switch to http mcp

.husky/pre-commit

@@ -8,5 +8,5 @@ if git diff --cached --name-only | grep -q "^package.json$"; then
     pnpm build
 
     # Add the built files and lockfile to the commit
-    git add entry mcp-server pnpm-lock.yaml
+    git add entry pnpm-lock.yaml
 fi

agents/codex.ts

@@ -128,7 +128,7 @@ const messageHandlers: {
         toolName: item.tool,
         input: {
           server: item.server,
-          ...((item as any).args || {}),
+          ...((item as any).arguments || {}),
         },
       });
     }
@@ -167,7 +167,7 @@ const messageHandlers: {
       const reasoningText = item.text.trim();
       // Remove markdown bold markers if present for cleaner output
       const cleanText = reasoningText.replace(/\*\*/g, "");
-      log.info(cleanText);
+      log.box(cleanText, { title: "Codex" });
     }
   },
   error: (event) => {
@@ -177,34 +177,30 @@ const messageHandlers: {
 
 /**
  * Configure MCP servers for Codex using the CLI.
- * Codex CLI syntax: codex mcp add <name> --env KEY=value -- <command> [args...]
+ * For HTTP-based servers, use: codex mcp add <name> --url <url>
  */
 function configureCodexMcpServers({ mcpServers, cliPath }: ConfigureMcpServersParams): void {
   for (const [serverName, serverConfig] of Object.entries(mcpServers)) {
-    const command = serverConfig.command;
-    const args = serverConfig.args || [];
-    const envVars = serverConfig.env || {};
+    if (serverConfig.type === "http") {
+      // HTTP-based MCP server - use --url flag
+      const addArgs = ["mcp", "add", serverName, "--url", serverConfig.url];
 
-    const addArgs = ["mcp", "add", serverName];
+      log.info(`Adding MCP server '${serverName}' at ${serverConfig.url}...`);
+      const addResult = spawnSync("node", [cliPath, ...addArgs], {
+        stdio: "pipe",
+        encoding: "utf-8",
+      });
 
-    // Add environment variables as --env flags first
-    for (const [key, value] of Object.entries(envVars)) {
-      addArgs.push("--env", `${key}=${value}`);
-    }
-
-    addArgs.push("--", command, ...args);
-
-    log.info(`Adding MCP server '${serverName}'...`);
-    const addResult = spawnSync("node", [cliPath, ...addArgs], {
-      stdio: "pipe",
-      encoding: "utf-8",
-    });
-
-    if (addResult.status !== 0) {
+      if (addResult.status !== 0) {
+        throw new Error(
+          `codex mcp add failed: ${addResult.stderr || addResult.stdout || "Unknown error"}`
+        );
+      }
+      log.info(`✓ MCP server '${serverName}' configured`);
+    } else {
       throw new Error(
-        `codex mcp add failed: ${addResult.stderr || addResult.stdout || "Unknown error"}`
+        `Unsupported MCP server type for Codex: ${(serverConfig as any).type || "unknown"}`
       );
     }
-    log.info(`✓ MCP server '${serverName}' configured`);
   }
 }

agents/cursor.ts

@@ -269,6 +269,22 @@ function configureCursorMcpServers({ mcpServers }: ConfigureMcpServersParams) {
   const cursorConfigDir = join(realHome, ".cursor");
   const mcpConfigPath = join(cursorConfigDir, "mcp.json");
   mkdirSync(cursorConfigDir, { recursive: true });
-  writeFileSync(mcpConfigPath, JSON.stringify({ mcpServers }, null, 2), "utf-8");
+
+  // Convert to Cursor's expected format (HTTP config)
+  const cursorMcpServers: Record<string, { type: string; url: string }> = {};
+  for (const [serverName, serverConfig] of Object.entries(mcpServers)) {
+    if (serverConfig.type !== "http") {
+      throw new Error(
+        `Unsupported MCP server type for Cursor: ${(serverConfig as any).type || "unknown"}`
+      );
+    }
+
+    cursorMcpServers[serverName] = {
+      type: "http",
+      url: serverConfig.url,
+    };
+  }
+
+  writeFileSync(mcpConfigPath, JSON.stringify({ mcpServers: cursorMcpServers }, null, 2), "utf-8");
   log.info(`MCP config written to ${mcpConfigPath}`);
 }

agents/gemini.ts

@@ -249,31 +249,31 @@ export const gemini = agent({
 
 /**
  * Configure MCP servers for Gemini using the CLI.
- * Gemini CLI syntax: gemini mcp add <name> <commandOrUrl> [args...] --env KEY=value
+ * Gemini CLI syntax: gemini mcp add <name> <commandOrUrl> [args...] --transport <type>
+ * For HTTP-based servers, use: gemini mcp add <name> <url> --transport http
  */
 function configureGeminiMcpServers({ mcpServers, cliPath }: ConfigureMcpServersParams): void {
   for (const [serverName, serverConfig] of Object.entries(mcpServers)) {
-    const command = serverConfig.command;
-    const args = serverConfig.args || [];
-    const envVars = serverConfig.env || {};
+    if (serverConfig.type === "http") {
+      // HTTP-based MCP server - use URL with --transport http flag
+      const addArgs = ["mcp", "add", serverName, serverConfig.url, "--transport", "http"];
 
-    const addArgs = ["mcp", "add", serverName, command, ...args];
+      log.info(`Adding MCP server '${serverName}' at ${serverConfig.url}...`);
+      const addResult = spawnSync("node", [cliPath, ...addArgs], {
+        stdio: "pipe",
+        encoding: "utf-8",
+      });
 
-    for (const [key, value] of Object.entries(envVars)) {
-      addArgs.push("--env", `${key}=${value}`);
-    }
-
-    log.info(`Adding MCP server '${serverName}'...`);
-    const addResult = spawnSync("node", [cliPath, ...addArgs], {
-      stdio: "pipe",
-      encoding: "utf-8",
-    });
-
-    if (addResult.status !== 0) {
+      if (addResult.status !== 0) {
+        throw new Error(
+          `gemini mcp add failed: ${addResult.stderr || addResult.stdout || "Unknown error"}`
+        );
+      }
+      log.info(`✓ MCP server '${serverName}' configured`);
+    } else {
       throw new Error(
-        `gemini mcp add failed: ${addResult.stderr || addResult.stdout || "Unknown error"}`
+        `Unsupported MCP server type for Gemini: ${(serverConfig as any).type || "unknown"}`
       );
     }
-    log.info(`✓ MCP server '${serverName}' configured`);
   }
 }

agents/shared.ts

@@ -4,7 +4,7 @@ import { mkdtemp } from "node:fs/promises";
 import { tmpdir } from "node:os";
 import { join } from "node:path";
 import { pipeline } from "node:stream/promises";
-import type { McpStdioServerConfig } from "@anthropic-ai/claude-agent-sdk";
+import type { McpHttpServerConfig } from "@anthropic-ai/claude-agent-sdk";
 import type { show } from "@ark/util";
 import { type AgentManifest, type AgentName, agentsManifest, type Payload } from "../external.ts";
 import { log } from "../utils/cli.ts";
@@ -26,7 +26,7 @@ export interface AgentConfig {
   apiKey: string;
   githubInstallationToken: string;
   payload: Payload;
-  mcpServers: Record<string, McpStdioServerConfig>;
+  mcpServers: Record<string, McpHttpServerConfig>;
   cliPath: string;
 }
 
@@ -34,7 +34,7 @@ export interface AgentConfig {
  * Parameters for configuring MCP servers
  */
 export interface ConfigureMcpServersParams {
-  mcpServers: Record<string, McpStdioServerConfig>;
+  mcpServers: Record<string, McpHttpServerConfig>;
   cliPath: string;
 }
 

esbuild.config.js

@@ -59,7 +59,7 @@ const sharedConfig = {
   drop: [],
 };
 
-// Build the main entry bundle (without MCP)
+// Build the main entry bundle
 await build({
   ...sharedConfig,
   entryPoints: ["./entry.ts"],
@@ -67,12 +67,4 @@ await build({
   plugins: [stripShebangPlugin],
 });
 
-// Build the MCP server bundle
-await build({
-  ...sharedConfig,
-  entryPoints: ["./mcp/server.ts"],
-  outfile: "./mcp-server",
-  plugins: [stripShebangPlugin],
-});
-
 console.log("✅ Build completed successfully!");

fixtures/basic.txt

@@ -1 +1 @@
-write a comment to https://github.com/pullfrogai/scratch/pull/29 that tells a joke
+use debug_shell_command tool to run 'git status' and explain the result

main.ts

@@ -10,6 +10,7 @@ import type { AgentResult } from "./agents/shared.ts";
 import type { AgentName, AgentName as AgentNameType, Payload } from "./external.ts";
 import { agentsManifest } from "./external.ts";
 import { createMcpConfigs } from "./mcp/config.ts";
+import { startMcpHttpServer } from "./mcp/server.ts";
 import { modes } from "./modes.ts";
 import packageJson from "./package.json" with { type: "json" };
 import { fetchRepoSettings } from "./utils/api.ts";
@@ -48,39 +49,29 @@ export interface MainResult {
 }
 
 export async function main(inputs: Inputs): Promise<MainResult> {
-  let githubInstallationToken: string | undefined;
   let pollInterval: NodeJS.Timeout | null = null;
+  let mcpServerClose: (() => Promise<void>) | undefined;
+  let githubInstallationToken: string | undefined;
 
   try {
     // parse payload early to extract agent
     const payload = parsePayload(inputs);
 
-    // resolve agent before initializing context
-    githubInstallationToken = await setupGitHubInstallationToken();
-    const repoContext = parseRepoContext();
-    const { agentName, agent } = await resolveAgent(
-      inputs,
-      payload,
-      githubInstallationToken,
-      repoContext
-    );
-
-    const partialCtx = await initializeContext(
-      inputs,
-      agentName,
-      agent,
-      githubInstallationToken,
-      repoContext
-    );
+    const partialCtx = await initializeContext(inputs, payload);
     const ctx = partialCtx as MainContext;
-    ctx.payload = payload;
+    githubInstallationToken = ctx.githubInstallationToken;
 
-    setupGitAuth(ctx.githubInstallationToken, ctx.repoContext);
+    setupGitAuth({
+      githubInstallationToken: ctx.githubInstallationToken,
+      repoContext: ctx.repoContext,
+    });
     await setupTempDirectory(ctx);
     setupMcpLogPolling(ctx);
     pollInterval = ctx.pollInterval;
 
     setupGitBranch(ctx.payload);
+    await startMcpServer(ctx);
+    mcpServerClose = ctx.mcpServerClose;
     setupMcpServers(ctx);
     await installAgentCli(ctx);
     validateApiKey(ctx);
@@ -99,6 +90,9 @@ export async function main(inputs: Inputs): Promise<MainResult> {
     if (pollInterval) {
       clearInterval(pollInterval);
     }
+    if (mcpServerClose) {
+      await mcpServerClose();
+    }
     if (githubInstallationToken) {
       await revokeInstallationToken(githubInstallationToken);
     }
@@ -179,6 +173,8 @@ interface MainContext {
   mcpLogPath: string;
   pollInterval: NodeJS.Timeout | null;
   payload: Payload;
+  mcpServerUrl: string;
+  mcpServerClose: () => Promise<void>;
   mcpServers: ReturnType<typeof createMcpConfigs>;
   cliPath: string;
   apiKey: string;
@@ -186,21 +182,33 @@ interface MainContext {
 
 async function initializeContext(
   inputs: Inputs,
-  agentName: AgentNameType,
-  agent: (typeof agents)[AgentNameType],
-  githubInstallationToken: string,
-  repoContext: RepoContext
-): Promise<Omit<MainContext, "payload" | "mcpServers" | "cliPath" | "apiKey">> {
+  payload: Payload
+): Promise<
+  Omit<MainContext, "mcpServerUrl" | "mcpServerClose" | "mcpServers" | "cliPath" | "apiKey">
+> {
   log.info(`🐸 Running pullfrog/action@${packageJson.version}...`);
   Inputs.assert(inputs);
   setupGitConfig();
 
+  const githubInstallationToken = await setupGitHubInstallationToken();
+  const repoContext = parseRepoContext();
+
+  // resolve agent and update payload with resolved agent name
+  const { agentName, agent } = await resolveAgent(
+    inputs,
+    payload,
+    githubInstallationToken,
+    repoContext
+  );
+  const resolvedPayload = { ...payload, agent: agentName };
+
   return {
     inputs,
     githubInstallationToken,
     repoContext,
     agentName,
     agent,
+    payload: resolvedPayload,
     sharedTempDir: "",
     mcpLogPath: "",
     pollInterval: null,
@@ -293,9 +301,27 @@ function parsePayload(inputs: Inputs): Payload {
   }
 }
 
-function setupMcpServers(ctx: MainContext): void {
+async function startMcpServer(ctx: MainContext): Promise<void> {
+  // Set environment variables for MCP server tools
+  const repoContext = parseRepoContext();
+  const githubRepository = `${repoContext.owner}/${repoContext.name}`;
   const allModes = [...modes, ...(ctx.payload.modes || [])];
-  ctx.mcpServers = createMcpConfigs(ctx.githubInstallationToken, allModes, ctx.payload);
+
+  process.env.GITHUB_INSTALLATION_TOKEN = ctx.githubInstallationToken;
+  process.env.GITHUB_REPOSITORY = githubRepository;
+  process.env.PULLFROG_MODES = JSON.stringify(allModes);
+  process.env.PULLFROG_PAYLOAD = JSON.stringify(ctx.payload);
+
+  // GITHUB_RUN_ID is already set in GitHub Actions, no need to set it here
+
+  const { url, close } = await startMcpHttpServer();
+  ctx.mcpServerUrl = url;
+  ctx.mcpServerClose = close;
+  log.info(`🚀 MCP server started at ${url}`);
+}
+
+function setupMcpServers(ctx: MainContext): void {
+  ctx.mcpServers = createMcpConfigs(ctx.mcpServerUrl);
   log.debug(`📋 MCP Config: ${JSON.stringify(ctx.mcpServers, null, 2)}`);
 }
 

mcp/comment.ts

@@ -15,7 +15,7 @@ function buildCommentFooter(payload: Payload): string {
   const agentDisplayName = agentInfo?.displayName || "Unknown Agent";
   const agentUrl = agentInfo?.url || "https://pullfrog.ai";
 
-  // build workflow run URL
+  // build workflow run URL: https://github.com/{owner}/{repo}/actions/runs/{runId}
   const workflowRunUrl = runId
     ? `https://github.com/${repoContext.owner}/${repoContext.name}/actions/runs/${runId}`
     : `https://github.com/${repoContext.owner}/${repoContext.name}`;

mcp/config.ts

@@ -2,47 +2,18 @@
  * Simple MCP configuration helper for adding our minimal GitHub comment server
  */
 
-import type { McpStdioServerConfig } from "@anthropic-ai/claude-agent-sdk";
-import { fromHere } from "@ark/fs";
-import type { Payload } from "../external.ts";
+import type { McpHttpServerConfig } from "@anthropic-ai/claude-agent-sdk";
 import { ghPullfrogMcpName } from "../external.ts";
-import type { Mode } from "../modes.ts";
-import { parseRepoContext } from "../utils/github.ts";
 
 export type McpName = typeof ghPullfrogMcpName;
 
-export type McpConfigs = Record<McpName, McpStdioServerConfig>;
-
-export function createMcpConfigs(
-  githubInstallationToken: string,
-  modes: Mode[],
-  payload: Payload
-): McpConfigs {
-  const repoContext = parseRepoContext();
-  const githubRepository = `${repoContext.owner}/${repoContext.name}`;
-
-  // In production (GitHub Actions), mcp-server is in same directory as entry.js (where this is bundled)
-  // In development, server.ts is in the same directory as this file (config.ts)
-  const serverPath = process.env.GITHUB_ACTIONS ? fromHere("mcp-server") : fromHere("server.ts");
-
-  const env: Record<string, string> = {
-    GITHUB_INSTALLATION_TOKEN: githubInstallationToken,
-    GITHUB_REPOSITORY: githubRepository,
-    PULLFROG_MODES: JSON.stringify(modes),
-    PULLFROG_PAYLOAD: JSON.stringify(payload),
-    PULLFROG_TEMP_DIR: process.env.PULLFROG_TEMP_DIR!,
-  };
-
-  // pass through GITHUB_RUN_ID if available (automatically set in GitHub Actions)
-  if (process.env.GITHUB_RUN_ID) {
-    env.GITHUB_RUN_ID = process.env.GITHUB_RUN_ID;
-  }
+export type McpConfigs = Record<McpName, McpHttpServerConfig>;
 
+export function createMcpConfigs(mcpServerUrl: string): McpConfigs {
   return {
     [ghPullfrogMcpName]: {
-      command: "node",
-      args: [serverPath],
-      env,
+      type: "http",
+      url: mcpServerUrl,
     },
   };
 }

mcp/debug.ts

@@ -0,0 +1,45 @@
+import { type } from "arktype";
+import { $ } from "../utils/shell.ts";
+import type { ToolResult } from "./shared.ts";
+import { tool } from "./shared.ts";
+
+export const DebugShellCommand = type({});
+
+export const DebugShellCommandTool = tool({
+  name: "debug_shell_command",
+  description:
+    "debug tool: runs 'git status' and returns the output. use this to test shell command execution in the MCP server.",
+  parameters: DebugShellCommand,
+  execute: async (): Promise<ToolResult> => {
+    try {
+      const result = $("git", ["status"]);
+
+      return {
+        content: [
+          {
+            type: "text",
+            text: JSON.stringify(
+              {
+                success: true,
+                command: "git status",
+                output: result.trim(),
+              },
+              null,
+              2
+            ),
+          },
+        ],
+      };
+    } catch (error) {
+      return {
+        content: [
+          {
+            type: "text",
+            text: `Error: ${error instanceof Error ? error.message : String(error)}`,
+          },
+        ],
+        isError: true,
+      };
+    }
+  },
+});

mcp/server.ts

@@ -1,5 +1,6 @@
 import "./arkConfig.ts";
 // this must be imported first
+import { createServer } from "node:net";
 import { FastMCP } from "fastmcp";
 import { ghPullfrogMcpName } from "../external.ts";
 import { GetCheckSuiteLogsTool } from "./checkSuite.ts";
@@ -9,6 +10,7 @@ import {
   EditCommentTool,
   UpdateWorkingCommentTool,
 } from "./comment.ts";
+import { DebugShellCommandTool } from "./debug.ts";
 import { IssueTool } from "./issue.ts";
 import { PullRequestTool } from "./pr.ts";
 import { PullRequestInfoTool } from "./prInfo.ts";
@@ -17,24 +19,79 @@ import { GetReviewCommentsTool, ListPullRequestReviewsTool } from "./reviewComme
 import { SelectModeTool } from "./selectMode.ts";
 import { addTools } from "./shared.ts";
 
-const server = new FastMCP({
-  name: ghPullfrogMcpName,
-  version: "0.0.1",
-});
+/**
+ * Find an available port starting from the given port
+ */
+async function findAvailablePort(startPort: number): Promise<number> {
+  const checkPort = (port: number): Promise<boolean> => {
+    return new Promise((resolve) => {
+      const server = createServer();
+      server.once("error", () => {
+        server.close();
+        resolve(false);
+      });
+      server.listen(port, () => {
+        server.close(() => {
+          resolve(true);
+        });
+      });
+    });
+  };
 
-addTools(server, [
-  SelectModeTool,
-  CreateCommentTool,
-  EditCommentTool,
-  CreateWorkingCommentTool,
-  UpdateWorkingCommentTool,
-  IssueTool,
-  PullRequestTool,
-  ReviewTool,
-  PullRequestInfoTool,
-  GetReviewCommentsTool,
-  ListPullRequestReviewsTool,
-  GetCheckSuiteLogsTool,
-]);
+  let port = startPort;
+  while (port < startPort + 100) {
+    if (await checkPort(port)) {
+      return port;
+    }
+    port++;
+  }
+  throw new Error(`Could not find available port starting from ${startPort}`);
+}
 
-server.start();
+/**
+ * Start the MCP HTTP server and return the URL and close function
+ */
+export async function startMcpHttpServer(): Promise<{ url: string; close: () => Promise<void> }> {
+  const server = new FastMCP({
+    name: ghPullfrogMcpName,
+    version: "0.0.1",
+  });
+
+  addTools(server, [
+    SelectModeTool,
+    CreateCommentTool,
+    EditCommentTool,
+    CreateWorkingCommentTool,
+    UpdateWorkingCommentTool,
+    IssueTool,
+    PullRequestTool,
+    ReviewTool,
+    PullRequestInfoTool,
+    GetReviewCommentsTool,
+    ListPullRequestReviewsTool,
+    GetCheckSuiteLogsTool,
+    DebugShellCommandTool,
+  ]);
+
+  const port = await findAvailablePort(3764);
+  const host = "127.0.0.1";
+  const endpoint = "/mcp";
+
+  await server.start({
+    transportType: "httpStream",
+    httpStream: {
+      port,
+      host,
+      endpoint,
+    },
+  });
+
+  const url = `http://${host}:${port}${endpoint}`;
+
+  return {
+    url,
+    close: async () => {
+      await server.stop();
+    },
+  };
+}

mcp/shared.ts

@@ -2,7 +2,6 @@ import { Octokit } from "@octokit/rest";
 import type { StandardSchemaV1 } from "@standard-schema/spec";
 import type { FastMCP, Tool } from "fastmcp";
 import type { Payload } from "../external.ts";
-import { log } from "../utils/cli.ts";
 import { parseRepoContext, type RepoContext } from "../utils/github.ts";
 
 export interface ToolResult {
@@ -48,42 +47,7 @@ export interface McpContext extends RepoContext {
   payload: Payload;
 }
 
-export const tool = <const params>(toolDef: Tool<any, StandardSchemaV1<params>>) => {
-  // Wrap the execute function to add logging with the tool name
-  const toolName = toolDef.name;
-  const originalExecute = toolDef.execute;
-
-  toolDef.execute = async (args: params, context: any) => {
-    try {
-      const result = await originalExecute(args, context);
-
-      // TOOL CALL LOGGING DISABLED — now handled by each agent
-
-      // Check if result is a ToolResult with isError property
-      // const isError =
-      //   result && typeof result === "object" && "isError" in result && result.isError === true;
-      // const resultData =
-      //   result && typeof result === "object" && "content" in result
-      //     ? (result as ToolResult).content[0]?.text
-      //     : undefined;
-
-      // if (isError && resultData) {
-      //   log.toolCall({ toolName, request: args, error: resultData });
-      // } else if (resultData) {
-      //   log.toolCall({ toolName, request: args, result: resultData });
-      // } else {
-      //   log.toolCall({ toolName, request: args });
-      // }
-      return result;
-    } catch (error) {
-      // const errorMessage = error instanceof Error ? error.message : String(error);
-      // log.toolCall({ toolName, request: args, error: errorMessage });
-      throw error;
-    }
-  };
-
-  return toolDef;
-};
+export const tool = <const params>(toolDef: Tool<any, StandardSchemaV1<params>>) => toolDef;
 
 export const addTools = (server: FastMCP, tools: Tool<any, any>[]) => {
   for (const tool of tools) {

modes.ts

@@ -6,7 +6,7 @@ export interface Mode {
   prompt: string;
 }
 
-const initialCommentInstruction = `Use ${ghPullfrogMcpName}/create_working_comment to create an initial Working Comment with a conversational description of what work you are about to perform.`;
+const initialCommentInstruction = `When the task is associated with an issue/PR, use ${ghPullfrogMcpName}/create_working_comment to create an initial Working Comment with a conversational description of what work you are about to perform.`;
 
 export const modes: Mode[] = [
   {

package.json

@@ -1,6 +1,6 @@
 {
   "name": "@pullfrog/action",
-  "version": "0.0.112",
+  "version": "0.0.113",
   "type": "module",
   "files": [
     "index.js",

play.ts

@@ -141,6 +141,8 @@ Examples:
     if (!result.success) {
       process.exit(1);
     }
+
+    process.exit(0);
   } catch (err) {
     log.error((err as Error).message);
     process.exit(1);

utils/setup.ts

@@ -43,20 +43,22 @@ export function setupTestRepo(options: SetupOptions): void {
 
 /**
  * Setup git configuration to avoid identity errors
- * Only runs in GitHub Actions environment to avoid overwriting local git config
+ * Uses --local flag to scope config to the current repo only
  */
 export function setupGitConfig(): void {
-  // Only set up git config in GitHub Actions environment
-  // In local development, use the user's existing git config
-  if (!process.env.GITHUB_ACTIONS) {
-    return;
-  }
-
+  const repoDir = process.cwd();
   log.info("🔧 Setting up git configuration...");
   try {
-    execSync('git config user.email "action@pullfrog.ai"', { stdio: "pipe" });
-    execSync('git config user.name "Pullfrog Action"', { stdio: "pipe" });
-    log.debug("setupGitConfig: ✓ Git configuration set successfully");
+    // Use --local to scope config to this repo only, preventing leakage to user's global config
+    execSync('git config --local user.email "action@pullfrog.ai"', {
+      cwd: repoDir,
+      stdio: "pipe",
+    });
+    execSync('git config --local user.name "Pullfrog Action"', {
+      cwd: repoDir,
+      stdio: "pipe",
+    });
+    log.debug("setupGitConfig: ✓ Git configuration set successfully (scoped to repo)");
   } catch (error) {
     // If git config fails, log warning but don't fail the action
     // This can happen if we're not in a git repo or git isn't available
@@ -67,30 +69,34 @@ export function setupGitConfig(): void {
 }
 
 /**
- * Setup git authentication using GitHub token
- * Only runs in GitHub Actions environment to avoid breaking local git remotes
+ * Setup git authentication using GitHub installation token
+ * Always uses the installation token, scoped to the current repo only
  */
-export function setupGitAuth(githubToken: string, repoContext: RepoContext): void {
-  // Only set up git auth in GitHub Actions environment
-  // In local testing, this would overwrite the real git remote with fake credentials
-  if (!process.env.GITHUB_ACTIONS) {
-    return;
-  }
+export function setupGitAuth(ctx: {
+  githubInstallationToken: string;
+  repoContext: RepoContext;
+}): void {
+  const repoDir = process.cwd();
 
   log.info("🔐 Setting up git authentication...");
 
   // Remove existing git auth headers that actions/checkout might have set
+  // Use --local to scope to this repo only
   try {
-    execSync("git config --unset-all http.https://github.com/.extraheader", { stdio: "inherit" });
+    execSync("git config --local --unset-all http.https://github.com/.extraheader", {
+      cwd: repoDir,
+      stdio: "pipe",
+    });
     log.info("✓ Removed existing authentication headers");
   } catch {
-    log.info("No existing authentication headers to remove");
+    log.debug("No existing authentication headers to remove");
   }
 
   // Update remote URL to embed the token
-  const remoteUrl = `https://x-access-token:${githubToken}@github.com/${repoContext.owner}/${repoContext.name}.git`;
-  $("git", ["remote", "set-url", "origin", remoteUrl]);
-  log.info("✓ Updated remote URL with authentication token");
+  // This is scoped to the repo's .git/config, not the user's global config
+  const remoteUrl = `https://x-access-token:${ctx.githubInstallationToken}@github.com/${ctx.repoContext.owner}/${ctx.repoContext.name}.git`;
+  $("git", ["remote", "set-url", "origin", remoteUrl], { cwd: repoDir });
+  log.info("✓ Updated remote URL with authentication token (scoped to repo)");
 }
 
 /**
@@ -99,6 +105,7 @@ export function setupGitAuth(githubToken: string, repoContext: RepoContext): voi
  */
 export function setupGitBranch(payload: Payload): void {
   const branch = payload.event.branch;
+  const repoDir = process.cwd();
 
   if (!branch) {
     log.debug("No branch specified in payload, using default branch");
@@ -110,11 +117,17 @@ export function setupGitBranch(payload: Payload): void {
   try {
     // Fetch the branch from origin
     log.debug(`Fetching branch from origin: ${branch}`);
-    execSync(`git fetch origin ${branch}`, { stdio: "pipe" });
+    execSync(`git fetch origin ${branch}`, {
+      cwd: repoDir,
+      stdio: "pipe",
+    });
 
     // Checkout the branch, creating local tracking branch
     log.debug(`Checking out branch: ${branch}`);
-    execSync(`git checkout -B ${branch} origin/${branch}`, { stdio: "pipe" });
+    execSync(`git checkout -B ${branch} origin/${branch}`, {
+      cwd: repoDir,
+      stdio: "pipe",
+    });
 
     log.info(`✓ Successfully checked out branch: ${branch}`);
   } catch (error) {

utils/shell.ts

@@ -29,8 +29,11 @@ interface ShellOptions {
  */
 export function $(cmd: string, args: string[], options?: ShellOptions): string {
   const encoding = options?.encoding ?? "utf-8";
+
+  // CRITICAL: use "ignore" for stdin instead of "inherit" to avoid breaking MCP transport
+  // when running inside an MCP server, stdin is used for JSON-RPC protocol
   const result = spawnSync(cmd, args, {
-    stdio: ["inherit", "pipe", "pipe"],
+    stdio: ["ignore", "pipe", "pipe"],
     encoding,
     cwd: options?.cwd,
   });
@@ -39,10 +42,19 @@ export function $(cmd: string, args: string[], options?: ShellOptions): string {
   const stderr = result.stderr ?? "";
 
   // Write output to process streams so it behaves like stdio: "inherit"
+  // CRITICAL: when running inside an MCP server, stdout is used for JSON-RPC protocol
+  // so we must write to stderr instead to avoid corrupting the protocol
   // Only log if log option is not explicitly set to false
   if (options?.log !== false) {
+    // if stdout is a TTY, it's safe to write to it; otherwise it's likely a pipe used for JSON-RPC
+    const canWriteToStdout = process.stdout.isTTY === true;
     if (stdout) {
-      process.stdout.write(stdout);
+      if (canWriteToStdout) {
+        process.stdout.write(stdout);
+      } else {
+        // stdout is a pipe (MCP context) - write to stderr instead
+        process.stderr.write(stdout);
+      }
     }
     if (stderr) {
       process.stderr.write(stderr);