fix: replace REST API branch listing with GraphQL query for better performance

- Replaced REST API listBranches call with GraphQL query that filters branches by prefix
- This fixes the issue where repositories with >100 branches could miss existing Claude branches
- The GraphQL query directly filters by prefix, making it more efficient and accurate

Co-authored-by: ashwin-ant <ashwin-ant@users.noreply.github.com>

.github/workflows/claude.yml

@@ -36,3 +36,4 @@ jobs:
           anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}
           allowed_tools: "Bash(bun install),Bash(bun test:*),Bash(bun run format),Bash(bun typecheck)"
           custom_instructions: "You have also been granted tools for editing files and running bun commands (install, run, test, typecheck) for testing your changes: bun install, bun test, bun run format, bun typecheck."
+          model: "claude-opus-4-20250514"

FAQ.md

@@ -6,7 +6,7 @@ This FAQ addresses common questions and gotchas when using the Claude Code GitHu
 
 ### Why doesn't tagging @claude from my automated workflow work?
 
-The `github-actions` user (and other GitHub Apps/bots) cannot trigger subsequent GitHub Actions workflows. This is a GitHub security feature to prevent infinite loops. To make this work, you need to use a Personal Access Token (PAT) instead, which will act as a regular user. When posting a comment on an issue or PR from your workflow, use your PAT instead of the `GITHUB_TOKEN` generated in your workflow.
+The `github-actions` user cannot trigger subsequent GitHub Actions workflows. This is a GitHub security feature to prevent infinite loops. To make this work, you need to use a Personal Access Token (PAT) instead, which will act as a regular user, or use a separate app token of your own. When posting a comment on an issue or PR from your workflow, use your PAT instead of the `GITHUB_TOKEN` generated in your workflow.
 
 ### Why does Claude say I don't have permission to trigger it?
 

src/create-prompt/index.ts

@@ -31,13 +31,24 @@ const BASE_ALLOWED_TOOLS = [
   "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): string {
+export function buildAllowedToolsString(
+  eventData: EventData,
+  customAllowedTools?: string,
+): string {
   let baseTools = [...BASE_ALLOWED_TOOLS];
 
+  // Add the appropriate comment tool based on event type
+  if (eventData.eventName === "pull_request_review_comment") {
+    // For inline PR review comments, only use PR comment tool
+    baseTools.push("mcp__github__update_pull_request_comment");
+  } else {
+    // For all other events (issue comments, PR reviews, issues), use issue comment tool
+    baseTools.push("mcp__github__update_issue_comment");
+  }
+
   let allAllowedTools = baseTools.join(",");
   if (customAllowedTools) {
     allAllowedTools = `${allAllowedTools},${customAllowedTools}`;
@@ -350,6 +361,7 @@ export function getEventTypeAndContext(envVars: PreparedContext): {
 export function generatePrompt(
   context: PreparedContext,
   githubData: FetchDataResult,
+  isReusedBranch?: boolean,
 ): string {
   const {
     contextData,
@@ -436,15 +448,33 @@ ${sanitizeContent(context.directPrompt)}
 </direct_prompt>`
     : ""
 }
-${`<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.
+${
+  eventData.eventName === "pull_request_review_comment"
+    ? `<comment_tool_info>
+IMPORTANT: For this inline PR review comment, you have been provided with ONLY the mcp__github__update_pull_request_comment tool to update this specific review comment.
 
-Tool usage example for mcp__github_file_ops__update_claude_comment:
+Tool usage example for mcp__github__update_pull_request_comment:
 {
+  "owner": "${context.repository.split("/")[0]}",
+  "repo": "${context.repository.split("/")[1]}",
+  "commentId": ${eventData.commentId || context.claudeCommentId},
   "body": "Your comment text here"
 }
-Only the body parameter is required - the tool automatically knows which comment to update.
-</comment_tool_info>`}
+All four parameters (owner, repo, commentId, body) are required.
+</comment_tool_info>`
+    : `<comment_tool_info>
+IMPORTANT: For this event type, you have been provided with ONLY the mcp__github__update_issue_comment tool to update comments.
+
+Tool usage example for mcp__github__update_issue_comment:
+{
+  "owner": "${context.repository.split("/")[0]}",
+  "repo": "${context.repository.split("/")[1]}",
+  "commentId": ${context.claudeCommentId},
+  "body": "Your comment text here"
+}
+All four parameters (owner, repo, commentId, body) are required.
+</comment_tool_info>`
+}
 
 Your task is to analyze the context, understand the request, and provide helpful responses and/or implement code changes as needed.
 
@@ -458,7 +488,7 @@ 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 ${eventData.eventName === "pull_request_review_comment" ? "mcp__github__update_pull_request_comment" : "mcp__github__update_issue_comment"} with each task completion.
 
 2. Gather Context:
    - Analyze the pre-fetched data provided above.
@@ -488,11 +518,11 @@ ${context.directPrompt ? `   - DIRECT INSTRUCTION: A direct instruction was prov
         - Look for bugs, security issues, performance problems, and other issues
         - Suggest improvements for readability and maintainability
         - Check for best practices and coding standards
-        - Reference specific code sections with file paths and line numbers${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__update_issue_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. This will be displayed as your PR review." : "Remember that this feedback must be posted to the GitHub comment."}
 
    B. For Straightforward Changes:
       - Use file system tools to make the change locally.
@@ -505,7 +535,7 @@ ${context.directPrompt ? `   - DIRECT INSTRUCTION: A direct instruction was prov
       - 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 TRIGGER_USERNAME is not "Unknown", include a "Co-authored-by: ${context.triggerUsername} <${context.triggerUsername}@users.noreply.github.com>" line in the commit message.`
           : `
-      - You are already on the correct branch (${eventData.claudeBranch || "the PR branch"}). Do not create a new branch.
+      - You are already on the correct branch (${eventData.claudeBranch || "the PR branch"}). Do not create a new branch.${isReusedBranch ? `\n      - NOTE: This branch (${eventData.claudeBranch}) was reused from a previous Claude invocation on this issue. It may already contain some work.` : ''}
       - 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 TRIGGER_USERNAME is not "Unknown", include a "Co-authored-by: ${context.triggerUsername} <${context.triggerUsername}@users.noreply.github.com>" line in the commit message.
@@ -547,8 +577,8 @@ ${context.directPrompt ? `   - DIRECT INSTRUCTION: A direct instruction was prov
 
 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.
-- 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." : ""}
+- Never create new comments. Only update the existing comment using ${eventData.eventName === "pull_request_review_comment" ? "mcp__github__update_pull_request_comment" : "mcp__github__update_issue_comment"} with comment_id: ${context.claudeCommentId}.
+- This includes ALL responses: code reviews, answers to questions, progress updates, and final results.${eventData.isPR ? "\n- PR CRITICAL: After reading files and forming your response, you MUST post it by calling mcp__github__update_issue_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.`}
@@ -612,6 +642,7 @@ export async function createPrompt(
   claudeBranch: string | undefined,
   githubData: FetchDataResult,
   context: ParsedGitHubContext,
+  isReusedBranch?: boolean,
 ) {
   try {
     const preparedContext = prepareContext(
@@ -624,7 +655,7 @@ export async function createPrompt(
     await mkdir("/tmp/claude-prompts", { recursive: true });
 
     // Generate the prompt
-    const promptContent = generatePrompt(preparedContext, githubData);
+    const promptContent = generatePrompt(preparedContext, githubData, isReusedBranch);
 
     // Log the final prompt to console
     console.log("===== FINAL PROMPT =====");
@@ -636,6 +667,7 @@ export async function createPrompt(
 
     // Set allowed tools
     const allAllowedTools = buildAllowedToolsString(
+      preparedContext.eventData,
       preparedContext.allowedTools,
     );
     const allDisallowedTools = buildDisallowedToolsString(

src/entrypoints/prepare.ts

@@ -81,6 +81,7 @@ async function run() {
       branchInfo.claudeBranch,
       githubData,
       context,
+      branchInfo.isReusedBranch,
     );
 
     // Step 11: Get MCP configuration
@@ -89,7 +90,6 @@ async function run() {
       context.repository.owner,
       context.repository.repo,
       branchInfo.currentBranch,
-      commentId.toString(),
     );
     core.setOutput("mcp_config", mcpConfig);
   } catch (error) {

src/entrypoints/update-comment-link.ts

@@ -87,13 +87,29 @@ async function run() {
     const currentBody = comment.body ?? "";
 
     // Check if we need to add branch link for new branches
-    const { shouldDeleteBranch, branchLink } = await checkAndDeleteEmptyBranch(
-      octokit,
-      owner,
-      repo,
-      claudeBranch,
-      baseBranch,
-    );
+    // For issues, we don't delete branches anymore to allow reuse
+    const skipBranchDeletion = !context.isPR && claudeBranch;
+    
+    let shouldDeleteBranch = false;
+    let branchLink = "";
+    
+    if (skipBranchDeletion) {
+      // For issue branches, just add the branch link without checking for deletion
+      const branchUrl = `${GITHUB_SERVER_URL}/${owner}/${repo}/tree/${claudeBranch}`;
+      branchLink = `\n[View branch](${branchUrl})`;
+      console.log(`Keeping issue branch ${claudeBranch} for potential reuse`);
+    } else {
+      // For PR branches, use the existing cleanup logic
+      const result = await checkAndDeleteEmptyBranch(
+        octokit,
+        owner,
+        repo,
+        claudeBranch,
+        baseBranch,
+      );
+      shouldDeleteBranch = result.shouldDeleteBranch;
+      branchLink = result.branchLink;
+    }
 
     // Check if we need to add PR URL when we have a new branch
     let prLink = "";

src/github/operations/branch.ts

@@ -17,6 +17,7 @@ export type BranchInfo = {
   baseBranch: string;
   claudeBranch?: string;
   currentBranch: string;
+  isReusedBranch?: boolean;
 };
 
 export async function setupBranch(
@@ -79,57 +80,127 @@ export async function setupBranch(
 
   // Creating a new branch for either an issue or closed/merged PR
   const entityType = isPR ? "pr" : "issue";
-  console.log(
-    `Creating new branch for ${entityType} #${entityNumber} from source branch: ${sourceBranch}...`,
-  );
-
-  const timestamp = new Date()
-    .toISOString()
-    .replace(/[:-]/g, "")
-    .replace(/\.\d{3}Z/, "")
-    .split("T")
-    .join("_");
-
-  const newBranch = `claude/${entityType}-${entityNumber}-${timestamp}`;
-
-  try {
-    // Get the SHA of the source branch
-    const sourceBranchRef = await octokits.rest.git.getRef({
-      owner,
-      repo,
-      ref: `heads/${sourceBranch}`,
-    });
-
-    const currentSHA = sourceBranchRef.data.object.sha;
-
-    console.log(`Current SHA: ${currentSHA}`);
-
-    // Create branch using GitHub API
-    await octokits.rest.git.createRef({
-      owner,
-      repo,
-      ref: `refs/heads/${newBranch}`,
-      sha: currentSHA,
-    });
-
-    // Checkout the new branch (shallow fetch for performance)
-    await $`git fetch origin --depth=1 ${newBranch}`;
-    await $`git checkout ${newBranch}`;
-
+  
+  // For issues, check if a Claude branch already exists
+  let branchToUse: string | null = null;
+  let isReusedBranch = false;
+  
+  if (!isPR) {
+    // Check for existing Claude branches for this issue
+    try {
+      // Use GraphQL to efficiently search for branches with a specific prefix
+      const query = `
+        query($owner: String!, $repo: String!, $prefix: String!) {
+          repository(owner: $owner, name: $repo) {
+            refs(refPrefix: "refs/heads/", query: $prefix, first: 100) {
+              nodes {
+                name
+              }
+            }
+          }
+        }
+      `;
+      
+      const response = await octokits.graphql<{
+        repository: {
+          refs: {
+            nodes: Array<{ name: string }>;
+          };
+        };
+      }>(query, {
+        owner,
+        repo,
+        prefix: `claude/issue-${entityNumber}-`,
+      });
+      
+      const branches = response.repository.refs.nodes;
+      
+      if (branches.length > 0) {
+        // Use the first matching branch (could be sorted by date in future)
+        branchToUse = branches[0].name;
+        isReusedBranch = true;
+        console.log(`Found existing Claude branch for issue #${entityNumber}: ${branchToUse}`);
+      }
+    } catch (error) {
+      console.error("Error checking for existing branches:", error);
+      // Continue with new branch creation if check fails
+    }
+  }
+  
+  // If no existing branch found or this is a PR, create a new branch
+  if (!branchToUse) {
     console.log(
-      `Successfully created and checked out new branch: ${newBranch}`,
+      `Creating new branch for ${entityType} #${entityNumber} from source branch: ${sourceBranch}...`,
     );
 
+    const timestamp = new Date()
+      .toISOString()
+      .replace(/[:-]/g, "")
+      .replace(/\.\d{3}Z/, "")
+      .split("T")
+      .join("_");
+
+    branchToUse = `claude/${entityType}-${entityNumber}-${timestamp}`;
+  }
+
+  try {
+    if (isReusedBranch) {
+      // For existing branches, just checkout
+      console.log(`Checking out existing branch: ${branchToUse}`);
+      
+      // Fetch the branch with more depth to allow for context
+      await $`git fetch origin --depth=20 ${branchToUse}`;
+      await $`git checkout ${branchToUse}`;
+      
+      console.log(
+        `Successfully checked out existing branch: ${branchToUse}`,
+      );
+      console.log(
+        `Note: This is a reused branch from a previous Claude invocation on issue #${entityNumber}`,
+      );
+    } else {
+      // Get the SHA of the source branch
+      const sourceBranchRef = await octokits.rest.git.getRef({
+        owner,
+        repo,
+        ref: `heads/${sourceBranch}`,
+      });
+
+      const currentSHA = sourceBranchRef.data.object.sha;
+
+      console.log(`Current SHA: ${currentSHA}`);
+
+      // Create branch using GitHub API
+      await octokits.rest.git.createRef({
+        owner,
+        repo,
+        ref: `refs/heads/${branchToUse}`,
+        sha: currentSHA,
+      });
+
+      // Checkout the new branch (shallow fetch for performance)
+      await $`git fetch origin --depth=1 ${branchToUse}`;
+      await $`git checkout ${branchToUse}`;
+
+      console.log(
+        `Successfully created and checked out new branch: ${branchToUse}`,
+      );
+    }
+
     // Set outputs for GitHub Actions
-    core.setOutput("CLAUDE_BRANCH", newBranch);
+    core.setOutput("CLAUDE_BRANCH", branchToUse);
     core.setOutput("BASE_BRANCH", sourceBranch);
+    if (isReusedBranch) {
+      core.setOutput("IS_REUSED_BRANCH", "true");
+    }
     return {
       baseBranch: sourceBranch,
-      claudeBranch: newBranch,
-      currentBranch: newBranch,
+      claudeBranch: branchToUse,
+      currentBranch: branchToUse,
+      isReusedBranch,
     };
   } catch (error) {
-    console.error("Error creating branch:", error);
+    console.error("Error setting up branch:", error);
     process.exit(1);
   }
 }

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

@@ -7,7 +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";
 
 type GitHubRef = {
   object: {
@@ -440,106 +439,6 @@ server.tool(
   },
 );
 
-// Update Claude comment 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);
-
-      // Create Octokit instance
-      const octokit = new Octokit({
-        auth: githubToken,
-      });
-
-      // Determine if this is a PR review comment based on event type
-      const isPullRequestReviewComment =
-        eventName === "pull_request_review_comment";
-
-      let response;
-
-      try {
-        if (isPullRequestReviewComment) {
-          // Try PR review comment API first
-          response = await octokit.rest.pulls.updateReviewComment({
-            owner,
-            repo,
-            comment_id: commentId,
-            body,
-          });
-        } else {
-          // Use issue comment API (works for both issues and PR general comments)
-          response = await octokit.rest.issues.updateComment({
-            owner,
-            repo,
-            comment_id: commentId,
-            body,
-          });
-        }
-      } catch (error: any) {
-        // If PR review comment update fails with 404, fall back to issue comment API
-        if (isPullRequestReviewComment && error.status === 404) {
-          response = await octokit.rest.issues.updateComment({
-            owner,
-            repo,
-            comment_id: commentId,
-            body,
-          });
-        } else {
-          throw error;
-        }
-      }
-
-      return {
-        content: [
-          {
-            type: "text",
-            text: JSON.stringify(
-              {
-                id: response.data.id,
-                html_url: response.data.html_url,
-                updated_at: response.data.updated_at,
-              },
-              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

@@ -5,7 +5,6 @@ export async function prepareMcpConfig(
   owner: string,
   repo: string,
   branch: string,
-  claudeCommentId?: string,
 ): Promise<string> {
   try {
     const mcpConfig = {
@@ -36,9 +35,6 @@ 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",
           },
         },
       },

test/create-prompt.test.ts

@@ -8,6 +8,7 @@ import {
   buildDisallowedToolsString,
 } from "../src/create-prompt";
 import type { PreparedContext } from "../src/create-prompt";
+import type { EventData } from "../src/create-prompt/types";
 
 describe("generatePrompt", () => {
   const mockGitHubData = {
@@ -618,7 +619,15 @@ describe("getEventTypeAndContext", () => {
 
 describe("buildAllowedToolsString", () => {
   test("should return issue comment tool for regular events", () => {
-    const result = buildAllowedToolsString();
+    const mockEventData: EventData = {
+      eventName: "issue_comment",
+      commentId: "123",
+      isPR: true,
+      prNumber: "456",
+      commentBody: "Test comment",
+    };
+
+    const result = buildAllowedToolsString(mockEventData);
 
     // The base tools should be in the result
     expect(result).toContain("Edit");
@@ -627,15 +636,22 @@ 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");
+    expect(result).toContain("mcp__github__update_issue_comment");
     expect(result).not.toContain("mcp__github__update_pull_request_comment");
     expect(result).toContain("mcp__github_file_ops__commit_files");
     expect(result).toContain("mcp__github_file_ops__delete_files");
   });
 
   test("should return PR comment tool for inline review comments", () => {
-    const result = buildAllowedToolsString();
+    const mockEventData: EventData = {
+      eventName: "pull_request_review_comment",
+      isPR: true,
+      prNumber: "456",
+      commentBody: "Test review comment",
+      commentId: "789",
+    };
+
+    const result = buildAllowedToolsString(mockEventData);
 
     // The base tools should be in the result
     expect(result).toContain("Edit");
@@ -644,16 +660,23 @@ 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");
-    expect(result).not.toContain("mcp__github__update_pull_request_comment");
+    expect(result).toContain("mcp__github__update_pull_request_comment");
     expect(result).toContain("mcp__github_file_ops__commit_files");
     expect(result).toContain("mcp__github_file_ops__delete_files");
   });
 
   test("should append custom tools when provided", () => {
+    const mockEventData: EventData = {
+      eventName: "issue_comment",
+      commentId: "123",
+      isPR: true,
+      prNumber: "456",
+      commentBody: "Test comment",
+    };
+
     const customTools = "Tool1,Tool2,Tool3";
-    const result = buildAllowedToolsString(customTools);
+    const result = buildAllowedToolsString(mockEventData, customTools);
 
     // Base tools should be present
     expect(result).toContain("Edit");