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/ISSUE_TEMPLATE/bug_report.md

@@ -0,0 +1,36 @@
+---
+name: Bug report
+about: Create a report to help us improve
+title: ""
+labels: bug
+assignees: ""
+---
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Workflow yml file**
+If it's not sensitive, consider including a paste of your full Claude workflow.yml file.
+
+**API Provider**
+
+[ ] Anthropic First-Party API (default)
+[ ] AWS Bedrock
+[ ] GCP Vertex
+
+**Additional context**
+Add any other context about the problem here.

.github/workflows/claude.yml

@@ -1,4 +1,4 @@
-name: Claude
+name: Claude Code
 
 on:
   issue_comment:
@@ -11,12 +11,12 @@ on:
     types: [submitted]
 
 jobs:
-  claude-pr:
+  claude:
     if: |
       (github.event_name == 'issue_comment' && contains(github.event.comment.body, '@claude')) ||
       (github.event_name == 'pull_request_review_comment' && contains(github.event.comment.body, '@claude')) ||
       (github.event_name == 'pull_request_review' && contains(github.event.review.body, '@claude')) ||
-      (github.event_name == 'issues' && contains(github.event.issue.body, '@claude'))
+      (github.event_name == 'issues' && (contains(github.event.issue.body, '@claude') || contains(github.event.issue.title, '@claude')))
     runs-on: ubuntu-latest
     permissions:
       contents: read
@@ -29,10 +29,11 @@ jobs:
         with:
           fetch-depth: 1
 
-      - name: Run Claude PR Agent
-        uses: anthropics/claude-code-action@main
+      - name: Run Claude Code
+        id: claude
+        uses: anthropics/claude-code-action@beta
         with:
-          timeout_minutes: "60"
           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) for testing your changes."
+          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"

.github/workflows/issue-triage.yml

@@ -0,0 +1,106 @@
+name: Claude Issue Triage
+description: Run Claude Code for issue triage in GitHub Actions
+on:
+  issues:
+    types: [opened]
+
+jobs:
+  triage-issue:
+    runs-on: ubuntu-latest
+    timeout-minutes: 10
+    permissions:
+      contents: read
+      issues: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Setup GitHub MCP Server
+        run: |
+          mkdir -p /tmp/mcp-config
+          cat > /tmp/mcp-config/mcp-servers.json << 'EOF'
+          {
+            "mcpServers": {
+              "github": {
+                "command": "docker",
+                "args": [
+                  "run",
+                  "-i",
+                  "--rm",
+                  "-e",
+                  "GITHUB_PERSONAL_ACCESS_TOKEN",
+                  "ghcr.io/github/github-mcp-server:sha-7aced2b"
+                ],
+                "env": {
+                  "GITHUB_PERSONAL_ACCESS_TOKEN": "${{ secrets.GITHUB_TOKEN }}"
+                }
+              }
+            }
+          }
+          EOF
+
+      - name: Create triage prompt
+        run: |
+          mkdir -p /tmp/claude-prompts
+          cat > /tmp/claude-prompts/triage-prompt.txt << 'EOF'
+          You're an issue triage assistant for GitHub issues. Your task is to analyze the issue and select appropriate labels from the provided list.
+
+          IMPORTANT: Don't post any comments or messages to the issue. Your only action should be to apply labels.
+
+          Issue Information:
+          - REPO: ${{ github.repository }}
+          - ISSUE_NUMBER: ${{ github.event.issue.number }}
+
+          TASK OVERVIEW:
+
+          1. First, fetch the list of labels available in this repository by running: `gh label list`. Run exactly this command with nothing else.
+
+          2. Next, use the GitHub tools to get context about the issue:
+             - You have access to these tools:
+               - mcp__github__get_issue: Use this to retrieve the current issue's details including title, description, and existing labels
+               - mcp__github__get_issue_comments: Use this to read any discussion or additional context provided in the comments
+               - mcp__github__update_issue: Use this to apply labels to the issue (do not use this for commenting)
+               - mcp__github__search_issues: Use this to find similar issues that might provide context for proper categorization and to identify potential duplicate issues
+               - mcp__github__list_issues: Use this to understand patterns in how other issues are labeled
+             - Start by using mcp__github__get_issue to get the issue details
+
+          3. Analyze the issue content, considering:
+             - The issue title and description
+             - The type of issue (bug report, feature request, question, etc.)
+             - Technical areas mentioned
+             - Severity or priority indicators
+             - User impact
+             - Components affected
+
+          4. Select appropriate labels from the available labels list provided above:
+             - Choose labels that accurately reflect the issue's nature
+             - Be specific but comprehensive
+             - Select priority labels if you can determine urgency (high-priority, med-priority, or low-priority)
+             - Consider platform labels (android, ios) if applicable
+             - If you find similar issues using mcp__github__search_issues, consider using a "duplicate" label if appropriate. Only do so if the issue is a duplicate of another OPEN issue.
+
+          5. Apply the selected labels:
+             - Use mcp__github__update_issue to apply your selected labels
+             - DO NOT post any comments explaining your decision
+             - DO NOT communicate directly with users
+             - If no labels are clearly applicable, do not apply any labels
+
+          IMPORTANT GUIDELINES:
+          - Be thorough in your analysis
+          - Only select labels from the provided list above
+          - DO NOT post any comments to the issue
+          - Your ONLY action should be to apply labels using mcp__github__update_issue
+          - It's okay to not add any labels if none are clearly applicable
+          EOF
+
+      - name: Run Claude Code for Issue Triage
+        uses: anthropics/claude-code-base-action@beta
+        with:
+          prompt_file: /tmp/claude-prompts/triage-prompt.txt
+          allowed_tools: "Bash(gh label list),mcp__github__get_issue,mcp__github__get_issue_comments,mcp__github__update_issue,mcp__github__search_issues,mcp__github__list_issues"
+          mcp_config: /tmp/mcp-config/mcp-servers.json
+          timeout_minutes: "5"
+          anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}

.gitignore

@@ -1,3 +1,4 @@
+.DS_Store
 node_modules
 
 **/.claude/settings.local.json

FAQ.md

@@ -0,0 +1,156 @@
+# Frequently Asked Questions (FAQ)
+
+This FAQ addresses common questions and gotchas when using the Claude Code GitHub Action.
+
+## Triggering and Authentication
+
+### Why doesn't tagging @claude from my automated workflow work?
+
+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?
+
+Only users with **write permissions** to the repository can trigger Claude. This is a security feature to prevent unauthorized use. Make sure the user commenting has at least write access to the repository.
+
+### Why am I getting OIDC authentication errors?
+
+If you're using the default GitHub App authentication, you must add the `id-token: write` permission to your workflow:
+
+```yaml
+permissions:
+  contents: read
+  id-token: write # Required for OIDC authentication
+```
+
+The OIDC token is required in order for the Claude GitHub app to function. If you wish to not use the GitHub app, you can instead provide a `github_token` input to the action for Claude to operate with. See the [Claude Code permissions documentation][perms] for more.
+
+## Claude's Capabilities and Limitations
+
+### Why won't Claude update workflow files when I ask it to?
+
+The GitHub App for Claude doesn't have workflow write access for security reasons. This prevents Claude from modifying CI/CD configurations that could potentially create unintended consequences. This is something we may reconsider in the future.
+
+### Why won't Claude rebase my branch?
+
+By default, Claude only uses commit tools for non-destructive changes to the branch. Claude is configured to:
+
+- Never push to branches other than where it was invoked (either its own branch or the PR branch)
+- Never force push or perform destructive operations
+
+You can grant additional tools via the `allowed_tools` input if needed:
+
+```yaml
+allowed_tools: "Bash(git rebase:*)" # Use with caution
+```
+
+### Why won't Claude create a pull request?
+
+Claude doesn't create PRs by default. Instead, it pushes commits to a branch and provides a link to a pre-filled PR submission page. This approach ensures your repository's branch protection rules are still adhered to and gives you final control over PR creation.
+
+### Why can't Claude run my tests or see CI results?
+
+Claude cannot access GitHub Actions logs, test results, or other CI/CD outputs by default. It only has access to the repository files. If you need Claude to see test results, you can either:
+
+1. Instruct Claude to run tests before making commits
+2. Copy and paste CI results into a comment for Claude to analyze
+
+This limitation exists for security reasons but may be reconsidered in the future based on user feedback.
+
+### Why does Claude only update one comment instead of creating new ones?
+
+Claude is configured to update a single comment to avoid cluttering PR/issue discussions. All of Claude's responses, including progress updates and final results, will appear in the same comment with checkboxes showing task progress.
+
+## Branch and Commit Behavior
+
+### Why did Claude create a new branch when commenting on a closed PR?
+
+Claude's branch behavior depends on the context:
+
+- **Open PRs**: Pushes directly to the existing PR branch
+- **Closed/Merged PRs**: Creates a new branch (cannot push to closed PR branches)
+- **Issues**: Always creates a new branch with a timestamp
+
+### Why are my commits shallow/missing history?
+
+For performance, Claude uses shallow clones:
+
+- PRs: `--depth=20` (last 20 commits)
+- New branches: `--depth=1` (single commit)
+
+If you need full history, you can configure this in your workflow before calling Claude in the `actions/checkout` step.
+
+```
+- uses: actions/checkout@v4
+  depth: 0 # will fetch full repo history
+```
+
+## Configuration and Tools
+
+### What's the difference between `direct_prompt` and `custom_instructions`?
+
+These inputs serve different purposes in how Claude responds:
+
+- **`direct_prompt`**: Bypasses trigger detection entirely. When provided, Claude executes this exact instruction regardless of comments or mentions. Perfect for automated workflows where you want Claude to perform a specific task on every run (e.g., "Update the API documentation based on changes in this PR").
+
+- **`custom_instructions`**: Additional context added to Claude's system prompt while still respecting normal triggers. These instructions modify Claude's behavior but don't replace the triggering comment. Use this to give Claude standing instructions like "You have been granted additional tools for ...".
+
+Example:
+
+```yaml
+# Using direct_prompt - runs automatically without @claude mention
+direct_prompt: "Review this PR for security vulnerabilities"
+
+# Using custom_instructions - still requires @claude trigger
+custom_instructions: "Focus on performance implications and suggest optimizations"
+```
+
+### Why doesn't Claude execute my bash commands?
+
+The Bash tool is **disabled by default** for security. To enable individual bash commands:
+
+```yaml
+allowed_tools: "Bash(npm:*),Bash(git:*)" # Allows only npm and git commands
+```
+
+### Can Claude work across multiple repositories?
+
+No, Claude's GitHub app token is sandboxed to the current repository only. It cannot push to any other repositories. It can, however, read public repositories, but to get access to this, you must configure it with tools to do so.
+
+## MCP Servers and Extended Functionality
+
+### What MCP servers are available by default?
+
+Claude Code Action automatically configures two MCP servers:
+
+1. **GitHub MCP server**: For GitHub API operations
+2. **File operations server**: For advanced file manipulation
+
+However, tools from these servers still need to be explicitly allowed via `allowed_tools`.
+
+## Troubleshooting
+
+### How can I debug what Claude is doing?
+
+Check the GitHub Action log for Claude's run for the full execution trace.
+
+### Why can't I trigger Claude with `@claude-mention` or `claude!`?
+
+The trigger uses word boundaries, so `@claude` must be a complete word. Variations like `@claude-bot`, `@claude!`, or `claude@mention` won't work unless you customize the `trigger_phrase`.
+
+## Best Practices
+
+1. **Always specify permissions explicitly** in your workflow file
+2. **Use GitHub Secrets** for API keys - never hardcode them
+3. **Be specific with `allowed_tools`** - only enable what's necessary
+4. **Test in a separate branch** before using on important PRs
+5. **Monitor Claude's token usage** to avoid hitting API limits
+6. **Review Claude's changes** carefully before merging
+
+## Getting Help
+
+If you encounter issues not covered here:
+
+1. Check the [GitHub Issues](https://github.com/anthropics/claude-code-action/issues)
+2. Review the [example workflows](https://github.com/anthropics/claude-code-action#examples)
+
+[perms]: https://docs.anthropic.com/en/docs/claude-code/settings#permissions

README.md

@@ -33,6 +33,10 @@ This command will guide you through setting up the GitHub app and required secre
 2. Add `ANTHROPIC_API_KEY` to your repository secrets ([Learn how to use secrets in GitHub Actions](https://docs.github.com/en/actions/security-for-github-actions/security-guides/using-secrets-in-github-actions))
 3. Copy the workflow file from [`examples/claude.yml`](./examples/claude.yml) into your repository's `.github/workflows/`
 
+## 📚 FAQ
+
+Having issues or questions? Check out our [Frequently Asked Questions](./FAQ.md) for solutions to common problems and detailed explanations of Claude's capabilities and limitations.
+
 ## Usage
 
 Add a workflow file to your repository (e.g., `.github/workflows/claude.yml`):
@@ -61,6 +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
@@ -78,13 +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
@@ -229,6 +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:
@@ -446,7 +528,7 @@ anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}
 ```
 
 This applies to all sensitive values including API keys, access tokens, and credentials.
-We also reccomend that you always use short-lived tokens when possible
+We also recommend that you always use short-lived tokens when possible
 
 ## License
 

action.yml

@@ -12,6 +12,9 @@ inputs:
   assignee_trigger:
     description: "The assignee username that triggers the action (e.g. @claude)"
     required: false
+  base_branch:
+    description: "The branch to use as the base/source when creating new branches (defaults to repository default branch)"
+    required: false
 
   # Claude Code configuration
   model:
@@ -36,6 +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:
@@ -67,7 +76,7 @@ runs:
   using: "composite"
   steps:
     - name: Install Bun
-      uses: oven-sh/setup-bun@v2
+      uses: oven-sh/setup-bun@735343b667d3e6f658f44d0eca948eb6282f2b76 # https://github.com/oven-sh/setup-bun/releases/tag/v2.0.2
       with:
         bun-version: 1.2.11
 
@@ -85,16 +94,18 @@ runs:
       env:
         TRIGGER_PHRASE: ${{ inputs.trigger_phrase }}
         ASSIGNEE_TRIGGER: ${{ inputs.assignee_trigger }}
+        BASE_BRANCH: ${{ inputs.base_branch }}
         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@beta
+      uses: anthropics/claude-code-base-action@ashwin/debug
       with:
         prompt_file: /tmp/claude-prompts/claude-prompt.txt
         allowed_tools: ${{ env.ALLOWED_TOOLS }}
@@ -105,11 +116,15 @@ 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 }}
         GITHUB_TOKEN: ${{ steps.prepare.outputs.GITHUB_TOKEN }}
 
+        # Provider configuration
+        ANTHROPIC_BASE_URL: ${{ env.ANTHROPIC_BASE_URL }}
+
         # AWS configuration
         AWS_REGION: ${{ env.AWS_REGION }}
         AWS_ACCESS_KEY_ID: ${{ env.AWS_ACCESS_KEY_ID }}
@@ -143,10 +158,12 @@ runs:
         TRIGGER_COMMENT_ID: ${{ github.event.comment.id }}
         CLAUDE_BRANCH: ${{ steps.prepare.outputs.CLAUDE_BRANCH }}
         IS_PR: ${{ github.event.issue.pull_request != null || github.event_name == 'pull_request_review_comment' }}
-        DEFAULT_BRANCH: ${{ steps.prepare.outputs.DEFAULT_BRANCH }}
+        BASE_BRANCH: ${{ steps.prepare.outputs.BASE_BRANCH }}
         CLAUDE_SUCCESS: ${{ steps.claude-code.outputs.conclusion == 'success' }}
         OUTPUT_FILE: ${{ steps.claude-code.outputs.execution_file || '' }}
         TRIGGER_USERNAME: ${{ github.event.comment.user.login || github.event.issue.user.login || github.event.pull_request.user.login || github.event.sender.login || github.triggering_actor || github.actor || '' }}
+        PREPARE_SUCCESS: ${{ steps.prepare.outcome == 'success' }}
+        PREPARE_ERROR: ${{ steps.prepare.outputs.prepare_error || '' }}
 
     - name: Display Claude Code Report
       if: steps.prepare.outputs.contains_trigger == 'true' && steps.claude-code.outputs.execution_file != ''

src/create-prompt/index.ts

@@ -9,8 +9,8 @@ import {
   formatComments,
   formatReviewComments,
   formatChangedFilesWithSHA,
-  stripHtmlComments,
 } from "../github/data/formatter";
+import { sanitizeContent } from "../github/utils/sanitizer";
 import {
   isIssuesEvent,
   isIssueCommentEvent,
@@ -31,37 +31,40 @@ 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(
-  eventData: EventData,
-  customAllowedTools?: string,
-): string {
+export function buildAllowedToolsString(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}`;
+  if (customAllowedTools && customAllowedTools.length > 0) {
+    allAllowedTools = `${allAllowedTools},${customAllowedTools.join(",")}`;
   }
   return allAllowedTools;
 }
 
 export function buildDisallowedToolsString(
-  customDisallowedTools?: string,
+  customDisallowedTools?: string[],
+  allowedTools?: string[],
 ): string {
-  let allDisallowedTools = DISALLOWED_TOOLS.join(",");
-  if (customDisallowedTools) {
-    allDisallowedTools = `${allDisallowedTools},${customDisallowedTools}`;
+  let disallowedTools = [...DISALLOWED_TOOLS];
+
+  // If user has explicitly allowed some hardcoded disallowed tools, remove them from disallowed list
+  if (allowedTools && allowedTools.length > 0) {
+    disallowedTools = disallowedTools.filter(
+      (tool) => !allowedTools.includes(tool),
+    );
+  }
+
+  let allDisallowedTools = disallowedTools.join(",");
+  if (customDisallowedTools && customDisallowedTools.length > 0) {
+    if (allDisallowedTools) {
+      allDisallowedTools = `${allDisallowedTools},${customDisallowedTools.join(",")}`;
+    } else {
+      allDisallowedTools = customDisallowedTools.join(",");
+    }
   }
   return allDisallowedTools;
 }
@@ -69,7 +72,7 @@ export function buildDisallowedToolsString(
 export function prepareContext(
   context: ParsedGitHubContext,
   claudeCommentId: string,
-  defaultBranch?: string,
+  baseBranch?: string,
   claudeBranch?: string,
 ): PreparedContext {
   const repository = context.repository.full_name;
@@ -114,8 +117,10 @@ export function prepareContext(
     triggerPhrase,
     ...(triggerUsername && { triggerUsername }),
     ...(customInstructions && { customInstructions }),
-    ...(allowedTools && { allowedTools }),
-    ...(disallowedTools && { disallowedTools }),
+    ...(allowedTools.length > 0 && { allowedTools: allowedTools.join(",") }),
+    ...(disallowedTools.length > 0 && {
+      disallowedTools: disallowedTools.join(","),
+    }),
     ...(directPrompt && { directPrompt }),
     ...(claudeBranch && { claudeBranch }),
   };
@@ -147,7 +152,7 @@ export function prepareContext(
         ...(commentId && { commentId }),
         commentBody,
         ...(claudeBranch && { claudeBranch }),
-        ...(defaultBranch && { defaultBranch }),
+        ...(baseBranch && { baseBranch }),
       };
       break;
 
@@ -169,7 +174,7 @@ export function prepareContext(
         prNumber,
         commentBody,
         ...(claudeBranch && { claudeBranch }),
-        ...(defaultBranch && { defaultBranch }),
+        ...(baseBranch && { baseBranch }),
       };
       break;
 
@@ -194,13 +199,13 @@ export function prepareContext(
           prNumber,
           commentBody,
           ...(claudeBranch && { claudeBranch }),
-          ...(defaultBranch && { defaultBranch }),
+          ...(baseBranch && { baseBranch }),
         };
         break;
       } else if (!claudeBranch) {
         throw new Error("CLAUDE_BRANCH is required for issue_comment event");
-      } else if (!defaultBranch) {
-        throw new Error("DEFAULT_BRANCH is required for issue_comment event");
+      } else if (!baseBranch) {
+        throw new Error("BASE_BRANCH is required for issue_comment event");
       } else if (!issueNumber) {
         throw new Error(
           "ISSUE_NUMBER is required for issue_comment event for issues",
@@ -212,7 +217,7 @@ export function prepareContext(
         commentId,
         isPR: false,
         claudeBranch: claudeBranch,
-        defaultBranch,
+        baseBranch,
         issueNumber,
         commentBody,
       };
@@ -228,8 +233,8 @@ export function prepareContext(
       if (isPR) {
         throw new Error("IS_PR must be false for issues event");
       }
-      if (!defaultBranch) {
-        throw new Error("DEFAULT_BRANCH is required for issues event");
+      if (!baseBranch) {
+        throw new Error("BASE_BRANCH is required for issues event");
       }
       if (!claudeBranch) {
         throw new Error("CLAUDE_BRANCH is required for issues event");
@@ -246,7 +251,7 @@ export function prepareContext(
           eventAction: "assigned",
           isPR: false,
           issueNumber,
-          defaultBranch,
+          baseBranch,
           claudeBranch,
           assigneeTrigger,
         };
@@ -256,7 +261,7 @@ export function prepareContext(
           eventAction: "opened",
           isPR: false,
           issueNumber,
-          defaultBranch,
+          baseBranch,
           claudeBranch,
         };
       } else {
@@ -277,7 +282,7 @@ export function prepareContext(
         isPR: true,
         prNumber,
         ...(claudeBranch && { claudeBranch }),
-        ...(defaultBranch && { defaultBranch }),
+        ...(baseBranch && { baseBranch }),
       };
       break;
 
@@ -419,26 +424,26 @@ ${
     eventData.eventName === "pull_request_review") &&
   eventData.commentBody
     ? `<trigger_comment>
-${stripHtmlComments(eventData.commentBody)}
+${sanitizeContent(eventData.commentBody)}
 </trigger_comment>`
     : ""
 }
 ${
   context.directPrompt
     ? `<direct_prompt>
-${stripHtmlComments(context.directPrompt)}
+${sanitizeContent(context.directPrompt)}
 </direct_prompt>`
     : ""
 }
-${
-  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.
-</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.
-</comment_tool_info>`
+${`<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.
+
+Tool usage example for mcp__github_file_ops__update_claude_comment:
+{
+  "body": "Your comment text here"
 }
+Only the body parameter is required - the tool automatically knows which comment to update.
+</comment_tool_info>`}
 
 Your task is to analyze the context, understand the request, and provide helpful responses and/or implement code changes as needed.
 
@@ -452,7 +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.
@@ -482,11 +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.
@@ -506,13 +511,13 @@ ${context.directPrompt ? `   - DIRECT INSTRUCTION: A direct instruction was prov
       ${
         eventData.claudeBranch
           ? `- Provide a URL to create a PR manually in this format:
-        [Create a PR](${GITHUB_SERVER_URL}/${context.repository}/compare/${eventData.defaultBranch}...<branch-name>?quick_pull=1&title=<url-encoded-title>&body=<url-encoded-body>)
+        [Create a PR](${GITHUB_SERVER_URL}/${context.repository}/compare/${eventData.baseBranch}...<branch-name>?quick_pull=1&title=<url-encoded-title>&body=<url-encoded-body>)
         - IMPORTANT: Use THREE dots (...) between branch names, not two (..)
           Example: ${GITHUB_SERVER_URL}/${context.repository}/compare/main...feature-branch (correct)
           NOT: ${GITHUB_SERVER_URL}/${context.repository}/compare/main..feature-branch (incorrect)
         - IMPORTANT: Ensure all URL parameters are properly encoded - spaces should be encoded as %20, not left as spaces
           Example: Instead of "fix: update welcome message", use "fix%3A%20update%20welcome%20message"
-        - The target-branch should be '${eventData.defaultBranch}'.
+        - The target-branch should be '${eventData.baseBranch}'.
         - The branch-name is the current branch: ${eventData.claudeBranch}
         - The body should include:
           - A clear description of the changes
@@ -541,12 +546,15 @@ ${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: ${context.claudeCommentId}.
-- This includes ALL responses: code reviews, answers to questions, progress updates, and final results.${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." : ""}
+- 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." : ""}
 - 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.
+  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"}
 - 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 (#).
@@ -573,6 +581,11 @@ What You CANNOT Do:
 - Execute commands outside the repository context
 - Run arbitrary Bash commands (unless explicitly allowed via allowed_tools configuration)
 - Perform branch operations (cannot merge branches, rebase, or perform other git operations beyond pushing commits)
+- Modify files in the .github/workflows directory (GitHub App permissions do not allow workflow modifications)
+- View CI/CD results or workflow run outputs (cannot access GitHub Actions logs or test results)
+
+When users ask you to perform actions you cannot do, politely explain the limitation and, when applicable, direct them to the FAQ for more information and workarounds:
+"I'm unable to [specific action] due to [reason]. You can find more information and potential workarounds in the [FAQ](https://github.com/anthropics/claude-code-action/blob/main/FAQ.md)."
 
 If a user asks for something outside these capabilities (and you have no other tools provided), politely explain that you cannot perform that action and suggest an alternative approach if possible.
 
@@ -594,7 +607,7 @@ f. If you are unable to complete certain steps, such as running a linter or test
 
 export async function createPrompt(
   claudeCommentId: number,
-  defaultBranch: string | undefined,
+  baseBranch: string | undefined,
   claudeBranch: string | undefined,
   githubData: FetchDataResult,
   context: ParsedGitHubContext,
@@ -603,7 +616,7 @@ export async function createPrompt(
     const preparedContext = prepareContext(
       context,
       claudeCommentId.toString(),
-      defaultBranch,
+      baseBranch,
       claudeBranch,
     );
 
@@ -622,11 +635,11 @@ export async function createPrompt(
 
     // Set allowed tools
     const allAllowedTools = buildAllowedToolsString(
-      preparedContext.eventData,
-      preparedContext.allowedTools,
+      context.inputs.allowedTools,
     );
     const allDisallowedTools = buildDisallowedToolsString(
-      preparedContext.disallowedTools,
+      context.inputs.disallowedTools,
+      context.inputs.allowedTools,
     );
 
     core.exportVariable("ALLOWED_TOOLS", allAllowedTools);

src/create-prompt/types.ts

@@ -16,7 +16,7 @@ type PullRequestReviewCommentEvent = {
   commentId?: string; // May be present for review comments
   commentBody: string;
   claudeBranch?: string;
-  defaultBranch?: string;
+  baseBranch?: string;
 };
 
 type PullRequestReviewEvent = {
@@ -25,7 +25,7 @@ type PullRequestReviewEvent = {
   prNumber: string;
   commentBody: string;
   claudeBranch?: string;
-  defaultBranch?: string;
+  baseBranch?: string;
 };
 
 type IssueCommentEvent = {
@@ -33,7 +33,7 @@ type IssueCommentEvent = {
   commentId: string;
   issueNumber: string;
   isPR: false;
-  defaultBranch: string;
+  baseBranch: string;
   claudeBranch: string;
   commentBody: string;
 };
@@ -46,7 +46,7 @@ type PullRequestCommentEvent = {
   isPR: true;
   commentBody: string;
   claudeBranch?: string;
-  defaultBranch?: string;
+  baseBranch?: string;
 };
 
 type IssueOpenedEvent = {
@@ -54,7 +54,7 @@ type IssueOpenedEvent = {
   eventAction: "opened";
   isPR: false;
   issueNumber: string;
-  defaultBranch: string;
+  baseBranch: string;
   claudeBranch: string;
 };
 
@@ -63,7 +63,7 @@ type IssueAssignedEvent = {
   eventAction: "assigned";
   isPR: false;
   issueNumber: string;
-  defaultBranch: string;
+  baseBranch: string;
   claudeBranch: string;
   assigneeTrigger: string;
 };
@@ -74,7 +74,7 @@ type PullRequestEvent = {
   isPR: true;
   prNumber: string;
   claudeBranch?: string;
-  defaultBranch?: string;
+  baseBranch?: string;
 };
 
 // Union type for all possible event types

src/entrypoints/prepare.ts

@@ -77,22 +77,29 @@ async function run() {
     // Step 10: Create prompt file
     await createPrompt(
       commentId,
-      branchInfo.defaultBranch,
+      branchInfo.baseBranch,
       branchInfo.claudeBranch,
       githubData,
       context,
     );
 
     // Step 11: Get MCP configuration
-    const mcpConfig = await prepareMcpConfig(
+    const additionalMcpConfig = process.env.MCP_CONFIG || "";
+    const mcpConfig = await prepareMcpConfig({
       githubToken,
-      context.repository.owner,
-      context.repository.repo,
-      branchInfo.currentBranch,
-    );
+      owner: context.repository.owner,
+      repo: context.repository.repo,
+      branch: branchInfo.currentBranch,
+      additionalMcpConfig,
+      claudeCommentId: commentId.toString(),
+      allowedTools: context.inputs.allowedTools,
+    });
     core.setOutput("mcp_config", mcpConfig);
   } catch (error) {
-    core.setFailed(`Prepare step failed with error: ${error}`);
+    const errorMessage = error instanceof Error ? error.message : String(error);
+    core.setFailed(`Prepare step failed with error: ${errorMessage}`);
+    // Also output the clean error message for the action to capture
+    core.setOutput("prepare_error", errorMessage);
     process.exit(1);
   }
 }

src/entrypoints/update-comment-link.ts

@@ -12,13 +12,14 @@ 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 {
     const commentId = parseInt(process.env.CLAUDE_COMMENT_ID!);
     const githubToken = process.env.GITHUB_TOKEN!;
     const claudeBranch = process.env.CLAUDE_BRANCH;
-    const defaultBranch = process.env.DEFAULT_BRANCH || "main";
+    const baseBranch = process.env.BASE_BRANCH || "main";
     const triggerUsername = process.env.TRIGGER_USERNAME;
 
     const context = parseGitHubContext();
@@ -92,7 +93,7 @@ async function run() {
       owner,
       repo,
       claudeBranch,
-      defaultBranch,
+      baseBranch,
     );
 
     // Check if we need to add PR URL when we have a new branch
@@ -102,7 +103,7 @@ async function run() {
       // Check if comment already contains a PR URL
       const serverUrlPattern = serverUrl.replace(/[.*+?^${}()|[\]\\]/g, "\\$&");
       const prUrlPattern = new RegExp(
-        `${serverUrlPattern}\\/.+\\/compare\\/${defaultBranch.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}\\.\\.\\.`,
+        `${serverUrlPattern}\\/.+\\/compare\\/${baseBranch.replace(/[.*+?^${}()|[\]\\]/g, "\\$&")}\\.\\.\\.`,
       );
       const containsPRUrl = currentBody.match(prUrlPattern);
 
@@ -113,7 +114,7 @@ async function run() {
             await octokit.rest.repos.compareCommitsWithBasehead({
               owner,
               repo,
-              basehead: `${defaultBranch}...${claudeBranch}`,
+              basehead: `${baseBranch}...${claudeBranch}`,
             });
 
           // If there are changes (commits or file changes), add the PR URL
@@ -128,7 +129,7 @@ async function run() {
             const prBody = encodeURIComponent(
               `This PR addresses ${entityType.toLowerCase()} #${context.entityNumber}\n\nGenerated with [Claude Code](https://claude.ai/code)`,
             );
-            const prUrl = `${serverUrl}/${owner}/${repo}/compare/${defaultBranch}...${claudeBranch}?quick_pull=1&title=${prTitle}&body=${prBody}`;
+            const prUrl = `${serverUrl}/${owner}/${repo}/compare/${baseBranch}...${claudeBranch}?quick_pull=1&title=${prTitle}&body=${prBody}`;
             prLink = `\n[Create a PR](${prUrl})`;
           }
         } catch (error) {
@@ -145,7 +146,16 @@ async function run() {
       duration_api_ms?: number;
     } | null = null;
     let actionFailed = false;
+    let errorDetails: string | undefined;
 
+    // First check if prepare step failed
+    const prepareSuccess = process.env.PREPARE_SUCCESS !== "false";
+    const prepareError = process.env.PREPARE_ERROR;
+
+    if (!prepareSuccess && prepareError) {
+      actionFailed = true;
+      errorDetails = prepareError;
+    } else {
       // Check for existence of output file and parse it if available
       try {
         const outputFile = process.env.OUTPUT_FILE;
@@ -157,7 +167,7 @@ async function run() {
           if (Array.isArray(outputData) && outputData.length > 0) {
             const lastElement = outputData[outputData.length - 1];
             if (
-            lastElement.role === "system" &&
+              lastElement.type === "result" &&
               "cost_usd" in lastElement &&
               "duration_ms" in lastElement
             ) {
@@ -170,7 +180,7 @@ async function run() {
           }
         }
 
-      // Check if the action failed by looking at the exit code or error marker
+        // Check if the Claude action failed
         const claudeSuccess = process.env.CLAUDE_SUCCESS !== "false";
         actionFailed = !claudeSuccess;
       } catch (error) {
@@ -178,6 +188,7 @@ async function run() {
         // If we can't read the file, check for any failure markers
         actionFailed = process.env.CLAUDE_SUCCESS === "false";
       }
+    }
 
     // Prepare input for updateCommentBody function
     const commentInput: CommentUpdateInput = {
@@ -189,27 +200,19 @@ async function run() {
       prLink,
       branchName: shouldDeleteBranch ? undefined : claudeBranch,
       triggerUsername,
+      errorDetails,
     };
 
     const updatedBody = updateCommentBody(commentInput);
 
-    // Update the comment using the appropriate API
     try {
-      if (isPRReviewComment) {
-        await octokit.rest.pulls.updateReviewComment({
+      await updateClaudeComment(octokit.rest, {
         owner,
         repo,
-          comment_id: commentId,
+        commentId,
         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/api/client.ts

@@ -9,7 +9,10 @@ export type Octokits = {
 
 export function createOctokit(token: string): Octokits {
   return {
-    rest: new Octokit({ auth: token }),
+    rest: new Octokit({
+      auth: token,
+      baseUrl: GITHUB_API_URL,
+    }),
     graphql: graphql.defaults({
       baseUrl: GITHUB_API_URL,
       headers: {

src/github/context.ts

@@ -28,10 +28,11 @@ export type ParsedGitHubContext = {
   inputs: {
     triggerPhrase: string;
     assigneeTrigger: string;
-    allowedTools: string;
-    disallowedTools: string;
+    allowedTools: string[];
+    disallowedTools: string[];
     customInstructions: string;
     directPrompt: string;
+    baseBranch?: string;
   };
 };
 
@@ -51,10 +52,17 @@ export function parseGitHubContext(): ParsedGitHubContext {
     inputs: {
       triggerPhrase: process.env.TRIGGER_PHRASE ?? "@claude",
       assigneeTrigger: process.env.ASSIGNEE_TRIGGER ?? "",
-      allowedTools: process.env.ALLOWED_TOOLS ?? "",
-      disallowedTools: process.env.DISALLOWED_TOOLS ?? "",
+      allowedTools: (process.env.ALLOWED_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/data/formatter.ts

@@ -6,10 +6,7 @@ import type {
   GitHubReview,
 } from "../types";
 import type { GitHubFileWithSHA } from "./fetcher";
-
-export function stripHtmlComments(text: string): string {
-  return text.replace(/<!--[\s\S]*?-->/g, "");
-}
+import { sanitizeContent } from "../utils/sanitizer";
 
 export function formatContext(
   contextData: GitHubPullRequest | GitHubIssue,
@@ -37,13 +34,14 @@ export function formatBody(
   body: string,
   imageUrlMap: Map<string, string>,
 ): string {
-  let processedBody = stripHtmlComments(body);
+  let processedBody = body;
 
-  // Replace image URLs with local paths
   for (const [originalUrl, localPath] of imageUrlMap) {
     processedBody = processedBody.replaceAll(originalUrl, localPath);
   }
 
+  processedBody = sanitizeContent(processedBody);
+
   return processedBody;
 }
 
@@ -53,15 +51,16 @@ export function formatComments(
 ): string {
   return comments
     .map((comment) => {
-      let body = stripHtmlComments(comment.body);
+      let body = comment.body;
 
-      // Replace image URLs with local paths if we have a mapping
       if (imageUrlMap && body) {
         for (const [originalUrl, localPath] of imageUrlMap) {
           body = body.replaceAll(originalUrl, localPath);
         }
       }
 
+      body = sanitizeContent(body);
+
       return `[${comment.author.login} at ${comment.createdAt}]: ${body}`;
     })
     .join("\n\n");
@@ -78,6 +77,19 @@ export function formatReviewComments(
   const formattedReviews = reviewData.nodes.map((review) => {
     let reviewOutput = `[Review by ${review.author.login} at ${review.submittedAt}]: ${review.state}`;
 
+    if (review.body && review.body.trim()) {
+      let body = review.body;
+
+      if (imageUrlMap) {
+        for (const [originalUrl, localPath] of imageUrlMap) {
+          body = body.replaceAll(originalUrl, localPath);
+        }
+      }
+
+      const sanitizedBody = sanitizeContent(body);
+      reviewOutput += `\n${sanitizedBody}`;
+    }
+
     if (
       review.comments &&
       review.comments.nodes &&
@@ -85,15 +97,16 @@ export function formatReviewComments(
     ) {
       const comments = review.comments.nodes
         .map((comment) => {
-          let body = stripHtmlComments(comment.body);
+          let body = comment.body;
 
-          // Replace image URLs with local paths if we have a mapping
           if (imageUrlMap) {
             for (const [originalUrl, localPath] of imageUrlMap) {
               body = body.replaceAll(originalUrl, localPath);
             }
           }
 
+          body = sanitizeContent(body);
+
           return `  [Comment on ${comment.path}:${comment.line || "?"}]: ${body}`;
         })
         .join("\n");

src/github/operations/branch-cleanup.ts

@@ -6,7 +6,7 @@ export async function checkAndDeleteEmptyBranch(
   owner: string,
   repo: string,
   claudeBranch: string | undefined,
-  defaultBranch: string,
+  baseBranch: string,
 ): Promise<{ shouldDeleteBranch: boolean; branchLink: string }> {
   let branchLink = "";
   let shouldDeleteBranch = false;
@@ -18,7 +18,7 @@ export async function checkAndDeleteEmptyBranch(
         await octokit.rest.repos.compareCommitsWithBasehead({
           owner,
           repo,
-          basehead: `${defaultBranch}...${claudeBranch}`,
+          basehead: `${baseBranch}...${claudeBranch}`,
         });
 
       // If there are no commits, mark branch for deletion

src/github/operations/branch.ts

@@ -14,7 +14,7 @@ import type { Octokits } from "../api/client";
 import type { FetchDataResult } from "../data/fetcher";
 
 export type BranchInfo = {
-  defaultBranch: string;
+  baseBranch: string;
   claudeBranch?: string;
   currentBranch: string;
 };
@@ -26,15 +26,9 @@ export async function setupBranch(
 ): Promise<BranchInfo> {
   const { owner, repo } = context.repository;
   const entityNumber = context.entityNumber;
+  const { baseBranch } = context.inputs;
   const isPR = context.isPR;
 
-  // Get the default branch first
-  const repoResponse = await octokits.rest.repos.get({
-    owner,
-    repo,
-  });
-  const defaultBranch = repoResponse.data.default_branch;
-
   if (isPR) {
     const prData = githubData.contextData as GitHubPullRequest;
     const prState = prData.state;
@@ -42,7 +36,7 @@ export async function setupBranch(
     // Check if PR is closed or merged
     if (prState === "CLOSED" || prState === "MERGED") {
       console.log(
-        `PR #${entityNumber} is ${prState}, creating new branch from default...`,
+        `PR #${entityNumber} is ${prState}, creating new branch from source...`,
       );
       // Fall through to create a new branch like we do for issues
     } else {
@@ -51,23 +45,43 @@ export async function setupBranch(
 
       const branchName = prData.headRefName;
 
-      // Execute git commands to checkout PR branch
-      await $`git fetch origin ${branchName}`;
+      // Execute git commands to checkout PR branch (shallow fetch for performance)
+      // Fetch the branch with a depth of 20 to avoid fetching too much history, while still allowing for some context
+      await $`git fetch origin --depth=20 ${branchName}`;
       await $`git checkout ${branchName}`;
 
       console.log(`Successfully checked out PR branch for PR #${entityNumber}`);
 
-      // For open PRs, return branch info
+      // For open PRs, we need to get the base branch of the PR
+      const baseBranch = prData.baseRefName;
+
       return {
-        defaultBranch,
+        baseBranch,
         currentBranch: branchName,
       };
     }
   }
 
+  // Determine source branch - use baseBranch if provided, otherwise fetch default
+  let sourceBranch: string;
+
+  if (baseBranch) {
+    // Use provided base branch for source
+    sourceBranch = baseBranch;
+  } else {
+    // No base branch provided, fetch the default branch to use as source
+    const repoResponse = await octokits.rest.repos.get({
+      owner,
+      repo,
+    });
+    sourceBranch = repoResponse.data.default_branch;
+  }
+
   // 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}...`);
+  console.log(
+    `Creating new branch for ${entityType} #${entityNumber} from source branch: ${sourceBranch}...`,
+  );
 
   const timestamp = new Date()
     .toISOString()
@@ -79,14 +93,14 @@ export async function setupBranch(
   const newBranch = `claude/${entityType}-${entityNumber}-${timestamp}`;
 
   try {
-    // Get the SHA of the default branch
-    const defaultBranchRef = await octokits.rest.git.getRef({
+    // Get the SHA of the source branch
+    const sourceBranchRef = await octokits.rest.git.getRef({
       owner,
       repo,
-      ref: `heads/${defaultBranch}`,
+      ref: `heads/${sourceBranch}`,
     });
 
-    const currentSHA = defaultBranchRef.data.object.sha;
+    const currentSHA = sourceBranchRef.data.object.sha;
 
     console.log(`Current SHA: ${currentSHA}`);
 
@@ -98,8 +112,8 @@ export async function setupBranch(
       sha: currentSHA,
     });
 
-    // Checkout the new branch
-    await $`git fetch origin ${newBranch}`;
+    // Checkout the new branch (shallow fetch for performance)
+    await $`git fetch origin --depth=1 ${newBranch}`;
     await $`git checkout ${newBranch}`;
 
     console.log(
@@ -108,9 +122,9 @@ export async function setupBranch(
 
     // Set outputs for GitHub Actions
     core.setOutput("CLAUDE_BRANCH", newBranch);
-    core.setOutput("DEFAULT_BRANCH", defaultBranch);
+    core.setOutput("BASE_BRANCH", sourceBranch);
     return {
-      defaultBranch,
+      baseBranch: sourceBranch,
       claudeBranch: newBranch,
       currentBranch: newBranch,
     };

src/github/operations/comment-logic.ts

@@ -15,6 +15,7 @@ export type CommentUpdateInput = {
   prLink?: string;
   branchName?: string;
   triggerUsername?: string;
+  errorDetails?: string;
 };
 
 export function ensureProperlyEncodedUrl(url: string): string | null {
@@ -75,6 +76,7 @@ export function updateCommentBody(input: CommentUpdateInput): string {
     actionFailed,
     branchName,
     triggerUsername,
+    errorDetails,
   } = input;
 
   // Extract content from the original comment body
@@ -177,7 +179,14 @@ export function updateCommentBody(input: CommentUpdateInput): string {
   }
 
   // Build the new body with blank line between header and separator
-  let newBody = `${header}${links}\n\n---\n`;
+  let newBody = `${header}${links}`;
+
+  // Add error details if available
+  if (actionFailed && errorDetails) {
+    newBody += `\n\n\`\`\`\n${errorDetails}\n\`\`\``;
+  }
+
+  newBody += `\n\n---\n`;
 
   // Clean up the body content
   // Remove any existing View job run, branch links from the bottom

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)) {
-      // For PR review comments (inline comments), use the pulls API
-      await octokit.rest.pulls.updateReviewComment({
+    const isPRReviewComment = isPullRequestReviewCommentEvent(context);
+
+    await updateClaudeComment(octokit.rest, {
       owner,
       repo,
-        comment_id: commentId,
+      commentId,
       body: updatedBody,
+      isPullRequestReviewComment: isPRReviewComment,
     });
-      console.log(`✅ Updated PR review comment ${commentId} with branch link`);
-    } else {
-      // For all other comments, use the issues API
-      await octokit.rest.issues.updateComment({
-        owner,
-        repo,
-        comment_id: commentId,
-        body: updatedBody,
-      });
-      console.log(`✅ Updated issue comment ${commentId} with branch link`);
-    }
+
+    console.log(
+      `✅ Updated ${isPRReviewComment ? "PR review" : "issue"} comment ${commentId} with branch link`,
+    );
   } catch (error) {
     console.error("Error updating comment with branch link:", error);
     throw error;

src/github/token.ts

@@ -39,25 +39,19 @@ async function retryWithBackoff<T>(
     }
   }
 
-  throw new Error(
-    `Operation failed after ${maxAttempts} attempts. Last error: ${
-      lastError?.message ?? "Unknown error"
-    }`,
-  );
+  console.error(`Operation failed after ${maxAttempts} attempts`);
+  throw lastError;
 }
 
 async function getOidcToken(): Promise<string> {
   try {
     const oidcToken = await core.getIDToken("claude-code-github-action");
 
-    if (!oidcToken) {
-      throw new Error("OIDC token not found");
-    }
-
     return oidcToken;
   } catch (error) {
+    console.error("Failed to get OIDC token:", error);
     throw new Error(
-      `Failed to get OIDC token: ${error instanceof Error ? error.message : String(error)}`,
+      "Could not fetch an OIDC token. Did you remember to add `id-token: write` to your workflow permissions?",
     );
   }
 }
@@ -74,9 +68,15 @@ async function exchangeForAppToken(oidcToken: string): Promise<string> {
   );
 
   if (!response.ok) {
-    throw new Error(
-      `App token exchange failed: ${response.status} ${response.statusText}`,
+    const responseJson = (await response.json()) as {
+      error?: {
+        message?: string;
+      };
+    };
+    console.error(
+      `App token exchange failed: ${response.status} ${response.statusText} - ${responseJson?.error?.message ?? "Unknown error"}`,
     );
+    throw new Error(`${responseJson?.error?.message ?? "Unknown error"}`);
   }
 
   const appTokenData = (await response.json()) as {
@@ -117,7 +117,9 @@ export async function setupGitHubToken(): Promise<string> {
     core.setOutput("GITHUB_TOKEN", appToken);
     return appToken;
   } catch (error) {
-    core.setFailed(`Failed to setup GitHub token: ${error}`);
+    core.setFailed(
+      `Failed to setup GitHub token: ${error}.\n\nIf you instead wish to use this action with a custom GitHub token or custom GitHub app, provide a \`github_token\` in the \`uses\` section of the app in your workflow yml file.`,
+    );
     process.exit(1);
   }
 }

src/github/utils/sanitizer.ts

@@ -0,0 +1,65 @@
+export function stripInvisibleCharacters(content: string): string {
+  content = content.replace(/[\u200B\u200C\u200D\uFEFF]/g, "");
+  content = content.replace(
+    /[\u0000-\u0008\u000B\u000C\u000E-\u001F\u007F-\u009F]/g,
+    "",
+  );
+  content = content.replace(/\u00AD/g, "");
+  content = content.replace(/[\u202A-\u202E\u2066-\u2069]/g, "");
+  return content;
+}
+
+export function stripMarkdownImageAltText(content: string): string {
+  return content.replace(/!\[[^\]]*\]\(/g, "![](");
+}
+
+export function stripMarkdownLinkTitles(content: string): string {
+  content = content.replace(/(\[[^\]]*\]\([^)]+)\s+"[^"]*"/g, "$1");
+  content = content.replace(/(\[[^\]]*\]\([^)]+)\s+'[^']*'/g, "$1");
+  return content;
+}
+
+export function stripHiddenAttributes(content: string): string {
+  content = content.replace(/\salt\s*=\s*["'][^"']*["']/gi, "");
+  content = content.replace(/\salt\s*=\s*[^\s>]+/gi, "");
+  content = content.replace(/\stitle\s*=\s*["'][^"']*["']/gi, "");
+  content = content.replace(/\stitle\s*=\s*[^\s>]+/gi, "");
+  content = content.replace(/\saria-label\s*=\s*["'][^"']*["']/gi, "");
+  content = content.replace(/\saria-label\s*=\s*[^\s>]+/gi, "");
+  content = content.replace(/\sdata-[a-zA-Z0-9-]+\s*=\s*["'][^"']*["']/gi, "");
+  content = content.replace(/\sdata-[a-zA-Z0-9-]+\s*=\s*[^\s>]+/gi, "");
+  content = content.replace(/\splaceholder\s*=\s*["'][^"']*["']/gi, "");
+  content = content.replace(/\splaceholder\s*=\s*[^\s>]+/gi, "");
+  return content;
+}
+
+export function normalizeHtmlEntities(content: string): string {
+  content = content.replace(/&#(\d+);/g, (_, dec) => {
+    const num = parseInt(dec, 10);
+    if (num >= 32 && num <= 126) {
+      return String.fromCharCode(num);
+    }
+    return "";
+  });
+  content = content.replace(/&#x([0-9a-fA-F]+);/g, (_, hex) => {
+    const num = parseInt(hex, 16);
+    if (num >= 32 && num <= 126) {
+      return String.fromCharCode(num);
+    }
+    return "";
+  });
+  return content;
+}
+
+export function sanitizeContent(content: string): string {
+  content = stripHtmlComments(content);
+  content = stripInvisibleCharacters(content);
+  content = stripMarkdownImageAltText(content);
+  content = stripMarkdownLinkTitles(content);
+  content = stripHiddenAttributes(content);
+  content = normalizeHtmlEntities(content);
+  return content;
+}
+
+export const stripHtmlComments = (content: string) =>
+  content.replace(/<!--[\s\S]*?-->/g, "");

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

@@ -4,8 +4,11 @@ import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
 import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
 import { z } from "zod";
 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: {
@@ -36,6 +39,7 @@ type GitHubNewCommit = {
 const REPO_OWNER = process.env.REPO_OWNER;
 const REPO_NAME = process.env.REPO_NAME;
 const BRANCH_NAME = process.env.BRANCH_NAME;
+const REPO_DIR = process.env.REPO_DIR || process.cwd();
 
 if (!REPO_OWNER || !REPO_NAME || !BRANCH_NAME) {
   console.error(
@@ -71,18 +75,9 @@ server.tool(
         throw new Error("GITHUB_TOKEN environment variable is required");
       }
 
-      // Convert absolute paths to relative if they match CWD
-      const cwd = process.cwd();
       const processedFiles = files.map((filePath) => {
         if (filePath.startsWith("/")) {
-          if (filePath.startsWith(cwd)) {
-            // Strip CWD from absolute path
-            return filePath.slice(cwd.length + 1);
-          } else {
-            throw new Error(
-              `Path '${filePath}' must be relative to repository root or within current working directory`,
-            );
-          }
+          return filePath.slice(1);
         }
         return filePath;
       });
@@ -126,7 +121,11 @@ server.tool(
       // 3. Create tree entries for all files
       const treeEntries = await Promise.all(
         processedFiles.map(async (filePath) => {
-          const content = await readFile(filePath, "utf-8");
+          const fullPath = filePath.startsWith("/")
+            ? filePath
+            : join(REPO_DIR, filePath);
+
+          const content = await readFile(fullPath, "utf-8");
           return {
             path: filePath,
             mode: "100644",
@@ -232,13 +231,16 @@ server.tool(
         ],
       };
     } catch (error) {
+      const errorMessage =
+        error instanceof Error ? error.message : String(error);
       return {
         content: [
           {
             type: "text",
-            text: `Error: ${error instanceof Error ? error.message : String(error)}`,
+            text: `Error: ${errorMessage}`,
           },
         ],
+        error: errorMessage,
         isError: true,
       };
     }
@@ -423,13 +425,79 @@ server.tool(
         ],
       };
     } catch (error) {
+      const errorMessage =
+        error instanceof Error ? error.message : String(error);
       return {
         content: [
           {
             type: "text",
-            text: `Error: ${error instanceof Error ? error.message : String(error)}`,
+            text: `Error: ${errorMessage}`,
           },
         ],
+        error: errorMessage,
+        isError: true,
+      };
+    }
+  },
+);
+
+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,
       };
     }

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,
-  owner: string,
-  repo: string,
-  branch: string,
+  params: PrepareConfigParams,
 ): 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: [
@@ -34,12 +42,65 @@ export async function prepareMcpConfig(
             REPO_OWNER: owner,
             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/comment-logic.test.ts

@@ -39,6 +39,25 @@ describe("updateCommentBody", () => {
       expect(result).toContain("**Claude encountered an error after 45s**");
     });
 
+    it("includes error details when provided", () => {
+      const input = {
+        ...baseInput,
+        currentBody: "Claude Code is working...",
+        actionFailed: true,
+        executionDetails: { duration_ms: 45000 },
+        errorDetails: "Failed to fetch issue data",
+      };
+
+      const result = updateCommentBody(input);
+      expect(result).toContain("**Claude encountered an error after 45s**");
+      expect(result).toContain("[View job]");
+      expect(result).toContain("```\nFailed to fetch issue data\n```");
+      // Ensure error details come after the header/links
+      const errorIndex = result.indexOf("```");
+      const headerIndex = result.indexOf("**Claude encountered an error");
+      expect(errorIndex).toBeGreaterThan(headerIndex);
+    });
+
     it("handles username extraction from content when not provided", () => {
       const input = {
         ...baseInput,

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 = {
@@ -127,7 +126,7 @@ describe("generatePrompt", () => {
         eventName: "issue_comment",
         commentId: "67890",
         isPR: false,
-        defaultBranch: "main",
+        baseBranch: "main",
         claudeBranch: "claude/issue-67890-20240101_120000",
         issueNumber: "67890",
         commentBody: "@claude please fix this",
@@ -183,7 +182,7 @@ describe("generatePrompt", () => {
         eventAction: "opened",
         isPR: false,
         issueNumber: "789",
-        defaultBranch: "main",
+        baseBranch: "main",
         claudeBranch: "claude/issue-789-20240101_120000",
       },
     };
@@ -210,7 +209,7 @@ describe("generatePrompt", () => {
         eventAction: "assigned",
         isPR: false,
         issueNumber: "999",
-        defaultBranch: "develop",
+        baseBranch: "develop",
         claudeBranch: "claude/issue-999-20240101_120000",
         assigneeTrigger: "claude-bot",
       },
@@ -238,7 +237,7 @@ describe("generatePrompt", () => {
         eventAction: "opened",
         isPR: false,
         issueNumber: "789",
-        defaultBranch: "main",
+        baseBranch: "main",
         claudeBranch: "claude/issue-789-20240101_120000",
       },
     };
@@ -285,7 +284,7 @@ describe("generatePrompt", () => {
         commentId: "67890",
         isPR: false,
         issueNumber: "123",
-        defaultBranch: "main",
+        baseBranch: "main",
         claudeBranch: "claude/issue-67890-20240101_120000",
         commentBody: "@claude please fix this",
       },
@@ -307,7 +306,7 @@ describe("generatePrompt", () => {
         commentId: "67890",
         isPR: false,
         issueNumber: "123",
-        defaultBranch: "main",
+        baseBranch: "main",
         claudeBranch: "claude/issue-67890-20240101_120000",
         commentBody: "@claude please fix this",
       },
@@ -362,7 +361,7 @@ describe("generatePrompt", () => {
         eventAction: "opened",
         isPR: false,
         issueNumber: "789",
-        defaultBranch: "main",
+        baseBranch: "main",
         claudeBranch: "claude/issue-789-20240101_120000",
       },
     };
@@ -400,7 +399,7 @@ describe("generatePrompt", () => {
         commentId: "67890",
         isPR: false,
         issueNumber: "123",
-        defaultBranch: "main",
+        baseBranch: "main",
         claudeBranch: "claude/issue-123-20240101_120000",
         commentBody: "@claude please fix this",
       },
@@ -432,7 +431,7 @@ describe("generatePrompt", () => {
         prNumber: "456",
         commentBody: "@claude please fix this",
         claudeBranch: "claude/pr-456-20240101_120000",
-        defaultBranch: "main",
+        baseBranch: "main",
       },
     };
 
@@ -470,7 +469,7 @@ describe("generatePrompt", () => {
         isPR: true,
         prNumber: "456",
         commentBody: "@claude please fix this",
-        // No claudeBranch or defaultBranch for open PRs
+        // No claudeBranch or baseBranch for open PRs
       },
     };
 
@@ -503,7 +502,7 @@ describe("generatePrompt", () => {
         prNumber: "789",
         commentBody: "@claude please update this",
         claudeBranch: "claude/pr-789-20240101_123000",
-        defaultBranch: "develop",
+        baseBranch: "develop",
       },
     };
 
@@ -531,7 +530,7 @@ describe("generatePrompt", () => {
         commentId: "review-comment-123",
         commentBody: "@claude fix this issue",
         claudeBranch: "claude/pr-999-20240101_140000",
-        defaultBranch: "main",
+        baseBranch: "main",
       },
     };
 
@@ -559,7 +558,7 @@ describe("generatePrompt", () => {
         isPR: true,
         prNumber: "555",
         claudeBranch: "claude/pr-555-20240101_150000",
-        defaultBranch: "main",
+        baseBranch: "main",
       },
     };
 
@@ -604,7 +603,7 @@ describe("getEventTypeAndContext", () => {
         eventAction: "assigned",
         isPR: false,
         issueNumber: "999",
-        defaultBranch: "main",
+        baseBranch: "main",
         claudeBranch: "claude/issue-999-20240101_120000",
         assigneeTrigger: "claude-bot",
       },
@@ -619,15 +618,7 @@ describe("getEventTypeAndContext", () => {
 
 describe("buildAllowedToolsString", () => {
   test("should return issue comment tool for regular events", () => {
-    const mockEventData: EventData = {
-      eventName: "issue_comment",
-      commentId: "123",
-      isPR: true,
-      prNumber: "456",
-      commentBody: "Test comment",
-    };
-
-    const result = buildAllowedToolsString(mockEventData);
+    const result = buildAllowedToolsString();
 
     // 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 = {
-      eventName: "pull_request_review_comment",
-      isPR: true,
-      prNumber: "456",
-      commentBody: "Test review comment",
-      commentId: "789",
-    };
-
-    const result = buildAllowedToolsString(mockEventData);
+    const result = buildAllowedToolsString();
 
     // 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 = {
-      eventName: "issue_comment",
-      commentId: "123",
-      isPR: true,
-      prNumber: "456",
-      commentBody: "Test comment",
-    };
-
-    const customTools = "Tool1,Tool2,Tool3";
-    const result = buildAllowedToolsString(mockEventData, customTools);
+    const customTools = ["Tool1", "Tool2", "Tool3"];
+    const result = buildAllowedToolsString(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
@@ -722,4 +699,51 @@ describe("buildDisallowedToolsString", () => {
     expect(parts).toContain("BadTool1");
     expect(parts).toContain("BadTool2");
   });
+
+  test("should remove hardcoded disallowed tools if they are in allowed tools", () => {
+    const customDisallowedTools = ["BadTool1", "BadTool2"];
+    const allowedTools = ["WebSearch", "SomeOtherTool"];
+    const result = buildDisallowedToolsString(
+      customDisallowedTools,
+      allowedTools,
+    );
+
+    // WebSearch should be removed from disallowed since it's in allowed
+    expect(result).not.toContain("WebSearch");
+
+    // WebFetch should still be disallowed since it's not in allowed
+    expect(result).toContain("WebFetch");
+
+    // Custom disallowed tools should still be present
+    expect(result).toContain("BadTool1");
+    expect(result).toContain("BadTool2");
+  });
+
+  test("should remove all hardcoded disallowed tools if they are all in allowed tools", () => {
+    const allowedTools = ["WebSearch", "WebFetch", "SomeOtherTool"];
+    const result = buildDisallowedToolsString(undefined, allowedTools);
+
+    // Both hardcoded disallowed tools should be removed
+    expect(result).not.toContain("WebSearch");
+    expect(result).not.toContain("WebFetch");
+
+    // Result should be empty since no custom disallowed tools provided
+    expect(result).toBe("");
+  });
+
+  test("should handle custom disallowed tools when all hardcoded tools are overridden", () => {
+    const customDisallowedTools = ["BadTool1", "BadTool2"];
+    const allowedTools = ["WebSearch", "WebFetch"];
+    const result = buildDisallowedToolsString(
+      customDisallowedTools,
+      allowedTools,
+    );
+
+    // Hardcoded tools should be removed
+    expect(result).not.toContain("WebSearch");
+    expect(result).not.toContain("WebFetch");
+
+    // Only custom disallowed tools should remain
+    expect(result).toBe("BadTool1,BadTool2");
+  });
 });

test/data-formatter.test.ts

@@ -6,7 +6,6 @@ import {
   formatReviewComments,
   formatChangedFiles,
   formatChangedFilesWithSHA,
-  stripHtmlComments,
 } from "../src/github/data/formatter";
 import type {
   GitHubPullRequest,
@@ -99,9 +98,9 @@ Some more text.`;
 
     const result = formatBody(body, imageUrlMap);
     expect(result)
-      .toBe(`Here is some text with an image: ![screenshot](/tmp/github-images/image-1234-0.png)
+      .toBe(`Here is some text with an image: ![](/tmp/github-images/image-1234-0.png)
     
-And another one: ![another](/tmp/github-images/image-1234-1.jpg)
+And another one: ![](/tmp/github-images/image-1234-1.jpg)
 
 Some more text.`);
   });
@@ -124,7 +123,7 @@ Some more text.`);
     ]);
 
     const result = formatBody(body, imageUrlMap);
-    expect(result).toBe("![image](https://example.com/image.png)");
+    expect(result).toBe("![](https://example.com/image.png)");
   });
 
   test("handles multiple occurrences of same image", () => {
@@ -139,8 +138,8 @@ Second: ![img](https://github.com/user-attachments/assets/test.png)`;
     ]);
 
     const result = formatBody(body, imageUrlMap);
-    expect(result).toBe(`First: ![img](/tmp/github-images/image-1234-0.png)
-Second: ![img](/tmp/github-images/image-1234-0.png)`);
+    expect(result).toBe(`First: ![](/tmp/github-images/image-1234-0.png)
+Second: ![](/tmp/github-images/image-1234-0.png)`);
   });
 });
 
@@ -205,7 +204,7 @@ describe("formatComments", () => {
 
     const result = formatComments(comments, imageUrlMap);
     expect(result).toBe(
-      `[user1 at 2023-01-01T00:00:00Z]: Check out this screenshot: ![screenshot](/tmp/github-images/image-1234-0.png)\n\n[user2 at 2023-01-02T00:00:00Z]: Here's another image: ![bug](/tmp/github-images/image-1234-1.jpg)`,
+      `[user1 at 2023-01-01T00:00:00Z]: Check out this screenshot: ![](/tmp/github-images/image-1234-0.png)\n\n[user2 at 2023-01-02T00:00:00Z]: Here's another image: ![](/tmp/github-images/image-1234-1.jpg)`,
     );
   });
 
@@ -233,7 +232,7 @@ describe("formatComments", () => {
 
     const result = formatComments(comments, imageUrlMap);
     expect(result).toBe(
-      `[user1 at 2023-01-01T00:00:00Z]: Two images: ![first](/tmp/github-images/image-1234-0.png) and ![second](/tmp/github-images/image-1234-1.png)`,
+      `[user1 at 2023-01-01T00:00:00Z]: Two images: ![](/tmp/github-images/image-1234-0.png) and ![](/tmp/github-images/image-1234-1.png)`,
     );
   });
 
@@ -250,7 +249,7 @@ describe("formatComments", () => {
 
     const result = formatComments(comments);
     expect(result).toBe(
-      `[user1 at 2023-01-01T00:00:00Z]: Image: ![test](https://github.com/user-attachments/assets/test.png)`,
+      `[user1 at 2023-01-01T00:00:00Z]: Image: ![](https://github.com/user-attachments/assets/test.png)`,
     );
   });
 });
@@ -294,7 +293,7 @@ describe("formatReviewComments", () => {
 
     const result = formatReviewComments(reviewData);
     expect(result).toBe(
-      `[Review by reviewer1 at 2023-01-01T00:00:00Z]: APPROVED\n  [Comment on src/index.ts:42]: Nice implementation\n  [Comment on src/utils.ts:?]: Consider adding error handling`,
+      `[Review by reviewer1 at 2023-01-01T00:00:00Z]: APPROVED\nThis is a great PR! LGTM.\n  [Comment on src/index.ts:42]: Nice implementation\n  [Comment on src/utils.ts:?]: Consider adding error handling`,
     );
   });
 
@@ -317,7 +316,7 @@ describe("formatReviewComments", () => {
 
     const result = formatReviewComments(reviewData);
     expect(result).toBe(
-      `[Review by reviewer1 at 2023-01-01T00:00:00Z]: APPROVED`,
+      `[Review by reviewer1 at 2023-01-01T00:00:00Z]: APPROVED\nLooks good to me!`,
     );
   });
 
@@ -384,7 +383,7 @@ describe("formatReviewComments", () => {
 
     const result = formatReviewComments(reviewData);
     expect(result).toBe(
-      `[Review by reviewer1 at 2023-01-01T00:00:00Z]: CHANGES_REQUESTED\n\n[Review by reviewer2 at 2023-01-02T00:00:00Z]: APPROVED`,
+      `[Review by reviewer1 at 2023-01-01T00:00:00Z]: CHANGES_REQUESTED\nNeeds changes\n\n[Review by reviewer2 at 2023-01-02T00:00:00Z]: APPROVED\nLGTM`,
     );
   });
 
@@ -438,7 +437,7 @@ describe("formatReviewComments", () => {
 
     const result = formatReviewComments(reviewData, imageUrlMap);
     expect(result).toBe(
-      `[Review by reviewer1 at 2023-01-01T00:00:00Z]: APPROVED\n  [Comment on src/index.ts:42]: Comment with image: ![comment-img](/tmp/github-images/image-1234-1.png)`,
+      `[Review by reviewer1 at 2023-01-01T00:00:00Z]: APPROVED\nReview with image: ![](/tmp/github-images/image-1234-0.png)\n  [Comment on src/index.ts:42]: Comment with image: ![](/tmp/github-images/image-1234-1.png)`,
     );
   });
 
@@ -482,7 +481,7 @@ describe("formatReviewComments", () => {
 
     const result = formatReviewComments(reviewData, imageUrlMap);
     expect(result).toBe(
-      `[Review by reviewer1 at 2023-01-01T00:00:00Z]: APPROVED\n  [Comment on src/main.ts:15]: Two issues: ![issue1](/tmp/github-images/image-1234-0.png) and ![issue2](/tmp/github-images/image-1234-1.png)`,
+      `[Review by reviewer1 at 2023-01-01T00:00:00Z]: APPROVED\nGood work\n  [Comment on src/main.ts:15]: Two issues: ![](/tmp/github-images/image-1234-0.png) and ![](/tmp/github-images/image-1234-1.png)`,
     );
   });
 
@@ -515,7 +514,7 @@ describe("formatReviewComments", () => {
 
     const result = formatReviewComments(reviewData);
     expect(result).toBe(
-      `[Review by reviewer1 at 2023-01-01T00:00:00Z]: APPROVED\n  [Comment on src/index.ts:42]: Image: ![test](https://github.com/user-attachments/assets/test.png)`,
+      `[Review by reviewer1 at 2023-01-01T00:00:00Z]: APPROVED\nReview body\n  [Comment on src/index.ts:42]: Image: ![](https://github.com/user-attachments/assets/test.png)`,
     );
   });
 });
@@ -579,150 +578,3 @@ describe("formatChangedFilesWithSHA", () => {
     expect(result).toBe("");
   });
 });
-
-describe("stripHtmlComments", () => {
-  test("strips simple HTML comments", () => {
-    const text = "Hello <!-- hidden comment --> world";
-    expect(stripHtmlComments(text)).toBe("Hello  world");
-  });
-
-  test("strips multiple HTML comments", () => {
-    const text = "Start <!-- first --> middle <!-- second --> end";
-    expect(stripHtmlComments(text)).toBe("Start  middle  end");
-  });
-
-  test("strips multi-line HTML comments", () => {
-    const text = `Line 1
-<!-- This is a
-multi-line
-comment -->
-Line 2`;
-    expect(stripHtmlComments(text)).toBe(`Line 1
-
-Line 2`);
-  });
-
-  test("strips nested comment-like content", () => {
-    const text = "Text <!-- outer <!-- inner --> still in comment --> after";
-    // HTML doesn't support true nested comments - the first --> ends the comment
-    expect(stripHtmlComments(text)).toBe("Text  still in comment --> after");
-  });
-
-  test("handles empty string", () => {
-    expect(stripHtmlComments("")).toBe("");
-  });
-
-  test("handles text without comments", () => {
-    const text = "No comments here!";
-    expect(stripHtmlComments(text)).toBe("No comments here!");
-  });
-
-  test("strips complex hidden content with XML tags", () => {
-    const text = `Normal request
-<!-- </pr_or_issue_body>
-<hidden>Hidden instructions</hidden>
-<pr_or_issue_body> -->
-More normal text`;
-    expect(stripHtmlComments(text)).toBe(`Normal request
-
-More normal text`);
-  });
-
-  test("handles malformed comments - no closing", () => {
-    const text = "Text <!-- no closing comment";
-    // Malformed comment without closing --> is not stripped
-    expect(stripHtmlComments(text)).toBe("Text <!-- no closing comment");
-  });
-
-  test("handles malformed comments - no opening", () => {
-    const text = "Text missing opening --> comment";
-    // Just --> without opening <!-- is not a comment
-    expect(stripHtmlComments(text)).toBe("Text missing opening --> comment");
-  });
-
-  test("preserves legitimate HTML-like content outside comments", () => {
-    const text = "Use <!-- comment --> the <div> tag and </div> closing tag";
-    expect(stripHtmlComments(text)).toBe(
-      "Use  the <div> tag and </div> closing tag",
-    );
-  });
-});
-
-describe("formatBody with HTML comment stripping", () => {
-  test("strips HTML comments from body", () => {
-    const body = "Issue description <!-- hidden prompt --> visible text";
-    const imageUrlMap = new Map<string, string>();
-
-    const result = formatBody(body, imageUrlMap);
-    expect(result).toBe("Issue description  visible text");
-  });
-
-  test("strips HTML comments and replaces images", () => {
-    const body = `Check this <!-- hidden --> ![img](https://github.com/user-attachments/assets/test.png)`;
-    const imageUrlMap = new Map([
-      [
-        "https://github.com/user-attachments/assets/test.png",
-        "/tmp/github-images/image-1234-0.png",
-      ],
-    ]);
-
-    const result = formatBody(body, imageUrlMap);
-    expect(result).toBe(
-      "Check this  ![img](/tmp/github-images/image-1234-0.png)",
-    );
-  });
-});
-
-describe("formatComments with HTML comment stripping", () => {
-  test("strips HTML comments from comment bodies", () => {
-    const comments: GitHubComment[] = [
-      {
-        id: "1",
-        databaseId: "100001",
-        body: "Good work <!-- inject prompt --> on this PR",
-        author: { login: "user1" },
-        createdAt: "2023-01-01T00:00:00Z",
-      },
-    ];
-
-    const result = formatComments(comments);
-    expect(result).toBe(
-      "[user1 at 2023-01-01T00:00:00Z]: Good work  on this PR",
-    );
-  });
-});
-
-describe("formatReviewComments with HTML comment stripping", () => {
-  test("strips HTML comments from review comment bodies", () => {
-    const reviewData = {
-      nodes: [
-        {
-          id: "review1",
-          databaseId: "300001",
-          author: { login: "reviewer1" },
-          body: "LGTM",
-          state: "APPROVED",
-          submittedAt: "2023-01-01T00:00:00Z",
-          comments: {
-            nodes: [
-              {
-                id: "comment1",
-                databaseId: "200001",
-                body: "Nice work <!-- malicious --> here",
-                author: { login: "reviewer1" },
-                createdAt: "2023-01-01T00:00:00Z",
-                path: "src/index.ts",
-                line: 42,
-              },
-            ],
-          },
-        },
-      ],
-    };
-
-    const result = formatReviewComments(reviewData);
-    expect(result).toBe(
-      `[Review by reviewer1 at 2023-01-01T00:00:00Z]: APPROVED\n  [Comment on src/index.ts:42]: Nice work  here`,
-    );
-  });
-});

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/integration-sanitization.test.ts

@@ -0,0 +1,134 @@
+import { describe, expect, it } from "bun:test";
+import { formatBody, formatComments } from "../src/github/data/formatter";
+import type { GitHubComment } from "../src/github/types";
+
+describe("Sanitization Integration", () => {
+  it("should sanitize complete issue/PR body with various hidden content patterns", () => {
+    const issueBody = `
+# Feature Request: Add user dashboard
+
+## Description
+We need a new dashboard for users to track their activity.
+
+<!-- HTML comment that should be removed -->
+
+## Technical Details
+The dashboard should display:
+- User statistics ![dashboard mockup with hidden​‌‍text](dashboard.png)
+- Activity graphs <img alt="example graph description" src="graph.jpg">
+- Recent actions
+
+## Implementation Notes
+See [documentation](https://docs.example.com "internal docs title") for API details.
+
+<div data-instruction="example instruction" aria-label="dashboard label" title="hover text">
+  The implementation should follow our standard patterns.
+</div>
+
+Additional notes: Text­with­soft­hyphens and &#72;&#105;&#100;&#100;&#101;&#110; encoded content.
+
+<input placeholder="search placeholder" type="text" />
+
+Direction override test: ‮reversed‬ text should be normalized.`;
+
+    const imageUrlMap = new Map<string, string>();
+    const result = formatBody(issueBody, imageUrlMap);
+
+    // Verify hidden content is removed
+    expect(result).not.toContain("<!-- HTML comment");
+    expect(result).not.toContain("hidden​‌‍text");
+    expect(result).not.toContain("example graph description");
+    expect(result).not.toContain("internal docs title");
+    expect(result).not.toContain("example instruction");
+    expect(result).not.toContain("dashboard label");
+    expect(result).not.toContain("hover text");
+    expect(result).not.toContain("search placeholder");
+    expect(result).not.toContain("\u200B");
+    expect(result).not.toContain("\u200C");
+    expect(result).not.toContain("\u200D");
+    expect(result).not.toContain("\u00AD");
+    expect(result).not.toContain("\u202E");
+    expect(result).not.toContain("&#72;");
+
+    // Verify legitimate content is preserved
+    expect(result).toContain("# Feature Request: Add user dashboard");
+    expect(result).toContain("## Description");
+    expect(result).toContain("We need a new dashboard");
+    expect(result).toContain("User statistics");
+    expect(result).toContain("![](dashboard.png)");
+    expect(result).toContain('<img src="graph.jpg">');
+    expect(result).toContain("[documentation](https://docs.example.com)");
+    expect(result).toContain(
+      "The implementation should follow our standard patterns",
+    );
+    expect(result).toContain("Hidden encoded content");
+    expect(result).toContain('<input type="text" />');
+  });
+
+  it("should sanitize GitHub comments preserving discussion flow", () => {
+    const comments: GitHubComment[] = [
+      {
+        id: "1",
+        databaseId: "100001",
+        body: `Great idea! Here are my thoughts:
+
+1. We should consider the performance impact
+2. The UI mockup looks good: ![ui design](mockup.png)
+3. Check the [API docs](https://api.example.com "api reference") for rate limits
+
+<div aria-label="comment metadata" data-comment-type="review">
+  This change would affect multiple systems.
+</div>
+
+Note: Implementation​should​follow​best​practices.`,
+        author: { login: "reviewer1" },
+        createdAt: "2023-01-01T10:00:00Z",
+      },
+      {
+        id: "2",
+        databaseId: "100002",
+        body: `Thanks for the feedback! 
+
+<!-- Internal note: discussed with team -->
+
+I've updated the proposal based on your suggestions.
+
+&#84;&#101;&#115;&#116; &#110;&#111;&#116;&#101;: All systems checked.
+
+<span title="status update" data-status="approved">Ready for implementation</span>`,
+        author: { login: "author1" },
+        createdAt: "2023-01-01T12:00:00Z",
+      },
+    ];
+
+    const result = formatComments(comments);
+
+    // Verify hidden content is removed
+    expect(result).not.toContain("<!-- Internal note");
+    expect(result).not.toContain("api reference");
+    expect(result).not.toContain("comment metadata");
+    expect(result).not.toContain('data-comment-type="review"');
+    expect(result).not.toContain("status update");
+    expect(result).not.toContain('data-status="approved"');
+    expect(result).not.toContain("\u200B");
+    expect(result).not.toContain("&#84;");
+
+    // Verify discussion flow is preserved
+    expect(result).toContain("Great idea! Here are my thoughts:");
+    expect(result).toContain("1. We should consider the performance impact");
+    expect(result).toContain("2. The UI mockup looks good: ![](mockup.png)");
+    expect(result).toContain(
+      "3. Check the [API docs](https://api.example.com)",
+    );
+    expect(result).toContain("This change would affect multiple systems.");
+    expect(result).toContain("Implementationshouldfollowbestpractices");
+    expect(result).toContain("Thanks for the feedback!");
+    expect(result).toContain(
+      "I've updated the proposal based on your suggestions.",
+    );
+    expect(result).toContain("Test note: All systems checked.");
+    expect(result).toContain("Ready for implementation");
+    expect(result).toContain("[reviewer1 at");
+    expect(result).toContain("[author1 at");
+  });
+});

test/mockContext.ts

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

test/permissions.test.ts

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

test/prepare-context.test.ts

@@ -34,7 +34,7 @@ describe("parseEnvVarsWithContext", () => {
       beforeEach(() => {
         process.env = {
           ...BASE_ENV,
-          DEFAULT_BRANCH: "main",
+          BASE_BRANCH: "main",
           CLAUDE_BRANCH: "claude/issue-67890-20240101_120000",
         };
       });
@@ -62,7 +62,7 @@ describe("parseEnvVarsWithContext", () => {
           expect(result.eventData.claudeBranch).toBe(
             "claude/issue-67890-20240101_120000",
           );
-          expect(result.eventData.defaultBranch).toBe("main");
+          expect(result.eventData.baseBranch).toBe("main");
           expect(result.eventData.commentBody).toBe(
             "@claude can you help explain how to configure the logging system?",
           );
@@ -75,7 +75,7 @@ describe("parseEnvVarsWithContext", () => {
         ).toThrow("CLAUDE_BRANCH is required for issue_comment event");
       });
 
-      test("should throw error when DEFAULT_BRANCH is missing", () => {
+      test("should throw error when BASE_BRANCH is missing", () => {
         expect(() =>
           prepareContext(
             mockIssueCommentContext,
@@ -83,7 +83,7 @@ describe("parseEnvVarsWithContext", () => {
             undefined,
             "claude/issue-67890-20240101_120000",
           ),
-        ).toThrow("DEFAULT_BRANCH is required for issue_comment event");
+        ).toThrow("BASE_BRANCH is required for issue_comment event");
       });
     });
 
@@ -151,7 +151,7 @@ describe("parseEnvVarsWithContext", () => {
     beforeEach(() => {
       process.env = {
         ...BASE_ENV,
-        DEFAULT_BRANCH: "main",
+        BASE_BRANCH: "main",
         CLAUDE_BRANCH: "claude/issue-42-20240101_120000",
       };
     });
@@ -172,7 +172,7 @@ describe("parseEnvVarsWithContext", () => {
         result.eventData.eventAction === "opened"
       ) {
         expect(result.eventData.issueNumber).toBe("42");
-        expect(result.eventData.defaultBranch).toBe("main");
+        expect(result.eventData.baseBranch).toBe("main");
         expect(result.eventData.claudeBranch).toBe(
           "claude/issue-42-20240101_120000",
         );
@@ -195,7 +195,7 @@ describe("parseEnvVarsWithContext", () => {
         result.eventData.eventAction === "assigned"
       ) {
         expect(result.eventData.issueNumber).toBe("123");
-        expect(result.eventData.defaultBranch).toBe("main");
+        expect(result.eventData.baseBranch).toBe("main");
         expect(result.eventData.claudeBranch).toBe(
           "claude/issue-123-20240101_120000",
         );
@@ -209,7 +209,7 @@ describe("parseEnvVarsWithContext", () => {
       ).toThrow("CLAUDE_BRANCH is required for issues event");
     });
 
-    test("should throw error when DEFAULT_BRANCH is missing for issues", () => {
+    test("should throw error when BASE_BRANCH is missing for issues", () => {
       expect(() =>
         prepareContext(
           mockIssueOpenedContext,
@@ -217,7 +217,7 @@ describe("parseEnvVarsWithContext", () => {
           undefined,
           "claude/issue-42-20240101_120000",
         ),
-      ).toThrow("DEFAULT_BRANCH is required for issues event");
+      ).toThrow("BASE_BRANCH is required for issues event");
     });
   });
 
@@ -242,7 +242,7 @@ describe("parseEnvVarsWithContext", () => {
         ...mockPullRequestCommentContext,
         inputs: {
           ...mockPullRequestCommentContext.inputs,
-          allowedTools: "Tool1,Tool2",
+          allowedTools: ["Tool1", "Tool2"],
         },
       });
       const result = prepareContext(contextWithAllowedTools, "12345");

test/sanitizer.test.ts

@@ -0,0 +1,259 @@
+import { describe, expect, it } from "bun:test";
+import {
+  stripInvisibleCharacters,
+  stripMarkdownImageAltText,
+  stripMarkdownLinkTitles,
+  stripHiddenAttributes,
+  normalizeHtmlEntities,
+  sanitizeContent,
+  stripHtmlComments,
+} from "../src/github/utils/sanitizer";
+
+describe("stripInvisibleCharacters", () => {
+  it("should remove zero-width characters", () => {
+    expect(stripInvisibleCharacters("Hello\u200BWorld")).toBe("HelloWorld");
+    expect(stripInvisibleCharacters("Text\u200C\u200D")).toBe("Text");
+    expect(stripInvisibleCharacters("\uFEFFStart")).toBe("Start");
+  });
+
+  it("should remove control characters", () => {
+    expect(stripInvisibleCharacters("Hello\u0000World")).toBe("HelloWorld");
+    expect(stripInvisibleCharacters("Text\u001F\u007F")).toBe("Text");
+  });
+
+  it("should preserve common whitespace", () => {
+    expect(stripInvisibleCharacters("Hello\nWorld")).toBe("Hello\nWorld");
+    expect(stripInvisibleCharacters("Tab\there")).toBe("Tab\there");
+    expect(stripInvisibleCharacters("Carriage\rReturn")).toBe(
+      "Carriage\rReturn",
+    );
+  });
+
+  it("should remove soft hyphens", () => {
+    expect(stripInvisibleCharacters("Soft\u00ADHyphen")).toBe("SoftHyphen");
+  });
+
+  it("should remove Unicode direction overrides", () => {
+    expect(stripInvisibleCharacters("Text\u202A\u202BMore")).toBe("TextMore");
+    expect(stripInvisibleCharacters("\u2066Isolated\u2069")).toBe("Isolated");
+  });
+});
+
+describe("stripMarkdownImageAltText", () => {
+  it("should remove alt text from markdown images", () => {
+    expect(stripMarkdownImageAltText("![example alt text](image.png)")).toBe(
+      "![](image.png)",
+    );
+    expect(
+      stripMarkdownImageAltText("Text ![description](pic.jpg) more text"),
+    ).toBe("Text ![](pic.jpg) more text");
+  });
+
+  it("should handle multiple images", () => {
+    expect(stripMarkdownImageAltText("![one](1.png) ![two](2.png)")).toBe(
+      "![](1.png) ![](2.png)",
+    );
+  });
+
+  it("should handle empty alt text", () => {
+    expect(stripMarkdownImageAltText("![](image.png)")).toBe("![](image.png)");
+  });
+});
+
+describe("stripMarkdownLinkTitles", () => {
+  it("should remove titles from markdown links", () => {
+    expect(stripMarkdownLinkTitles('[Link](url.com "example title")')).toBe(
+      "[Link](url.com)",
+    );
+    expect(stripMarkdownLinkTitles("[Link](url.com 'example title')")).toBe(
+      "[Link](url.com)",
+    );
+  });
+
+  it("should handle multiple links", () => {
+    expect(
+      stripMarkdownLinkTitles('[One](1.com "first") [Two](2.com "second")'),
+    ).toBe("[One](1.com) [Two](2.com)");
+  });
+
+  it("should preserve links without titles", () => {
+    expect(stripMarkdownLinkTitles("[Link](url.com)")).toBe("[Link](url.com)");
+  });
+});
+
+describe("stripHiddenAttributes", () => {
+  it("should remove alt attributes", () => {
+    expect(
+      stripHiddenAttributes('<img alt="example text" src="pic.jpg">'),
+    ).toBe('<img src="pic.jpg">');
+    expect(stripHiddenAttributes("<img alt='example' src=\"pic.jpg\">")).toBe(
+      '<img src="pic.jpg">',
+    );
+    expect(stripHiddenAttributes('<img alt=example src="pic.jpg">')).toBe(
+      '<img src="pic.jpg">',
+    );
+  });
+
+  it("should remove title attributes", () => {
+    expect(
+      stripHiddenAttributes('<a title="example text" href="#">Link</a>'),
+    ).toBe('<a href="#">Link</a>');
+    expect(stripHiddenAttributes("<div title='example'>Content</div>")).toBe(
+      "<div>Content</div>",
+    );
+  });
+
+  it("should remove aria-label attributes", () => {
+    expect(
+      stripHiddenAttributes('<button aria-label="example">Click</button>'),
+    ).toBe("<button>Click</button>");
+  });
+
+  it("should remove data-* attributes", () => {
+    expect(
+      stripHiddenAttributes(
+        '<div data-test="example" data-info="more example">Text</div>',
+      ),
+    ).toBe("<div>Text</div>");
+  });
+
+  it("should remove placeholder attributes", () => {
+    expect(
+      stripHiddenAttributes('<input placeholder="example text" type="text">'),
+    ).toBe('<input type="text">');
+  });
+
+  it("should handle multiple attributes", () => {
+    expect(
+      stripHiddenAttributes(
+        '<img alt="example" title="test" src="pic.jpg" class="image">',
+      ),
+    ).toBe('<img src="pic.jpg" class="image">');
+  });
+});
+
+describe("normalizeHtmlEntities", () => {
+  it("should decode numeric entities", () => {
+    expect(normalizeHtmlEntities("&#72;&#101;&#108;&#108;&#111;")).toBe(
+      "Hello",
+    );
+    expect(normalizeHtmlEntities("&#65;&#66;&#67;")).toBe("ABC");
+  });
+
+  it("should decode hex entities", () => {
+    expect(normalizeHtmlEntities("&#x48;&#x65;&#x6C;&#x6C;&#x6F;")).toBe(
+      "Hello",
+    );
+    expect(normalizeHtmlEntities("&#x41;&#x42;&#x43;")).toBe("ABC");
+  });
+
+  it("should remove non-printable entities", () => {
+    expect(normalizeHtmlEntities("&#0;&#31;")).toBe("");
+    expect(normalizeHtmlEntities("&#x00;&#x1F;")).toBe("");
+  });
+
+  it("should preserve normal text", () => {
+    expect(normalizeHtmlEntities("Normal text")).toBe("Normal text");
+  });
+});
+
+describe("sanitizeContent", () => {
+  it("should apply all sanitization measures", () => {
+    const testContent = `
+      <!-- This is a comment -->
+      <img alt="example alt text" src="image.jpg">
+      ![example image description](screenshot.png)
+      [click here](https://example.com "example title")
+      <div data-prompt="example data" aria-label="example label">
+        Normal text with hidden\u200Bcharacters
+      </div>
+      &#72;&#105;&#100;&#100;&#101;&#110; message
+    `;
+
+    const sanitized = sanitizeContent(testContent);
+
+    expect(sanitized).not.toContain("<!-- This is a comment -->");
+    expect(sanitized).not.toContain("example alt text");
+    expect(sanitized).not.toContain("example image description");
+    expect(sanitized).not.toContain("example title");
+    expect(sanitized).not.toContain("example data");
+    expect(sanitized).not.toContain("example label");
+    expect(sanitized).not.toContain("\u200B");
+    expect(sanitized).not.toContain("alt=");
+    expect(sanitized).not.toContain("data-prompt=");
+    expect(sanitized).not.toContain("aria-label=");
+
+    expect(sanitized).toContain("Normal text with hiddencharacters");
+    expect(sanitized).toContain("Hidden message");
+    expect(sanitized).toContain('<img src="image.jpg">');
+    expect(sanitized).toContain("![](screenshot.png)");
+    expect(sanitized).toContain("[click here](https://example.com)");
+  });
+
+  it("should handle complex nested patterns", () => {
+    const complexContent = `
+      Text with ![alt \u200B text](image.png) and more.
+      <a href="#" title="example\u00ADtitle">Link</a>
+      <div data-x="&#72;&#105;">Content</div>
+    `;
+
+    const sanitized = sanitizeContent(complexContent);
+
+    expect(sanitized).not.toContain("\u200B");
+    expect(sanitized).not.toContain("\u00AD");
+    expect(sanitized).not.toContain("alt ");
+    expect(sanitized).not.toContain('title="');
+    expect(sanitized).not.toContain('data-x="');
+    expect(sanitized).toContain("![](image.png)");
+    expect(sanitized).toContain('<a href="#">Link</a>');
+  });
+
+  it("should preserve legitimate markdown and HTML", () => {
+    const legitimateContent = `
+      # Heading
+      
+      This is **bold** and *italic* text.
+      
+      Here's a normal image: ![](normal.jpg)
+      And a normal link: [Click here](https://example.com)
+      
+      <div class="container">
+        <p id="para">Normal paragraph</p>
+        <input type="text" name="field">
+      </div>
+    `;
+
+    const sanitized = sanitizeContent(legitimateContent);
+
+    expect(sanitized).toBe(legitimateContent);
+  });
+
+  it("should handle entity-encoded text", () => {
+    const encodedText = `
+      &#72;&#105;&#100;&#100;&#101;&#110; &#109;&#101;&#115;&#115;&#97;&#103;&#101;
+      <div title="&#101;&#120;&#97;&#109;&#112;&#108;&#101;">Test</div>
+    `;
+
+    const sanitized = sanitizeContent(encodedText);
+
+    expect(sanitized).toContain("Hidden message");
+    expect(sanitized).not.toContain('title="');
+    expect(sanitized).toContain("<div>Test</div>");
+  });
+});
+
+describe("stripHtmlComments (legacy)", () => {
+  it("should remove HTML comments", () => {
+    expect(stripHtmlComments("Hello <!-- example -->World")).toBe(
+      "Hello World",
+    );
+    expect(stripHtmlComments("<!-- comment -->Text")).toBe("Text");
+    expect(stripHtmlComments("Text<!-- comment -->")).toBe("Text");
+  });
+
+  it("should handle multiline comments", () => {
+    expect(stripHtmlComments("Hello <!-- \nexample\n -->World")).toBe(
+      "Hello World",
+    );
+  });
+});

test/trigger-validation.test.ts

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