fix: move critical outputs to immediately after prepare step

Previously, outputs like GITHUB_TOKEN and branch_name were set after Claude execution completed. This caused issues if Claude failed, as downstream cleanup steps wouldn't have access to these outputs.

Now outputs are set immediately after prepare() completes, ensuring they're available even if Claude execution fails.

action.yml

@@ -118,10 +118,10 @@ inputs:
 outputs:
   execution_file:
     description: "Path to the Claude Code execution output file"
-    value: ${{ steps.claude-code.outputs.execution_file }}
+    value: ${{ steps.claude.outputs.execution_file }}
   branch_name:
     description: "The branch created by Claude Code for this execution"
-    value: ${{ steps.prepare.outputs.CLAUDE_BRANCH }}
+    value: ${{ steps.claude.outputs.CLAUDE_BRANCH }}
 
 runs:
   using: "composite"
@@ -137,20 +137,36 @@ runs:
         cd ${GITHUB_ACTION_PATH}
         bun install
 
-    - name: Prepare action
-      id: prepare
+    - name: Run Claude
+      id: claude
       shell: bash
       run: |
-        bun run ${GITHUB_ACTION_PATH}/src/entrypoints/prepare.ts
+        # Install base-action dependencies
+        echo "Installing base-action dependencies..."
+        cd ${GITHUB_ACTION_PATH}/base-action
+        bun install
+        echo "Base-action dependencies installed"
+        cd -
+
+        # Install Claude Code globally
+        bun install -g @anthropic-ai/claude-code@1.0.67
+
+        # Setup network restrictions if needed
+        if [[ "${{ inputs.experimental_allowed_domains }}" != "" ]]; then
+          chmod +x ${GITHUB_ACTION_PATH}/scripts/setup-network-restrictions.sh
+          ${GITHUB_ACTION_PATH}/scripts/setup-network-restrictions.sh
+        fi
+
+        # Run the unified entrypoint
+        bun run ${GITHUB_ACTION_PATH}/src/entrypoints/run.ts
       env:
+        # Mode and trigger configuration
         MODE: ${{ inputs.mode }}
         TRIGGER_PHRASE: ${{ inputs.trigger_phrase }}
         ASSIGNEE_TRIGGER: ${{ inputs.assignee_trigger }}
         LABEL_TRIGGER: ${{ inputs.label_trigger }}
         BASE_BRANCH: ${{ inputs.base_branch }}
         BRANCH_PREFIX: ${{ inputs.branch_prefix }}
-        ALLOWED_TOOLS: ${{ inputs.allowed_tools }}
-        DISALLOWED_TOOLS: ${{ inputs.disallowed_tools }}
         CUSTOM_INSTRUCTIONS: ${{ inputs.custom_instructions }}
         DIRECT_PROMPT: ${{ inputs.direct_prompt }}
         OVERRIDE_PROMPT: ${{ inputs.override_prompt }}
@@ -161,57 +177,21 @@ runs:
         DEFAULT_WORKFLOW_TOKEN: ${{ github.token }}
         ADDITIONAL_PERMISSIONS: ${{ inputs.additional_permissions }}
         USE_COMMIT_SIGNING: ${{ inputs.use_commit_signing }}
-
-    - name: Install Base Action Dependencies
-      if: steps.prepare.outputs.contains_trigger == 'true'
-      shell: bash
-      run: |
-        echo "Installing base-action dependencies..."
-        cd ${GITHUB_ACTION_PATH}/base-action
-        bun install
-        echo "Base-action dependencies installed"
-        cd -
-        # Install Claude Code globally
-        bun install -g @anthropic-ai/claude-code@1.0.69
-
-    - name: Setup Network Restrictions
-      if: steps.prepare.outputs.contains_trigger == 'true' && inputs.experimental_allowed_domains != ''
-      shell: bash
-      run: |
-        chmod +x ${GITHUB_ACTION_PATH}/scripts/setup-network-restrictions.sh
-        ${GITHUB_ACTION_PATH}/scripts/setup-network-restrictions.sh
-      env:
         EXPERIMENTAL_ALLOWED_DOMAINS: ${{ inputs.experimental_allowed_domains }}
 
-    - name: Run Claude Code
-      id: claude-code
-      if: steps.prepare.outputs.contains_trigger == 'true'
-      shell: bash
-      run: |
-
-        # Run the base-action
-        bun run ${GITHUB_ACTION_PATH}/base-action/src/index.ts
-      env:
-        # Base-action inputs
-        CLAUDE_CODE_ACTION: "1"
-        INPUT_PROMPT_FILE: ${{ runner.temp }}/claude-prompts/claude-prompt.txt
-        INPUT_ALLOWED_TOOLS: ${{ env.ALLOWED_TOOLS }}
-        INPUT_DISALLOWED_TOOLS: ${{ env.DISALLOWED_TOOLS }}
-        INPUT_MAX_TURNS: ${{ inputs.max_turns }}
-        INPUT_MCP_CONFIG: ${{ steps.prepare.outputs.mcp_config }}
-        INPUT_SETTINGS: ${{ inputs.settings }}
-        INPUT_SYSTEM_PROMPT: ""
-        INPUT_APPEND_SYSTEM_PROMPT: ${{ env.APPEND_SYSTEM_PROMPT }}
-        INPUT_TIMEOUT_MINUTES: ${{ inputs.timeout_minutes }}
-        INPUT_CLAUDE_ENV: ${{ inputs.claude_env }}
-        INPUT_FALLBACK_MODEL: ${{ inputs.fallback_model }}
+        # Claude configuration
+        ALLOWED_TOOLS: ${{ inputs.allowed_tools }}
+        DISALLOWED_TOOLS: ${{ inputs.disallowed_tools }}
+        MAX_TURNS: ${{ inputs.max_turns }}
+        SETTINGS: ${{ inputs.settings }}
+        TIMEOUT_MINUTES: ${{ inputs.timeout_minutes }}
+        CLAUDE_ENV: ${{ inputs.claude_env }}
+        FALLBACK_MODEL: ${{ inputs.fallback_model }}
         INPUT_EXPERIMENTAL_SLASH_COMMANDS_DIR: ${{ github.action_path }}/slash-commands
 
         # Model configuration
+        MODEL: ${{ inputs.model }}
         ANTHROPIC_MODEL: ${{ inputs.model || inputs.anthropic_model }}
-        GITHUB_TOKEN: ${{ steps.prepare.outputs.GITHUB_TOKEN }}
-        NODE_VERSION: ${{ env.NODE_VERSION }}
-        DETAILED_PERMISSION_MESSAGES: "1"
 
         # Provider configuration
         ANTHROPIC_API_KEY: ${{ inputs.anthropic_api_key }}
@@ -239,35 +219,35 @@ runs:
         VERTEX_REGION_CLAUDE_3_7_SONNET: ${{ env.VERTEX_REGION_CLAUDE_3_7_SONNET }}
 
     - name: Update comment with job link
-      if: steps.prepare.outputs.contains_trigger == 'true' && steps.prepare.outputs.claude_comment_id && always()
+      if: steps.claude.outputs.contains_trigger == 'true' && steps.claude.outputs.claude_comment_id && always()
       shell: bash
       run: |
         bun run ${GITHUB_ACTION_PATH}/src/entrypoints/update-comment-link.ts
       env:
         REPOSITORY: ${{ github.repository }}
         PR_NUMBER: ${{ github.event.issue.number || github.event.pull_request.number }}
-        CLAUDE_COMMENT_ID: ${{ steps.prepare.outputs.claude_comment_id }}
+        CLAUDE_COMMENT_ID: ${{ steps.claude.outputs.claude_comment_id }}
         GITHUB_RUN_ID: ${{ github.run_id }}
-        GITHUB_TOKEN: ${{ steps.prepare.outputs.GITHUB_TOKEN }}
+        GITHUB_TOKEN: ${{ steps.claude.outputs.GITHUB_TOKEN }}
         GITHUB_EVENT_NAME: ${{ github.event_name }}
         TRIGGER_COMMENT_ID: ${{ github.event.comment.id }}
-        CLAUDE_BRANCH: ${{ steps.prepare.outputs.CLAUDE_BRANCH }}
+        CLAUDE_BRANCH: ${{ steps.claude.outputs.CLAUDE_BRANCH }}
         IS_PR: ${{ github.event.issue.pull_request != null || github.event_name == 'pull_request_review_comment' }}
-        BASE_BRANCH: ${{ steps.prepare.outputs.BASE_BRANCH }}
-        CLAUDE_SUCCESS: ${{ steps.claude-code.outputs.conclusion == 'success' }}
-        OUTPUT_FILE: ${{ steps.claude-code.outputs.execution_file || '' }}
+        BASE_BRANCH: ${{ steps.claude.outputs.BASE_BRANCH }}
+        CLAUDE_SUCCESS: ${{ steps.claude.outputs.conclusion == 'success' }}
+        OUTPUT_FILE: ${{ steps.claude.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 || '' }}
+        PREPARE_SUCCESS: ${{ steps.claude.outcome == 'success' }}
+        PREPARE_ERROR: ${{ steps.claude.outputs.prepare_error || '' }}
         USE_STICKY_COMMENT: ${{ inputs.use_sticky_comment }}
         USE_COMMIT_SIGNING: ${{ inputs.use_commit_signing }}
 
     - name: Display Claude Code Report
-      if: steps.prepare.outputs.contains_trigger == 'true' && steps.claude-code.outputs.execution_file != ''
+      if: steps.claude.outputs.contains_trigger == 'true' && steps.claude.outputs.execution_file != ''
       shell: bash
       run: |
         # Try to format the turns, but if it fails, dump the raw JSON
-        if bun run ${{ github.action_path }}/src/entrypoints/format-turns.ts "${{ steps.claude-code.outputs.execution_file }}" >> $GITHUB_STEP_SUMMARY 2>/dev/null; then
+        if bun run ${{ github.action_path }}/src/entrypoints/format-turns.ts "${{ steps.claude.outputs.execution_file }}" >> $GITHUB_STEP_SUMMARY 2>/dev/null; then
           echo "Successfully formatted Claude Code report"
         else
           echo "## Claude Code Report (Raw Output)" >> $GITHUB_STEP_SUMMARY
@@ -275,7 +255,7 @@ runs:
           echo "Failed to format output (please report). Here's the raw JSON:" >> $GITHUB_STEP_SUMMARY
           echo "" >> $GITHUB_STEP_SUMMARY
           echo '```json' >> $GITHUB_STEP_SUMMARY
-          cat "${{ steps.claude-code.outputs.execution_file }}" >> $GITHUB_STEP_SUMMARY
+          cat "${{ steps.claude.outputs.execution_file }}" >> $GITHUB_STEP_SUMMARY
           echo '```' >> $GITHUB_STEP_SUMMARY
         fi
 
@@ -286,6 +266,6 @@ runs:
         curl -L \
           -X DELETE \
           -H "Accept: application/vnd.github+json" \
-          -H "Authorization: Bearer ${{ steps.prepare.outputs.GITHUB_TOKEN }}" \
+          -H "Authorization: Bearer ${{ steps.claude.outputs.GITHUB_TOKEN }}" \
           -H "X-GitHub-Api-Version: 2022-11-28" \
           ${GITHUB_API_URL:-https://api.github.com}/installation/token

base-action/src/index.ts

@@ -2,7 +2,7 @@
 
 import * as core from "@actions/core";
 import { preparePrompt } from "./prepare-prompt";
-import { runClaude } from "./run-claude";
+import { runClaudeCore } from "./run-claude-core";
 import { setupClaudeCodeSettings } from "./setup-claude-code-settings";
 import { validateEnvironmentVariables } from "./validate-env";
 
@@ -21,7 +21,9 @@ async function run() {
       promptFile: process.env.INPUT_PROMPT_FILE || "",
     });
 
-    await runClaude(promptConfig.path, {
+    await runClaudeCore({
+      promptFile: promptConfig.path,
+      settings: process.env.INPUT_SETTINGS,
       allowedTools: process.env.INPUT_ALLOWED_TOOLS,
       disallowedTools: process.env.INPUT_DISALLOWED_TOOLS,
       maxTurns: process.env.INPUT_MAX_TURNS,
@@ -31,6 +33,7 @@ async function run() {
       claudeEnv: process.env.INPUT_CLAUDE_ENV,
       fallbackModel: process.env.INPUT_FALLBACK_MODEL,
       model: process.env.ANTHROPIC_MODEL,
+      timeoutMinutes: process.env.INPUT_TIMEOUT_MINUTES,
     });
   } catch (error) {
     core.setFailed(`Action failed with error: ${error}`);

base-action/src/run-claude-core.ts

@@ -0,0 +1,366 @@
+#!/usr/bin/env bun
+
+import * as core from "@actions/core";
+import { exec } from "child_process";
+import { promisify } from "util";
+import { unlink, writeFile, stat } from "fs/promises";
+import { createWriteStream } from "fs";
+import { spawn } from "child_process";
+
+const execAsync = promisify(exec);
+
+const PIPE_PATH = `${process.env.RUNNER_TEMP}/claude_prompt_pipe`;
+const EXECUTION_FILE = `${process.env.RUNNER_TEMP}/claude-execution-output.json`;
+const BASE_ARGS = ["-p", "--verbose", "--output-format", "stream-json"];
+
+export type ClaudeOptions = {
+  allowedTools?: string;
+  disallowedTools?: string;
+  maxTurns?: string;
+  mcpConfig?: string;
+  systemPrompt?: string;
+  appendSystemPrompt?: string;
+  claudeEnv?: string;
+  fallbackModel?: string;
+  model?: string;
+  timeoutMinutes?: string;
+};
+
+export type RunClaudeConfig = {
+  promptFile: string;
+  settings?: string;
+  allowedTools?: string;
+  disallowedTools?: string;
+  maxTurns?: string;
+  mcpConfig?: string;
+  systemPrompt?: string;
+  appendSystemPrompt?: string;
+  claudeEnv?: string;
+  fallbackModel?: string;
+  model?: string;
+  timeoutMinutes?: string;
+  env?: Record<string, string>;
+};
+
+function parseCustomEnvVars(claudeEnv?: string): Record<string, string> {
+  if (!claudeEnv || claudeEnv.trim() === "") {
+    return {};
+  }
+
+  const customEnv: Record<string, string> = {};
+
+  // Split by lines and parse each line as KEY: VALUE
+  const lines = claudeEnv.split("\n");
+
+  for (const line of lines) {
+    const trimmedLine = line.trim();
+    if (trimmedLine === "" || trimmedLine.startsWith("#")) {
+      continue; // Skip empty lines and comments
+    }
+
+    const colonIndex = trimmedLine.indexOf(":");
+    if (colonIndex === -1) {
+      continue; // Skip lines without colons
+    }
+
+    const key = trimmedLine.substring(0, colonIndex).trim();
+    const value = trimmedLine.substring(colonIndex + 1).trim();
+
+    if (key) {
+      customEnv[key] = value;
+    }
+  }
+
+  return customEnv;
+}
+
+function prepareClaudeArgs(config: RunClaudeConfig): string[] {
+  const claudeArgs = [...BASE_ARGS];
+
+  if (config.allowedTools) {
+    claudeArgs.push("--allowedTools", config.allowedTools);
+  }
+  if (config.disallowedTools) {
+    claudeArgs.push("--disallowedTools", config.disallowedTools);
+  }
+  if (config.maxTurns) {
+    const maxTurnsNum = parseInt(config.maxTurns, 10);
+    if (isNaN(maxTurnsNum) || maxTurnsNum <= 0) {
+      throw new Error(
+        `maxTurns must be a positive number, got: ${config.maxTurns}`,
+      );
+    }
+    claudeArgs.push("--max-turns", config.maxTurns);
+  }
+  if (config.mcpConfig) {
+    claudeArgs.push("--mcp-config", config.mcpConfig);
+  }
+  if (config.systemPrompt) {
+    claudeArgs.push("--system-prompt", config.systemPrompt);
+  }
+  if (config.appendSystemPrompt) {
+    claudeArgs.push("--append-system-prompt", config.appendSystemPrompt);
+  }
+  if (config.fallbackModel) {
+    claudeArgs.push("--fallback-model", config.fallbackModel);
+  }
+  if (config.model) {
+    claudeArgs.push("--model", config.model);
+  }
+  if (config.timeoutMinutes) {
+    const timeoutMinutesNum = parseInt(config.timeoutMinutes, 10);
+    if (isNaN(timeoutMinutesNum) || timeoutMinutesNum <= 0) {
+      throw new Error(
+        `timeoutMinutes must be a positive number, got: ${config.timeoutMinutes}`,
+      );
+    }
+  }
+
+  return claudeArgs;
+}
+
+export function prepareRunConfig(
+  promptPath: string,
+  options: ClaudeOptions,
+): { claudeArgs: string[]; promptPath: string; env: Record<string, string> } {
+  const config: RunClaudeConfig = {
+    promptFile: promptPath,
+    ...options,
+  };
+
+  const claudeArgs = prepareClaudeArgs(config);
+  const customEnv = parseCustomEnvVars(config.claudeEnv);
+  const mergedEnv = {
+    ...customEnv,
+    ...(config.env || {}),
+  };
+
+  return {
+    claudeArgs,
+    promptPath,
+    env: mergedEnv,
+  };
+}
+
+export async function runClaudeCore(config: RunClaudeConfig) {
+  const claudeArgs = prepareClaudeArgs(config);
+
+  // Parse custom environment variables from claudeEnv
+  const customEnv = parseCustomEnvVars(config.claudeEnv);
+
+  // Merge with additional env vars passed in config
+  const mergedEnv = {
+    ...customEnv,
+    ...(config.env || {}),
+  };
+
+  // Create a named pipe
+  try {
+    await unlink(PIPE_PATH);
+  } catch (e) {
+    // Ignore if file doesn't exist
+  }
+
+  // Create the named pipe
+  await execAsync(`mkfifo "${PIPE_PATH}"`);
+
+  // Log prompt file size
+  let promptSize = "unknown";
+  try {
+    const stats = await stat(config.promptFile);
+    promptSize = stats.size.toString();
+  } catch (e) {
+    // Ignore error
+  }
+
+  console.log(`Prompt file size: ${promptSize} bytes`);
+
+  // Log custom environment variables if any
+  const totalEnvVars = Object.keys(mergedEnv).length;
+  if (totalEnvVars > 0) {
+    const envKeys = Object.keys(mergedEnv).join(", ");
+    console.log(`Custom environment variables (${totalEnvVars}): ${envKeys}`);
+  }
+
+  // Output to console
+  console.log(`Running Claude with prompt from file: ${config.promptFile}`);
+
+  // Start sending prompt to pipe in background
+  const catProcess = spawn("cat", [config.promptFile], {
+    stdio: ["ignore", "pipe", "inherit"],
+  });
+  const pipeStream = createWriteStream(PIPE_PATH);
+  catProcess.stdout.pipe(pipeStream);
+
+  catProcess.on("error", (error) => {
+    console.error("Error reading prompt file:", error);
+    pipeStream.destroy();
+  });
+
+  const claudeProcess = spawn("claude", claudeArgs, {
+    stdio: ["pipe", "pipe", "inherit"],
+    env: {
+      ...process.env,
+      ...mergedEnv,
+    },
+  });
+
+  // Handle Claude process errors
+  claudeProcess.on("error", (error) => {
+    console.error("Error spawning Claude process:", error);
+    pipeStream.destroy();
+  });
+
+  // Capture output for parsing execution metrics
+  let output = "";
+  claudeProcess.stdout.on("data", (data) => {
+    const text = data.toString();
+
+    // Try to parse as JSON and pretty print if it's on a single line
+    const lines = text.split("\n");
+    lines.forEach((line: string, index: number) => {
+      if (line.trim() === "") return;
+
+      try {
+        // Check if this line is a JSON object
+        const parsed = JSON.parse(line);
+        const prettyJson = JSON.stringify(parsed, null, 2);
+        process.stdout.write(prettyJson);
+        if (index < lines.length - 1 || text.endsWith("\n")) {
+          process.stdout.write("\n");
+        }
+      } catch (e) {
+        // Not a JSON object, print as is
+        process.stdout.write(line);
+        if (index < lines.length - 1 || text.endsWith("\n")) {
+          process.stdout.write("\n");
+        }
+      }
+    });
+
+    output += text;
+  });
+
+  // Handle stdout errors
+  claudeProcess.stdout.on("error", (error) => {
+    console.error("Error reading Claude stdout:", error);
+  });
+
+  // Pipe from named pipe to Claude
+  const pipeProcess = spawn("cat", [PIPE_PATH]);
+  pipeProcess.stdout.pipe(claudeProcess.stdin);
+
+  // Handle pipe process errors
+  pipeProcess.on("error", (error) => {
+    console.error("Error reading from named pipe:", error);
+    claudeProcess.kill("SIGTERM");
+  });
+
+  // Wait for Claude to finish with timeout
+  let timeoutMs = 10 * 60 * 1000; // Default 10 minutes
+  if (config.timeoutMinutes) {
+    timeoutMs = parseInt(config.timeoutMinutes, 10) * 60 * 1000;
+  } else if (process.env.INPUT_TIMEOUT_MINUTES) {
+    const envTimeout = parseInt(process.env.INPUT_TIMEOUT_MINUTES, 10);
+    if (isNaN(envTimeout) || envTimeout <= 0) {
+      throw new Error(
+        `INPUT_TIMEOUT_MINUTES must be a positive number, got: ${process.env.INPUT_TIMEOUT_MINUTES}`,
+      );
+    }
+    timeoutMs = envTimeout * 60 * 1000;
+  }
+  const exitCode = await new Promise<number>((resolve) => {
+    let resolved = false;
+
+    // Set a timeout for the process
+    const timeoutId = setTimeout(() => {
+      if (!resolved) {
+        console.error(
+          `Claude process timed out after ${timeoutMs / 1000} seconds`,
+        );
+        claudeProcess.kill("SIGTERM");
+        // Give it 5 seconds to terminate gracefully, then force kill
+        setTimeout(() => {
+          try {
+            claudeProcess.kill("SIGKILL");
+          } catch (e) {
+            // Process may already be dead
+          }
+        }, 5000);
+        resolved = true;
+        resolve(124); // Standard timeout exit code
+      }
+    }, timeoutMs);
+
+    claudeProcess.on("close", (code) => {
+      if (!resolved) {
+        clearTimeout(timeoutId);
+        resolved = true;
+        resolve(code || 0);
+      }
+    });
+
+    claudeProcess.on("error", (error) => {
+      if (!resolved) {
+        console.error("Claude process error:", error);
+        clearTimeout(timeoutId);
+        resolved = true;
+        resolve(1);
+      }
+    });
+  });
+
+  // Clean up processes
+  try {
+    catProcess.kill("SIGTERM");
+  } catch (e) {
+    // Process may already be dead
+  }
+  try {
+    pipeProcess.kill("SIGTERM");
+  } catch (e) {
+    // Process may already be dead
+  }
+
+  // Clean up pipe file
+  try {
+    await unlink(PIPE_PATH);
+  } catch (e) {
+    // Ignore errors during cleanup
+  }
+
+  // Set conclusion based on exit code
+  if (exitCode === 0) {
+    // Try to process the output and save execution metrics
+    try {
+      await writeFile("output.txt", output);
+
+      // Process output.txt into JSON and save to execution file
+      const { stdout: jsonOutput } = await execAsync("jq -s '.' output.txt");
+      await writeFile(EXECUTION_FILE, jsonOutput);
+
+      console.log(`Log saved to ${EXECUTION_FILE}`);
+    } catch (e) {
+      core.warning(`Failed to process output for execution metrics: ${e}`);
+    }
+
+    core.setOutput("conclusion", "success");
+    core.setOutput("execution_file", EXECUTION_FILE);
+  } else {
+    core.setOutput("conclusion", "failure");
+
+    // Still try to save execution file if we have output
+    if (output) {
+      try {
+        await writeFile("output.txt", output);
+        const { stdout: jsonOutput } = await execAsync("jq -s '.' output.txt");
+        await writeFile(EXECUTION_FILE, jsonOutput);
+        core.setOutput("execution_file", EXECUTION_FILE);
+      } catch (e) {
+        // Ignore errors when processing output during failure
+      }
+    }
+
+    process.exit(exitCode);
+  }
+}

base-action/src/run-claude.ts

@@ -1,331 +1,44 @@
+#!/usr/bin/env bun
+
 import * as core from "@actions/core";
-import { exec } from "child_process";
-import { promisify } from "util";
-import { unlink, writeFile, stat } from "fs/promises";
-import { createWriteStream } from "fs";
-import { spawn } from "child_process";
+import { preparePrompt } from "./prepare-prompt";
+import { runClaudeCore } from "./run-claude-core";
+export { prepareRunConfig, type ClaudeOptions } from "./run-claude-core";
+import { setupClaudeCodeSettings } from "./setup-claude-code-settings";
+import { validateEnvironmentVariables } from "./validate-env";
 
-const execAsync = promisify(exec);
-
-const PIPE_PATH = `${process.env.RUNNER_TEMP}/claude_prompt_pipe`;
-const EXECUTION_FILE = `${process.env.RUNNER_TEMP}/claude-execution-output.json`;
-const BASE_ARGS = ["-p", "--verbose", "--output-format", "stream-json"];
-
-export type ClaudeOptions = {
-  allowedTools?: string;
-  disallowedTools?: string;
-  maxTurns?: string;
-  mcpConfig?: string;
-  systemPrompt?: string;
-  appendSystemPrompt?: string;
-  claudeEnv?: string;
-  fallbackModel?: string;
-  timeoutMinutes?: string;
-  model?: string;
-};
-
-type PreparedConfig = {
-  claudeArgs: string[];
-  promptPath: string;
-  env: Record<string, string>;
-};
-
-function parseCustomEnvVars(claudeEnv?: string): Record<string, string> {
-  if (!claudeEnv || claudeEnv.trim() === "") {
-    return {};
-  }
-
-  const customEnv: Record<string, string> = {};
-
-  // Split by lines and parse each line as KEY: VALUE
-  const lines = claudeEnv.split("\n");
-
-  for (const line of lines) {
-    const trimmedLine = line.trim();
-    if (trimmedLine === "" || trimmedLine.startsWith("#")) {
-      continue; // Skip empty lines and comments
-    }
-
-    const colonIndex = trimmedLine.indexOf(":");
-    if (colonIndex === -1) {
-      continue; // Skip lines without colons
-    }
-
-    const key = trimmedLine.substring(0, colonIndex).trim();
-    const value = trimmedLine.substring(colonIndex + 1).trim();
-
-    if (key) {
-      customEnv[key] = value;
-    }
-  }
-
-  return customEnv;
-}
-
-export function prepareRunConfig(
-  promptPath: string,
-  options: ClaudeOptions,
-): PreparedConfig {
-  const claudeArgs = [...BASE_ARGS];
-
-  if (options.allowedTools) {
-    claudeArgs.push("--allowedTools", options.allowedTools);
-  }
-  if (options.disallowedTools) {
-    claudeArgs.push("--disallowedTools", options.disallowedTools);
-  }
-  if (options.maxTurns) {
-    const maxTurnsNum = parseInt(options.maxTurns, 10);
-    if (isNaN(maxTurnsNum) || maxTurnsNum <= 0) {
-      throw new Error(
-        `maxTurns must be a positive number, got: ${options.maxTurns}`,
-      );
-    }
-    claudeArgs.push("--max-turns", options.maxTurns);
-  }
-  if (options.mcpConfig) {
-    claudeArgs.push("--mcp-config", options.mcpConfig);
-  }
-  if (options.systemPrompt) {
-    claudeArgs.push("--system-prompt", options.systemPrompt);
-  }
-  if (options.appendSystemPrompt) {
-    claudeArgs.push("--append-system-prompt", options.appendSystemPrompt);
-  }
-  if (options.fallbackModel) {
-    claudeArgs.push("--fallback-model", options.fallbackModel);
-  }
-  if (options.model) {
-    claudeArgs.push("--model", options.model);
-  }
-  if (options.timeoutMinutes) {
-    const timeoutMinutesNum = parseInt(options.timeoutMinutes, 10);
-    if (isNaN(timeoutMinutesNum) || timeoutMinutesNum <= 0) {
-      throw new Error(
-        `timeoutMinutes must be a positive number, got: ${options.timeoutMinutes}`,
-      );
-    }
-  }
-
-  // Parse custom environment variables
-  const customEnv = parseCustomEnvVars(options.claudeEnv);
-
-  return {
-    claudeArgs,
-    promptPath,
-    env: customEnv,
-  };
-}
-
-export async function runClaude(promptPath: string, options: ClaudeOptions) {
-  const config = prepareRunConfig(promptPath, options);
-
-  // Create a named pipe
+async function run() {
   try {
-    await unlink(PIPE_PATH);
-  } catch (e) {
-    // Ignore if file doesn't exist
-  }
+    validateEnvironmentVariables();
 
-  // Create the named pipe
-  await execAsync(`mkfifo "${PIPE_PATH}"`);
+    await setupClaudeCodeSettings(process.env.INPUT_SETTINGS);
 
-  // Log prompt file size
-  let promptSize = "unknown";
-  try {
-    const stats = await stat(config.promptPath);
-    promptSize = stats.size.toString();
-  } catch (e) {
-    // Ignore error
-  }
-
-  console.log(`Prompt file size: ${promptSize} bytes`);
-
-  // Log custom environment variables if any
-  if (Object.keys(config.env).length > 0) {
-    const envKeys = Object.keys(config.env).join(", ");
-    console.log(`Custom environment variables: ${envKeys}`);
-  }
-
-  // Output to console
-  console.log(`Running Claude with prompt from file: ${config.promptPath}`);
-
-  // Start sending prompt to pipe in background
-  const catProcess = spawn("cat", [config.promptPath], {
-    stdio: ["ignore", "pipe", "inherit"],
-  });
-  const pipeStream = createWriteStream(PIPE_PATH);
-  catProcess.stdout.pipe(pipeStream);
-
-  catProcess.on("error", (error) => {
-    console.error("Error reading prompt file:", error);
-    pipeStream.destroy();
-  });
-
-  const claudeProcess = spawn("claude", config.claudeArgs, {
-    stdio: ["pipe", "pipe", "inherit"],
-    env: {
-      ...process.env,
-      ...config.env,
-    },
-  });
-
-  // Handle Claude process errors
-  claudeProcess.on("error", (error) => {
-    console.error("Error spawning Claude process:", error);
-    pipeStream.destroy();
-  });
-
-  // Capture output for parsing execution metrics
-  let output = "";
-  claudeProcess.stdout.on("data", (data) => {
-    const text = data.toString();
-
-    // Try to parse as JSON and pretty print if it's on a single line
-    const lines = text.split("\n");
-    lines.forEach((line: string, index: number) => {
-      if (line.trim() === "") return;
-
-      try {
-        // Check if this line is a JSON object
-        const parsed = JSON.parse(line);
-        const prettyJson = JSON.stringify(parsed, null, 2);
-        process.stdout.write(prettyJson);
-        if (index < lines.length - 1 || text.endsWith("\n")) {
-          process.stdout.write("\n");
-        }
-      } catch (e) {
-        // Not a JSON object, print as is
-        process.stdout.write(line);
-        if (index < lines.length - 1 || text.endsWith("\n")) {
-          process.stdout.write("\n");
-        }
-      }
+    const promptConfig = await preparePrompt({
+      prompt: process.env.INPUT_PROMPT || "",
+      promptFile: process.env.INPUT_PROMPT_FILE || "",
     });
 
-    output += text;
-  });
-
-  // Handle stdout errors
-  claudeProcess.stdout.on("error", (error) => {
-    console.error("Error reading Claude stdout:", error);
-  });
-
-  // Pipe from named pipe to Claude
-  const pipeProcess = spawn("cat", [PIPE_PATH]);
-  pipeProcess.stdout.pipe(claudeProcess.stdin);
-
-  // Handle pipe process errors
-  pipeProcess.on("error", (error) => {
-    console.error("Error reading from named pipe:", error);
-    claudeProcess.kill("SIGTERM");
-  });
-
-  // Wait for Claude to finish with timeout
-  let timeoutMs = 10 * 60 * 1000; // Default 10 minutes
-  if (options.timeoutMinutes) {
-    timeoutMs = parseInt(options.timeoutMinutes, 10) * 60 * 1000;
-  } else if (process.env.INPUT_TIMEOUT_MINUTES) {
-    const envTimeout = parseInt(process.env.INPUT_TIMEOUT_MINUTES, 10);
-    if (isNaN(envTimeout) || envTimeout <= 0) {
-      throw new Error(
-        `INPUT_TIMEOUT_MINUTES must be a positive number, got: ${process.env.INPUT_TIMEOUT_MINUTES}`,
-      );
-    }
-    timeoutMs = envTimeout * 60 * 1000;
-  }
-  const exitCode = await new Promise<number>((resolve) => {
-    let resolved = false;
-
-    // Set a timeout for the process
-    const timeoutId = setTimeout(() => {
-      if (!resolved) {
-        console.error(
-          `Claude process timed out after ${timeoutMs / 1000} seconds`,
-        );
-        claudeProcess.kill("SIGTERM");
-        // Give it 5 seconds to terminate gracefully, then force kill
-        setTimeout(() => {
-          try {
-            claudeProcess.kill("SIGKILL");
-          } catch (e) {
-            // Process may already be dead
-          }
-        }, 5000);
-        resolved = true;
-        resolve(124); // Standard timeout exit code
-      }
-    }, timeoutMs);
-
-    claudeProcess.on("close", (code) => {
-      if (!resolved) {
-        clearTimeout(timeoutId);
-        resolved = true;
-        resolve(code || 0);
-      }
+    await runClaudeCore({
+      promptFile: promptConfig.path,
+      settings: process.env.INPUT_SETTINGS,
+      allowedTools: process.env.INPUT_ALLOWED_TOOLS,
+      disallowedTools: process.env.INPUT_DISALLOWED_TOOLS,
+      maxTurns: process.env.INPUT_MAX_TURNS,
+      mcpConfig: process.env.INPUT_MCP_CONFIG,
+      systemPrompt: process.env.INPUT_SYSTEM_PROMPT,
+      appendSystemPrompt: process.env.INPUT_APPEND_SYSTEM_PROMPT,
+      claudeEnv: process.env.INPUT_CLAUDE_ENV,
+      fallbackModel: process.env.INPUT_FALLBACK_MODEL,
+      model: process.env.ANTHROPIC_MODEL,
+      timeoutMinutes: process.env.INPUT_TIMEOUT_MINUTES,
     });
-
-    claudeProcess.on("error", (error) => {
-      if (!resolved) {
-        console.error("Claude process error:", error);
-        clearTimeout(timeoutId);
-        resolved = true;
-        resolve(1);
-      }
-    });
-  });
-
-  // Clean up processes
-  try {
-    catProcess.kill("SIGTERM");
-  } catch (e) {
-    // Process may already be dead
-  }
-  try {
-    pipeProcess.kill("SIGTERM");
-  } catch (e) {
-    // Process may already be dead
-  }
-
-  // Clean up pipe file
-  try {
-    await unlink(PIPE_PATH);
-  } catch (e) {
-    // Ignore errors during cleanup
-  }
-
-  // Set conclusion based on exit code
-  if (exitCode === 0) {
-    // Try to process the output and save execution metrics
-    try {
-      await writeFile("output.txt", output);
-
-      // Process output.txt into JSON and save to execution file
-      const { stdout: jsonOutput } = await execAsync("jq -s '.' output.txt");
-      await writeFile(EXECUTION_FILE, jsonOutput);
-
-      console.log(`Log saved to ${EXECUTION_FILE}`);
-    } catch (e) {
-      core.warning(`Failed to process output for execution metrics: ${e}`);
-    }
-
-    core.setOutput("conclusion", "success");
-    core.setOutput("execution_file", EXECUTION_FILE);
-  } else {
+  } catch (error) {
+    core.setFailed(`Action failed with error: ${error}`);
     core.setOutput("conclusion", "failure");
-
-    // Still try to save execution file if we have output
-    if (output) {
-      try {
-        await writeFile("output.txt", output);
-        const { stdout: jsonOutput } = await execAsync("jq -s '.' output.txt");
-        await writeFile(EXECUTION_FILE, jsonOutput);
-        core.setOutput("execution_file", EXECUTION_FILE);
-      } catch (e) {
-        // Ignore errors when processing output during failure
-      }
-    }
-
-    process.exit(exitCode);
+    process.exit(1);
   }
 }
+
+if (import.meta.main) {
+  run();
+}

src/create-prompt/index.ts

@@ -811,12 +811,18 @@ f. If you are unable to complete certain steps, such as running a linter or test
   return promptContent;
 }
 
+export type CreatePromptResult = {
+  promptFile: string;
+  allowedTools: string;
+  disallowedTools: string;
+};
+
 export async function createPrompt(
   mode: Mode,
   modeContext: ModeContext,
   githubData: FetchDataResult,
   context: ParsedGitHubContext,
-) {
+): Promise<CreatePromptResult> {
   try {
     // Prepare the context for prompt generation
     let claudeCommentId: string = "";
@@ -888,8 +894,17 @@ export async function createPrompt(
       combinedAllowedTools,
     );
 
+    // TODO: Remove these environment variable exports once modes are updated to use return values
     core.exportVariable("ALLOWED_TOOLS", allAllowedTools);
     core.exportVariable("DISALLOWED_TOOLS", allDisallowedTools);
+
+    const promptFile = `${process.env.RUNNER_TEMP}/claude-prompts/claude-prompt.txt`;
+
+    return {
+      promptFile,
+      allowedTools: allAllowedTools,
+      disallowedTools: allDisallowedTools,
+    };
   } catch (error) {
     core.setFailed(`Create prompt failed with error: ${error}`);
     process.exit(1);

src/entrypoints/run.ts

@@ -0,0 +1,145 @@
+#!/usr/bin/env bun
+
+/**
+ * Unified entrypoint that combines prepare and run-claude steps
+ */
+
+import * as core from "@actions/core";
+import { setupGitHubToken } from "../github/token";
+import { checkWritePermissions } from "../github/validation/permissions";
+import { createOctokit } from "../github/api/client";
+import { parseGitHubContext, isEntityContext } from "../github/context";
+import { getMode, isValidMode, DEFAULT_MODE } from "../modes/registry";
+import type { ModeName } from "../modes/types";
+import { prepare } from "../prepare";
+import { runClaudeCore } from "../../base-action/src/run-claude-core";
+import { validateEnvironmentVariables } from "../../base-action/src/validate-env";
+import { setupClaudeCodeSettings } from "../../base-action/src/setup-claude-code-settings";
+
+async function run() {
+  try {
+    // Step 1: Get mode first to determine authentication method
+    const modeInput = process.env.MODE || DEFAULT_MODE;
+
+    // Validate mode input
+    if (!isValidMode(modeInput)) {
+      throw new Error(`Invalid mode: ${modeInput}`);
+    }
+    const validatedMode: ModeName = modeInput;
+
+    // Step 2: Setup GitHub token based on mode
+    let githubToken: string;
+    if (validatedMode === "experimental-review") {
+      // For experimental-review mode, use the default GitHub Action token
+      githubToken = process.env.DEFAULT_WORKFLOW_TOKEN || "";
+      if (!githubToken) {
+        throw new Error(
+          "DEFAULT_WORKFLOW_TOKEN not found for experimental-review mode",
+        );
+      }
+      console.log("Using default GitHub Action token for review mode");
+    } else {
+      // For other modes, use the existing token exchange
+      githubToken = await setupGitHubToken();
+    }
+    const octokit = createOctokit(githubToken);
+
+    // Step 3: Parse GitHub context (once for all operations)
+    const context = parseGitHubContext();
+
+    // Step 4: Check write permissions (only for entity contexts)
+    if (isEntityContext(context)) {
+      const hasWritePermissions = await checkWritePermissions(
+        octokit.rest,
+        context,
+      );
+      if (!hasWritePermissions) {
+        throw new Error(
+          "Actor does not have write permissions to the repository",
+        );
+      }
+    }
+
+    // Step 5: Get mode and check trigger conditions
+    const mode = getMode(validatedMode, context);
+    const containsTrigger = mode.shouldTrigger(context);
+
+    // Set output for action.yml to check (in case it's still needed)
+    core.setOutput("contains_trigger", containsTrigger.toString());
+
+    if (!containsTrigger) {
+      console.log("No trigger found, skipping remaining steps");
+      return;
+    }
+
+    // Step 6: Use the modular prepare function
+    const prepareResult = await prepare({
+      context,
+      octokit,
+      mode,
+      githubToken,
+    });
+
+    // Set critical outputs immediately after prepare completes
+    // This ensures they're available for cleanup even if Claude fails
+    core.setOutput("GITHUB_TOKEN", githubToken);
+    core.setOutput("mcp_config", prepareResult.mcpConfig);
+    if (prepareResult.branchInfo.claudeBranch) {
+      core.setOutput("branch_name", prepareResult.branchInfo.claudeBranch);
+      core.setOutput("CLAUDE_BRANCH", prepareResult.branchInfo.claudeBranch);
+    }
+    core.setOutput("BASE_BRANCH", prepareResult.branchInfo.baseBranch);
+    if (prepareResult.commentId) {
+      core.setOutput("claude_comment_id", prepareResult.commentId.toString());
+    }
+
+    // Step 7: The mode.prepare() call already created the prompt and set up tools
+    // We need to get the allowed/disallowed tools from environment variables
+    // TODO: Update Mode interface to return tools from prepare() instead of relying on env vars
+    const allowedTools = process.env.ALLOWED_TOOLS || "";
+    const disallowedTools = process.env.DISALLOWED_TOOLS || "";
+    const promptFile = `${process.env.RUNNER_TEMP}/claude-prompts/claude-prompt.txt`;
+
+    // Step 8: Validate environment and setup Claude settings
+    validateEnvironmentVariables();
+    await setupClaudeCodeSettings(process.env.SETTINGS);
+
+    // Step 9: Run Claude Code
+    console.log("Running Claude Code...");
+
+    // Build environment object to pass to Claude
+    const claudeEnvObject: Record<string, string> = {
+      GITHUB_TOKEN: githubToken,
+      NODE_VERSION: process.env.NODE_VERSION || "18.x",
+      DETAILED_PERMISSION_MESSAGES: "1",
+      CLAUDE_CODE_ACTION: "1",
+    };
+
+    await runClaudeCore({
+      promptFile,
+      settings: process.env.SETTINGS,
+      allowedTools,
+      disallowedTools,
+      maxTurns: process.env.MAX_TURNS,
+      mcpConfig: prepareResult.mcpConfig,
+      systemPrompt: "",
+      appendSystemPrompt: "",
+      claudeEnv: process.env.CLAUDE_ENV,
+      fallbackModel: process.env.FALLBACK_MODEL,
+      model: process.env.ANTHROPIC_MODEL || process.env.MODEL,
+      timeoutMinutes: process.env.TIMEOUT_MINUTES || "30",
+      env: claudeEnvObject,
+    });
+  } catch (error) {
+    const errorMessage = error instanceof Error ? error.message : String(error);
+    core.setFailed(`Action failed with error: ${errorMessage}`);
+    // Also output the clean error message for the action to capture
+    core.setOutput("prepare_error", errorMessage);
+    core.setOutput("conclusion", "failure");
+    process.exit(1);
+  }
+}
+
+if (import.meta.main) {
+  run();
+}

src/mcp/github-inline-comment-server.ts

@@ -0,0 +1,178 @@
+#!/usr/bin/env node
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { StdioServerTransport } from "@modelcontextprotocol/sdk/server/stdio.js";
+import { z } from "zod";
+import { createOctokit } from "../github/api/client";
+
+// Get repository and PR information from environment variables
+const REPO_OWNER = process.env.REPO_OWNER;
+const REPO_NAME = process.env.REPO_NAME;
+const PR_NUMBER = process.env.PR_NUMBER;
+
+if (!REPO_OWNER || !REPO_NAME || !PR_NUMBER) {
+  console.error(
+    "Error: REPO_OWNER, REPO_NAME, and PR_NUMBER environment variables are required",
+  );
+  process.exit(1);
+}
+
+// GitHub Inline Comment MCP Server - Provides inline PR comment functionality
+// Provides an inline comment tool without exposing full PR review capabilities, so that
+// Claude can't accidentally approve a PR
+const server = new McpServer({
+  name: "GitHub Inline Comment Server",
+  version: "0.0.1",
+});
+
+server.tool(
+  "create_inline_comment",
+  "Create an inline comment on a specific line or lines in a PR file",
+  {
+    path: z
+      .string()
+      .describe("The file path to comment on (e.g., 'src/index.js')"),
+    body: z
+      .string()
+      .describe(
+        "The comment text (supports markdown and GitHub code suggestion blocks). " +
+          "For code suggestions, use: ```suggestion\\nreplacement code\\n```. " +
+          "IMPORTANT: The suggestion block will REPLACE the ENTIRE line range (single line or startLine to line). " +
+          "Ensure the replacement is syntactically complete and valid - it must work as a drop-in replacement for the selected lines.",
+      ),
+    line: z
+      .number()
+      .optional()
+      .describe(
+        "Line number for single-line comments (required if startLine is not provided)",
+      ),
+    startLine: z
+      .number()
+      .optional()
+      .describe(
+        "Start line for multi-line comments (use with line parameter for the end line)",
+      ),
+    side: z
+      .enum(["LEFT", "RIGHT"])
+      .optional()
+      .default("RIGHT")
+      .describe(
+        "Side of the diff to comment on: LEFT (old code) or RIGHT (new code)",
+      ),
+    commit_id: z
+      .string()
+      .optional()
+      .describe(
+        "Specific commit SHA to comment on (defaults to latest commit)",
+      ),
+  },
+  async ({ path, body, line, startLine, side, commit_id }) => {
+    try {
+      const githubToken = process.env.GITHUB_TOKEN;
+
+      if (!githubToken) {
+        throw new Error("GITHUB_TOKEN environment variable is required");
+      }
+
+      const owner = REPO_OWNER;
+      const repo = REPO_NAME;
+      const pull_number = parseInt(PR_NUMBER, 10);
+
+      const octokit = createOctokit(githubToken).rest;
+
+      // Validate that either line or both startLine and line are provided
+      if (!line && !startLine) {
+        throw new Error(
+          "Either 'line' for single-line comments or both 'startLine' and 'line' for multi-line comments must be provided",
+        );
+      }
+
+      // If only line is provided, it's a single-line comment
+      // If both startLine and line are provided, it's a multi-line comment
+      const isSingleLine = !startLine;
+
+      const pr = await octokit.pulls.get({
+        owner,
+        repo,
+        pull_number,
+      });
+
+      const params: Parameters<
+        typeof octokit.rest.pulls.createReviewComment
+      >[0] = {
+        owner,
+        repo,
+        pull_number,
+        body,
+        path,
+        side: side || "RIGHT",
+        commit_id: commit_id || pr.data.head.sha,
+      };
+
+      if (isSingleLine) {
+        // Single-line comment
+        params.line = line;
+      } else {
+        // Multi-line comment
+        params.start_line = startLine;
+        params.start_side = side || "RIGHT";
+        params.line = line;
+      }
+
+      const result = await octokit.rest.pulls.createReviewComment(params);
+
+      return {
+        content: [
+          {
+            type: "text",
+            text: JSON.stringify(
+              {
+                success: true,
+                comment_id: result.data.id,
+                html_url: result.data.html_url,
+                path: result.data.path,
+                line: result.data.line || result.data.original_line,
+                message: `Inline comment created successfully on ${path}${isSingleLine ? ` at line ${line}` : ` from line ${startLine} to ${line}`}`,
+              },
+              null,
+              2,
+            ),
+          },
+        ],
+      };
+    } catch (error) {
+      const errorMessage =
+        error instanceof Error ? error.message : String(error);
+
+      // Provide more helpful error messages for common issues
+      let helpMessage = "";
+      if (errorMessage.includes("Validation Failed")) {
+        helpMessage =
+          "\n\nThis usually means the line number doesn't exist in the diff or the file path is incorrect. Make sure you're commenting on lines that are part of the PR's changes.";
+      } else if (errorMessage.includes("Not Found")) {
+        helpMessage =
+          "\n\nThis usually means the PR number, repository, or file path is incorrect.";
+      }
+
+      return {
+        content: [
+          {
+            type: "text",
+            text: `Error creating inline comment: ${errorMessage}${helpMessage}`,
+          },
+        ],
+        error: errorMessage,
+        isError: true,
+      };
+    }
+  },
+);
+
+async function runServer() {
+  const transport = new StdioServerTransport();
+  await server.connect(transport);
+  process.on("exit", () => {
+    server.close();
+  });
+}
+
+runServer().catch(console.error);

src/mcp/install-mcp-server.ts

@@ -111,6 +111,24 @@ export async function prepareMcpConfig(
       };
     }
 
+    // Include inline comment server for experimental review mode
+    if (context.inputs.mode === "experimental-review" && context.isPR) {
+      baseMcpConfig.mcpServers.github_inline_comment = {
+        command: "bun",
+        args: [
+          "run",
+          `${process.env.GITHUB_ACTION_PATH}/src/mcp/github-inline-comment-server.ts`,
+        ],
+        env: {
+          GITHUB_TOKEN: githubToken,
+          REPO_OWNER: owner,
+          REPO_NAME: repo,
+          PR_NUMBER: context.entityNumber?.toString() || "",
+          GITHUB_API_URL: GITHUB_API_URL,
+        },
+      };
+    }
+
     // Only add CI server if we have actions:read permission and we're in a PR context
     const hasActionsReadPermission =
       context.inputs.additionalPermissions.get("actions") === "read";

src/modes/review/index.ts

@@ -60,20 +60,8 @@ export const reviewMode: Mode = {
 
   getAllowedTools() {
     return [
-      // Context tools - to know who the current user is
-      "mcp__github__get_me",
-      // Core review tools
-      "mcp__github__create_pending_pull_request_review",
-      "mcp__github__add_comment_to_pending_review",
-      "mcp__github__submit_pending_pull_request_review",
-      "mcp__github__delete_pending_pull_request_review",
-      "mcp__github__create_and_submit_pull_request_review",
-      // Comment tools
-      "mcp__github__add_issue_comment",
-      // PR information tools
-      "mcp__github__get_pull_request",
-      "mcp__github__get_pull_request_reviews",
-      "mcp__github__get_pull_request_status",
+      "Bash(gh issue comment:*)",
+      "mcp__github_inline_comment__create_inline_comment",
     ];
   },
 
@@ -163,17 +151,13 @@ REVIEW MODE WORKFLOW:
 
 1. First, understand the PR context:
    - You are reviewing PR #${eventData.isPR && eventData.prNumber ? eventData.prNumber : "[PR number]"} in ${context.repository}
-   - Use mcp__github__get_pull_request to get PR metadata
    - Use the Read, Grep, and Glob tools to examine the modified files directly from disk
    - This provides the full context and latest state of the code
    - Look at the changed_files section above to see which files were modified
 
-2. Create a pending review:
-   - Use mcp__github__create_pending_pull_request_review to start your review
-   - This allows you to batch comments before submitting
-
-3. Add inline comments:
-   - Use mcp__github__add_comment_to_pending_review for each issue or suggestion
+2. Add comments:
+   - use Bash(gh issue comment:*) to add top-level comments
+   - Use mcp__github_inline_comment__create_inline_comment to add inline comments (prefer this where possible)
    - Parameters:
      * path: The file path (e.g., "src/index.js")
      * line: Line number for single-line comments
@@ -182,49 +166,6 @@ REVIEW MODE WORKFLOW:
      * subjectType: "line" for line-level comments
      * body: Your comment text
    
-   - When to use multi-line comments:
-     * When replacing multiple consecutive lines
-     * When the fix requires changes across several lines
-     * Example: To replace lines 19-20, use startLine: 19, line: 20
-   
-   - For code suggestions, use this EXACT format in the body:
-     \`\`\`suggestion
-     corrected code here
-     \`\`\`
-   
-   CRITICAL: GitHub suggestion blocks must ONLY contain the replacement for the specific line(s) being commented on:
-   - For single-line comments: Replace ONLY that line
-   - For multi-line comments: Replace ONLY the lines in the range
-   - Do NOT include surrounding context or function signatures
-   - Do NOT suggest changes that span beyond the commented lines
-   
-   Example for line 19 \`var name = user.name;\`:
-   WRONG:
-   \\\`\\\`\\\`suggestion
-   function processUser(user) {
-       if (!user) throw new Error('Invalid user');
-       const name = user.name;
-   \\\`\\\`\\\`
-   
-   CORRECT:
-   \\\`\\\`\\\`suggestion
-   const name = user.name;
-   \\\`\\\`\\\`
-   
-   For validation suggestions, comment on the function declaration line or create separate comments for each concern.
-
-4. Submit your review:
-   - Use mcp__github__submit_pending_pull_request_review
-   - Parameters:
-     * event: "COMMENT" (general feedback), "REQUEST_CHANGES" (issues found), or "APPROVE" (if appropriate)
-     * body: Write a comprehensive review summary that includes:
-       - Overview of what was reviewed (files, scope, focus areas)
-       - Summary of all issues found (with counts by severity if applicable)
-       - Key recommendations and action items
-       - Highlights of good practices observed
-       - Overall assessment and recommendation
-   - The body should be detailed and informative since it's the main review content
-   - Structure the body with clear sections using markdown headers
 
 REVIEW GUIDELINES:
 
@@ -301,6 +242,7 @@ This ensures users get value from the review even before checking individual inl
       claudeBranch: branchInfo.claudeBranch,
     });
 
+    // TODO: Capture and return the allowed/disallowed tools from createPrompt
     await createPrompt(reviewMode, modeContext, githubData, context);
 
     // Export tool environment variables for review mode

src/modes/tag/index.ts

@@ -98,6 +98,7 @@ export const tagMode: Mode = {
       claudeBranch: branchInfo.claudeBranch,
     });
 
+    // TODO: Capture and return the allowed/disallowed tools from createPrompt
     await createPrompt(tagMode, modeContext, githubData, context);
 
     // Get MCP configuration

src/prepare/types.ts

@@ -10,6 +10,7 @@ export type PrepareResult = {
     currentBranch: string;
   };
   mcpConfig: string;
+  // TODO: Add allowedTools and disallowedTools here once modes are updated
 };
 
 export type PrepareOptions = {