Fix MCP file discovery errors (#9)

* fix tool errors

*QA

utils/setup.ts

@@ -1,6 +1,7 @@
 import { execSync } from "node:child_process";
 import { existsSync, rmSync } from "node:fs";
 import type { Context } from "../main.ts";
+import { checkoutPrBranch } from "../mcp/checkout.ts";
 import { log } from "./cli.ts";
 import { $ } from "./shell.ts";
 
@@ -72,11 +73,11 @@ export function setupGitConfig(): void {
 
 /**
  * Setup git authentication for the repository.
- * PR checkout is handled dynamically by the checkout_pr MCP tool.
+ * For PR events, uses the shared checkoutPrBranch helper (also used by checkout_pr MCP tool).
  *
- * FORK PR ARCHITECTURE (handled by checkout_pr tool):
+ * FORK PR ARCHITECTURE:
  * - origin: always points to BASE REPO (where PR targets)
- * - checkout_pr sets per-branch pushRemote config for fork PRs
+ * - checkoutPrBranch sets per-branch pushRemote config for fork PRs
  * - diff operations use: git diff origin/<base>..HEAD
  */
 export async function setupGit(ctx: Context): Promise<void> {
@@ -95,8 +96,21 @@ export async function setupGit(ctx: Context): Promise<void> {
     log.debug("no existing authentication headers to remove");
   }
 
-  // authenticate origin - needed for all fetch operations including PR fetches
+  // non-PR events: set up origin with token, stay on default branch
+  if (ctx.payload.event.is_pr !== true || !ctx.payload.event.issue_number) {
+    const originUrl = `https://x-access-token:${ctx.githubInstallationToken}@github.com/${ctx.owner}/${ctx.name}.git`;
+    $("git", ["remote", "set-url", "origin", originUrl], { cwd: repoDir });
+    log.info("✓ Updated origin URL with authentication token");
+    return;
+  }
+
+  // PR event: checkout PR branch using shared helper
+  const prNumber = ctx.payload.event.issue_number;
+
+  // ensure origin is configured with auth token before checkout
   const originUrl = `https://x-access-token:${ctx.githubInstallationToken}@github.com/${ctx.owner}/${ctx.name}.git`;
   $("git", ["remote", "set-url", "origin", originUrl], { cwd: repoDir });
-  log.info("✓ updated origin URL with authentication token");
+
+  // use shared checkout helper (handles fork remotes, push config, etc.)
+  await checkoutPrBranch(ctx, prNumber);
 }