml

@@ -33,4 +33,6 @@ jobs:
         uses: anthropics/claude-code-action@beta
         with:
           anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}
+          # Or use OAuth token instead:
+          # claude_code_oauth_token: ${{ secrets.CLAUDE_CODE_OAUTH_TOKEN }}
           timeout_minutes: "60"

src/create-prompt/index.ts

@@ -30,18 +30,40 @@ const BASE_ALLOWED_TOOLS = [
   "LS",
   "Read",
   "Write",
-  "mcp__github_file_ops__commit_files",
-  "mcp__github_file_ops__delete_files",
-  "mcp__github_file_ops__update_claude_comment",
 ];
 const DISALLOWED_TOOLS = ["WebSearch", "WebFetch"];
 
 export function buildAllowedToolsString(
   customAllowedTools?: string[],
   includeActionsTools: boolean = false,
+  useCommitSigning: boolean = false,
 ): string {
   let baseTools = [...BASE_ALLOWED_TOOLS];
 
+  // Always include the comment update tool from the comment server
+  baseTools.push("mcp__github_comment__update_claude_comment");
+
+  // Add commit signing tools if enabled
+  if (useCommitSigning) {
+    baseTools.push(
+      "mcp__github_file_ops__commit_files",
+      "mcp__github_file_ops__delete_files",
+    );
+  } else {
+    // When not using commit signing, add specific Bash git commands only
+    baseTools.push(
+      "Bash(git add:*)",
+      "Bash(git commit:*)",
+      "Bash(git push:*)",
+      "Bash(git status:*)",
+      "Bash(git diff:*)",
+      "Bash(git log:*)",
+      "Bash(git rm:*)",
+      "Bash(git config user.name:*)",
+      "Bash(git config user.email:*)",
+    );
+  }
+
   // Add GitHub Actions MCP tools if enabled
   if (includeActionsTools) {
     baseTools.push(
@@ -380,9 +402,68 @@ export function getEventTypeAndContext(envVars: PreparedContext): {
   }
 }
 
+function getCommitInstructions(
+  eventData: EventData,
+  githubData: FetchDataResult,
+  context: PreparedContext,
+  useCommitSigning: boolean,
+): string {
+  const coAuthorLine =
+    (githubData.triggerDisplayName ?? context.triggerUsername !== "Unknown")
+      ? `Co-authored-by: ${githubData.triggerDisplayName ?? context.triggerUsername} <${context.triggerUsername}@users.noreply.github.com>`
+      : "";
+
+  if (useCommitSigning) {
+    if (eventData.isPR && !eventData.claudeBranch) {
+      return `
+      - Push directly using mcp__github_file_ops__commit_files to the existing branch (works for both new and existing files).
+      - Use mcp__github_file_ops__commit_files to commit files atomically in a single commit (supports single or multiple files).
+      - When pushing changes with this tool and the trigger user is not "Unknown", include a Co-authored-by trailer in the commit message.
+      - Use: "${coAuthorLine}"`;
+    } else {
+      return `
+      - You are already on the correct branch (${eventData.claudeBranch || "the PR branch"}). Do not create a new branch.
+      - Push changes directly to the current branch using mcp__github_file_ops__commit_files (works for both new and existing files)
+      - Use mcp__github_file_ops__commit_files to commit files atomically in a single commit (supports single or multiple files).
+      - When pushing changes and the trigger user is not "Unknown", include a Co-authored-by trailer in the commit message.
+      - Use: "${coAuthorLine}"`;
+    }
+  } else {
+    // Non-signing instructions
+    if (eventData.isPR && !eventData.claudeBranch) {
+      return `
+      - Use git commands via the Bash tool to commit and push your changes:
+        - Stage files: Bash(git add <files>)
+        - Commit with a descriptive message: Bash(git commit -m "<message>")
+        ${
+          coAuthorLine
+            ? `- When committing and the trigger user is not "Unknown", include a Co-authored-by trailer:
+          Bash(git commit -m "<message>\\n\\n${coAuthorLine}")`
+            : ""
+        }
+        - Push to the remote: Bash(git push origin HEAD)`;
+    } else {
+      const branchName = eventData.claudeBranch || eventData.baseBranch;
+      return `
+      - You are already on the correct branch (${eventData.claudeBranch || "the PR branch"}). Do not create a new branch.
+      - Use git commands via the Bash tool to commit and push your changes:
+        - Stage files: Bash(git add <files>)
+        - Commit with a descriptive message: Bash(git commit -m "<message>")
+        ${
+          coAuthorLine
+            ? `- When committing and the trigger user is not "Unknown", include a Co-authored-by trailer:
+          Bash(git commit -m "<message>\\n\\n${coAuthorLine}")`
+            : ""
+        }
+        - Push to the remote: Bash(git push origin ${branchName})`;
+    }
+  }
+}
+
 export function generatePrompt(
   context: PreparedContext,
   githubData: FetchDataResult,
+  useCommitSigning: boolean,
 ): string {
   const {
     contextData,
@@ -471,9 +552,9 @@ ${sanitizeContent(context.directPrompt)}
     : ""
 }
 ${`<comment_tool_info>
-IMPORTANT: You have been provided with the mcp__github_file_ops__update_claude_comment tool to update your comment. This tool automatically handles both issue and PR comments.
+IMPORTANT: You have been provided with the mcp__github_comment__update_claude_comment tool to update your comment. This tool automatically handles both issue and PR comments.
 
-Tool usage example for mcp__github_file_ops__update_claude_comment:
+Tool usage example for mcp__github_comment__update_claude_comment:
 {
   "body": "Your comment text here"
 }
@@ -492,7 +573,7 @@ Follow these steps:
 1. Create a Todo List:
    - Use your GitHub comment to maintain a detailed task list based on the request.
    - Format todos as a checklist (- [ ] for incomplete, - [x] for complete).
-   - Update the comment using mcp__github_file_ops__update_claude_comment with each task completion.
+   - Update the comment using mcp__github_comment__update_claude_comment with each task completion.
 
 2. Gather Context:
    - Analyze the pre-fetched data provided above.
@@ -523,29 +604,16 @@ ${context.directPrompt ? `   - DIRECT INSTRUCTION: A direct instruction was prov
         - Look for bugs, security issues, performance problems, and other issues
         - Suggest improvements for readability and maintainability
         - Check for best practices and coding standards
-        - Reference specific code sections with file paths and line numbers${eventData.isPR ? "\n      - AFTER reading files and analyzing code, you MUST call mcp__github_file_ops__update_claude_comment to post your review" : ""}
+        - Reference specific code sections with file paths and line numbers${eventData.isPR ? `\n      - AFTER reading files and analyzing code, you MUST call mcp__github_comment__update_claude_comment to post your review` : ""}
       - Formulate a concise, technical, and helpful response based on the context.
       - Reference specific code with inline formatting or code blocks.
       - Include relevant file paths and line numbers when applicable.
-      - ${eventData.isPR ? "IMPORTANT: Submit your review feedback by updating the Claude comment using mcp__github_file_ops__update_claude_comment. This will be displayed as your PR review." : "Remember that this feedback must be posted to the GitHub comment using mcp__github_file_ops__update_claude_comment."}
+      - ${eventData.isPR ? `IMPORTANT: Submit your review feedback by updating the Claude comment using mcp__github_comment__update_claude_comment. This will be displayed as your PR review.` : `Remember that this feedback must be posted to the GitHub comment using mcp__github_comment__update_claude_comment.`}
 
    B. For Straightforward Changes:
       - Use file system tools to make the change locally.
       - If you discover related tasks (e.g., updating tests), add them to the todo list.
-      - Mark each subtask as completed as you progress.
+      - Mark each subtask as completed as you progress.${getCommitInstructions(eventData, githubData, context, useCommitSigning)}
-      ${
-        eventData.isPR && !eventData.claudeBranch
-          ? `
-      - Push directly using mcp__github_file_ops__commit_files to the existing branch (works for both new and existing files).
-      - Use mcp__github_file_ops__commit_files to commit files atomically in a single commit (supports single or multiple files).
-      - When pushing changes with this tool and the trigger user is not "Unknown", include a Co-authored-by trailer in the commit message.
-      - Use: "Co-authored-by: ${githubData.triggerDisplayName ?? context.triggerUsername} <${context.triggerUsername}@users.noreply.github.com>"`
-          : `
-      - You are already on the correct branch (${eventData.claudeBranch || "the PR branch"}). Do not create a new branch.
-      - Push changes directly to the current branch using mcp__github_file_ops__commit_files (works for both new and existing files)
-      - Use mcp__github_file_ops__commit_files to commit files atomically in a single commit (supports single or multiple files).
-      - When pushing changes and the trigger user is not "Unknown", include a Co-authored-by trailer in the commit message.
-      - Use: "Co-authored-by: ${githubData.triggerDisplayName ?? context.triggerUsername} <${context.triggerUsername}@users.noreply.github.com>"
       ${
         eventData.claudeBranch
           ? `- Provide a URL to create a PR manually in this format:
@@ -563,7 +631,6 @@ ${context.directPrompt ? `   - DIRECT INSTRUCTION: A direct instruction was prov
           - The signature: "Generated with [Claude Code](https://claude.ai/code)"
         - Just include the markdown link with text "Create a PR" - do not add explanatory text before it like "You can create a PR using this link"`
           : ""
-      }`
       }
 
    C. For Complex Changes:
@@ -579,20 +646,31 @@ ${context.directPrompt ? `   - DIRECT INSTRUCTION: A direct instruction was prov
    - Always update the GitHub comment to reflect the current todo state.
    - When all todos are completed, remove the spinner and add a brief summary of what was accomplished, and what was not done.
    - Note: If you see previous Claude comments with headers like "**Claude finished @user's task**" followed by "---", do not include this in your comment. The system adds this automatically.
-   - If you changed any files locally, you must update them in the remote branch via mcp__github_file_ops__commit_files before saying that you're done.
+   - If you changed any files locally, you must update them in the remote branch via ${useCommitSigning ? "mcp__github_file_ops__commit_files" : "git commands (add, commit, push)"} before saying that you're done.
    ${eventData.claudeBranch ? `- If you created anything in your branch, your comment must include the PR URL with prefilled title and body mentioned above.` : ""}
 
 Important Notes:
 - All communication must happen through GitHub PR comments.
-- Never create new comments. Only update the existing comment using mcp__github_file_ops__update_claude_comment.
+- Never create new comments. Only update the existing comment using mcp__github_comment__update_claude_comment.
-- This includes ALL responses: code reviews, answers to questions, progress updates, and final results.${eventData.isPR ? "\n- PR CRITICAL: After reading files and forming your response, you MUST post it by calling mcp__github_file_ops__update_claude_comment. Do NOT just respond with a normal response, the user will not see it." : ""}
+- This includes ALL responses: code reviews, answers to questions, progress updates, and final results.${eventData.isPR ? `\n- PR CRITICAL: After reading files and forming your response, you MUST post it by calling mcp__github_comment__update_claude_comment. Do NOT just respond with a normal response, the user will not see it.` : ""}
 - You communicate exclusively by editing your single comment - not through any other means.
 - Use this spinner HTML when work is in progress: <img src="https://github.com/user-attachments/assets/5ac382c7-e004-429b-8e35-7feb3e8f9c6f" width="14px" height="14px" style="vertical-align: middle; margin-left: 4px;" />
 ${eventData.isPR && !eventData.claudeBranch ? `- Always push to the existing branch when triggered on a PR.` : `- IMPORTANT: You are already on the correct branch (${eventData.claudeBranch || "the created branch"}). Never create new branches when triggered on issues or closed/merged PRs.`}
-- Use mcp__github_file_ops__commit_files for making commits (works for both new and existing files, single or multiple). Use mcp__github_file_ops__delete_files for deleting files (supports deleting single or multiple files atomically), or mcp__github__delete_file for deleting a single file. Edit files locally, and the tool will read the content from the same path on disk.
+${
+  useCommitSigning
+    ? `- Use mcp__github_file_ops__commit_files for making commits (works for both new and existing files, single or multiple). Use mcp__github_file_ops__delete_files for deleting files (supports deleting single or multiple files atomically), or mcp__github__delete_file for deleting a single file. Edit files locally, and the tool will read the content from the same path on disk.
   Tool usage examples:
   - mcp__github_file_ops__commit_files: {"files": ["path/to/file1.js", "path/to/file2.py"], "message": "feat: add new feature"}
-  - mcp__github_file_ops__delete_files: {"files": ["path/to/old.js"], "message": "chore: remove deprecated file"}
+  - mcp__github_file_ops__delete_files: {"files": ["path/to/old.js"], "message": "chore: remove deprecated file"}`
+    : `- Use git commands via the Bash tool for version control (you have access to specific git commands only):
+  - Stage files: Bash(git add <files>)
+  - Commit changes: Bash(git commit -m "<message>")
+  - Push to remote: Bash(git push origin <branch>) (NEVER force push)
+  - Delete files: Bash(git rm <files>) followed by commit and push
+  - Check status: Bash(git status)
+  - View diff: Bash(git diff)
+  - Configure git user: Bash(git config user.name "...") and Bash(git config user.email "...")`
+}
 - Display the todo list as a checklist in the GitHub comment and mark things off as you go.
 - REPOSITORY SETUP INSTRUCTIONS: The repository's CLAUDE.md file(s) contain critical repo-specific setup instructions, development guidelines, and preferences. Always read and follow these files, particularly the root CLAUDE.md, as they provide essential context for working with the codebase effectively.
 - Use h3 headers (###) for section titles in your comments, not h1 headers (#).
@@ -663,7 +741,11 @@ export async function createPrompt(
     });
 
     // Generate the prompt
-    const promptContent = generatePrompt(preparedContext, githubData);
+    const promptContent = generatePrompt(
+      preparedContext,
+      githubData,
+      context.inputs.useCommitSigning,
+    );
 
     // Log the final prompt to console
     console.log("===== FINAL PROMPT =====");
@@ -683,6 +765,7 @@ export async function createPrompt(
     const allAllowedTools = buildAllowedToolsString(
       context.inputs.allowedTools,
       hasActionsReadPermission,
+      context.inputs.useCommitSigning,
     );
     const allDisallowedTools = buildDisallowedToolsString(
       context.inputs.disallowedTools,

src/entrypoints/prepare.ts

@@ -12,7 +12,7 @@ import { checkHumanActor } from "../github/validation/actor";
 import { checkWritePermissions } from "../github/validation/permissions";
 import { createInitialComment } from "../github/operations/comments/create-initial";
 import { setupBranch } from "../github/operations/branch";
-import { updateTrackingComment } from "../github/operations/comments/update-with-branch";
+import { configureGitAuth } from "../github/operations/git-config";
 import { prepareMcpConfig } from "../mcp/install-mcp-server";
 import { createPrompt } from "../create-prompt";
 import { createOctokit } from "../github/api/client";
@@ -51,7 +51,8 @@ async function run() {
     await checkHumanActor(octokit.rest, context);
 
     // Step 6: Create initial tracking comment
-    const commentId = await createInitialComment(octokit.rest, context);
+    const commentData = await createInitialComment(octokit.rest, context);
+    const commentId = commentData.id;
 
     // Step 7: Fetch GitHub data (once for both branch setup and prompt creation)
     const githubData = await fetchGitHubData({
@@ -65,14 +66,14 @@ async function run() {
     // Step 8: Setup branch
     const branchInfo = await setupBranch(octokit, githubData, context);
 
-    // Step 9: Update initial comment with branch link (only for issues that created a new branch)
+    // Step 9: Configure git authentication if not using commit signing
-    if (branchInfo.claudeBranch) {
+    if (!context.inputs.useCommitSigning) {
-      await updateTrackingComment(
+      try {
-        octokit,
+        await configureGitAuth(githubToken, context, commentData.user);
-        context,
+      } catch (error) {
-        commentId,
+        console.error("Failed to configure git authentication:", error);
-        branchInfo.claudeBranch,
+        throw error;
-      );
+      }
     }
 
     // Step 10: Create prompt file

src/entrypoints/update-comment-link.ts

@@ -11,7 +11,7 @@ import {
   isPullRequestReviewCommentEvent,
 } from "../github/context";
 import { GITHUB_SERVER_URL } from "../github/api/config";
-import { checkAndDeleteEmptyBranch } from "../github/operations/branch-cleanup";
+import { checkAndCommitOrDeleteBranch } from "../github/operations/branch-cleanup";
 import { updateClaudeComment } from "../github/operations/comments/update-claude-comment";
 
 async function run() {
@@ -88,13 +88,16 @@ async function run() {
     const currentBody = comment.body ?? "";
 
     // Check if we need to add branch link for new branches
-    const { shouldDeleteBranch, branchLink } = await checkAndDeleteEmptyBranch(
+    const useCommitSigning = process.env.USE_COMMIT_SIGNING === "true";
-      octokit,
+    const { shouldDeleteBranch, branchLink } =
-      owner,
+      await checkAndCommitOrDeleteBranch(
-      repo,
+        octokit,
-      claudeBranch,
+        owner,
-      baseBranch,
+        repo,
-    );
+        claudeBranch,
+        baseBranch,
+        useCommitSigning,
+      );
 
     // Check if we need to add PR URL when we have a new branch
     let prLink = "";
@@ -198,7 +201,7 @@ async function run() {
       jobUrl,
       branchLink,
       prLink,
-      branchName: shouldDeleteBranch ? undefined : claudeBranch,
+      branchName: shouldDeleteBranch || !branchLink ? undefined : claudeBranch,
       triggerUsername,
       errorDetails,
     };

src/github/context.ts

@@ -38,6 +38,7 @@ export type ParsedGitHubContext = {
     branchPrefix: string;
     useStickyComment: boolean;
     additionalPermissions: Map<string, string>;
+    useCommitSigning: boolean;
   };
 };
 
@@ -68,6 +69,7 @@ export function parseGitHubContext(): ParsedGitHubContext {
       additionalPermissions: parseAdditionalPermissions(
         process.env.ADDITIONAL_PERMISSIONS ?? "",
       ),
+      useCommitSigning: process.env.USE_COMMIT_SIGNING === "true",
     },
   };
 

src/github/operations/branch-cleanup.ts

@@ -1,17 +1,44 @@
 import type { Octokits } from "../api/client";
 import { GITHUB_SERVER_URL } from "../api/config";
+import { $ } from "bun";
 
-export async function checkAndDeleteEmptyBranch(
+export async function checkAndCommitOrDeleteBranch(
   octokit: Octokits,
   owner: string,
   repo: string,
   claudeBranch: string | undefined,
   baseBranch: string,
+  useCommitSigning: boolean,
 ): Promise<{ shouldDeleteBranch: boolean; branchLink: string }> {
   let branchLink = "";
   let shouldDeleteBranch = false;
 
   if (claudeBranch) {
+    // First check if the branch exists remotely
+    let branchExistsRemotely = false;
+    try {
+      await octokit.rest.repos.getBranch({
+        owner,
+        repo,
+        branch: claudeBranch,
+      });
+      branchExistsRemotely = true;
+    } catch (error: any) {
+      if (error.status === 404) {
+        console.log(`Branch ${claudeBranch} does not exist remotely`);
+      } else {
+        console.error("Error checking if branch exists:", error);
+      }
+    }
+
+    // Only proceed if branch exists remotely
+    if (!branchExistsRemotely) {
+      console.log(
+        `Branch ${claudeBranch} does not exist remotely, no branch link will be added`,
+      );
+      return { shouldDeleteBranch: false, branchLink: "" };
+    }
+
     // Check if Claude made any commits to the branch
     try {
       const { data: comparison } =
@@ -21,20 +48,66 @@ export async function checkAndDeleteEmptyBranch(
           basehead: `${baseBranch}...${claudeBranch}`,
         });
 
-      // If there are no commits, mark branch for deletion
+      // If there are no commits, check for uncommitted changes if not using commit signing
       if (comparison.total_commits === 0) {
-        console.log(
+        if (!useCommitSigning) {
-          `Branch ${claudeBranch} has no commits from Claude, will delete it`,
+          console.log(
-        );
+            `Branch ${claudeBranch} has no commits from Claude, checking for uncommitted changes...`,
-        shouldDeleteBranch = true;
+          );
+
+          // Check for uncommitted changes using git status
+          try {
+            const gitStatus = await $`git status --porcelain`.quiet();
+            const hasUncommittedChanges =
+              gitStatus.stdout.toString().trim().length > 0;
+
+            if (hasUncommittedChanges) {
+              console.log("Found uncommitted changes, committing them...");
+
+              // Add all changes
+              await $`git add -A`;
+
+              // Commit with a descriptive message
+              const runId = process.env.GITHUB_RUN_ID || "unknown";
+              const commitMessage = `Auto-commit: Save uncommitted changes from Claude\n\nRun ID: ${runId}`;
+              await $`git commit -m ${commitMessage}`;
+
+              // Push the changes
+              await $`git push origin ${claudeBranch}`;
+
+              console.log(
+                "✅ Successfully committed and pushed uncommitted changes",
+              );
+
+              // Set branch link since we now have commits
+              const branchUrl = `${GITHUB_SERVER_URL}/${owner}/${repo}/tree/${claudeBranch}`;
+              branchLink = `\n[View branch](${branchUrl})`;
+            } else {
+              console.log(
+                "No uncommitted changes found, marking branch for deletion",
+              );
+              shouldDeleteBranch = true;
+            }
+          } catch (gitError) {
+            console.error("Error checking/committing changes:", gitError);
+            // If we can't check git status, assume the branch might have changes
+            const branchUrl = `${GITHUB_SERVER_URL}/${owner}/${repo}/tree/${claudeBranch}`;
+            branchLink = `\n[View branch](${branchUrl})`;
+          }
+        } else {
+          console.log(
+            `Branch ${claudeBranch} has no commits from Claude, will delete it`,
+          );
+          shouldDeleteBranch = true;
+        }
       } else {
         // Only add branch link if there are commits
         const branchUrl = `${GITHUB_SERVER_URL}/${owner}/${repo}/tree/${claudeBranch}`;
         branchLink = `\n[View branch](${branchUrl})`;
       }
     } catch (error) {
-      console.error("Error checking for commits on Claude branch:", error);
+      console.error("Error comparing commits on Claude branch:", error);
-      // If we can't check, assume the branch has commits to be safe
+      // If we can't compare but the branch exists remotely, include the branch link
       const branchUrl = `${GITHUB_SERVER_URL}/${owner}/${repo}/tree/${claudeBranch}`;
       branchLink = `\n[View branch](${branchUrl})`;
     }

src/github/operations/branch.ts

@@ -84,12 +84,8 @@ export async function setupBranch(
     sourceBranch = repoResponse.data.default_branch;
   }
 
-  // Creating a new branch for either an issue or closed/merged PR
+  // Generate branch name for either an issue or closed/merged PR
   const entityType = isPR ? "pr" : "issue";
-  console.log(
-    `Creating new branch for ${entityType} #${entityNumber} from source branch: ${sourceBranch}...`,
-  );
-
   const timestamp = new Date()
     .toISOString()
     .replace(/[:-]/g, "")
@@ -100,7 +96,7 @@ export async function setupBranch(
   const newBranch = `${branchPrefix}${entityType}-${entityNumber}-${timestamp}`;
 
   try {
-    // Get the SHA of the source branch
+    // Get the SHA of the source branch to verify it exists
     const sourceBranchRef = await octokits.rest.git.getRef({
       owner,
       repo,
@@ -108,23 +104,34 @@ export async function setupBranch(
     });
 
     const currentSHA = sourceBranchRef.data.object.sha;
+    console.log(`Source branch SHA: ${currentSHA}`);
 
-    console.log(`Current SHA: ${currentSHA}`);
+    // For commit signing, defer branch creation to the file ops server
+    if (context.inputs.useCommitSigning) {
+      console.log(
+        `Branch name generated: ${newBranch} (will be created by file ops server on first commit)`,
+      );
 
-    // Create branch using GitHub API
+      // Set outputs for GitHub Actions
-    await octokits.rest.git.createRef({
+      core.setOutput("CLAUDE_BRANCH", newBranch);
-      owner,
+      core.setOutput("BASE_BRANCH", sourceBranch);
-      repo,
+      return {
-      ref: `refs/heads/${newBranch}`,
+        baseBranch: sourceBranch,
-      sha: currentSHA,
+        claudeBranch: newBranch,
-    });
+        currentBranch: sourceBranch, // Stay on source branch for now
+      };
+    }
 
-    // Checkout the new branch (shallow fetch for performance)
+    // For non-signing case, create and checkout the branch locally only
-    await $`git fetch origin --depth=1 ${newBranch}`;
+    console.log(
-    await $`git checkout ${newBranch}`;
+      `Creating local branch ${newBranch} for ${entityType} #${entityNumber} from source branch: ${sourceBranch}...`,
+    );
+
+    // Create and checkout the new branch locally
+    await $`git checkout -b ${newBranch}`;
 
     console.log(
-      `Successfully created and checked out new branch: ${newBranch}`,
+      `Successfully created and checked out local branch: ${newBranch}`,
     );
 
     // Set outputs for GitHub Actions
@@ -136,7 +143,7 @@ export async function setupBranch(
       currentBranch: newBranch,
     };
   } catch (error) {
-    console.error("Error creating branch:", error);
+    console.error("Error in branch setup:", error);
     process.exit(1);
   }
 }

src/github/operations/comments/create-initial.ts

@@ -14,6 +14,8 @@ import {
 } from "../../context";
 import type { Octokit } from "@octokit/rest";
 
+const CLAUDE_APP_BOT_ID = 209825114;
+
 export async function createInitialComment(
   octokit: Octokit,
   context: ParsedGitHubContext,
@@ -36,16 +38,15 @@ export async function createInitialComment(
         repo,
         issue_number: context.entityNumber,
       });
-      console.log("users");
+      const existingComment = comments.data.find((comment) => {
-      comments.data.forEach((comment) => {
+        const idMatch = comment.user?.id === CLAUDE_APP_BOT_ID;
-        console.log(comment.user);
+        const botNameMatch =
-      });
+          comment.user?.type === "Bot" &&
+          comment.user?.login.toLowerCase().includes("claude");
+        const bodyMatch = comment.body === initialBody;
 
-      const existingComment = comments.data.find(
+        return idMatch || botNameMatch || bodyMatch;
-        (comment) =>
+      });
-          comment.user?.login.indexOf("claude[bot]") !== -1 ||
-          comment.body === initialBody,
-      );
       if (existingComment) {
         response = await octokit.rest.issues.updateComment({
           owner,
@@ -85,7 +86,7 @@ export async function createInitialComment(
     const githubOutput = process.env.GITHUB_OUTPUT!;
     appendFileSync(githubOutput, `claude_comment_id=${response.data.id}\n`);
     console.log(`✅ Created initial comment with ID: ${response.data.id}`);
-    return response.data.id;
+    return response.data;
   } catch (error) {
     console.error("Error in initial comment:", error);
 
@@ -101,7 +102,7 @@ export async function createInitialComment(
       const githubOutput = process.env.GITHUB_OUTPUT!;
       appendFileSync(githubOutput, `claude_comment_id=${response.data.id}\n`);
       console.log(`✅ Created fallback comment with ID: ${response.data.id}`);
-      return response.data.id;
+      return response.data;
     } catch (fallbackError) {
       console.error("Error creating fallback comment:", fallbackError);
       throw fallbackError;

src/github/operations/git-config.ts

@@ -0,0 +1,56 @@
+#!/usr/bin/env bun
+
+/**
+ * Configure git authentication for non-signing mode
+ * Sets up git user and authentication to work with GitHub App tokens
+ */
+
+import { $ } from "bun";
+import type { ParsedGitHubContext } from "../context";
+import { GITHUB_SERVER_URL } from "../api/config";
+
+type GitUser = {
+  login: string;
+  id: number;
+};
+
+export async function configureGitAuth(
+  githubToken: string,
+  context: ParsedGitHubContext,
+  user: GitUser | null,
+) {
+  console.log("Configuring git authentication for non-signing mode");
+
+  // Configure git user based on the comment creator
+  console.log("Configuring git user...");
+  if (user) {
+    const botName = user.login;
+    const botId = user.id;
+    console.log(`Setting git user as ${botName}...`);
+    await $`git config user.name "${botName}"`;
+    await $`git config user.email "${botId}+${botName}@users.noreply.github.com"`;
+    console.log(`✓ Set git user as ${botName}`);
+  } else {
+    console.log("No user data in comment, using default bot user");
+    await $`git config user.name "github-actions[bot]"`;
+    await $`git config user.email "41898282+github-actions[bot]@users.noreply.github.com"`;
+  }
+
+  // Remove the authorization header that actions/checkout sets
+  console.log("Removing existing git authentication headers...");
+  try {
+    await $`git config --unset-all http.${GITHUB_SERVER_URL}/.extraheader`;
+    console.log("✓ Removed existing authentication headers");
+  } catch (e) {
+    console.log("No existing authentication headers to remove");
+  }
+
+  // Update the remote URL to include the token for authentication
+  console.log("Updating remote URL with authentication...");
+  const serverUrl = new URL(GITHUB_SERVER_URL);
+  const remoteUrl = `https://x-access-token:${githubToken}@${serverUrl.host}/${context.repository.owner}/${context.repository.repo}.git`;
+  await $`git remote set-url origin ${remoteUrl}`;
+  console.log("✓ Updated remote URL with authentication token");
+
+  console.log("Git authentication configured successfully");
+}

src/mcp/github-comment-server.ts

@@ -0,0 +1,98 @@
+#!/usr/bin/env node
+// GitHub Comment MCP Server - Minimal server that only provides comment update functionality
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
+import { z } from "zod";
+import { GITHUB_API_URL } from "../github/api/config";
+import { Octokit } from "@octokit/rest";
+import { updateClaudeComment } from "../github/operations/comments/update-claude-comment";
+
+// Get repository information from environment variables
+const REPO_OWNER = process.env.REPO_OWNER;
+const REPO_NAME = process.env.REPO_NAME;
+
+if (!REPO_OWNER || !REPO_NAME) {
+  console.error(
+    "Error: REPO_OWNER and REPO_NAME environment variables are required",
+  );
+  process.exit(1);
+}
+
+const server = new McpServer({
+  name: "GitHub Comment Server",
+  version: "0.0.1",
+});
+
+server.tool(
+  "update_claude_comment",
+  "Update the Claude comment with progress and results (automatically handles both issue and PR comments)",
+  {
+    body: z.string().describe("The updated comment content"),
+  },
+  async ({ body }) => {
+    try {
+      const githubToken = process.env.GITHUB_TOKEN;
+      const claudeCommentId = process.env.CLAUDE_COMMENT_ID;
+      const eventName = process.env.GITHUB_EVENT_NAME;
+
+      if (!githubToken) {
+        throw new Error("GITHUB_TOKEN environment variable is required");
+      }
+      if (!claudeCommentId) {
+        throw new Error("CLAUDE_COMMENT_ID environment variable is required");
+      }
+
+      const owner = REPO_OWNER;
+      const repo = REPO_NAME;
+      const commentId = parseInt(claudeCommentId, 10);
+
+      const octokit = new Octokit({
+        auth: githubToken,
+        baseUrl: GITHUB_API_URL,
+      });
+
+      const isPullRequestReviewComment =
+        eventName === "pull_request_review_comment";
+
+      const result = await updateClaudeComment(octokit, {
+        owner,
+        repo,
+        commentId,
+        body,
+        isPullRequestReviewComment,
+      });
+
+      return {
+        content: [
+          {
+            type: "text",
+            text: JSON.stringify(result, null, 2),
+          },
+        ],
+      };
+    } catch (error) {
+      const errorMessage =
+        error instanceof Error ? error.message : String(error);
+      return {
+        content: [
+          {
+            type: "text",
+            text: `Error: ${errorMessage}`,
+          },
+        ],
+        error: errorMessage,
+        isError: true,
+      };
+    }
+  },
+);
+
+async function runServer() {
+  const transport = new StdioServerTransport();
+  await server.connect(transport);
+  process.on("exit", () => {
+    server.close();
+  });
+}
+
+runServer().catch(console.error);

src/mcp/github-file-ops-server.ts

@@ -7,8 +7,6 @@ import { readFile } from "fs/promises";
 import { join } from "path";
 import fetch from "node-fetch";
 import { GITHUB_API_URL } from "../github/api/config";
-import { Octokit } from "@octokit/rest";
-import { updateClaudeComment } from "../github/operations/comments/update-claude-comment";
 import { retryWithBackoff } from "../utils/retry";
 
 type GitHubRef = {
@@ -54,6 +52,120 @@ const server = new McpServer({
   version: "0.0.1",
 });
 
+// Helper function to get or create branch reference
+async function getOrCreateBranchRef(
+  owner: string,
+  repo: string,
+  branch: string,
+  githubToken: string,
+): Promise<string> {
+  // Try to get the branch reference
+  const refUrl = `${GITHUB_API_URL}/repos/${owner}/${repo}/git/refs/heads/${branch}`;
+  const refResponse = await fetch(refUrl, {
+    headers: {
+      Accept: "application/vnd.github+json",
+      Authorization: `Bearer ${githubToken}`,
+      "X-GitHub-Api-Version": "2022-11-28",
+    },
+  });
+
+  if (refResponse.ok) {
+    const refData = (await refResponse.json()) as GitHubRef;
+    return refData.object.sha;
+  }
+
+  if (refResponse.status !== 404) {
+    throw new Error(`Failed to get branch reference: ${refResponse.status}`);
+  }
+
+  // Branch doesn't exist, need to create it
+  console.log(`Branch ${branch} does not exist, creating it...`);
+
+  // Get base branch from environment or determine it
+  const baseBranch = process.env.BASE_BRANCH || "main";
+
+  // Get the SHA of the base branch
+  const baseRefUrl = `${GITHUB_API_URL}/repos/${owner}/${repo}/git/refs/heads/${baseBranch}`;
+  const baseRefResponse = await fetch(baseRefUrl, {
+    headers: {
+      Accept: "application/vnd.github+json",
+      Authorization: `Bearer ${githubToken}`,
+      "X-GitHub-Api-Version": "2022-11-28",
+    },
+  });
+
+  let baseSha: string;
+
+  if (!baseRefResponse.ok) {
+    // If base branch doesn't exist, try default branch
+    const repoUrl = `${GITHUB_API_URL}/repos/${owner}/${repo}`;
+    const repoResponse = await fetch(repoUrl, {
+      headers: {
+        Accept: "application/vnd.github+json",
+        Authorization: `Bearer ${githubToken}`,
+        "X-GitHub-Api-Version": "2022-11-28",
+      },
+    });
+
+    if (!repoResponse.ok) {
+      throw new Error(`Failed to get repository info: ${repoResponse.status}`);
+    }
+
+    const repoData = (await repoResponse.json()) as {
+      default_branch: string;
+    };
+    const defaultBranch = repoData.default_branch;
+
+    // Try default branch
+    const defaultRefUrl = `${GITHUB_API_URL}/repos/${owner}/${repo}/git/refs/heads/${defaultBranch}`;
+    const defaultRefResponse = await fetch(defaultRefUrl, {
+      headers: {
+        Accept: "application/vnd.github+json",
+        Authorization: `Bearer ${githubToken}`,
+        "X-GitHub-Api-Version": "2022-11-28",
+      },
+    });
+
+    if (!defaultRefResponse.ok) {
+      throw new Error(
+        `Failed to get default branch reference: ${defaultRefResponse.status}`,
+      );
+    }
+
+    const defaultRefData = (await defaultRefResponse.json()) as GitHubRef;
+    baseSha = defaultRefData.object.sha;
+  } else {
+    const baseRefData = (await baseRefResponse.json()) as GitHubRef;
+    baseSha = baseRefData.object.sha;
+  }
+
+  // Create the new branch
+  const createRefUrl = `${GITHUB_API_URL}/repos/${owner}/${repo}/git/refs`;
+  const createRefResponse = await fetch(createRefUrl, {
+    method: "POST",
+    headers: {
+      Accept: "application/vnd.github+json",
+      Authorization: `Bearer ${githubToken}`,
+      "X-GitHub-Api-Version": "2022-11-28",
+      "Content-Type": "application/json",
+    },
+    body: JSON.stringify({
+      ref: `refs/heads/${branch}`,
+      sha: baseSha,
+    }),
+  });
+
+  if (!createRefResponse.ok) {
+    const errorText = await createRefResponse.text();
+    throw new Error(
+      `Failed to create branch: ${createRefResponse.status} - ${errorText}`,
+    );
+  }
+
+  console.log(`Successfully created branch ${branch}`);
+  return baseSha;
+}
+
 // Commit files tool
 server.tool(
   "commit_files",
@@ -83,24 +195,13 @@ server.tool(
         return filePath;
       });
 
-      // 1. Get the branch reference
+      // 1. Get the branch reference (create if doesn't exist)
-      const refUrl = `${GITHUB_API_URL}/repos/${owner}/${repo}/git/refs/heads/${branch}`;
+      const baseSha = await getOrCreateBranchRef(
-      const refResponse = await fetch(refUrl, {
+        owner,
-        headers: {
+        repo,
-          Accept: "application/vnd.github+json",
+        branch,
-          Authorization: `Bearer ${githubToken}`,
+        githubToken,
-          "X-GitHub-Api-Version": "2022-11-28",
+      );
-        },
-      });
-
-      if (!refResponse.ok) {
-        throw new Error(
-          `Failed to get branch reference: ${refResponse.status}`,
-        );
-      }
-
-      const refData = (await refResponse.json()) as GitHubRef;
-      const baseSha = refData.object.sha;
 
       // 2. Get the base commit
       const commitUrl = `${GITHUB_API_URL}/repos/${owner}/${repo}/git/commits/${baseSha}`;
@@ -262,7 +363,6 @@ server.tool(
 
             // Only retry on 403 errors - these are the intermittent failures we're targeting
             if (updateRefResponse.status === 403) {
-              console.log("Received 403 error, will retry...");
               throw error;
             }
 
@@ -355,24 +455,13 @@ server.tool(
         return filePath;
       });
 
-      // 1. Get the branch reference
+      // 1. Get the branch reference (create if doesn't exist)
-      const refUrl = `${GITHUB_API_URL}/repos/${owner}/${repo}/git/refs/heads/${branch}`;
+      const baseSha = await getOrCreateBranchRef(
-      const refResponse = await fetch(refUrl, {
+        owner,
-        headers: {
+        repo,
-          Accept: "application/vnd.github+json",
+        branch,
-          Authorization: `Bearer ${githubToken}`,
+        githubToken,
-          "X-GitHub-Api-Version": "2022-11-28",
+      );
-        },
-      });
-
-      if (!refResponse.ok) {
-        throw new Error(
-          `Failed to get branch reference: ${refResponse.status}`,
-        );
-      }
-
-      const refData = (await refResponse.json()) as GitHubRef;
-      const baseSha = refData.object.sha;
 
       // 2. Get the base commit
       const commitUrl = `${GITHUB_API_URL}/repos/${owner}/${repo}/git/commits/${baseSha}`;
@@ -535,70 +624,6 @@ server.tool(
   },
 );
 
-server.tool(
-  "update_claude_comment",
-  "Update the Claude comment with progress and results (automatically handles both issue and PR comments)",
-  {
-    body: z.string().describe("The updated comment content"),
-  },
-  async ({ body }) => {
-    try {
-      const githubToken = process.env.GITHUB_TOKEN;
-      const claudeCommentId = process.env.CLAUDE_COMMENT_ID;
-      const eventName = process.env.GITHUB_EVENT_NAME;
-
-      if (!githubToken) {
-        throw new Error("GITHUB_TOKEN environment variable is required");
-      }
-      if (!claudeCommentId) {
-        throw new Error("CLAUDE_COMMENT_ID environment variable is required");
-      }
-
-      const owner = REPO_OWNER;
-      const repo = REPO_NAME;
-      const commentId = parseInt(claudeCommentId, 10);
-
-      const octokit = new Octokit({
-        auth: githubToken,
-        baseUrl: GITHUB_API_URL,
-      });
-
-      const isPullRequestReviewComment =
-        eventName === "pull_request_review_comment";
-
-      const result = await updateClaudeComment(octokit, {
-        owner,
-        repo,
-        commentId,
-        body,
-        isPullRequestReviewComment,
-      });
-
-      return {
-        content: [
-          {
-            type: "text",
-            text: JSON.stringify(result, null, 2),
-          },
-        ],
-      };
-    } catch (error) {
-      const errorMessage =
-        error instanceof Error ? error.message : String(error);
-      return {
-        content: [
-          {
-            type: "text",
-            text: `Error: ${errorMessage}`,
-          },
-        ],
-        error: errorMessage,
-        isError: true,
-      };
-    }
-  },
-);
-
 async function runServer() {
   const transport = new StdioServerTransport();
   await server.connect(transport);

src/mcp/install-mcp-server.ts

@@ -67,28 +67,48 @@ export async function prepareMcpConfig(
     );
 
     const baseMcpConfig: { mcpServers: Record<string, unknown> } = {
-      mcpServers: {
+      mcpServers: {},
-        github_file_ops: {
+    };
-          command: "bun",
+
-          args: [
+    // Always include comment server for updating Claude comments
-            "run",
+    baseMcpConfig.mcpServers.github_comment = {
-            `${process.env.GITHUB_ACTION_PATH}/src/mcp/github-file-ops-server.ts`,
+      command: "bun",
-          ],
+      args: [
-          env: {
+        "run",
-            GITHUB_TOKEN: githubToken,
+        `${process.env.GITHUB_ACTION_PATH}/src/mcp/github-comment-server.ts`,
-            REPO_OWNER: owner,
+      ],
-            REPO_NAME: repo,
+      env: {
-            BRANCH_NAME: branch,
+        GITHUB_TOKEN: githubToken,
-            REPO_DIR: process.env.GITHUB_WORKSPACE || process.cwd(),
+        REPO_OWNER: owner,
-            ...(claudeCommentId && { CLAUDE_COMMENT_ID: claudeCommentId }),
+        REPO_NAME: repo,
-            GITHUB_EVENT_NAME: process.env.GITHUB_EVENT_NAME || "",
+        ...(claudeCommentId && { CLAUDE_COMMENT_ID: claudeCommentId }),
-            IS_PR: process.env.IS_PR || "false",
+        GITHUB_EVENT_NAME: process.env.GITHUB_EVENT_NAME || "",
-            GITHUB_API_URL: GITHUB_API_URL,
+        GITHUB_API_URL: GITHUB_API_URL,
-          },
-        },
       },
     };
 
+    // Include file ops server when commit signing is enabled
+    if (context.inputs.useCommitSigning) {
+      baseMcpConfig.mcpServers.github_file_ops = {
+        command: "bun",
+        args: [
+          "run",
+          `${process.env.GITHUB_ACTION_PATH}/src/mcp/github-file-ops-server.ts`,
+        ],
+        env: {
+          GITHUB_TOKEN: githubToken,
+          REPO_OWNER: owner,
+          REPO_NAME: repo,
+          BRANCH_NAME: branch,
+          BASE_BRANCH: process.env.BASE_BRANCH || "",
+          REPO_DIR: process.env.GITHUB_WORKSPACE || process.cwd(),
+          GITHUB_EVENT_NAME: process.env.GITHUB_EVENT_NAME || "",
+          IS_PR: process.env.IS_PR || "false",
+          GITHUB_API_URL: GITHUB_API_URL,
+        },
+      };
+    }
+
     // Only add CI server if we have actions:read permission and we're in a PR context
     const hasActionsReadPermission =
       context.inputs.additionalPermissions.get("actions") === "read";
@@ -134,7 +154,7 @@ export async function prepareMcpConfig(
           "--rm",
           "-e",
           "GITHUB_PERSONAL_ACCESS_TOKEN",
-          "ghcr.io/github/github-mcp-server:sha-6d69797", // https://github.com/github/github-mcp-server/releases/tag/v0.5.0
+          "ghcr.io/github/github-mcp-server:sha-721fd3e", // https://github.com/github/github-mcp-server/releases/tag/v0.6.0
         ],
         env: {
           GITHUB_PERSONAL_ACCESS_TOKEN: githubToken,

test/branch-cleanup.test.ts

@@ -1,9 +1,9 @@
 import { describe, test, expect, beforeEach, afterEach, spyOn } from "bun:test";
-import { checkAndDeleteEmptyBranch } from "../src/github/operations/branch-cleanup";
+import { checkAndCommitOrDeleteBranch } from "../src/github/operations/branch-cleanup";
 import type { Octokits } from "../src/github/api/client";
 import { GITHUB_SERVER_URL } from "../src/github/api/config";
 
-describe("checkAndDeleteEmptyBranch", () => {
+describe("checkAndCommitOrDeleteBranch", () => {
   let consoleLogSpy: any;
   let consoleErrorSpy: any;
 
@@ -21,6 +21,7 @@ describe("checkAndDeleteEmptyBranch", () => {
   const createMockOctokit = (
     compareResponse?: any,
     deleteRefError?: Error,
+    branchExists: boolean = true,
   ): Octokits => {
     return {
       rest: {
@@ -28,6 +29,14 @@ describe("checkAndDeleteEmptyBranch", () => {
           compareCommitsWithBasehead: async () => ({
             data: compareResponse || { total_commits: 0 },
           }),
+          getBranch: async () => {
+            if (!branchExists) {
+              const error: any = new Error("Not Found");
+              error.status = 404;
+              throw error;
+            }
+            return { data: {} };
+          },
         },
         git: {
           deleteRef: async () => {
@@ -43,12 +52,13 @@ describe("checkAndDeleteEmptyBranch", () => {
 
   test("should return no branch link and not delete when branch is undefined", async () => {
     const mockOctokit = createMockOctokit();
-    const result = await checkAndDeleteEmptyBranch(
+    const result = await checkAndCommitOrDeleteBranch(
       mockOctokit,
       "owner",
       "repo",
       undefined,
       "main",
+      false,
     );
 
     expect(result.shouldDeleteBranch).toBe(false);
@@ -56,14 +66,15 @@ describe("checkAndDeleteEmptyBranch", () => {
     expect(consoleLogSpy).not.toHaveBeenCalled();
   });
 
-  test("should delete branch and return no link when branch has no commits", async () => {
+  test("should mark branch for deletion when commit signing is enabled and no commits", async () => {
     const mockOctokit = createMockOctokit({ total_commits: 0 });
-    const result = await checkAndDeleteEmptyBranch(
+    const result = await checkAndCommitOrDeleteBranch(
       mockOctokit,
       "owner",
       "repo",
       "claude/issue-123-20240101_123456",
       "main",
+      true, // commit signing enabled
     );
 
     expect(result.shouldDeleteBranch).toBe(true);
@@ -71,19 +82,17 @@ describe("checkAndDeleteEmptyBranch", () => {
     expect(consoleLogSpy).toHaveBeenCalledWith(
       "Branch claude/issue-123-20240101_123456 has no commits from Claude, will delete it",
     );
-    expect(consoleLogSpy).toHaveBeenCalledWith(
-      "✅ Deleted empty branch: claude/issue-123-20240101_123456",
-    );
   });
 
   test("should not delete branch and return link when branch has commits", async () => {
     const mockOctokit = createMockOctokit({ total_commits: 3 });
-    const result = await checkAndDeleteEmptyBranch(
+    const result = await checkAndCommitOrDeleteBranch(
       mockOctokit,
       "owner",
       "repo",
       "claude/issue-123-20240101_123456",
       "main",
+      false,
     );
 
     expect(result.shouldDeleteBranch).toBe(false);
@@ -102,6 +111,7 @@ describe("checkAndDeleteEmptyBranch", () => {
           compareCommitsWithBasehead: async () => {
             throw new Error("API error");
           },
+          getBranch: async () => ({ data: {} }), // Branch exists
         },
         git: {
           deleteRef: async () => ({ data: {} }),
@@ -109,12 +119,13 @@ describe("checkAndDeleteEmptyBranch", () => {
       },
     } as any as Octokits;
 
-    const result = await checkAndDeleteEmptyBranch(
+    const result = await checkAndCommitOrDeleteBranch(
       mockOctokit,
       "owner",
       "repo",
       "claude/issue-123-20240101_123456",
       "main",
+      false,
     );
 
     expect(result.shouldDeleteBranch).toBe(false);
@@ -122,7 +133,7 @@ describe("checkAndDeleteEmptyBranch", () => {
       `\n[View branch](${GITHUB_SERVER_URL}/owner/repo/tree/claude/issue-123-20240101_123456)`,
     );
     expect(consoleErrorSpy).toHaveBeenCalledWith(
-      "Error checking for commits on Claude branch:",
+      "Error comparing commits on Claude branch:",
       expect.any(Error),
     );
   });
@@ -131,12 +142,13 @@ describe("checkAndDeleteEmptyBranch", () => {
     const deleteError = new Error("Delete failed");
     const mockOctokit = createMockOctokit({ total_commits: 0 }, deleteError);
 
-    const result = await checkAndDeleteEmptyBranch(
+    const result = await checkAndCommitOrDeleteBranch(
       mockOctokit,
       "owner",
       "repo",
       "claude/issue-123-20240101_123456",
       "main",
+      true, // commit signing enabled - will try to delete
     );
 
     expect(result.shouldDeleteBranch).toBe(true);
@@ -146,4 +158,30 @@ describe("checkAndDeleteEmptyBranch", () => {
       deleteError,
     );
   });
+
+  test("should return no branch link when branch doesn't exist remotely", async () => {
+    const mockOctokit = createMockOctokit(
+      { total_commits: 0 },
+      undefined,
+      false, // branch doesn't exist
+    );
+
+    const result = await checkAndCommitOrDeleteBranch(
+      mockOctokit,
+      "owner",
+      "repo",
+      "claude/issue-123-20240101_123456",
+      "main",
+      false,
+    );
+
+    expect(result.shouldDeleteBranch).toBe(false);
+    expect(result.branchLink).toBe("");
+    expect(consoleLogSpy).toHaveBeenCalledWith(
+      "Branch claude/issue-123-20240101_123456 does not exist remotely",
+    );
+    expect(consoleLogSpy).toHaveBeenCalledWith(
+      "Branch claude/issue-123-20240101_123456 does not exist remotely, no branch link will be added",
+    );
+  });
 });

test/comment-logic.test.ts

@@ -1,5 +1,8 @@
 import { describe, it, expect } from "bun:test";
-import { updateCommentBody } from "../src/github/operations/comment-logic";
+import {
+  updateCommentBody,
+  type CommentUpdateInput,
+} from "../src/github/operations/comment-logic";
 
 describe("updateCommentBody", () => {
   const baseInput = {
@@ -417,5 +420,27 @@ describe("updateCommentBody", () => {
         "• [Create PR ➔](https://github.com/owner/repo/compare/main...claude/issue-123-20240101_120000)",
       );
     });
+
+    it("should not show branch name when branch doesn't exist remotely", () => {
+      const input: CommentUpdateInput = {
+        currentBody: "@claude can you help with this?",
+        actionFailed: false,
+        executionDetails: { duration_ms: 90000 },
+        jobUrl: "https://github.com/owner/repo/actions/runs/123",
+        branchLink: "", // Empty branch link means branch doesn't exist remotely
+        branchName: undefined, // Should be undefined when branchLink is empty
+        triggerUsername: "claude",
+        prLink: "",
+      };
+
+      const result = updateCommentBody(input);
+
+      expect(result).toContain("Claude finished @claude's task in 1m 30s");
+      expect(result).toContain(
+        "[View job](https://github.com/owner/repo/actions/runs/123)",
+      );
+      expect(result).not.toContain("claude/issue-123");
+      expect(result).not.toContain("tree/claude/issue-123");
+    });
   });
 });

test/create-prompt.test.ts

@@ -133,7 +133,7 @@ describe("generatePrompt", () => {
       },
     };
 
-    const prompt = generatePrompt(envVars, mockGitHubData);
+    const prompt = generatePrompt(envVars, mockGitHubData, false);
 
     expect(prompt).toContain("You are Claude, an AI assistant");
     expect(prompt).toContain("<event_type>GENERAL_COMMENT</event_type>");
@@ -161,7 +161,7 @@ describe("generatePrompt", () => {
       },
     };
 
-    const prompt = generatePrompt(envVars, mockGitHubData);
+    const prompt = generatePrompt(envVars, mockGitHubData, false);
 
     expect(prompt).toContain("<event_type>PR_REVIEW</event_type>");
     expect(prompt).toContain("<is_pr>true</is_pr>");
@@ -187,7 +187,7 @@ describe("generatePrompt", () => {
       },
     };
 
-    const prompt = generatePrompt(envVars, mockGitHubData);
+    const prompt = generatePrompt(envVars, mockGitHubData, false);
 
     expect(prompt).toContain("<event_type>ISSUE_CREATED</event_type>");
     expect(prompt).toContain(
@@ -215,7 +215,7 @@ describe("generatePrompt", () => {
       },
     };
 
-    const prompt = generatePrompt(envVars, mockGitHubData);
+    const prompt = generatePrompt(envVars, mockGitHubData, false);
 
     expect(prompt).toContain("<event_type>ISSUE_ASSIGNED</event_type>");
     expect(prompt).toContain(
@@ -242,7 +242,7 @@ describe("generatePrompt", () => {
       },
     };
 
-    const prompt = generatePrompt(envVars, mockGitHubData);
+    const prompt = generatePrompt(envVars, mockGitHubData, false);
 
     expect(prompt).toContain("<event_type>ISSUE_LABELED</event_type>");
     expect(prompt).toContain(
@@ -269,7 +269,7 @@ describe("generatePrompt", () => {
       },
     };
 
-    const prompt = generatePrompt(envVars, mockGitHubData);
+    const prompt = generatePrompt(envVars, mockGitHubData, false);
 
     expect(prompt).toContain("<direct_prompt>");
     expect(prompt).toContain("Fix the bug in the login form");
@@ -292,7 +292,7 @@ describe("generatePrompt", () => {
       },
     };
 
-    const prompt = generatePrompt(envVars, mockGitHubData);
+    const prompt = generatePrompt(envVars, mockGitHubData, false);
 
     expect(prompt).toContain("<event_type>PULL_REQUEST</event_type>");
     expect(prompt).toContain("<is_pr>true</is_pr>");
@@ -317,7 +317,7 @@ describe("generatePrompt", () => {
       },
     };
 
-    const prompt = generatePrompt(envVars, mockGitHubData);
+    const prompt = generatePrompt(envVars, mockGitHubData, false);
 
     expect(prompt).toContain("CUSTOM INSTRUCTIONS:\nAlways use TypeScript");
   });
@@ -339,11 +339,12 @@ describe("generatePrompt", () => {
       },
     };
 
-    const prompt = generatePrompt(envVars, mockGitHubData);
+    const prompt = generatePrompt(envVars, mockGitHubData, false);
 
     expect(prompt).toContain("<trigger_username>johndoe</trigger_username>");
+    // With commit signing disabled, co-author info appears in git commit instructions
     expect(prompt).toContain(
-      'Use: "Co-authored-by: johndoe <johndoe@users.noreply.github.com>"',
+      "Co-authored-by: johndoe <johndoe@users.noreply.github.com>",
     );
   });
 
@@ -360,12 +361,10 @@ describe("generatePrompt", () => {
       },
     };
 
-    const prompt = generatePrompt(envVars, mockGitHubData);
+    const prompt = generatePrompt(envVars, mockGitHubData, false);
 
-    // Should contain PR-specific instructions
+    // Should contain PR-specific instructions (git commands when not using signing)
-    expect(prompt).toContain(
+    expect(prompt).toContain("git push");
-      "Push directly using mcp__github_file_ops__commit_files to the existing branch",
-    );
     expect(prompt).toContain(
       "Always push to the existing branch when triggered on a PR",
     );
@@ -393,7 +392,7 @@ describe("generatePrompt", () => {
       },
     };
 
-    const prompt = generatePrompt(envVars, mockGitHubData);
+    const prompt = generatePrompt(envVars, mockGitHubData, false);
 
     // Should contain Issue-specific instructions
     expect(prompt).toContain(
@@ -432,7 +431,7 @@ describe("generatePrompt", () => {
       },
     };
 
-    const prompt = generatePrompt(envVars, mockGitHubData);
+    const prompt = generatePrompt(envVars, mockGitHubData, false);
 
     // Should contain the actual branch name with timestamp
     expect(prompt).toContain(
@@ -462,7 +461,7 @@ describe("generatePrompt", () => {
       },
     };
 
-    const prompt = generatePrompt(envVars, mockGitHubData);
+    const prompt = generatePrompt(envVars, mockGitHubData, false);
 
     // Should contain branch-specific instructions like issues
     expect(prompt).toContain(
@@ -500,12 +499,10 @@ describe("generatePrompt", () => {
       },
     };
 
-    const prompt = generatePrompt(envVars, mockGitHubData);
+    const prompt = generatePrompt(envVars, mockGitHubData, false);
 
-    // Should contain open PR instructions
+    // Should contain open PR instructions (git commands when not using signing)
-    expect(prompt).toContain(
+    expect(prompt).toContain("git push");
-      "Push directly using mcp__github_file_ops__commit_files to the existing branch",
-    );
     expect(prompt).toContain(
       "Always push to the existing branch when triggered on a PR",
     );
@@ -533,7 +530,7 @@ describe("generatePrompt", () => {
       },
     };
 
-    const prompt = generatePrompt(envVars, mockGitHubData);
+    const prompt = generatePrompt(envVars, mockGitHubData, false);
 
     // Should contain new branch instructions
     expect(prompt).toContain(
@@ -561,7 +558,7 @@ describe("generatePrompt", () => {
       },
     };
 
-    const prompt = generatePrompt(envVars, mockGitHubData);
+    const prompt = generatePrompt(envVars, mockGitHubData, false);
 
     // Should contain new branch instructions
     expect(prompt).toContain(
@@ -589,7 +586,7 @@ describe("generatePrompt", () => {
       },
     };
 
-    const prompt = generatePrompt(envVars, mockGitHubData);
+    const prompt = generatePrompt(envVars, mockGitHubData, false);
 
     // Should contain new branch instructions
     expect(prompt).toContain(
@@ -598,6 +595,61 @@ describe("generatePrompt", () => {
     expect(prompt).toContain("Create a PR](https://github.com/");
     expect(prompt).toContain("Reference to the original PR");
   });
+
+  test("should include git commands when useCommitSigning is false", () => {
+    const envVars: PreparedContext = {
+      repository: "owner/repo",
+      claudeCommentId: "12345",
+      triggerPhrase: "@claude",
+      eventData: {
+        eventName: "issue_comment",
+        commentId: "67890",
+        isPR: true,
+        prNumber: "123",
+        commentBody: "@claude fix the bug",
+      },
+    };
+
+    const prompt = generatePrompt(envVars, mockGitHubData, false);
+
+    // Should have git command instructions
+    expect(prompt).toContain("Use git commands via the Bash tool");
+    expect(prompt).toContain("git add");
+    expect(prompt).toContain("git commit");
+    expect(prompt).toContain("git push");
+
+    // Should use the minimal comment tool
+    expect(prompt).toContain("mcp__github_comment__update_claude_comment");
+
+    // Should not have commit signing tool references
+    expect(prompt).not.toContain("mcp__github_file_ops__commit_files");
+  });
+
+  test("should include commit signing tools when useCommitSigning is true", () => {
+    const envVars: PreparedContext = {
+      repository: "owner/repo",
+      claudeCommentId: "12345",
+      triggerPhrase: "@claude",
+      eventData: {
+        eventName: "issue_comment",
+        commentId: "67890",
+        isPR: true,
+        prNumber: "123",
+        commentBody: "@claude fix the bug",
+      },
+    };
+
+    const prompt = generatePrompt(envVars, mockGitHubData, true);
+
+    // Should have commit signing tool instructions
+    expect(prompt).toContain("mcp__github_file_ops__commit_files");
+    expect(prompt).toContain("mcp__github_file_ops__delete_files");
+    // Comment tool should always be from comment server, not file ops
+    expect(prompt).toContain("mcp__github_comment__update_claude_comment");
+
+    // Should not have git command instructions
+    expect(prompt).not.toContain("Use git commands via the Bash tool");
+  });
 });
 
 describe("getEventTypeAndContext", () => {
@@ -689,7 +741,7 @@ describe("getEventTypeAndContext", () => {
 });
 
 describe("buildAllowedToolsString", () => {
-  test("should return issue comment tool for regular events", () => {
+  test("should return correct tools for regular events (default no signing)", () => {
     const result = buildAllowedToolsString();
 
     // The base tools should be in the result
@@ -699,15 +751,20 @@ describe("buildAllowedToolsString", () => {
     expect(result).toContain("LS");
     expect(result).toContain("Read");
     expect(result).toContain("Write");
-    expect(result).toContain("mcp__github_file_ops__update_claude_comment");
+
-    expect(result).not.toContain("mcp__github__update_issue_comment");
+    // Default is no commit signing, so should have specific Bash git commands
-    expect(result).not.toContain("mcp__github__update_pull_request_comment");
+    expect(result).toContain("Bash(git add:*)");
-    expect(result).toContain("mcp__github_file_ops__commit_files");
+    expect(result).toContain("Bash(git commit:*)");
-    expect(result).toContain("mcp__github_file_ops__delete_files");
+    expect(result).toContain("Bash(git push:*)");
+    expect(result).toContain("mcp__github_comment__update_claude_comment");
+
+    // Should not have commit signing tools
+    expect(result).not.toContain("mcp__github_file_ops__commit_files");
+    expect(result).not.toContain("mcp__github_file_ops__delete_files");
   });
 
-  test("should return PR comment tool for inline review comments", () => {
+  test("should return correct tools with default parameters", () => {
-    const result = buildAllowedToolsString();
+    const result = buildAllowedToolsString([], false, false);
 
     // The base tools should be in the result
     expect(result).toContain("Edit");
@@ -716,11 +773,15 @@ describe("buildAllowedToolsString", () => {
     expect(result).toContain("LS");
     expect(result).toContain("Read");
     expect(result).toContain("Write");
-    expect(result).toContain("mcp__github_file_ops__update_claude_comment");
+
-    expect(result).not.toContain("mcp__github__update_issue_comment");
+    // Should have specific Bash git commands for non-signing mode
-    expect(result).not.toContain("mcp__github__update_pull_request_comment");
+    expect(result).toContain("Bash(git add:*)");
-    expect(result).toContain("mcp__github_file_ops__commit_files");
+    expect(result).toContain("Bash(git commit:*)");
-    expect(result).toContain("mcp__github_file_ops__delete_files");
+    expect(result).toContain("mcp__github_comment__update_claude_comment");
+
+    // Should not have commit signing tools
+    expect(result).not.toContain("mcp__github_file_ops__commit_files");
+    expect(result).not.toContain("mcp__github_file_ops__delete_files");
   });
 
   test("should append custom tools when provided", () => {
@@ -773,6 +834,79 @@ describe("buildAllowedToolsString", () => {
     expect(result).toContain("mcp__github_ci__get_workflow_run_details");
     expect(result).toContain("mcp__github_ci__download_job_log");
   });
+
+  test("should include commit signing tools when useCommitSigning is true", () => {
+    const result = buildAllowedToolsString([], false, true);
+
+    // Base tools should be present
+    expect(result).toContain("Edit");
+    expect(result).toContain("Glob");
+    expect(result).toContain("Grep");
+    expect(result).toContain("LS");
+    expect(result).toContain("Read");
+    expect(result).toContain("Write");
+
+    // Commit signing tools should be included
+    expect(result).toContain("mcp__github_file_ops__commit_files");
+    expect(result).toContain("mcp__github_file_ops__delete_files");
+    // Comment tool should always be from github_comment server
+    expect(result).toContain("mcp__github_comment__update_claude_comment");
+
+    // Bash should NOT be included when using commit signing (except in comment tool name)
+    expect(result).not.toContain("Bash(");
+  });
+
+  test("should include specific Bash git commands when useCommitSigning is false", () => {
+    const result = buildAllowedToolsString([], false, false);
+
+    // Base tools should be present
+    expect(result).toContain("Edit");
+    expect(result).toContain("Glob");
+    expect(result).toContain("Grep");
+    expect(result).toContain("LS");
+    expect(result).toContain("Read");
+    expect(result).toContain("Write");
+
+    // Specific Bash git commands should be included
+    expect(result).toContain("Bash(git add:*)");
+    expect(result).toContain("Bash(git commit:*)");
+    expect(result).toContain("Bash(git push:*)");
+    expect(result).toContain("Bash(git status:*)");
+    expect(result).toContain("Bash(git diff:*)");
+    expect(result).toContain("Bash(git log:*)");
+    expect(result).toContain("Bash(git rm:*)");
+    expect(result).toContain("Bash(git config user.name:*)");
+    expect(result).toContain("Bash(git config user.email:*)");
+
+    // Comment tool from minimal server should be included
+    expect(result).toContain("mcp__github_comment__update_claude_comment");
+
+    // Commit signing tools should NOT be included
+    expect(result).not.toContain("mcp__github_file_ops__commit_files");
+    expect(result).not.toContain("mcp__github_file_ops__delete_files");
+  });
+
+  test("should handle all combinations of options", () => {
+    const customTools = ["CustomTool1", "CustomTool2"];
+    const result = buildAllowedToolsString(customTools, true, false);
+
+    // Base tools should be present
+    expect(result).toContain("Edit");
+    expect(result).toContain("Bash(git add:*)");
+
+    // Custom tools should be included
+    expect(result).toContain("CustomTool1");
+    expect(result).toContain("CustomTool2");
+
+    // GitHub Actions tools should be included
+    expect(result).toContain("mcp__github_ci__get_ci_status");
+
+    // Comment tool from minimal server should be included
+    expect(result).toContain("mcp__github_comment__update_claude_comment");
+
+    // Commit signing tools should NOT be included
+    expect(result).not.toContain("mcp__github_file_ops__commit_files");
+  });
 });
 
 describe("buildDisallowedToolsString", () => {

test/install-mcp-server.test.ts

@@ -34,6 +34,7 @@ describe("prepareMcpConfig", () => {
       branchPrefix: "",
       useStickyComment: false,
       additionalPermissions: new Map(),
+      useCommitSigning: false,
     },
   };
 
@@ -44,6 +45,22 @@ describe("prepareMcpConfig", () => {
     entityNumber: 456,
   };
 
+  const mockContextWithSigning: ParsedGitHubContext = {
+    ...mockContext,
+    inputs: {
+      ...mockContext.inputs,
+      useCommitSigning: true,
+    },
+  };
+
+  const mockPRContextWithSigning: ParsedGitHubContext = {
+    ...mockPRContext,
+    inputs: {
+      ...mockPRContext.inputs,
+      useCommitSigning: true,
+    },
+  };
+
   beforeEach(() => {
     consoleInfoSpy = spyOn(core, "info").mockImplementation(() => {});
     consoleWarningSpy = spyOn(core, "warning").mockImplementation(() => {});
@@ -65,7 +82,7 @@ describe("prepareMcpConfig", () => {
     processExitSpy.mockRestore();
   });
 
-  test("should return base config when no additional config is provided and no allowed_tools", async () => {
+  test("should return comment server when commit signing is disabled", async () => {
     const result = await prepareMcpConfig({
       githubToken: "test-token",
       owner: "test-owner",
@@ -78,6 +95,37 @@ describe("prepareMcpConfig", () => {
     const parsed = JSON.parse(result);
     expect(parsed.mcpServers).toBeDefined();
     expect(parsed.mcpServers.github).not.toBeDefined();
+    expect(parsed.mcpServers.github_file_ops).not.toBeDefined();
+    expect(parsed.mcpServers.github_comment).toBeDefined();
+    expect(parsed.mcpServers.github_comment.env.GITHUB_TOKEN).toBe(
+      "test-token",
+    );
+    expect(parsed.mcpServers.github_comment.env.REPO_OWNER).toBe("test-owner");
+    expect(parsed.mcpServers.github_comment.env.REPO_NAME).toBe("test-repo");
+  });
+
+  test("should return file ops server when commit signing is enabled", async () => {
+    const contextWithSigning = {
+      ...mockContext,
+      inputs: {
+        ...mockContext.inputs,
+        useCommitSigning: true,
+      },
+    };
+
+    const result = await prepareMcpConfig({
+      githubToken: "test-token",
+      owner: "test-owner",
+      repo: "test-repo",
+      branch: "test-branch",
+      allowedTools: [],
+      context: contextWithSigning,
+    });
+
+    const parsed = JSON.parse(result);
+    expect(parsed.mcpServers).toBeDefined();
+    expect(parsed.mcpServers.github).not.toBeDefined();
+    expect(parsed.mcpServers.github_comment).toBeDefined();
     expect(parsed.mcpServers.github_file_ops).toBeDefined();
     expect(parsed.mcpServers.github_file_ops.env.GITHUB_TOKEN).toBe(
       "test-token",
@@ -105,13 +153,22 @@ describe("prepareMcpConfig", () => {
     const parsed = JSON.parse(result);
     expect(parsed.mcpServers).toBeDefined();
     expect(parsed.mcpServers.github).toBeDefined();
-    expect(parsed.mcpServers.github_file_ops).toBeDefined();
+    expect(parsed.mcpServers.github_comment).toBeDefined();
+    expect(parsed.mcpServers.github_file_ops).not.toBeDefined();
     expect(parsed.mcpServers.github.env.GITHUB_PERSONAL_ACCESS_TOKEN).toBe(
       "test-token",
     );
   });
 
   test("should not include github MCP server when only file_ops tools are allowed", async () => {
+    const contextWithSigning = {
+      ...mockContext,
+      inputs: {
+        ...mockContext.inputs,
+        useCommitSigning: true,
+      },
+    };
+
     const result = await prepareMcpConfig({
       githubToken: "test-token",
       owner: "test-owner",
@@ -121,7 +178,7 @@ describe("prepareMcpConfig", () => {
         "mcp__github_file_ops__commit_files",
         "mcp__github_file_ops__update_claude_comment",
       ],
-      context: mockContext,
+      context: contextWithSigning,
     });
 
     const parsed = JSON.parse(result);
@@ -130,7 +187,7 @@ describe("prepareMcpConfig", () => {
     expect(parsed.mcpServers.github_file_ops).toBeDefined();
   });
 
-  test("should include file_ops server even when no GitHub tools are allowed", async () => {
+  test("should include comment server when no GitHub tools are allowed and signing disabled", async () => {
     const result = await prepareMcpConfig({
       githubToken: "test-token",
       owner: "test-owner",
@@ -143,7 +200,8 @@ describe("prepareMcpConfig", () => {
     const parsed = JSON.parse(result);
     expect(parsed.mcpServers).toBeDefined();
     expect(parsed.mcpServers.github).not.toBeDefined();
-    expect(parsed.mcpServers.github_file_ops).toBeDefined();
+    expect(parsed.mcpServers.github_file_ops).not.toBeDefined();
+    expect(parsed.mcpServers.github_comment).toBeDefined();
   });
 
   test("should return base config when additional config is empty string", async () => {
@@ -160,7 +218,7 @@ describe("prepareMcpConfig", () => {
     const parsed = JSON.parse(result);
     expect(parsed.mcpServers).toBeDefined();
     expect(parsed.mcpServers.github).not.toBeDefined();
-    expect(parsed.mcpServers.github_file_ops).toBeDefined();
+    expect(parsed.mcpServers.github_comment).toBeDefined();
     expect(consoleWarningSpy).not.toHaveBeenCalled();
   });
 
@@ -178,7 +236,7 @@ describe("prepareMcpConfig", () => {
     const parsed = JSON.parse(result);
     expect(parsed.mcpServers).toBeDefined();
     expect(parsed.mcpServers.github).not.toBeDefined();
-    expect(parsed.mcpServers.github_file_ops).toBeDefined();
+    expect(parsed.mcpServers.github_comment).toBeDefined();
     expect(consoleWarningSpy).not.toHaveBeenCalled();
   });
 
@@ -205,7 +263,7 @@ describe("prepareMcpConfig", () => {
         "mcp__github__create_issue",
         "mcp__github_file_ops__commit_files",
       ],
-      context: mockContext,
+      context: mockContextWithSigning,
     });
 
     const parsed = JSON.parse(result);
@@ -243,7 +301,7 @@ describe("prepareMcpConfig", () => {
         "mcp__github__create_issue",
         "mcp__github_file_ops__commit_files",
       ],
-      context: mockContext,
+      context: mockContextWithSigning,
     });
 
     const parsed = JSON.parse(result);
@@ -281,7 +339,7 @@ describe("prepareMcpConfig", () => {
       branch: "test-branch",
       additionalMcpConfig: additionalConfig,
       allowedTools: [],
-      context: mockContext,
+      context: mockContextWithSigning,
     });
 
     const parsed = JSON.parse(result);
@@ -301,7 +359,7 @@ describe("prepareMcpConfig", () => {
       branch: "test-branch",
       additionalMcpConfig: invalidJson,
       allowedTools: [],
-      context: mockContext,
+      context: mockContextWithSigning,
     });
 
     const parsed = JSON.parse(result);
@@ -322,7 +380,7 @@ describe("prepareMcpConfig", () => {
       branch: "test-branch",
       additionalMcpConfig: nonObjectJson,
       allowedTools: [],
-      context: mockContext,
+      context: mockContextWithSigning,
     });
 
     const parsed = JSON.parse(result);
@@ -346,7 +404,7 @@ describe("prepareMcpConfig", () => {
       branch: "test-branch",
       additionalMcpConfig: nullJson,
       allowedTools: [],
-      context: mockContext,
+      context: mockContextWithSigning,
     });
 
     const parsed = JSON.parse(result);
@@ -370,7 +428,7 @@ describe("prepareMcpConfig", () => {
       branch: "test-branch",
       additionalMcpConfig: arrayJson,
       allowedTools: [],
-      context: mockContext,
+      context: mockContextWithSigning,
     });
 
     const parsed = JSON.parse(result);
@@ -417,7 +475,7 @@ describe("prepareMcpConfig", () => {
       branch: "test-branch",
       additionalMcpConfig: additionalConfig,
       allowedTools: [],
-      context: mockContext,
+      context: mockContextWithSigning,
     });
 
     const parsed = JSON.parse(result);
@@ -439,7 +497,7 @@ describe("prepareMcpConfig", () => {
       repo: "test-repo",
       branch: "test-branch",
       allowedTools: [],
-      context: mockContext,
+      context: mockContextWithSigning,
     });
 
     const parsed = JSON.parse(result);
@@ -460,7 +518,7 @@ describe("prepareMcpConfig", () => {
       repo: "test-repo",
       branch: "test-branch",
       allowedTools: [],
-      context: mockContext,
+      context: mockContextWithSigning,
     });
 
     const parsed = JSON.parse(result);
@@ -478,6 +536,7 @@ describe("prepareMcpConfig", () => {
       inputs: {
         ...mockPRContext.inputs,
         additionalPermissions: new Map([["actions", "read"]]),
+        useCommitSigning: true,
       },
     };
 
@@ -506,7 +565,7 @@ describe("prepareMcpConfig", () => {
       repo: "test-repo",
       branch: "test-branch",
       allowedTools: [],
-      context: mockContext,
+      context: mockContextWithSigning,
     });
 
     const parsed = JSON.parse(result);
@@ -524,7 +583,7 @@ describe("prepareMcpConfig", () => {
       repo: "test-repo",
       branch: "test-branch",
       allowedTools: [],
-      context: mockPRContext,
+      context: mockPRContextWithSigning,
     });
 
     const parsed = JSON.parse(result);

test/mockContext.ts

@@ -22,6 +22,7 @@ const defaultInputs = {
   branchPrefix: "claude/",
   useStickyComment: false,
   additionalPermissions: new Map<string, string>(),
+  useCommitSigning: false,
 };
 
 const defaultRepository = {

test/permissions.test.ts

@@ -70,6 +70,7 @@ describe("checkWritePermissions", () => {
       branchPrefix: "claude/",
       useStickyComment: false,
       additionalPermissions: new Map(),
+      useCommitSigning: false,
     },
   });
 

test/trigger-validation.test.ts

@@ -38,6 +38,7 @@ describe("checkContainsTrigger", () => {
           branchPrefix: "claude/",
           useStickyComment: false,
           additionalPermissions: new Map(),
+          useCommitSigning: false,
         },
       });
       expect(checkContainsTrigger(context)).toBe(true);
@@ -68,6 +69,7 @@ describe("checkContainsTrigger", () => {
           branchPrefix: "claude/",
           useStickyComment: false,
           additionalPermissions: new Map(),
+          useCommitSigning: false,
         },
       });
       expect(checkContainsTrigger(context)).toBe(false);
@@ -282,6 +284,7 @@ describe("checkContainsTrigger", () => {
           branchPrefix: "claude/",
           useStickyComment: false,
           additionalPermissions: new Map(),
+          useCommitSigning: false,
         },
       });
       expect(checkContainsTrigger(context)).toBe(true);
@@ -313,6 +316,7 @@ describe("checkContainsTrigger", () => {
           branchPrefix: "claude/",
           useStickyComment: false,
           additionalPermissions: new Map(),
+          useCommitSigning: false,
         },
       });
       expect(checkContainsTrigger(context)).toBe(true);
@@ -344,6 +348,7 @@ describe("checkContainsTrigger", () => {
           branchPrefix: "claude/",
           useStickyComment: false,
           additionalPermissions: new Map(),
+          useCommitSigning: false,
         },
       });
       expect(checkContainsTrigger(context)).toBe(false);