debug mode

* fix: only load GitHub MCP server when its tools are allowed

- Add allowedTools parameter to prepareMcpConfig
- Check for mcp__github__ and mcp__github_file_ops__ tool prefixes
- Only include MCP servers when their tools are in allowed_tools
- Maintain backward compatibility when allowed_tools is not specified
- Update tests to reflect the new conditional loading behavior

This optimizes resource usage by not loading unnecessary MCP servers
when their tools are not allowed in the configuration.

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

* fix: always load github_file_ops server regardless of allowed_tools

- Only apply conditional loading to the github MCP server
- Always load github_file_ops server as it contains essential tools
- Update tests to reflect this behavior

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

* refactor: move allowedTools/disallowedTools parsing to parseGitHubContext

- Change allowedTools and disallowedTools from string to string[] in ParsedGitHubContext type
- Parse comma-separated environment variables into arrays in parseGitHubContext function
- Update create-prompt and install-mcp-server to use pre-parsed arrays
- Update all affected test files to use array syntax
- Eliminate duplicate parsing logic across the codebase

* style: apply prettier formatting

---------

Co-authored-by: claude[bot] <209825114+claude[bot]@users.noreply.github.com>
Co-authored-by: ashwin-ant <ashwin-ant@users.noreply.github.com>

.github/workflows/issue-triage.yml

@@ -23,18 +23,20 @@ jobs:
           mkdir -p /tmp/mcp-config
           cat > /tmp/mcp-config/mcp-servers.json << 'EOF'
           {
-            "github": {
+            "mcpServers": {
-              "command": "docker",
+              "github": {
-              "args": [
+                "command": "docker",
-                "run",
+                "args": [
-                "-i",
+                  "run",
-                "--rm",
+                  "-i",
-                "-e",
+                  "--rm",
-                "GITHUB_PERSONAL_ACCESS_TOKEN",
+                  "-e",
-                "ghcr.io/github/github-mcp-server:sha-7aced2b"
+                  "GITHUB_PERSONAL_ACCESS_TOKEN",
-              ],
+                  "ghcr.io/github/github-mcp-server:sha-7aced2b"
-              "env": {
+                ],
-                "GITHUB_PERSONAL_ACCESS_TOKEN": "${{ secrets.GITHUB_TOKEN }}"
+                "env": {
+                  "GITHUB_PERSONAL_ACCESS_TOKEN": "${{ secrets.GITHUB_TOKEN }}"
+                }
               }
             }
           }

README.md

@@ -65,6 +65,11 @@ jobs:
           # trigger_phrase: "/claude"
           # Optional: add assignee trigger for issues
           # assignee_trigger: "claude"
+          # Optional: add custom environment variables (YAML format)
+          # claude_env: |
+          #   NODE_ENV: test
+          #   DEBUG: true
+          #   API_URL: https://api.example.com
 ```
 
 ## Inputs
@@ -82,13 +87,70 @@ jobs:
 | `allowed_tools`       | Additional tools for Claude to use (the base GitHub tools will always be included)                                   | No       | ""        |
 | `disallowed_tools`    | Tools that Claude should never use                                                                                   | No       | ""        |
 | `custom_instructions` | Additional custom instructions to include in the prompt for Claude                                                   | No       | ""        |
+| `mcp_config`          | Additional MCP configuration (JSON string) that merges with the built-in GitHub MCP servers                          | 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` |
+| `claude_env`          | Custom environment variables to pass to Claude Code execution (YAML format)                                          | No       | ""        |
 
 \*Required when using direct Anthropic API (default and when not using Bedrock or Vertex)
 
 > **Note**: This action is currently in beta. Features and APIs may change as we continue to improve the integration.
 
+### Using Custom MCP Configuration
+
+The `mcp_config` input allows you to add custom MCP (Model Context Protocol) servers to extend Claude's capabilities. These servers merge with the built-in GitHub MCP servers.
+
+#### Basic Example: Adding a Sequential Thinking Server
+
+```yaml
+- uses: anthropics/claude-code-action@beta
+  with:
+    anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}
+    mcp_config: |
+      {
+        "mcpServers": {
+          "sequential-thinking": {
+            "command": "npx",
+            "args": [
+              "-y",
+              "@modelcontextprotocol/server-sequential-thinking"
+            ]
+          }
+        }
+      }
+    allowed_tools: "mcp__sequential-thinking__sequentialthinking" # Important: Each MCP tool from your server must be listed here, comma-separated
+    # ... other inputs
+```
+
+#### Passing Secrets to MCP Servers
+
+For MCP servers that require sensitive information like API keys or tokens, use GitHub Secrets in the environment variables:
+
+```yaml
+- uses: anthropics/claude-code-action@beta
+  with:
+    anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}
+    mcp_config: |
+      {
+        "mcpServers": {
+          "custom-api-server": {
+            "command": "npx",
+            "args": ["-y", "@example/api-server"],
+            "env": {
+              "API_KEY": "${{ secrets.CUSTOM_API_KEY }}",
+              "BASE_URL": "https://api.example.com"
+            }
+          }
+        }
+      }
+    # ... other inputs
+```
+
+**Important**:
+
+- Always use GitHub Secrets (`${{ secrets.SECRET_NAME }}`) for sensitive values like API keys, tokens, or passwords. Never hardcode secrets directly in the workflow file.
+- Your custom servers will override any built-in servers with the same name.
+
 ## Examples
 
 ### Ways to Tag @claude
@@ -233,6 +295,22 @@ This action is built on top of [`anthropics/claude-code-base-action`](https://gi
 
 ## Advanced Configuration
 
+### Custom Environment Variables
+
+You can pass custom environment variables to Claude Code execution using the `claude_env` input. This is useful for CI/test setups that require specific environment variables:
+
+```yaml
+- uses: anthropics/claude-code-action@beta
+  with:
+    claude_env: |
+      NODE_ENV: test
+      CI: true
+      DATABASE_URL: postgres://test:test@localhost:5432/test_db
+    # ... other inputs
+```
+
+The `claude_env` input accepts YAML format where each line defines a key-value pair. These environment variables will be available to Claude Code during execution, allowing it to run tests, build processes, or other commands that depend on specific environment configurations.
+
 ### Custom Tools
 
 By default, Claude only has access to:

action.yml

@@ -39,6 +39,12 @@ inputs:
     description: "Direct instruction for Claude (bypasses normal trigger detection)"
     required: false
     default: ""
+  mcp_config:
+    description: "Additional MCP configuration (JSON string) that merges with the built-in GitHub MCP servers"
+  claude_env:
+    description: "Custom environment variables to pass to Claude Code execution (YAML format)"
+    required: false
+    default: ""
 
   # Auth configuration
   anthropic_api_key:
@@ -92,13 +98,14 @@ runs:
         ALLOWED_TOOLS: ${{ inputs.allowed_tools }}
         CUSTOM_INSTRUCTIONS: ${{ inputs.custom_instructions }}
         DIRECT_PROMPT: ${{ inputs.direct_prompt }}
+        MCP_CONFIG: ${{ inputs.mcp_config }}
         OVERRIDE_GITHUB_TOKEN: ${{ inputs.github_token }}
         GITHUB_RUN_ID: ${{ github.run_id }}
 
     - name: Run Claude Code
       id: claude-code
       if: steps.prepare.outputs.contains_trigger == 'true'
-      uses: anthropics/claude-code-base-action@c8e31bd52d9a149b3f8309d7978c6edaa282688d # v0.0.8
+      uses: anthropics/claude-code-base-action@ashwin/debug
       with:
         prompt_file: /tmp/claude-prompts/claude-prompt.txt
         allowed_tools: ${{ env.ALLOWED_TOOLS }}
@@ -109,6 +116,7 @@ runs:
         use_bedrock: ${{ inputs.use_bedrock }}
         use_vertex: ${{ inputs.use_vertex }}
         anthropic_api_key: ${{ inputs.anthropic_api_key }}
+        claude_env: ${{ inputs.claude_env }}
       env:
         # Model configuration
         ANTHROPIC_MODEL: ${{ inputs.model || inputs.anthropic_model }}

src/create-prompt/index.ts

@@ -31,53 +31,39 @@ 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(
+export function buildAllowedToolsString(customAllowedTools?: string[]): string {
-  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) {
+  if (customAllowedTools && customAllowedTools.length > 0) {
-    allAllowedTools = `${allAllowedTools},${customAllowedTools}`;
+    allAllowedTools = `${allAllowedTools},${customAllowedTools.join(",")}`;
   }
   return allAllowedTools;
 }
 
 export function buildDisallowedToolsString(
-  customDisallowedTools?: string,
+  customDisallowedTools?: string[],
-  allowedTools?: string,
+  allowedTools?: string[],
 ): string {
   let disallowedTools = [...DISALLOWED_TOOLS];
 
   // If user has explicitly allowed some hardcoded disallowed tools, remove them from disallowed list
-  if (allowedTools) {
+  if (allowedTools && allowedTools.length > 0) {
-    const allowedToolsArray = allowedTools
-      .split(",")
-      .map((tool) => tool.trim());
     disallowedTools = disallowedTools.filter(
-      (tool) => !allowedToolsArray.includes(tool),
+      (tool) => !allowedTools.includes(tool),
     );
   }
 
   let allDisallowedTools = disallowedTools.join(",");
-  if (customDisallowedTools) {
+  if (customDisallowedTools && customDisallowedTools.length > 0) {
     if (allDisallowedTools) {
-      allDisallowedTools = `${allDisallowedTools},${customDisallowedTools}`;
+      allDisallowedTools = `${allDisallowedTools},${customDisallowedTools.join(",")}`;
     } else {
-      allDisallowedTools = customDisallowedTools;
+      allDisallowedTools = customDisallowedTools.join(",");
     }
   }
   return allDisallowedTools;
@@ -131,8 +117,10 @@ export function prepareContext(
     triggerPhrase,
     ...(triggerUsername && { triggerUsername }),
     ...(customInstructions && { customInstructions }),
-    ...(allowedTools && { allowedTools }),
+    ...(allowedTools.length > 0 && { allowedTools: allowedTools.join(",") }),
-    ...(disallowedTools && { disallowedTools }),
+    ...(disallowedTools.length > 0 && {
+      disallowedTools: disallowedTools.join(","),
+    }),
     ...(directPrompt && { directPrompt }),
     ...(claudeBranch && { claudeBranch }),
   };
@@ -447,33 +435,15 @@ ${sanitizeContent(context.directPrompt)}
 </direct_prompt>`
     : ""
 }
-${
+${`<comment_tool_info>
-  eventData.eventName === "pull_request_review_comment"
+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.
-    ? `<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__update_pull_request_comment:
+Tool usage example for mcp__github_file_ops__update_claude_comment:
 {
-  "owner": "${context.repository.split("/")[0]}",
-  "repo": "${context.repository.split("/")[1]}",
-  "commentId": ${eventData.commentId || context.claudeCommentId},
   "body": "Your comment text here"
 }
-All four parameters (owner, repo, commentId, body) are required.
+Only the body parameter is required - the tool automatically knows which comment to update.
-</comment_tool_info>`
+</comment_tool_info>`}
-    : `<comment_tool_info>
-IMPORTANT: For this event type, you have been provided with ONLY the mcp__github__update_issue_comment tool to update comments.
-
-Tool usage example for mcp__github__update_issue_comment:
-{
-  "owner": "${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.
 
@@ -487,7 +457,7 @@ 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 ${eventData.eventName === "pull_request_review_comment" ? "mcp__github__update_pull_request_comment" : "mcp__github__update_issue_comment"} with each task completion.
+   - Update the comment using mcp__github_file_ops__update_claude_comment with each task completion.
 
 2. Gather Context:
    - Analyze the pre-fetched data provided above.
@@ -517,11 +487,11 @@ ${context.directPrompt ? `   - DIRECT INSTRUCTION: A direct instruction was prov
         - Look for bugs, security issues, performance problems, and other issues
         - Suggest improvements for readability and maintainability
         - Check for best practices and coding standards
-        - Reference specific code sections with file paths and line numbers${eventData.isPR ? "\n      - AFTER reading files and analyzing code, you MUST call mcp__github__update_issue_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_file_ops__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. This will be displayed as your PR review." : "Remember that this feedback must be posted to the GitHub comment."}
+      - ${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."}
 
    B. For Straightforward Changes:
       - Use file system tools to make the change locally.
@@ -576,8 +546,8 @@ ${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 ${eventData.eventName === "pull_request_review_comment" ? "mcp__github__update_pull_request_comment" : "mcp__github__update_issue_comment"} with comment_id: ${context.claudeCommentId}.
+- Never create new comments. Only update the existing comment using mcp__github_file_ops__update_claude_comment.
-- This includes ALL responses: code reviews, answers to questions, progress updates, and final results.${eventData.isPR ? "\n- PR CRITICAL: After reading files and forming your response, you MUST post it by calling mcp__github__update_issue_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_file_ops__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.`}
@@ -665,12 +635,11 @@ export async function createPrompt(
 
     // Set allowed tools
     const allAllowedTools = buildAllowedToolsString(
-      preparedContext.eventData,
+      context.inputs.allowedTools,
-      preparedContext.allowedTools,
     );
     const allDisallowedTools = buildDisallowedToolsString(
-      preparedContext.disallowedTools,
+      context.inputs.disallowedTools,
-      preparedContext.allowedTools,
+      context.inputs.allowedTools,
     );
 
     core.exportVariable("ALLOWED_TOOLS", allAllowedTools);

src/entrypoints/prepare.ts

@@ -84,12 +84,16 @@ async function run() {
     );
 
     // Step 11: Get MCP configuration
-    const mcpConfig = await prepareMcpConfig(
+    const additionalMcpConfig = process.env.MCP_CONFIG || "";
+    const mcpConfig = await prepareMcpConfig({
       githubToken,
-      context.repository.owner,
+      owner: context.repository.owner,
-      context.repository.repo,
+      repo: context.repository.repo,
-      branchInfo.currentBranch,
+      branch: branchInfo.currentBranch,
-    );
+      additionalMcpConfig,
+      claudeCommentId: commentId.toString(),
+      allowedTools: context.inputs.allowedTools,
+    });
     core.setOutput("mcp_config", mcpConfig);
   } catch (error) {
     const errorMessage = error instanceof Error ? error.message : String(error);

src/entrypoints/update-comment-link.ts

@@ -12,6 +12,7 @@ import {
 } from "../github/context";
 import { GITHUB_SERVER_URL } from "../github/api/config";
 import { checkAndDeleteEmptyBranch } from "../github/operations/branch-cleanup";
+import { updateClaudeComment } from "../github/operations/comments/update-claude-comment";
 
 async function run() {
   try {
@@ -204,23 +205,14 @@ async function run() {
 
     const updatedBody = updateCommentBody(commentInput);
 
-    // Update the comment using the appropriate API
     try {
-      if (isPRReviewComment) {
+      await updateClaudeComment(octokit.rest, {
-        await octokit.rest.pulls.updateReviewComment({
+        owner,
-          owner,
+        repo,
-          repo,
+        commentId,
-          comment_id: commentId,
+        body: updatedBody,
-          body: updatedBody,
+        isPullRequestReviewComment: isPRReviewComment,
-        });
+      });
-      } else {
-        await octokit.rest.issues.updateComment({
-          owner,
-          repo,
-          comment_id: commentId,
-          body: updatedBody,
-        });
-      }
       console.log(
         `✅ Updated ${isPRReviewComment ? "PR review" : "issue"} comment ${commentId} with job link`,
       );

src/github/context.ts

@@ -28,8 +28,8 @@ export type ParsedGitHubContext = {
   inputs: {
     triggerPhrase: string;
     assigneeTrigger: string;
-    allowedTools: string;
+    allowedTools: string[];
-    disallowedTools: string;
+    disallowedTools: string[];
     customInstructions: string;
     directPrompt: string;
     baseBranch?: string;
@@ -52,8 +52,14 @@ export function parseGitHubContext(): ParsedGitHubContext {
     inputs: {
       triggerPhrase: process.env.TRIGGER_PHRASE ?? "@claude",
       assigneeTrigger: process.env.ASSIGNEE_TRIGGER ?? "",
-      allowedTools: process.env.ALLOWED_TOOLS ?? "",
+      allowedTools: (process.env.ALLOWED_TOOLS ?? "")
-      disallowedTools: process.env.DISALLOWED_TOOLS ?? "",
+        .split(",")
+        .map((tool) => tool.trim())
+        .filter((tool) => tool.length > 0),
+      disallowedTools: (process.env.DISALLOWED_TOOLS ?? "")
+        .split(",")
+        .map((tool) => tool.trim())
+        .filter((tool) => tool.length > 0),
       customInstructions: process.env.CUSTOM_INSTRUCTIONS ?? "",
       directPrompt: process.env.DIRECT_PROMPT ?? "",
       baseBranch: process.env.BASE_BRANCH,

src/github/data/fetcher.ts

@@ -1,17 +1,17 @@
 import { execSync } from "child_process";
+import type { Octokits } from "../api/client";
+import { ISSUE_QUERY, PR_QUERY } from "../api/queries/github";
 import type {
-  GitHubPullRequest,
-  GitHubIssue,
   GitHubComment,
   GitHubFile,
+  GitHubIssue,
+  GitHubPullRequest,
   GitHubReview,
-  PullRequestQueryResponse,
   IssueQueryResponse,
+  PullRequestQueryResponse,
 } from "../types";
-import { PR_QUERY, ISSUE_QUERY } from "../api/queries/github";
-import type { Octokits } from "../api/client";
-import { downloadCommentImages } from "../utils/image-downloader";
 import type { CommentWithImages } from "../utils/image-downloader";
+import { downloadCommentImages } from "../utils/image-downloader";
 
 type FetchDataParams = {
   octokits: Octokits;
@@ -101,6 +101,14 @@ export async function fetchGitHubData({
   let changedFilesWithSHA: GitHubFileWithSHA[] = [];
   if (isPR && changedFiles.length > 0) {
     changedFilesWithSHA = changedFiles.map((file) => {
+      // Don't compute SHA for deleted files
+      if (file.changeType === "DELETED") {
+        return {
+          ...file,
+          sha: "deleted",
+        };
+      }
+
       try {
         // Use git hash-object to compute the SHA for the current file content
         const sha = execSync(`git hash-object "${file.path}"`, {

src/github/operations/comments/update-claude-comment.ts

@@ -0,0 +1,70 @@
+import { Octokit } from "@octokit/rest";
+
+export type UpdateClaudeCommentParams = {
+  owner: string;
+  repo: string;
+  commentId: number;
+  body: string;
+  isPullRequestReviewComment: boolean;
+};
+
+export type UpdateClaudeCommentResult = {
+  id: number;
+  html_url: string;
+  updated_at: string;
+};
+
+/**
+ * Updates a Claude comment on GitHub (either an issue/PR comment or a PR review comment)
+ *
+ * @param octokit - Authenticated Octokit instance
+ * @param params - Parameters for updating the comment
+ * @returns The updated comment details
+ * @throws Error if the update fails
+ */
+export async function updateClaudeComment(
+  octokit: Octokit,
+  params: UpdateClaudeCommentParams,
+): Promise<UpdateClaudeCommentResult> {
+  const { owner, repo, commentId, body, isPullRequestReviewComment } = params;
+
+  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 {
+    id: response.data.id,
+    html_url: response.data.html_url,
+    updated_at: response.data.updated_at,
+  };
+}

src/github/operations/comments/update-with-branch.ts

@@ -15,6 +15,7 @@ import {
   isPullRequestReviewCommentEvent,
   type ParsedGitHubContext,
 } from "../../context";
+import { updateClaudeComment } from "./update-claude-comment";
 
 export async function updateTrackingComment(
   octokit: Octokits,
@@ -36,25 +37,19 @@ export async function updateTrackingComment(
 
   // Update the existing comment with the branch link
   try {
-    if (isPullRequestReviewCommentEvent(context)) {
+    const isPRReviewComment = isPullRequestReviewCommentEvent(context);
-      // For PR review comments (inline comments), use the pulls API
+
-      await octokit.rest.pulls.updateReviewComment({
+    await updateClaudeComment(octokit.rest, {
-        owner,
+      owner,
-        repo,
+      repo,
-        comment_id: commentId,
+      commentId,
-        body: updatedBody,
+      body: updatedBody,
-      });
+      isPullRequestReviewComment: isPRReviewComment,
-      console.log(`✅ Updated PR review comment ${commentId} with branch link`);
+    });
-    } else {
+
-      // For all other comments, use the issues API
+    console.log(
-      await octokit.rest.issues.updateComment({
+      `✅ Updated ${isPRReviewComment ? "PR review" : "issue"} comment ${commentId} with branch link`,
-        owner,
+    );
-        repo,
-        comment_id: commentId,
-        body: updatedBody,
-      });
-      console.log(`✅ Updated issue comment ${commentId} with branch link`);
-    }
   } catch (error) {
     console.error("Error updating comment with branch link:", error);
     throw error;

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

@@ -7,6 +7,8 @@ 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";
 
 type GitHubRef = {
   object: {
@@ -439,6 +441,69 @@ 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,
+      });
+
+      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

@@ -1,28 +1,36 @@
 import * as core from "@actions/core";
 
+type PrepareConfigParams = {
+  githubToken: string;
+  owner: string;
+  repo: string;
+  branch: string;
+  additionalMcpConfig?: string;
+  claudeCommentId?: string;
+  allowedTools: string[];
+};
+
 export async function prepareMcpConfig(
-  githubToken: string,
+  params: PrepareConfigParams,
-  owner: string,
-  repo: string,
-  branch: string,
 ): Promise<string> {
+  const {
+    githubToken,
+    owner,
+    repo,
+    branch,
+    additionalMcpConfig,
+    claudeCommentId,
+    allowedTools,
+  } = params;
   try {
-    const mcpConfig = {
+    const allowedToolsList = allowedTools || [];
+
+    const hasGitHubMcpTools = allowedToolsList.some((tool) =>
+      tool.startsWith("mcp__github__"),
+    );
+
+    const baseMcpConfig: { mcpServers: Record<string, unknown> } = {
       mcpServers: {
-        github: {
-          command: "docker",
-          args: [
-            "run",
-            "-i",
-            "--rm",
-            "-e",
-            "GITHUB_PERSONAL_ACCESS_TOKEN",
-            "ghcr.io/anthropics/github-mcp-server:sha-7382253",
-          ],
-          env: {
-            GITHUB_PERSONAL_ACCESS_TOKEN: githubToken,
-          },
-        },
         github_file_ops: {
           command: "bun",
           args: [
@@ -35,12 +43,64 @@ 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",
           },
         },
       },
     };
 
-    return JSON.stringify(mcpConfig, null, 2);
+    if (hasGitHubMcpTools) {
+      baseMcpConfig.mcpServers.github = {
+        command: "docker",
+        args: [
+          "run",
+          "-i",
+          "--rm",
+          "-e",
+          "GITHUB_PERSONAL_ACCESS_TOKEN",
+          "ghcr.io/github/github-mcp-server:sha-e9f748f", // https://github.com/github/github-mcp-server/releases/tag/v0.4.0
+        ],
+        env: {
+          GITHUB_PERSONAL_ACCESS_TOKEN: githubToken,
+        },
+      };
+    }
+
+    // Merge with additional MCP config if provided
+    if (additionalMcpConfig && additionalMcpConfig.trim()) {
+      try {
+        const additionalConfig = JSON.parse(additionalMcpConfig);
+
+        // Validate that parsed JSON is an object
+        if (typeof additionalConfig !== "object" || additionalConfig === null) {
+          throw new Error("MCP config must be a valid JSON object");
+        }
+
+        core.info(
+          "Merging additional MCP server configuration with built-in servers",
+        );
+
+        // Merge configurations with user config overriding built-in servers
+        const mergedConfig = {
+          ...baseMcpConfig,
+          ...additionalConfig,
+          mcpServers: {
+            ...baseMcpConfig.mcpServers,
+            ...additionalConfig.mcpServers,
+          },
+        };
+
+        return JSON.stringify(mergedConfig, null, 2);
+      } catch (parseError) {
+        core.warning(
+          `Failed to parse additional MCP config: ${parseError}. Using base config only.`,
+        );
+      }
+    }
+
+    return JSON.stringify(baseMcpConfig, null, 2);
   } catch (error) {
     core.setFailed(`Install MCP server failed with error: ${error}`);
     process.exit(1);

test/create-prompt.test.ts

@@ -8,7 +8,6 @@ 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 = {
@@ -619,15 +618,7 @@ describe("getEventTypeAndContext", () => {
 
 describe("buildAllowedToolsString", () => {
   test("should return issue comment tool for regular events", () => {
-    const mockEventData: EventData = {
+    const result = buildAllowedToolsString();
-      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");
@@ -636,22 +627,15 @@ describe("buildAllowedToolsString", () => {
     expect(result).toContain("LS");
     expect(result).toContain("Read");
     expect(result).toContain("Write");
-    expect(result).toContain("mcp__github__update_issue_comment");
+    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_file_ops__commit_files");
     expect(result).toContain("mcp__github_file_ops__delete_files");
   });
 
   test("should return PR comment tool for inline review comments", () => {
-    const mockEventData: EventData = {
+    const result = buildAllowedToolsString();
-      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");
@@ -660,23 +644,16 @@ 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_pull_request_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 append custom tools when provided", () => {
-    const mockEventData: EventData = {
+    const customTools = ["Tool1", "Tool2", "Tool3"];
-      eventName: "issue_comment",
+    const result = buildAllowedToolsString(customTools);
-      commentId: "123",
-      isPR: true,
-      prNumber: "456",
-      commentBody: "Test comment",
-    };
-
-    const customTools = "Tool1,Tool2,Tool3";
-    const result = buildAllowedToolsString(mockEventData, customTools);
 
     // Base tools should be present
     expect(result).toContain("Edit");
@@ -706,7 +683,7 @@ describe("buildDisallowedToolsString", () => {
   });
 
   test("should append custom disallowed tools when provided", () => {
-    const customDisallowedTools = "BadTool1,BadTool2";
+    const customDisallowedTools = ["BadTool1", "BadTool2"];
     const result = buildDisallowedToolsString(customDisallowedTools);
 
     // Base disallowed tools should be present
@@ -724,8 +701,8 @@ describe("buildDisallowedToolsString", () => {
   });
 
   test("should remove hardcoded disallowed tools if they are in allowed tools", () => {
-    const customDisallowedTools = "BadTool1,BadTool2";
+    const customDisallowedTools = ["BadTool1", "BadTool2"];
-    const allowedTools = "WebSearch,SomeOtherTool";
+    const allowedTools = ["WebSearch", "SomeOtherTool"];
     const result = buildDisallowedToolsString(
       customDisallowedTools,
       allowedTools,
@@ -743,7 +720,7 @@ describe("buildDisallowedToolsString", () => {
   });
 
   test("should remove all hardcoded disallowed tools if they are all in allowed tools", () => {
-    const allowedTools = "WebSearch,WebFetch,SomeOtherTool";
+    const allowedTools = ["WebSearch", "WebFetch", "SomeOtherTool"];
     const result = buildDisallowedToolsString(undefined, allowedTools);
 
     // Both hardcoded disallowed tools should be removed
@@ -755,8 +732,8 @@ describe("buildDisallowedToolsString", () => {
   });
 
   test("should handle custom disallowed tools when all hardcoded tools are overridden", () => {
-    const customDisallowedTools = "BadTool1,BadTool2";
+    const customDisallowedTools = ["BadTool1", "BadTool2"];
-    const allowedTools = "WebSearch,WebFetch";
+    const allowedTools = ["WebSearch", "WebFetch"];
     const result = buildDisallowedToolsString(
       customDisallowedTools,
       allowedTools,

test/install-mcp-server.test.ts

@@ -0,0 +1,414 @@
+import { describe, test, expect, beforeEach, afterEach, spyOn } from "bun:test";
+import { prepareMcpConfig } from "../src/mcp/install-mcp-server";
+import * as core from "@actions/core";
+
+describe("prepareMcpConfig", () => {
+  let consoleInfoSpy: any;
+  let consoleWarningSpy: any;
+  let setFailedSpy: any;
+  let processExitSpy: any;
+
+  beforeEach(() => {
+    consoleInfoSpy = spyOn(core, "info").mockImplementation(() => {});
+    consoleWarningSpy = spyOn(core, "warning").mockImplementation(() => {});
+    setFailedSpy = spyOn(core, "setFailed").mockImplementation(() => {});
+    processExitSpy = spyOn(process, "exit").mockImplementation(() => {
+      throw new Error("Process exit");
+    });
+  });
+
+  afterEach(() => {
+    consoleInfoSpy.mockRestore();
+    consoleWarningSpy.mockRestore();
+    setFailedSpy.mockRestore();
+    processExitSpy.mockRestore();
+  });
+
+  test("should return base config when no additional config is provided and no allowed_tools", async () => {
+    const result = await prepareMcpConfig({
+      githubToken: "test-token",
+      owner: "test-owner",
+      repo: "test-repo",
+      branch: "test-branch",
+      allowedTools: [],
+    });
+
+    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.env.GITHUB_TOKEN).toBe(
+      "test-token",
+    );
+    expect(parsed.mcpServers.github_file_ops.env.REPO_OWNER).toBe("test-owner");
+    expect(parsed.mcpServers.github_file_ops.env.REPO_NAME).toBe("test-repo");
+    expect(parsed.mcpServers.github_file_ops.env.BRANCH_NAME).toBe(
+      "test-branch",
+    );
+  });
+
+  test("should include github MCP server when mcp__github__ tools are allowed", async () => {
+    const result = await prepareMcpConfig({
+      githubToken: "test-token",
+      owner: "test-owner",
+      repo: "test-repo",
+      branch: "test-branch",
+      allowedTools: [
+        "mcp__github__create_issue",
+        "mcp__github_file_ops__commit_files",
+      ],
+    });
+
+    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.env.GITHUB_PERSONAL_ACCESS_TOKEN).toBe(
+      "test-token",
+    );
+  });
+
+  test("should not include github MCP server when only file_ops tools are allowed", async () => {
+    const result = await prepareMcpConfig({
+      githubToken: "test-token",
+      owner: "test-owner",
+      repo: "test-repo",
+      branch: "test-branch",
+      allowedTools: [
+        "mcp__github_file_ops__commit_files",
+        "mcp__github_file_ops__update_claude_comment",
+      ],
+    });
+
+    const parsed = JSON.parse(result);
+    expect(parsed.mcpServers).toBeDefined();
+    expect(parsed.mcpServers.github).not.toBeDefined();
+    expect(parsed.mcpServers.github_file_ops).toBeDefined();
+  });
+
+  test("should include file_ops server even when no GitHub tools are allowed", async () => {
+    const result = await prepareMcpConfig({
+      githubToken: "test-token",
+      owner: "test-owner",
+      repo: "test-repo",
+      branch: "test-branch",
+      allowedTools: ["Edit", "Read", "Write"],
+    });
+
+    const parsed = JSON.parse(result);
+    expect(parsed.mcpServers).toBeDefined();
+    expect(parsed.mcpServers.github).not.toBeDefined();
+    expect(parsed.mcpServers.github_file_ops).toBeDefined();
+  });
+
+  test("should return base config when additional config is empty string", async () => {
+    const result = await prepareMcpConfig({
+      githubToken: "test-token",
+      owner: "test-owner",
+      repo: "test-repo",
+      branch: "test-branch",
+      additionalMcpConfig: "",
+      allowedTools: [],
+    });
+
+    const parsed = JSON.parse(result);
+    expect(parsed.mcpServers).toBeDefined();
+    expect(parsed.mcpServers.github).not.toBeDefined();
+    expect(parsed.mcpServers.github_file_ops).toBeDefined();
+    expect(consoleWarningSpy).not.toHaveBeenCalled();
+  });
+
+  test("should return base config when additional config is whitespace only", async () => {
+    const result = await prepareMcpConfig({
+      githubToken: "test-token",
+      owner: "test-owner",
+      repo: "test-repo",
+      branch: "test-branch",
+      additionalMcpConfig: "   \n\t  ",
+      allowedTools: [],
+    });
+
+    const parsed = JSON.parse(result);
+    expect(parsed.mcpServers).toBeDefined();
+    expect(parsed.mcpServers.github).not.toBeDefined();
+    expect(parsed.mcpServers.github_file_ops).toBeDefined();
+    expect(consoleWarningSpy).not.toHaveBeenCalled();
+  });
+
+  test("should merge valid additional config with base config", async () => {
+    const additionalConfig = JSON.stringify({
+      mcpServers: {
+        custom_server: {
+          command: "custom-command",
+          args: ["arg1", "arg2"],
+          env: {
+            CUSTOM_ENV: "custom-value",
+          },
+        },
+      },
+    });
+
+    const result = await prepareMcpConfig({
+      githubToken: "test-token",
+      owner: "test-owner",
+      repo: "test-repo",
+      branch: "test-branch",
+      additionalMcpConfig: additionalConfig,
+      allowedTools: [
+        "mcp__github__create_issue",
+        "mcp__github_file_ops__commit_files",
+      ],
+    });
+
+    const parsed = JSON.parse(result);
+    expect(consoleInfoSpy).toHaveBeenCalledWith(
+      "Merging additional MCP server configuration with built-in servers",
+    );
+    expect(parsed.mcpServers.github).toBeDefined();
+    expect(parsed.mcpServers.github_file_ops).toBeDefined();
+    expect(parsed.mcpServers.custom_server).toBeDefined();
+    expect(parsed.mcpServers.custom_server.command).toBe("custom-command");
+    expect(parsed.mcpServers.custom_server.args).toEqual(["arg1", "arg2"]);
+    expect(parsed.mcpServers.custom_server.env.CUSTOM_ENV).toBe("custom-value");
+  });
+
+  test("should override built-in servers when additional config has same server names", async () => {
+    const additionalConfig = JSON.stringify({
+      mcpServers: {
+        github: {
+          command: "overridden-command",
+          args: ["overridden-arg"],
+          env: {
+            OVERRIDDEN_ENV: "overridden-value",
+          },
+        },
+      },
+    });
+
+    const result = await prepareMcpConfig({
+      githubToken: "test-token",
+      owner: "test-owner",
+      repo: "test-repo",
+      branch: "test-branch",
+      additionalMcpConfig: additionalConfig,
+      allowedTools: [
+        "mcp__github__create_issue",
+        "mcp__github_file_ops__commit_files",
+      ],
+    });
+
+    const parsed = JSON.parse(result);
+    expect(consoleInfoSpy).toHaveBeenCalledWith(
+      "Merging additional MCP server configuration with built-in servers",
+    );
+    expect(parsed.mcpServers.github.command).toBe("overridden-command");
+    expect(parsed.mcpServers.github.args).toEqual(["overridden-arg"]);
+    expect(parsed.mcpServers.github.env.OVERRIDDEN_ENV).toBe(
+      "overridden-value",
+    );
+    expect(
+      parsed.mcpServers.github.env.GITHUB_PERSONAL_ACCESS_TOKEN,
+    ).toBeUndefined();
+    expect(parsed.mcpServers.github_file_ops).toBeDefined();
+  });
+
+  test("should merge additional root-level properties", async () => {
+    const additionalConfig = JSON.stringify({
+      customProperty: "custom-value",
+      anotherProperty: {
+        nested: "value",
+      },
+      mcpServers: {
+        custom_server: {
+          command: "custom",
+        },
+      },
+    });
+
+    const result = await prepareMcpConfig({
+      githubToken: "test-token",
+      owner: "test-owner",
+      repo: "test-repo",
+      branch: "test-branch",
+      additionalMcpConfig: additionalConfig,
+      allowedTools: [],
+    });
+
+    const parsed = JSON.parse(result);
+    expect(parsed.customProperty).toBe("custom-value");
+    expect(parsed.anotherProperty).toEqual({ nested: "value" });
+    expect(parsed.mcpServers.github).not.toBeDefined();
+    expect(parsed.mcpServers.custom_server).toBeDefined();
+  });
+
+  test("should handle invalid JSON gracefully", async () => {
+    const invalidJson = "{ invalid json }";
+
+    const result = await prepareMcpConfig({
+      githubToken: "test-token",
+      owner: "test-owner",
+      repo: "test-repo",
+      branch: "test-branch",
+      additionalMcpConfig: invalidJson,
+      allowedTools: [],
+    });
+
+    const parsed = JSON.parse(result);
+    expect(consoleWarningSpy).toHaveBeenCalledWith(
+      expect.stringContaining("Failed to parse additional MCP config:"),
+    );
+    expect(parsed.mcpServers.github).not.toBeDefined();
+    expect(parsed.mcpServers.github_file_ops).toBeDefined();
+  });
+
+  test("should handle non-object JSON values", async () => {
+    const nonObjectJson = JSON.stringify("string value");
+
+    const result = await prepareMcpConfig({
+      githubToken: "test-token",
+      owner: "test-owner",
+      repo: "test-repo",
+      branch: "test-branch",
+      additionalMcpConfig: nonObjectJson,
+      allowedTools: [],
+    });
+
+    const parsed = JSON.parse(result);
+    expect(consoleWarningSpy).toHaveBeenCalledWith(
+      expect.stringContaining("Failed to parse additional MCP config:"),
+    );
+    expect(consoleWarningSpy).toHaveBeenCalledWith(
+      expect.stringContaining("MCP config must be a valid JSON object"),
+    );
+    expect(parsed.mcpServers.github).not.toBeDefined();
+    expect(parsed.mcpServers.github_file_ops).toBeDefined();
+  });
+
+  test("should handle null JSON value", async () => {
+    const nullJson = JSON.stringify(null);
+
+    const result = await prepareMcpConfig({
+      githubToken: "test-token",
+      owner: "test-owner",
+      repo: "test-repo",
+      branch: "test-branch",
+      additionalMcpConfig: nullJson,
+      allowedTools: [],
+    });
+
+    const parsed = JSON.parse(result);
+    expect(consoleWarningSpy).toHaveBeenCalledWith(
+      expect.stringContaining("Failed to parse additional MCP config:"),
+    );
+    expect(consoleWarningSpy).toHaveBeenCalledWith(
+      expect.stringContaining("MCP config must be a valid JSON object"),
+    );
+    expect(parsed.mcpServers.github).not.toBeDefined();
+    expect(parsed.mcpServers.github_file_ops).toBeDefined();
+  });
+
+  test("should handle array JSON value", async () => {
+    const arrayJson = JSON.stringify([1, 2, 3]);
+
+    const result = await prepareMcpConfig({
+      githubToken: "test-token",
+      owner: "test-owner",
+      repo: "test-repo",
+      branch: "test-branch",
+      additionalMcpConfig: arrayJson,
+      allowedTools: [],
+    });
+
+    const parsed = JSON.parse(result);
+    // Arrays are objects in JavaScript, so they pass the object check
+    // But they'll fail when trying to spread or access mcpServers property
+    expect(consoleInfoSpy).toHaveBeenCalledWith(
+      "Merging additional MCP server configuration with built-in servers",
+    );
+    expect(parsed.mcpServers.github).not.toBeDefined();
+    expect(parsed.mcpServers.github_file_ops).toBeDefined();
+    // The array will be spread into the config (0: 1, 1: 2, 2: 3)
+    expect(parsed[0]).toBe(1);
+    expect(parsed[1]).toBe(2);
+    expect(parsed[2]).toBe(3);
+  });
+
+  test("should merge complex nested configurations", async () => {
+    const additionalConfig = JSON.stringify({
+      mcpServers: {
+        server1: {
+          command: "cmd1",
+          env: { KEY1: "value1" },
+        },
+        server2: {
+          command: "cmd2",
+          env: { KEY2: "value2" },
+        },
+        github_file_ops: {
+          command: "overridden",
+          env: { CUSTOM: "value" },
+        },
+      },
+      otherConfig: {
+        nested: {
+          deeply: "value",
+        },
+      },
+    });
+
+    const result = await prepareMcpConfig({
+      githubToken: "test-token",
+      owner: "test-owner",
+      repo: "test-repo",
+      branch: "test-branch",
+      additionalMcpConfig: additionalConfig,
+      allowedTools: [],
+    });
+
+    const parsed = JSON.parse(result);
+    expect(parsed.mcpServers.server1).toBeDefined();
+    expect(parsed.mcpServers.server2).toBeDefined();
+    expect(parsed.mcpServers.github).not.toBeDefined();
+    expect(parsed.mcpServers.github_file_ops.command).toBe("overridden");
+    expect(parsed.mcpServers.github_file_ops.env.CUSTOM).toBe("value");
+    expect(parsed.otherConfig.nested.deeply).toBe("value");
+  });
+
+  test("should preserve GITHUB_ACTION_PATH in file_ops server args", async () => {
+    const oldEnv = process.env.GITHUB_ACTION_PATH;
+    process.env.GITHUB_ACTION_PATH = "/test/action/path";
+
+    const result = await prepareMcpConfig({
+      githubToken: "test-token",
+      owner: "test-owner",
+      repo: "test-repo",
+      branch: "test-branch",
+      allowedTools: [],
+    });
+
+    const parsed = JSON.parse(result);
+    expect(parsed.mcpServers.github_file_ops.args[1]).toBe(
+      "/test/action/path/src/mcp/github-file-ops-server.ts",
+    );
+
+    process.env.GITHUB_ACTION_PATH = oldEnv;
+  });
+
+  test("should use process.cwd() when GITHUB_WORKSPACE is not set", async () => {
+    const oldEnv = process.env.GITHUB_WORKSPACE;
+    delete process.env.GITHUB_WORKSPACE;
+
+    const result = await prepareMcpConfig({
+      githubToken: "test-token",
+      owner: "test-owner",
+      repo: "test-repo",
+      branch: "test-branch",
+      allowedTools: [],
+    });
+
+    const parsed = JSON.parse(result);
+    expect(parsed.mcpServers.github_file_ops.env.REPO_DIR).toBe(process.cwd());
+
+    process.env.GITHUB_WORKSPACE = oldEnv;
+  });
+});

test/mockContext.ts

@@ -11,8 +11,8 @@ const defaultInputs = {
   triggerPhrase: "/claude",
   assigneeTrigger: "",
   anthropicModel: "claude-3-7-sonnet-20250219",
-  allowedTools: "",
+  allowedTools: [] as string[],
-  disallowedTools: "",
+  disallowedTools: [] as string[],
   customInstructions: "",
   directPrompt: "",
   useBedrock: false,

test/permissions.test.ts

@@ -62,8 +62,8 @@ describe("checkWritePermissions", () => {
     inputs: {
       triggerPhrase: "@claude",
       assigneeTrigger: "",
-      allowedTools: "",
+      allowedTools: [],
-      disallowedTools: "",
+      disallowedTools: [],
       customInstructions: "",
       directPrompt: "",
     },

test/prepare-context.test.ts

@@ -242,7 +242,7 @@ describe("parseEnvVarsWithContext", () => {
         ...mockPullRequestCommentContext,
         inputs: {
           ...mockPullRequestCommentContext.inputs,
-          allowedTools: "Tool1,Tool2",
+          allowedTools: ["Tool1", "Tool2"],
         },
       });
       const result = prepareContext(contextWithAllowedTools, "12345");

test/trigger-validation.test.ts

@@ -30,8 +30,8 @@ describe("checkContainsTrigger", () => {
           triggerPhrase: "/claude",
           assigneeTrigger: "",
           directPrompt: "Fix the bug in the login form",
-          allowedTools: "",
+          allowedTools: [],
-          disallowedTools: "",
+          disallowedTools: [],
           customInstructions: "",
         },
       });
@@ -56,8 +56,8 @@ describe("checkContainsTrigger", () => {
           triggerPhrase: "/claude",
           assigneeTrigger: "",
           directPrompt: "",
-          allowedTools: "",
+          allowedTools: [],
-          disallowedTools: "",
+          disallowedTools: [],
           customInstructions: "",
         },
       });
@@ -228,8 +228,8 @@ describe("checkContainsTrigger", () => {
           triggerPhrase: "@claude",
           assigneeTrigger: "",
           directPrompt: "",
-          allowedTools: "",
+          allowedTools: [],
-          disallowedTools: "",
+          disallowedTools: [],
           customInstructions: "",
         },
       });
@@ -255,8 +255,8 @@ describe("checkContainsTrigger", () => {
           triggerPhrase: "@claude",
           assigneeTrigger: "",
           directPrompt: "",
-          allowedTools: "",
+          allowedTools: [],
-          disallowedTools: "",
+          disallowedTools: [],
           customInstructions: "",
         },
       });
@@ -282,8 +282,8 @@ describe("checkContainsTrigger", () => {
           triggerPhrase: "@claude",
           assigneeTrigger: "",
           directPrompt: "",
-          allowedTools: "",
+          allowedTools: [],
-          disallowedTools: "",
+          disallowedTools: [],
           customInstructions: "",
         },
       });

test/update-claude-comment.test.ts

@@ -0,0 +1,413 @@
+import { describe, test, expect, jest, beforeEach } from "bun:test";
+import { Octokit } from "@octokit/rest";
+import {
+  updateClaudeComment,
+  type UpdateClaudeCommentParams,
+} from "../src/github/operations/comments/update-claude-comment";
+
+describe("updateClaudeComment", () => {
+  let mockOctokit: Octokit;
+
+  beforeEach(() => {
+    mockOctokit = {
+      rest: {
+        issues: {
+          updateComment: jest.fn(),
+        },
+        pulls: {
+          updateReviewComment: jest.fn(),
+        },
+      },
+    } as any as Octokit;
+  });
+
+  test("should update issue comment successfully", async () => {
+    const mockResponse = {
+      data: {
+        id: 123456,
+        html_url: "https://github.com/owner/repo/issues/1#issuecomment-123456",
+        updated_at: "2024-01-01T00:00:00Z",
+        body: "Updated comment",
+      },
+    };
+
+    // @ts-expect-error Mock implementation doesn't match full type signature
+    mockOctokit.rest.issues.updateComment = jest
+      .fn()
+      .mockResolvedValue(mockResponse);
+
+    const params: UpdateClaudeCommentParams = {
+      owner: "testowner",
+      repo: "testrepo",
+      commentId: 123456,
+      body: "Updated comment",
+      isPullRequestReviewComment: false,
+    };
+
+    const result = await updateClaudeComment(mockOctokit, params);
+
+    expect(mockOctokit.rest.issues.updateComment).toHaveBeenCalledWith({
+      owner: "testowner",
+      repo: "testrepo",
+      comment_id: 123456,
+      body: "Updated comment",
+    });
+
+    expect(result).toEqual({
+      id: 123456,
+      html_url: "https://github.com/owner/repo/issues/1#issuecomment-123456",
+      updated_at: "2024-01-01T00:00:00Z",
+    });
+  });
+
+  test("should update PR comment successfully", async () => {
+    const mockResponse = {
+      data: {
+        id: 789012,
+        html_url: "https://github.com/owner/repo/pull/2#issuecomment-789012",
+        updated_at: "2024-01-02T00:00:00Z",
+        body: "Updated PR comment",
+      },
+    };
+
+    // @ts-expect-error Mock implementation doesn't match full type signature
+    mockOctokit.rest.issues.updateComment = jest
+      .fn()
+      .mockResolvedValue(mockResponse);
+
+    const params: UpdateClaudeCommentParams = {
+      owner: "testowner",
+      repo: "testrepo",
+      commentId: 789012,
+      body: "Updated PR comment",
+      isPullRequestReviewComment: false,
+    };
+
+    const result = await updateClaudeComment(mockOctokit, params);
+
+    expect(mockOctokit.rest.issues.updateComment).toHaveBeenCalledWith({
+      owner: "testowner",
+      repo: "testrepo",
+      comment_id: 789012,
+      body: "Updated PR comment",
+    });
+
+    expect(result).toEqual({
+      id: 789012,
+      html_url: "https://github.com/owner/repo/pull/2#issuecomment-789012",
+      updated_at: "2024-01-02T00:00:00Z",
+    });
+  });
+
+  test("should update PR review comment successfully", async () => {
+    const mockResponse = {
+      data: {
+        id: 345678,
+        html_url: "https://github.com/owner/repo/pull/3#discussion_r345678",
+        updated_at: "2024-01-03T00:00:00Z",
+        body: "Updated review comment",
+      },
+    };
+
+    // @ts-expect-error Mock implementation doesn't match full type signature
+    mockOctokit.rest.pulls.updateReviewComment = jest
+      .fn()
+      .mockResolvedValue(mockResponse);
+
+    const params: UpdateClaudeCommentParams = {
+      owner: "testowner",
+      repo: "testrepo",
+      commentId: 345678,
+      body: "Updated review comment",
+      isPullRequestReviewComment: true,
+    };
+
+    const result = await updateClaudeComment(mockOctokit, params);
+
+    expect(mockOctokit.rest.pulls.updateReviewComment).toHaveBeenCalledWith({
+      owner: "testowner",
+      repo: "testrepo",
+      comment_id: 345678,
+      body: "Updated review comment",
+    });
+
+    expect(result).toEqual({
+      id: 345678,
+      html_url: "https://github.com/owner/repo/pull/3#discussion_r345678",
+      updated_at: "2024-01-03T00:00:00Z",
+    });
+  });
+
+  test("should fallback to issue comment API when PR review comment update fails with 404", async () => {
+    const mockError = new Error("Not Found") as any;
+    mockError.status = 404;
+
+    const mockResponse = {
+      data: {
+        id: 456789,
+        html_url: "https://github.com/owner/repo/pull/4#issuecomment-456789",
+        updated_at: "2024-01-04T00:00:00Z",
+        body: "Updated via fallback",
+      },
+    };
+
+    // @ts-expect-error Mock implementation doesn't match full type signature
+    mockOctokit.rest.pulls.updateReviewComment = jest
+      .fn()
+      .mockRejectedValue(mockError);
+    // @ts-expect-error Mock implementation doesn't match full type signature
+    mockOctokit.rest.issues.updateComment = jest
+      .fn()
+      .mockResolvedValue(mockResponse);
+
+    const params: UpdateClaudeCommentParams = {
+      owner: "testowner",
+      repo: "testrepo",
+      commentId: 456789,
+      body: "Updated via fallback",
+      isPullRequestReviewComment: true,
+    };
+
+    const result = await updateClaudeComment(mockOctokit, params);
+
+    expect(mockOctokit.rest.pulls.updateReviewComment).toHaveBeenCalledWith({
+      owner: "testowner",
+      repo: "testrepo",
+      comment_id: 456789,
+      body: "Updated via fallback",
+    });
+
+    expect(mockOctokit.rest.issues.updateComment).toHaveBeenCalledWith({
+      owner: "testowner",
+      repo: "testrepo",
+      comment_id: 456789,
+      body: "Updated via fallback",
+    });
+
+    expect(result).toEqual({
+      id: 456789,
+      html_url: "https://github.com/owner/repo/pull/4#issuecomment-456789",
+      updated_at: "2024-01-04T00:00:00Z",
+    });
+  });
+
+  test("should propagate error when PR review comment update fails with non-404 error", async () => {
+    const mockError = new Error("Internal Server Error") as any;
+    mockError.status = 500;
+
+    // @ts-expect-error Mock implementation doesn't match full type signature
+    mockOctokit.rest.pulls.updateReviewComment = jest
+      .fn()
+      .mockRejectedValue(mockError);
+
+    const params: UpdateClaudeCommentParams = {
+      owner: "testowner",
+      repo: "testrepo",
+      commentId: 567890,
+      body: "This will fail",
+      isPullRequestReviewComment: true,
+    };
+
+    await expect(updateClaudeComment(mockOctokit, params)).rejects.toEqual(
+      mockError,
+    );
+
+    expect(mockOctokit.rest.pulls.updateReviewComment).toHaveBeenCalledWith({
+      owner: "testowner",
+      repo: "testrepo",
+      comment_id: 567890,
+      body: "This will fail",
+    });
+
+    // Ensure fallback wasn't attempted
+    expect(mockOctokit.rest.issues.updateComment).not.toHaveBeenCalled();
+  });
+
+  test("should propagate error when issue comment update fails", async () => {
+    const mockError = new Error("Forbidden");
+
+    // @ts-expect-error Mock implementation doesn't match full type signature
+    mockOctokit.rest.issues.updateComment = jest
+      .fn()
+      .mockRejectedValue(mockError);
+
+    const params: UpdateClaudeCommentParams = {
+      owner: "testowner",
+      repo: "testrepo",
+      commentId: 678901,
+      body: "This will also fail",
+      isPullRequestReviewComment: false,
+    };
+
+    await expect(updateClaudeComment(mockOctokit, params)).rejects.toEqual(
+      mockError,
+    );
+
+    expect(mockOctokit.rest.issues.updateComment).toHaveBeenCalledWith({
+      owner: "testowner",
+      repo: "testrepo",
+      comment_id: 678901,
+      body: "This will also fail",
+    });
+  });
+
+  test("should handle empty body", async () => {
+    const mockResponse = {
+      data: {
+        id: 111222,
+        html_url: "https://github.com/owner/repo/issues/5#issuecomment-111222",
+        updated_at: "2024-01-05T00:00:00Z",
+        body: "",
+      },
+    };
+
+    // @ts-expect-error Mock implementation doesn't match full type signature
+    mockOctokit.rest.issues.updateComment = jest
+      .fn()
+      .mockResolvedValue(mockResponse);
+
+    const params: UpdateClaudeCommentParams = {
+      owner: "testowner",
+      repo: "testrepo",
+      commentId: 111222,
+      body: "",
+      isPullRequestReviewComment: false,
+    };
+
+    const result = await updateClaudeComment(mockOctokit, params);
+
+    expect(result).toEqual({
+      id: 111222,
+      html_url: "https://github.com/owner/repo/issues/5#issuecomment-111222",
+      updated_at: "2024-01-05T00:00:00Z",
+    });
+  });
+
+  test("should handle very long body", async () => {
+    const longBody = "x".repeat(10000);
+    const mockResponse = {
+      data: {
+        id: 333444,
+        html_url: "https://github.com/owner/repo/issues/6#issuecomment-333444",
+        updated_at: "2024-01-06T00:00:00Z",
+        body: longBody,
+      },
+    };
+
+    // @ts-expect-error Mock implementation doesn't match full type signature
+    mockOctokit.rest.issues.updateComment = jest
+      .fn()
+      .mockResolvedValue(mockResponse);
+
+    const params: UpdateClaudeCommentParams = {
+      owner: "testowner",
+      repo: "testrepo",
+      commentId: 333444,
+      body: longBody,
+      isPullRequestReviewComment: false,
+    };
+
+    const result = await updateClaudeComment(mockOctokit, params);
+
+    expect(mockOctokit.rest.issues.updateComment).toHaveBeenCalledWith({
+      owner: "testowner",
+      repo: "testrepo",
+      comment_id: 333444,
+      body: longBody,
+    });
+
+    expect(result).toEqual({
+      id: 333444,
+      html_url: "https://github.com/owner/repo/issues/6#issuecomment-333444",
+      updated_at: "2024-01-06T00:00:00Z",
+    });
+  });
+
+  test("should handle markdown formatting in body", async () => {
+    const markdownBody = `
+# Header
+- List item 1
+- List item 2
+
+\`\`\`typescript
+const code = "example";
+\`\`\`
+
+[Link](https://example.com)
+    `.trim();
+
+    const mockResponse = {
+      data: {
+        id: 555666,
+        html_url: "https://github.com/owner/repo/issues/7#issuecomment-555666",
+        updated_at: "2024-01-07T00:00:00Z",
+        body: markdownBody,
+      },
+    };
+
+    // @ts-expect-error Mock implementation doesn't match full type signature
+    mockOctokit.rest.issues.updateComment = jest
+      .fn()
+      .mockResolvedValue(mockResponse);
+
+    const params: UpdateClaudeCommentParams = {
+      owner: "testowner",
+      repo: "testrepo",
+      commentId: 555666,
+      body: markdownBody,
+      isPullRequestReviewComment: false,
+    };
+
+    const result = await updateClaudeComment(mockOctokit, params);
+
+    expect(mockOctokit.rest.issues.updateComment).toHaveBeenCalledWith({
+      owner: "testowner",
+      repo: "testrepo",
+      comment_id: 555666,
+      body: markdownBody,
+    });
+
+    expect(result).toEqual({
+      id: 555666,
+      html_url: "https://github.com/owner/repo/issues/7#issuecomment-555666",
+      updated_at: "2024-01-07T00:00:00Z",
+    });
+  });
+
+  test("should handle different response data fields", async () => {
+    const mockResponse = {
+      data: {
+        id: 777888,
+        html_url: "https://github.com/owner/repo/pull/8#discussion_r777888",
+        updated_at: "2024-01-08T12:30:45Z",
+        body: "Updated",
+        // Additional fields that might be in the response
+        created_at: "2024-01-01T00:00:00Z",
+        user: { login: "bot" },
+        node_id: "MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDc3Nzg4OA==",
+      },
+    };
+
+    // @ts-expect-error Mock implementation doesn't match full type signature
+    mockOctokit.rest.pulls.updateReviewComment = jest
+      .fn()
+      .mockResolvedValue(mockResponse);
+
+    const params: UpdateClaudeCommentParams = {
+      owner: "testowner",
+      repo: "testrepo",
+      commentId: 777888,
+      body: "Updated",
+      isPullRequestReviewComment: true,
+    };
+
+    const result = await updateClaudeComment(mockOctokit, params);
+
+    // Should only return the specific fields we care about
+    expect(result).toEqual({
+      id: 777888,
+      html_url: "https://github.com/owner/repo/pull/8#discussion_r777888",
+      updated_at: "2024-01-08T12:30:45Z",
+    });
+  });
+});