Fix: Pass GitHub token to MCP servers in agent mode

The token was being obtained successfully but not outputted from the prepare step for use in later steps. Added explicit output of the GitHub token and debug logging.

.claude/agents/deep-thinker.md

@@ -1,31 +0,0 @@
----
-name: deep-thinker
-description: A subagent that performs deep analysis with extended thinking
-tools:
-  - "*"
-proactive: false
----
-
-# Deep Thinker Subagent
-
-You are a specialized subagent designed to perform deep, thorough analysis of complex problems using extended thinking capabilities.
-
-## Your Purpose
-
-You excel at:
-- Breaking down complex problems into smaller components
-- Analyzing trade-offs and implications
-- Providing comprehensive, well-reasoned solutions
-- Exploring edge cases and potential issues
-
-## Instructions
-
-When given a task:
-1. Use extended thinking to thoroughly analyze the problem
-2. Consider multiple approaches and their trade-offs
-3. Identify potential issues or edge cases
-4. Provide a detailed, well-structured response
-
-## Important
-
-Always think deeply before responding. Take your time to ensure thoroughness and accuracy in your analysis.

.claude/commands/fix-ci-commit.md

@@ -1,54 +0,0 @@
----
-description: Fix CI failures and commit changes (for use when branch already exists)
-allowed_tools: "*"
----
-
-# Fix CI Failures and Commit
-
-You are on a branch that was created to fix CI failures. Your task is to fix the issues and commit the changes.
-
-## CI Failure Information
-
-$ARGUMENTS
-
-## Your Tasks
-
-1. **Analyze the failures** - Understand what went wrong from the logs
-2. **Fix the issues** - Make the necessary code changes
-3. **Commit your fixes** - Use git to commit all changes
-
-## Step-by-Step Instructions
-
-### 1. Fix the Issues
-
-Based on the error logs:
-- Fix syntax errors
-- Fix formatting issues  
-- Fix test failures
-- Fix any other CI problems
-
-### 2. Commit Your Changes (REQUIRED)
-
-After fixing ALL issues, you MUST:
-
-Use the `mcp__github_file_ops__commit_files` tool to commit all your changes with a descriptive message like:
-
-```
-Fix CI failures
-
-- Fixed syntax errors
-- Fixed formatting issues  
-- Fixed test failures
-[List actual fixes made]
-```
-
-**IMPORTANT**: You MUST use the MCP file ops tool to commit your changes. The workflow expects you to commit your changes.
-
-### 3. Verify (Optional)
-
-If possible, run verification commands:
-- `bun run format:check` for formatting
-- `bun test` for tests
-- `bun run typecheck` for TypeScript
-
-Begin by analyzing the failure logs and then fix the issues.

.claude/commands/fix-ci.md

@@ -1,67 +0,0 @@
----
-description: Analyze and fix CI failures by examining logs and making targeted fixes
-allowed_tools: "*"
----
-
-# Fix CI Failures
-
-You are tasked with analyzing CI failure logs and fixing the issues. Follow these steps:
-
-## Context Provided
-
-$ARGUMENTS
-
-## Step 1: Analyze the Failure
-
-Parse the provided CI failure information to understand:
-- Which jobs failed and why
-- The specific error messages and stack traces
-- Whether failures are test-related, build-related, or linting issues
-
-## Step 2: Search and Understand the Codebase
-
-Use search tools to locate the failing code:
-- Search for the failing test names or functions
-- Find the source files mentioned in error messages
-- Review related configuration files (package.json, tsconfig.json, etc.)
-
-## Step 3: Apply Targeted Fixes
-
-Make minimal, focused changes:
-- **For test failures**: Determine if the test or implementation needs fixing
-- **For type errors**: Fix type definitions or correct the code logic
-- **For linting issues**: Apply formatting using the project's tools
-- **For build errors**: Resolve dependency or configuration issues
-- **For missing imports**: Add the necessary imports or install packages
-
-Requirements:
-- Only fix the actual CI failures, avoid unrelated changes
-- Follow existing code patterns and conventions
-- Ensure changes are production-ready, not temporary hacks
-- Preserve existing functionality while fixing issues
-
-## Step 4: Commit Changes
-
-After applying ALL fixes:
-1. Use the `mcp__github_file_ops__commit_files` tool to commit your changes
-2. Include a descriptive commit message explaining what was fixed
-3. Document which CI jobs/tests were addressed in the commit message
-4. Important: Use the MCP file ops tool, not git commands directly
-
-## Step 5: Verify Fixes Locally
-
-Run available verification commands:
-- Execute the failing tests locally to confirm they pass
-- Run the project's lint command (check package.json for scripts)
-- Run type checking if available
-- Execute any build commands to ensure compilation succeeds
-
-## Important Guidelines
-
-- Focus exclusively on fixing the reported CI failures
-- Maintain code quality and follow the project's established patterns
-- If a fix requires significant refactoring, document why it's necessary
-- When multiple solutions exist, choose the simplest one that maintains code quality
-- Add clear comments only if the fix is non-obvious
-
-Begin by analyzing the failure details provided above.

.claude/commands/review.md

@@ -1,22 +0,0 @@
----
-allowed-tools: Bash(gh pr comment:*), Bash(gh pr diff:*), Bash(gh pr view:*), Read, Glob, Grep
-description: Code review a pull request
----
-
-Review the current pull request and provide feedback.
-
-1. Use `gh pr view` to get the PR details and `gh pr diff` to see the changes
-2. Look for potential bugs, issues, or improvements
-3. Always post a comment with your findings using `gh pr comment`
-
-Format your comment like this:
-
-## Code Review
-
-[Your feedback here - be specific and constructive]
-
-- If you find issues, describe them clearly
-- If everything looks good, say so
-- Link to specific lines when relevant
-
-🤖 Generated with [Claude Code](https://claude.ai/code)

.github/workflows/auto-fix-ci-inline.yml

@@ -1,177 +0,0 @@
-name: Auto Fix CI Failures (Inline)
-
-on:
-  workflow_run:
-    workflows: ["CI"]
-    types:
-      - completed
-
-permissions:
-  contents: write
-  pull-requests: write
-  actions: read
-  issues: write
-
-jobs:
-  auto-fix:
-    if: |
-      github.event.workflow_run.conclusion == 'failure' &&
-      github.event.workflow_run.name != 'Auto Fix CI Failures' &&
-      github.event.workflow_run.name != 'Auto Fix CI Failures (Inline)'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-        with:
-          ref: ${{ github.event.workflow_run.head_branch }}
-          fetch-depth: 0
-          token: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Setup git
-        run: |
-          git config --global user.name "claude[bot]"
-          git config --global user.email "198276+claude[bot]@users.noreply.github.com"
-
-      - name: Create fix branch
-        id: branch
-        run: |
-          BRANCH_NAME="claude-auto-fix-ci-${{ github.event.workflow_run.head_branch }}-${{ github.run_id }}"
-          git checkout -b "$BRANCH_NAME"
-          echo "branch_name=$BRANCH_NAME" >> $GITHUB_OUTPUT
-
-      - name: Get CI failure details
-        id: failure_details
-        uses: actions/github-script@v7
-        with:
-          script: |
-            const run = await github.rest.actions.getWorkflowRun({
-              owner: context.repo.owner,
-              repo: context.repo.repo,
-              run_id: ${{ github.event.workflow_run.id }}
-            });
-            
-            const jobs = await github.rest.actions.listJobsForWorkflowRun({
-              owner: context.repo.owner,
-              repo: context.repo.repo,
-              run_id: ${{ github.event.workflow_run.id }}
-            });
-            
-            const failedJobs = jobs.data.jobs.filter(job => job.conclusion === 'failure');
-            
-            let errorLogs = [];
-            for (const job of failedJobs) {
-              const logs = await github.rest.actions.downloadJobLogsForWorkflowRun({
-                owner: context.repo.owner,
-                repo: context.repo.repo,
-                job_id: job.id
-              });
-              errorLogs.push({
-                jobName: job.name,
-                logs: logs.data
-              });
-            }
-            
-            return {
-              runUrl: run.data.html_url,
-              failedJobs: failedJobs.map(j => j.name),
-              errorLogs: errorLogs
-            };
-
-      - name: Fix CI failures with Claude
-        uses: anthropics/claude-code-action@v1-dev
-        with:
-          prompt: |
-            You are tasked with analyzing CI failure logs and fixing the issues. Follow these steps:
-            
-            ## Context Provided
-            
-            Failed CI Run: ${{ fromJSON(steps.failure_details.outputs.result).runUrl }}
-            Failed Jobs: ${{ join(fromJSON(steps.failure_details.outputs.result).failedJobs, ', ') }}
-            
-            Error logs:
-            ${{ toJSON(fromJSON(steps.failure_details.outputs.result).errorLogs) }}
-            
-            ## Step 1: Analyze the Failure
-            
-            Parse the provided CI failure information to understand:
-            - Which jobs failed and why
-            - The specific error messages and stack traces
-            - Whether failures are test-related, build-related, or linting issues
-            
-            ## Step 2: Search and Understand the Codebase
-            
-            Use search tools to locate the failing code:
-            - Search for the failing test names or functions
-            - Find the source files mentioned in error messages
-            - Review related configuration files (package.json, tsconfig.json, etc.)
-            
-            ## Step 3: Apply Targeted Fixes
-            
-            Make minimal, focused changes:
-            - **For test failures**: Determine if the test or implementation needs fixing
-            - **For type errors**: Fix type definitions or correct the code logic
-            - **For linting issues**: Apply formatting using the project's tools
-            - **For build errors**: Resolve dependency or configuration issues
-            - **For missing imports**: Add the necessary imports or install packages
-            
-            Requirements:
-            - Only fix the actual CI failures, avoid unrelated changes
-            - Follow existing code patterns and conventions
-            - Ensure changes are production-ready, not temporary hacks
-            - Preserve existing functionality while fixing issues
-            
-            ## Step 4: Commit Changes
-            
-            After applying ALL fixes:
-            1. Stage all modified files with `git add -A` 
-            2. Commit with: `git commit -m "Fix CI failures: prettier formatting and syntax errors"`
-            3. Important: You MUST commit your changes - the branch already exists
-            
-            ## Step 5: Verify Fixes Locally
-            
-            Run available verification commands:
-            - Execute the failing tests locally to confirm they pass
-            - Run the project's lint command (check package.json for scripts)
-            - Run type checking if available
-            - Execute any build commands to ensure compilation succeeds
-            
-            ## Important Guidelines
-            
-            - Focus exclusively on fixing the reported CI failures
-            - Maintain code quality and follow the project's established patterns
-            - If a fix requires significant refactoring, document why it's necessary
-            - When multiple solutions exist, choose the simplest one that maintains code quality
-            
-            Begin by analyzing the failure details provided above.
-          anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          timeout_minutes: "30"
-          use_sticky_comment: "true"
-          use_commit_signing: "true"
-          allowed_tools: "Edit,MultiEdit,Write,Read,Glob,Grep,LS,Bash,mcp__github_file_ops__commit_files,mcp__github_file_ops__delete_files"
-          claude_args: "--max-turns 15"
-
-      - name: Push fix branch
-        if: success()
-        run: |
-          git push origin ${{ steps.branch.outputs.branch_name }}
-
-      - name: Create pull request comment
-        if: success()
-        uses: actions/github-script@v7
-        with:
-          script: |
-            const branchName = '${{ steps.branch.outputs.branch_name }}';
-            const baseBranch = '${{ github.event.workflow_run.head_branch }}';
-            const prUrl = `https://github.com/${context.repo.owner}/${context.repo.repo}/compare/${baseBranch}...${branchName}?quick_pull=1`;
-            
-            const issueNumber = ${{ github.event.workflow_run.pull_requests[0] && github.event.workflow_run.pull_requests[0].number || 'null' }};
-            
-            if (issueNumber) {
-              await github.rest.issues.createComment({
-                owner: context.repo.owner,
-                repo: context.repo.repo,
-                issue_number: issueNumber,
-                body: `## 🤖 CI Auto-Fix Available\n\nClaude has analyzed the CI failures and prepared fixes.\n\n[**→ Create pull request to fix CI**](${prUrl})\n\n_This fix was generated automatically based on the [failed CI run](${{ fromJSON(steps.failure_details.outputs.result).runUrl }})._`
-              });
-            }

.github/workflows/auto-fix-ci.yml

@@ -1,119 +0,0 @@
-name: Auto Fix CI Failures
-
-on:
-  workflow_run:
-    workflows: ["CI"]
-    types:
-      - completed
-
-permissions:
-  contents: write
-  pull-requests: write
-  actions: read
-  issues: write
-
-jobs:
-  auto-fix:
-    if: |
-      github.event.workflow_run.conclusion == 'failure' &&
-      github.event.workflow_run.name != 'Auto Fix CI Failures'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Checkout code
-        uses: actions/checkout@v4
-        with:
-          ref: ${{ github.event.workflow_run.head_branch }}
-          fetch-depth: 0
-          token: ${{ secrets.GITHUB_TOKEN }}
-
-      - name: Setup git
-        run: |
-          git config --global user.name "claude[bot]"
-          git config --global user.email "198276+claude[bot]@users.noreply.github.com"
-
-      - name: Create fix branch
-        id: branch
-        run: |
-          BRANCH_NAME="claude-auto-fix-ci-${{ github.event.workflow_run.head_branch }}-${{ github.run_id }}"
-          git checkout -b "$BRANCH_NAME"
-          echo "branch_name=$BRANCH_NAME" >> $GITHUB_OUTPUT
-
-      - name: Get CI failure details
-        id: failure_details
-        uses: actions/github-script@v7
-        with:
-          script: |
-            const run = await github.rest.actions.getWorkflowRun({
-              owner: context.repo.owner,
-              repo: context.repo.repo,
-              run_id: ${{ github.event.workflow_run.id }}
-            });
-            
-            const jobs = await github.rest.actions.listJobsForWorkflowRun({
-              owner: context.repo.owner,
-              repo: context.repo.repo,
-              run_id: ${{ github.event.workflow_run.id }}
-            });
-            
-            const failedJobs = jobs.data.jobs.filter(job => job.conclusion === 'failure');
-            
-            let errorLogs = [];
-            for (const job of failedJobs) {
-              const logs = await github.rest.actions.downloadJobLogsForWorkflowRun({
-                owner: context.repo.owner,
-                repo: context.repo.repo,
-                job_id: job.id
-              });
-              errorLogs.push({
-                jobName: job.name,
-                logs: logs.data
-              });
-            }
-            
-            return {
-              runUrl: run.data.html_url,
-              failedJobs: failedJobs.map(j => j.name),
-              errorLogs: errorLogs
-            };
-
-      - name: Fix CI failures with Claude
-        uses: anthropics/claude-code-action@v1-dev
-        with:
-          prompt: |
-            /fix-ci-commit Failed CI Run: ${{ fromJSON(steps.failure_details.outputs.result).runUrl }}
-            Failed Jobs: ${{ join(fromJSON(steps.failure_details.outputs.result).failedJobs, ', ') }}
-            
-            Error logs:
-            ${{ toJSON(fromJSON(steps.failure_details.outputs.result).errorLogs) }}
-          anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}
-          github_token: ${{ secrets.GITHUB_TOKEN }}
-          timeout_minutes: "30"
-          use_sticky_comment: "true"
-          use_commit_signing: "true"
-          allowed_tools: "Edit,MultiEdit,Write,Read,Glob,Grep,LS,Bash,mcp__github_file_ops__commit_files,mcp__github_file_ops__delete_files"
-          claude_args: "--max-turns 15"
-
-      - name: Push fix branch
-        if: success()
-        run: |
-          git push origin ${{ steps.branch.outputs.branch_name }}
-
-      - name: Create pull request comment
-        if: success()
-        uses: actions/github-script@v7
-        with:
-          script: |
-            const branchName = '${{ steps.branch.outputs.branch_name }}';
-            const baseBranch = '${{ github.event.workflow_run.head_branch }}';
-            const prUrl = `https://github.com/${context.repo.owner}/${context.repo.repo}/compare/${baseBranch}...${branchName}?quick_pull=1`;
-            
-            const issueNumber = ${{ github.event.workflow_run.pull_requests[0] && github.event.workflow_run.pull_requests[0].number || 'null' }};
-            
-            if (issueNumber) {
-              await github.rest.issues.createComment({
-                owner: context.repo.owner,
-                repo: context.repo.repo,
-                issue_number: issueNumber,
-                body: `## 🤖 CI Auto-Fix Available\n\nClaude has analyzed the CI failures and prepared fixes.\n\n[**→ Create pull request to fix CI**](${prUrl})\n\n_This fix was generated automatically based on the [failed CI run](${{ fromJSON(steps.failure_details.outputs.result).runUrl }})._`
-              });
-            }

.github/workflows/claude-auto-review.yml

@@ -1,26 +0,0 @@
-name: Auto Review PRs
-
-on:
-  pull_request:
-    types: [opened, synchronize]
-
-jobs:
-  auto-review:
-    runs-on: ubuntu-latest
-    permissions:
-      contents: read
-      pull-requests: write
-      issues: write
-      id-token: write
-    
-    steps:
-      - name: Checkout repository
-        uses: actions/checkout@v4
-        with:
-          fetch-depth: 0
-          
-      - name: Auto review PR
-        uses: anthropics/claude-code-action@v1-dev
-        with:
-          anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}
-          prompt: /review

.github/workflows/claude.yml

@@ -31,13 +31,9 @@ jobs:
 
       - name: Run Claude Code
         id: claude
-        uses: janeapp/claude-code-action@main
+        uses: anthropics/claude-code-action@beta
         with:
           anthropic_api_key: ${{ secrets.ANTHROPIC_API_KEY }}
           allowed_tools: "Bash(bun install),Bash(bun test:*),Bash(bun run format),Bash(bun typecheck)"
           custom_instructions: "You have also been granted tools for editing files and running bun commands (install, run, test, typecheck) for testing your changes: bun install, bun test, bun run format, bun typecheck."
           model: "claude-opus-4-1-20250805"
-          # Testing PR 411 - sticky comment customization
-          use_sticky_comment: true
-          sticky_comment_app_bot_id: "209825114"
-          sticky_comment_app_bot_name: "claude"

README.md

@@ -1,6 +1,6 @@
 ![Claude Code Action responding to a comment](https://github.com/user-attachments/assets/1d60c2e9-82ed-4ee5-b749-f9e021c85f4d)
 
-# Claude Code Action (Final Test)
+# Claude Code Action - No Approval Test
 
 A general-purpose [Claude Code](https://claude.ai/code) action for GitHub PRs and issues that can answer questions and implement code changes. This action listens for a trigger phrase in comments and activates Claude act on the request. It supports multiple authentication methods including Anthropic direct API, Amazon Bedrock, and Google Vertex AI.
 

action.yml

@@ -81,10 +81,6 @@ inputs:
     description: "Enable commit signing using GitHub's commit signature verification. When false, Claude uses standard git commands"
     required: false
     default: "false"
-  allowed_tools:
-    description: "Comma-separated list of tools to allow Claude to use (e.g., 'Edit,MultiEdit,Write,Read'). If not set, mode defaults apply."
-    required: false
-    default: ""
   experimental_allowed_domains:
     description: "Restrict network access to these domains only (newline-separated). If not set, no restrictions are applied. Provider domains are auto-detected."
     required: false
@@ -134,7 +130,6 @@ runs:
         ADDITIONAL_PERMISSIONS: ${{ inputs.additional_permissions }}
         CLAUDE_ARGS: ${{ inputs.claude_args }}
         MCP_CONFIG: ${{ inputs.mcp_config }}
-        ALLOWED_TOOLS: ${{ inputs.allowed_tools }}
 
     - name: Install Base Action Dependencies
       if: steps.prepare.outputs.contains_trigger == 'true'

base-action/src/setup-claude-code-settings.ts

@@ -79,37 +79,4 @@ export async function setupClaudeCodeSettings(
       console.log(`Slash commands directory not found or error copying: ${e}`);
     }
   }
-
-  // Copy subagent files from repository to Claude's agents directory
-  // CLAUDE_WORKING_DIR is set by the action to point to the repo being processed
-  const workingDir = process.env.CLAUDE_WORKING_DIR || process.cwd();
-  const repoAgentsDir = `${workingDir}/.claude/agents`;
-  const targetAgentsDir = `${home}/.claude/agents`;
-  
-  try {
-    const agentsDirExists = await $`test -d ${repoAgentsDir}`.quiet().nothrow();
-    if (agentsDirExists.exitCode === 0) {
-      console.log(`Found subagents directory at ${repoAgentsDir}`);
-      
-      // Create target agents directory if it doesn't exist
-      await $`mkdir -p ${targetAgentsDir}`.quiet();
-      console.log(`Created target agents directory at ${targetAgentsDir}`);
-      
-      // Copy all .md files from repo agents to Claude's agents directory
-      const copyResult = await $`cp -r ${repoAgentsDir}/*.md ${targetAgentsDir}/ 2>/dev/null`.quiet().nothrow();
-      
-      if (copyResult.exitCode === 0) {
-        // List copied agents for logging
-        const agents = await $`ls -la ${targetAgentsDir}/*.md 2>/dev/null | wc -l`.quiet().text();
-        const agentCount = parseInt(agents.trim()) || 0;
-        console.log(`Successfully copied ${agentCount} subagent(s) to ${targetAgentsDir}`);
-      } else {
-        console.log(`No subagent files found in ${repoAgentsDir}`);
-      }
-    } else {
-      console.log(`No subagents directory found at ${repoAgentsDir}`);
-    }
-  } catch (e) {
-    console.log(`Error handling subagents: ${e}`);
-  }
 }

slash-commands/fix-ci-commit.md

@@ -1,54 +0,0 @@
----
-description: Fix CI failures and commit changes (for use when branch already exists)
-allowed_tools: "*"
----
-
-# Fix CI Failures and Commit
-
-You are on a branch that was created to fix CI failures. Your task is to fix the issues and commit the changes.
-
-## CI Failure Information
-
-$ARGUMENTS
-
-## Your Tasks
-
-1. **Analyze the failures** - Understand what went wrong from the logs
-2. **Fix the issues** - Make the necessary code changes
-3. **Commit your fixes** - Use git to commit all changes
-
-## Step-by-Step Instructions
-
-### 1. Fix the Issues
-
-Based on the error logs:
-- Fix syntax errors
-- Fix formatting issues  
-- Fix test failures
-- Fix any other CI problems
-
-### 2. Commit Your Changes (REQUIRED)
-
-After fixing ALL issues, you MUST:
-
-Use the `mcp__github_file_ops__commit_files` tool to commit all your changes with a descriptive message like:
-
-```
-Fix CI failures
-
-- Fixed syntax errors
-- Fixed formatting issues  
-- Fixed test failures
-[List actual fixes made]
-```
-
-**IMPORTANT**: You MUST use the MCP file ops tool to commit your changes. The workflow expects you to commit your changes.
-
-### 3. Verify (Optional)
-
-If possible, run verification commands:
-- `bun run format:check` for formatting
-- `bun test` for tests
-- `bun run typecheck` for TypeScript
-
-Begin by analyzing the failure logs and then fix the issues.

slash-commands/fix-ci.md

@@ -1,67 +0,0 @@
----
-description: Analyze and fix CI failures by examining logs and making targeted fixes
-allowed_tools: "*"
----
-
-# Fix CI Failures
-
-You are tasked with analyzing CI failure logs and fixing the issues. Follow these steps:
-
-## Context Provided
-
-$ARGUMENTS
-
-## Step 1: Analyze the Failure
-
-Parse the provided CI failure information to understand:
-- Which jobs failed and why
-- The specific error messages and stack traces
-- Whether failures are test-related, build-related, or linting issues
-
-## Step 2: Search and Understand the Codebase
-
-Use search tools to locate the failing code:
-- Search for the failing test names or functions
-- Find the source files mentioned in error messages
-- Review related configuration files (package.json, tsconfig.json, etc.)
-
-## Step 3: Apply Targeted Fixes
-
-Make minimal, focused changes:
-- **For test failures**: Determine if the test or implementation needs fixing
-- **For type errors**: Fix type definitions or correct the code logic
-- **For linting issues**: Apply formatting using the project's tools
-- **For build errors**: Resolve dependency or configuration issues
-- **For missing imports**: Add the necessary imports or install packages
-
-Requirements:
-- Only fix the actual CI failures, avoid unrelated changes
-- Follow existing code patterns and conventions
-- Ensure changes are production-ready, not temporary hacks
-- Preserve existing functionality while fixing issues
-
-## Step 4: Commit Changes
-
-After applying fixes:
-1. Use the `mcp__github_file_ops__commit_files` tool to commit your changes
-2. Include a descriptive commit message explaining what was fixed
-3. Document which CI jobs/tests were addressed in the commit message
-4. Important: Use the MCP file ops tool to commit your changes
-
-## Step 5: Verify Fixes Locally
-
-Run available verification commands:
-- Execute the failing tests locally to confirm they pass
-- Run the project's lint command (check package.json for scripts)
-- Run type checking if available
-- Execute any build commands to ensure compilation succeeds
-
-## Important Guidelines
-
-- Focus exclusively on fixing the reported CI failures
-- Maintain code quality and follow the project's established patterns
-- If a fix requires significant refactoring, document why it's necessary
-- When multiple solutions exist, choose the simplest one that maintains code quality
-- Add clear comments only if the fix is non-obvious
-
-Begin by analyzing the failure details provided above.

src/entrypoints/prepare.ts

@@ -56,6 +56,7 @@ async function run() {
       mode,
       githubToken,
     });
+    core.setOutput("GITHUB_TOKEN", githubToken);
 
     // MCP config is handled by individual modes (tag/agent) and included in their claude_args output
 

src/modes/agent/index.ts

@@ -42,6 +42,8 @@ export const agentMode: Mode = {
   async prepare({ context, githubToken }: ModeOptions): Promise<ModeResult> {
     // Agent mode handles automation events and any event with explicit prompts
     
+    console.log(`Agent mode: githubToken provided: ${!!githubToken}, length: ${githubToken?.length || 0}`);
+
     // TODO: handle by createPrompt (similar to tag and review modes)
     // Create prompt directory
     await mkdir(`${process.env.RUNNER_TEMP}/claude-prompts`, {
@@ -83,29 +85,6 @@ export const agentMode: Mode = {
       },
     };
 
-    // Add GitHub file ops server when using commit signing
-    if (context.inputs?.useCommitSigning) {
-      mcpConfig.mcpServers["github-file-ops-server"] = {
-        command: "bun",
-        args: [
-          "run",
-          `${process.env.GITHUB_ACTION_PATH}/src/mcp/github-file-ops-server.ts`,
-        ],
-        env: {
-          GITHUB_TOKEN: githubToken || "",
-          REPO_OWNER: context.repository.owner,
-          REPO_NAME: context.repository.repo,
-          BRANCH_NAME: "", // Agent mode doesn't pre-create branches
-          BASE_BRANCH: "",
-          REPO_DIR: process.env.GITHUB_WORKSPACE || process.cwd(),
-          GITHUB_EVENT_NAME: process.env.GITHUB_EVENT_NAME || "",
-          IS_PR: "false", // Agent mode doesn't create PRs by default
-          GITHUB_API_URL:
-            process.env.GITHUB_API_URL || "https://api.github.com",
-        },
-      };
-    }
-
     // Add user-provided additional MCP config if any
     const additionalMcpConfig = process.env.MCP_CONFIG || "";
     if (additionalMcpConfig.trim()) {
@@ -124,23 +103,12 @@ export const agentMode: Mode = {
       }
     }
 
-    // Agent mode: pass through user's claude_args with MCP config and allowed_tools
+    // Agent mode: pass through user's claude_args with MCP config
     const userClaudeArgs = process.env.CLAUDE_ARGS || "";
-    const userAllowedTools = process.env.ALLOWED_TOOLS || "";
     const escapedMcpConfig = JSON.stringify(mcpConfig).replace(/'/g, "'\\''");
-    let claudeArgs = `--mcp-config '${escapedMcpConfig}'`;
+    const claudeArgs =
-    
+      `--mcp-config '${escapedMcpConfig}' ${userClaudeArgs}`.trim();
-    // Add allowed_tools if specified
+    core.setOutput("claude_args", claudeArgs);
-    if (userAllowedTools) {
-      claudeArgs += ` --allowedTools "${userAllowedTools}"`;
-    }
-    
-    // Add user's additional claude_args
-    if (userClaudeArgs) {
-      claudeArgs += ` ${userClaudeArgs}`;
-    }
-    
-    core.setOutput("claude_args", claudeArgs.trim());
 
     return {
       commentId: undefined,

test-failure.ts

@@ -1,13 +0,0 @@
-// This file intentionally has TypeScript errors to trigger CI failure
-// Testing auto-fix with MCP file ops enabled
-const testFunction = (param: string): number => {
-  // Type error: returning string instead of number
-  return "this should be a number";
-}
-
-// Syntax error: missing closing brace
-function brokenFunction() {
-  console.log("missing closing brace"
-}
-
-export { testFunction, brokenFunction };