feat: add use_commit_signing input with default false (#238)

* feat: add use_commit_signing input with default false

- Add new input 'use_commit_signing' to action.yml (defaults to false)
- Separate comment update functionality into standalone github-comment-server.ts
- Update MCP server configuration to conditionally load servers based on signing preference
- When commit signing is disabled, use specific Bash git commands (e.g., Bash(git add:*))
- When commit signing is enabled, use github-file-ops-server for atomic commits with signing
- Always include github-comment-server for comment updates regardless of signing mode
- Update prompt generation to provide appropriate instructions based on signing preference
- Add comprehensive test coverage for new functionality

This change simplifies the default setup for users who don't need commit signing,
while maintaining the option to enable it for those who require GitHub's commit
signature verification.

🤖 Generated with [Claude Code](https://claude.ai/code)

Co-Authored-By: Claude <noreply@anthropic.com>

* feat: auto-commit uncommitted changes when commit signing is disabled

- Check for uncommitted changes after Claude finishes (non-signing mode only)
- Automatically commit and push any uncommitted work to preserve Claude's changes
- Update tests to avoid actual git operations during test runs
- Pass use_commit_signing flag to branch cleanup logic

---------

Co-authored-by: Claude <noreply@anthropic.com>

action.yml

@@ -92,6 +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:
@@ -133,6 +137,7 @@ 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
@@ -201,6 +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 != ''

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

@@ -13,6 +13,7 @@ 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 +52,8 @@ 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({
@@ -75,7 +77,17 @@ async function run() {
       );
     }
 
-    // Step 10: Create prompt file
+    // Step 10: Configure git authentication if not using commit signing
+    if (!context.inputs.useCommitSigning) {
+      try {
+        await configureGitAuth(githubToken, context, commentData.user);
+      } catch (error) {
+        console.error("Failed to configure git authentication:", error);
+        throw error;
+      }
+    }
+
+    // Step 11: Create prompt file
     await createPrompt(
       commentId,
       branchInfo.baseBranch,
@@ -84,7 +96,7 @@ async function run() {
       context,
     );
 
-    // Step 11: Get MCP configuration
+    // Step 12: Get MCP configuration
     const additionalMcpConfig = process.env.MCP_CONFIG || "";
     const mcpConfig = await prepareMcpConfig({
       githubToken,

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() {
@@ -88,12 +88,15 @@ 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";
+    const { shouldDeleteBranch, branchLink } =
+      await checkAndCommitOrDeleteBranch(
         octokit,
         owner,
         repo,
         claudeBranch,
         baseBranch,
+        useCommitSigning,
       );
 
     // Check if we need to add PR URL when we have a new branch

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

@@ -1,12 +1,14 @@
 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;
@@ -21,12 +23,58 @@ 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) {
+        if (!useCommitSigning) {
+          console.log(
+            `Branch ${claudeBranch} has no commits from Claude, checking for uncommitted changes...`,
+          );
+
+          // 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}`;

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

@@ -86,7 +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);
 
@@ -102,7 +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 = {
@@ -535,70 +533,6 @@ 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

@@ -67,8 +67,29 @@ export async function prepareMcpConfig(
     );
 
     const baseMcpConfig: { mcpServers: Record<string, unknown> } = {
-      mcpServers: {
+      mcpServers: {},
-        github_file_ops: {
+    };
+
+    // Always include comment server for updating Claude comments
+    baseMcpConfig.mcpServers.github_comment = {
+      command: "bun",
+      args: [
+        "run",
+        `${process.env.GITHUB_ACTION_PATH}/src/mcp/github-comment-server.ts`,
+      ],
+      env: {
+        GITHUB_TOKEN: githubToken,
+        REPO_OWNER: owner,
+        REPO_NAME: repo,
+        ...(claudeCommentId && { CLAUDE_COMMENT_ID: claudeCommentId }),
+        GITHUB_EVENT_NAME: process.env.GITHUB_EVENT_NAME || "",
+        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",
@@ -80,14 +101,12 @@ export async function prepareMcpConfig(
           REPO_NAME: repo,
           BRANCH_NAME: branch,
           REPO_DIR: process.env.GITHUB_WORKSPACE || process.cwd(),
-            ...(claudeCommentId && { CLAUDE_COMMENT_ID: claudeCommentId }),
           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 =

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;
 
@@ -43,12 +43,13 @@ 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 +57,15 @@ 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 +73,17 @@ 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);
@@ -109,12 +109,13 @@ 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);
@@ -131,12 +132,13 @@ 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);

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);