From bd203156c54ed7c1c59101f203d98ae0457d7e7f Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 14 May 2026 06:20:40 +0000
Subject: [PATCH 01/10] Initial plan


From fbcb7aa69651bebbab16d8b71be40e445d7a312f Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 14 May 2026 06:27:36 +0000
Subject: [PATCH 02/10] Fix safe output bundle fetch for checked-out branches

Co-authored-by: mrjf <180956+mrjf@users.noreply.github.com>
---
 actions/setup/js/create_pull_request.cjs      | 19 +++++++--
 actions/setup/js/create_pull_request.test.cjs | 41 +++++++++++++++++--
 2 files changed, 54 insertions(+), 6 deletions(-)

diff --git a/actions/setup/js/create_pull_request.cjs b/actions/setup/js/create_pull_request.cjs
index d8acf98de4a..732f28617a7 100644
--- a/actions/setup/js/create_pull_request.cjs
+++ b/actions/setup/js/create_pull_request.cjs
@@ -1266,13 +1266,17 @@ async function main(config = {}) {
       // unlike git format-patch which flattens history and drops merge resolution content.
       core.info(`Applying changes from bundle: ${bundleFilePath}`);
       let bundleBranchRef = `refs/heads/${originalAgentBranch || branchName}`;
+      const bundleTargetRef = `refs/heads/${branchName}`;
+      const bundleTempRef = `refs/bundles/create-pr-${branchName.replace(/[^a-zA-Z0-9-]/g, "-")}`;
       try {
         await ensureFullHistoryForBundle(exec);
 
-        // Fetch from bundle: creates a local branch pointing to the bundle's tip commit.
+        // Fetch from bundle into a temporary ref, then update the target branch.
+        // Fetching directly into refs/heads/<branch> fails when that branch is
+        // currently checked out in the safe_outputs job.
         // bundleBranchRef is the source ref inside the bundle (typically refs/heads/<agent-branch>).
         try {
-          await exec.exec("git", ["fetch", bundleFilePath, `${bundleBranchRef}:refs/heads/${branchName}`]);
+          await exec.exec("git", ["fetch", bundleFilePath, `${bundleBranchRef}:${bundleTempRef}`]);
         } catch (initialFetchError) {
           // Fallback: resolve the source ref directly from the bundle contents.
           // Some agents may emit a JSONL branch name that differs from the ref embedded in the bundle.
@@ -1287,17 +1291,26 @@ async function main(config = {}) {
           if (branchRefs.length === 1) {
             bundleBranchRef = branchRefs[0];
             core.info(`Resolved bundle source ref from list-heads: ${bundleBranchRef}`);
-            await exec.exec("git", ["fetch", bundleFilePath, `${bundleBranchRef}:refs/heads/${branchName}`]);
+            await exec.exec("git", ["fetch", bundleFilePath, `${bundleBranchRef}:${bundleTempRef}`]);
           } else {
             throw new Error(`Failed to resolve bundle branch ref from list-heads: expected exactly 1 refs/heads entry, found ${branchRefs.length}`, { cause: initialFetchError });
           }
         }
+        core.info(`Fetched bundle to ${bundleTempRef}`);
+        await exec.exec("git", ["update-ref", bundleTargetRef, bundleTempRef]);
         core.info(`Created local branch ${branchName} from bundle`);
         await exec.exec("git", ["checkout", branchName]);
+        await exec.exec("git", ["reset", "--hard"]);
         core.info(`Checked out branch ${branchName} from bundle`);
       } catch (bundleError) {
         core.error(`Failed to apply bundle: ${bundleError instanceof Error ? bundleError.message : String(bundleError)}`);
         return { success: false, error: "Failed to apply bundle" };
+      } finally {
+        try {
+          await exec.exec("git", ["update-ref", "-d", bundleTempRef]);
+        } catch {
+          // Non-fatal cleanup
+        }
       }
 
       // Push the commits from the bundle to the remote branch
diff --git a/actions/setup/js/create_pull_request.test.cjs b/actions/setup/js/create_pull_request.test.cjs
index ca3ce36bdca..36e244dea75 100644
--- a/actions/setup/js/create_pull_request.test.cjs
+++ b/actions/setup/js/create_pull_request.test.cjs
@@ -251,7 +251,9 @@ index 0000000..abc1234
 
     expect(result.success).toBe(true);
     expect(global.exec.exec).toHaveBeenCalledWith("git", ["fetch", "--unshallow", "origin"], expect.any(Object));
-    expect(global.exec.exec).toHaveBeenCalledWith("git", ["fetch", bundlePath, "refs/heads/feature/test:refs/heads/feature/test"]);
+    expect(global.exec.exec).toHaveBeenCalledWith("git", ["fetch", bundlePath, "refs/heads/feature/test:refs/bundles/create-pr-feature-test"]);
+    expect(global.exec.exec).toHaveBeenCalledWith("git", ["update-ref", "refs/heads/feature/test", "refs/bundles/create-pr-feature-test"]);
+    expect(global.exec.exec).toHaveBeenCalledWith("git", ["reset", "--hard"]);
     const unshallowCallIndex = global.exec.exec.mock.calls.findIndex(([, args]) => Array.isArray(args) && args[0] === "fetch" && args[1] === "--unshallow");
     const bundleFetchCallIndex = global.exec.exec.mock.calls.findIndex(([, args]) => Array.isArray(args) && args[0] === "fetch" && args[1] === bundlePath);
     expect(unshallowCallIndex).toBeGreaterThanOrEqual(0);
@@ -282,7 +284,7 @@ index 0000000..abc1234
     fs.writeFileSync(bundlePath, "bundle content");
 
     global.exec.exec.mockImplementation((cmd, args) => {
-      if (cmd === "git" && Array.isArray(args) && args[0] === "fetch" && args[1] === bundlePath && args[2] === "refs/heads/ops-review-may09-2026:refs/heads/ops-review-may09-2026") {
+      if (cmd === "git" && Array.isArray(args) && args[0] === "fetch" && args[1] === bundlePath && args[2] === "refs/heads/ops-review-may09-2026:refs/bundles/create-pr-ops-review-may09-2026") {
         throw new Error("fatal: couldn't find remote ref refs/heads/ops-review-may09-2026");
       }
       return Promise.resolve(0);
@@ -314,7 +316,40 @@ index 0000000..abc1234
 
     expect(result.success).toBe(true);
     expect(global.exec.getExecOutput).toHaveBeenCalledWith("git", ["bundle", "list-heads", bundlePath]);
-    expect(global.exec.exec).toHaveBeenCalledWith("git", ["fetch", bundlePath, "refs/heads/main:refs/heads/ops-review-may09-2026"]);
+    expect(global.exec.exec).toHaveBeenCalledWith("git", ["fetch", bundlePath, "refs/heads/main:refs/bundles/create-pr-ops-review-may09-2026"]);
+  });
+
+  it("should not fetch a bundle directly into the target branch", async () => {
+    const patchPath = path.join(tempDir, "test.patch");
+    fs.writeFileSync(
+      patchPath,
+      `From abc123 Mon Sep 17 00:00:00 2001
+From: Test Author <test@example.com>
+Date: Mon, 1 Jan 2024 00:00:00 +0000
+Subject: [PATCH] Test commit
+
+diff --git a/test.txt b/test.txt
+new file mode 100644
+index 0000000..abc1234
+--- /dev/null
++++ b/test.txt
+@@ -0,0 +1 @@
++Hello World
+--
+2.34.1
+`
+    );
+    const bundlePath = path.join(tempDir, "test.bundle");
+    fs.writeFileSync(bundlePath, "bundle content");
+
+    const { main } = require("./create_pull_request.cjs");
+    const handler = await main({ base_branch: "main", preserve_branch_name: true });
+    const result = await handler({ title: "Test PR", body: "Test body", branch: "autoloop/perf-comparison", patch_path: patchPath, bundle_path: bundlePath }, {});
+
+    expect(result.success).toBe(true);
+    expect(global.exec.exec).not.toHaveBeenCalledWith("git", ["fetch", bundlePath, "refs/heads/autoloop/perf-comparison:refs/heads/autoloop/perf-comparison"]);
+    expect(global.exec.exec).toHaveBeenCalledWith("git", ["fetch", bundlePath, "refs/heads/autoloop/perf-comparison:refs/bundles/create-pr-autoloop-perf-comparison"]);
+    expect(global.exec.exec).toHaveBeenCalledWith("git", ["update-ref", "refs/heads/autoloop/perf-comparison", "refs/bundles/create-pr-autoloop-perf-comparison"]);
   });
 });
 

From 3810fa7e7b72b166bd9d24d453d5432389a824d8 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 14 May 2026 11:38:24 +0000
Subject: [PATCH 03/10] Add bundle fetch integration test

Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>
---
 actions/setup/js/create_pull_request.cjs      | 104 +++++++++-------
 ...e_pull_request_bundle_integration.test.cjs | 115 ++++++++++++++++++
 2 files changed, 175 insertions(+), 44 deletions(-)
 create mode 100644 actions/setup/js/create_pull_request_bundle_integration.test.cjs

diff --git a/actions/setup/js/create_pull_request.cjs b/actions/setup/js/create_pull_request.cjs
index 732f28617a7..ad8d9044505 100644
--- a/actions/setup/js/create_pull_request.cjs
+++ b/actions/setup/js/create_pull_request.cjs
@@ -69,6 +69,62 @@ const HANDLER_TYPE = "create_pull_request";
 /** @type {string} Label always added to fallback issues so the triage system can find them */
 const MANAGED_FALLBACK_ISSUE_LABEL = "agentic-workflows";
 
+/**
+ * Apply a git bundle to a local branch without fetching directly into the branch ref.
+ * Fetching directly into refs/heads/<branch> fails when that branch is currently checked out.
+ *
+ * @param {string} bundleFilePath - Path to the bundle file
+ * @param {string} branchName - Target branch name
+ * @param {string} originalAgentBranch - Original source branch name from the agent, if different
+ * @param {{ exec: Function, getExecOutput: Function }} execApi - GitHub Actions exec API
+ * @returns {Promise<void>}
+ */
+async function applyBundleToBranch(bundleFilePath, branchName, originalAgentBranch, execApi) {
+  let bundleBranchRef = `refs/heads/${originalAgentBranch || branchName}`;
+  const bundleTargetRef = `refs/heads/${branchName}`;
+  const bundleTempRef = `refs/bundles/create-pr-${branchName.replace(/[^a-zA-Z0-9-]/g, "-")}`;
+
+  try {
+    await ensureFullHistoryForBundle(execApi);
+
+    // Fetch from bundle into a temporary ref, then update the target branch.
+    // bundleBranchRef is the source ref inside the bundle (typically refs/heads/<agent-branch>).
+    try {
+      await execApi.exec("git", ["fetch", bundleFilePath, `${bundleBranchRef}:${bundleTempRef}`]);
+    } catch (initialFetchError) {
+      // Fallback: resolve the source ref directly from the bundle contents.
+      // Some agents may emit a JSONL branch name that differs from the ref embedded in the bundle.
+      const initialFetchErrorMessage = initialFetchError instanceof Error ? initialFetchError.message : String(initialFetchError);
+      core.warning(`Bundle fetch with ${bundleBranchRef} failed: ${initialFetchErrorMessage}; resolving branch ref from bundle heads`);
+      const { stdout: bundleHeadsOutput } = await execApi.getExecOutput("git", ["bundle", "list-heads", bundleFilePath]);
+      const branchRefs = bundleHeadsOutput
+        .split("\n")
+        .map(line => line.trim().split(/\s+/)[1] || "")
+        .filter(ref => /^refs\/heads\/[A-Za-z0-9._][A-Za-z0-9._/-]*$/.test(ref));
+
+      if (branchRefs.length === 1) {
+        bundleBranchRef = branchRefs[0];
+        core.info(`Resolved bundle source ref from list-heads: ${bundleBranchRef}`);
+        await execApi.exec("git", ["fetch", bundleFilePath, `${bundleBranchRef}:${bundleTempRef}`]);
+      } else {
+        throw new Error(`Failed to resolve bundle branch ref from list-heads: expected exactly 1 refs/heads entry, found ${branchRefs.length}`, { cause: initialFetchError });
+      }
+    }
+    core.info(`Fetched bundle to ${bundleTempRef}`);
+    await execApi.exec("git", ["update-ref", bundleTargetRef, bundleTempRef]);
+    core.info(`Created local branch ${branchName} from bundle`);
+    await execApi.exec("git", ["checkout", branchName]);
+    await execApi.exec("git", ["reset", "--hard"]);
+    core.info(`Checked out branch ${branchName} from bundle`);
+  } finally {
+    try {
+      await execApi.exec("git", ["update-ref", "-d", bundleTempRef]);
+    } catch {
+      // Non-fatal cleanup
+    }
+  }
+}
+
 /**
  * Determines if a label API error is transient and worth retrying.
  * Returns true for:
@@ -1265,52 +1321,12 @@ async function main(config = {}) {
       // This preserves merge commit topology and per-commit metadata (messages, authorship)
       // unlike git format-patch which flattens history and drops merge resolution content.
       core.info(`Applying changes from bundle: ${bundleFilePath}`);
-      let bundleBranchRef = `refs/heads/${originalAgentBranch || branchName}`;
-      const bundleTargetRef = `refs/heads/${branchName}`;
-      const bundleTempRef = `refs/bundles/create-pr-${branchName.replace(/[^a-zA-Z0-9-]/g, "-")}`;
+      const bundleSourceRef = `refs/heads/${originalAgentBranch || branchName}`;
       try {
-        await ensureFullHistoryForBundle(exec);
-
-        // Fetch from bundle into a temporary ref, then update the target branch.
-        // Fetching directly into refs/heads/<branch> fails when that branch is
-        // currently checked out in the safe_outputs job.
-        // bundleBranchRef is the source ref inside the bundle (typically refs/heads/<agent-branch>).
-        try {
-          await exec.exec("git", ["fetch", bundleFilePath, `${bundleBranchRef}:${bundleTempRef}`]);
-        } catch (initialFetchError) {
-          // Fallback: resolve the source ref directly from the bundle contents.
-          // Some agents may emit a JSONL branch name that differs from the ref embedded in the bundle.
-          const initialFetchErrorMessage = initialFetchError instanceof Error ? initialFetchError.message : String(initialFetchError);
-          core.warning(`Bundle fetch with ${bundleBranchRef} failed: ${initialFetchErrorMessage}; resolving branch ref from bundle heads`);
-          const { stdout: bundleHeadsOutput } = await exec.getExecOutput("git", ["bundle", "list-heads", bundleFilePath]);
-          const branchRefs = bundleHeadsOutput
-            .split("\n")
-            .map(line => line.trim().split(/\s+/)[1] || "")
-            .filter(ref => /^refs\/heads\/[A-Za-z0-9._][A-Za-z0-9._/-]*$/.test(ref));
-
-          if (branchRefs.length === 1) {
-            bundleBranchRef = branchRefs[0];
-            core.info(`Resolved bundle source ref from list-heads: ${bundleBranchRef}`);
-            await exec.exec("git", ["fetch", bundleFilePath, `${bundleBranchRef}:${bundleTempRef}`]);
-          } else {
-            throw new Error(`Failed to resolve bundle branch ref from list-heads: expected exactly 1 refs/heads entry, found ${branchRefs.length}`, { cause: initialFetchError });
-          }
-        }
-        core.info(`Fetched bundle to ${bundleTempRef}`);
-        await exec.exec("git", ["update-ref", bundleTargetRef, bundleTempRef]);
-        core.info(`Created local branch ${branchName} from bundle`);
-        await exec.exec("git", ["checkout", branchName]);
-        await exec.exec("git", ["reset", "--hard"]);
-        core.info(`Checked out branch ${branchName} from bundle`);
+        await applyBundleToBranch(bundleFilePath, branchName, originalAgentBranch, exec);
       } catch (bundleError) {
         core.error(`Failed to apply bundle: ${bundleError instanceof Error ? bundleError.message : String(bundleError)}`);
         return { success: false, error: "Failed to apply bundle" };
-      } finally {
-        try {
-          await exec.exec("git", ["update-ref", "-d", bundleTempRef]);
-        } catch {
-          // Non-fatal cleanup
-        }
       }
 
       // Push the commits from the bundle to the remote branch
@@ -1367,7 +1383,7 @@ To create a pull request with the changes:
 gh run download ${runId} -n agent -D /tmp/agent-${runId}
 
 # Fetch the bundle into a local branch
-git fetch /tmp/agent-${runId}/${artifactFileName} ${bundleBranchRef}:refs/heads/${branchName}
+git fetch /tmp/agent-${runId}/${artifactFileName} ${bundleSourceRef}:refs/heads/${branchName}
 git checkout ${branchName}
 
 # Push the branch to origin
@@ -2072,4 +2088,4 @@ ${patchPreview}`;
   }; // End of handleCreatePullRequest
 } // End of main
 
-module.exports = { main, enforcePullRequestLimits, countUniquePatchFiles, parseDiffGitHeader };
+module.exports = { main, enforcePullRequestLimits, countUniquePatchFiles, parseDiffGitHeader, applyBundleToBranch };
diff --git a/actions/setup/js/create_pull_request_bundle_integration.test.cjs b/actions/setup/js/create_pull_request_bundle_integration.test.cjs
new file mode 100644
index 00000000000..393c99a79fa
--- /dev/null
+++ b/actions/setup/js/create_pull_request_bundle_integration.test.cjs
@@ -0,0 +1,115 @@
+/**
+ * Integration tests for create_pull_request bundle application.
+ *
+ * These tests run real git commands against temporary repositories to verify
+ * bundle handling for checked-out target branches.
+ */
+
+import { describe, it, expect, afterEach, vi } from "vitest";
+import { createRequire } from "module";
+import fs from "fs";
+import os from "os";
+import path from "path";
+import { spawnSync } from "child_process";
+
+const require = createRequire(import.meta.url);
+
+global.core = {
+  debug: vi.fn(),
+  error: vi.fn(),
+  info: vi.fn(),
+  warning: vi.fn(),
+};
+
+function execGit(args, options = {}) {
+  const result = spawnSync("git", args, {
+    encoding: "utf8",
+    ...options,
+  });
+  if (result.error) {
+    throw result.error;
+  }
+  if (result.status !== 0 && !options.allowFailure) {
+    throw new Error(`git ${args.join(" ")} failed: ${result.stderr}`);
+  }
+  return result;
+}
+
+function createRepo(prefix) {
+  const repoDir = fs.mkdtempSync(path.join(os.tmpdir(), prefix));
+  execGit(["init"], { cwd: repoDir });
+  execGit(["config", "user.name", "Test User"], { cwd: repoDir });
+  execGit(["config", "user.email", "test@example.com"], { cwd: repoDir });
+  return repoDir;
+}
+
+function createExecApi(cwd) {
+  return {
+    async exec(command, args = []) {
+      if (command !== "git") {
+        throw new Error(`unexpected command: ${command}`);
+      }
+      const result = execGit(args, { cwd, allowFailure: true });
+      if (result.status !== 0) {
+        throw new Error(result.stderr || result.stdout);
+      }
+      return result.status;
+    },
+    async getExecOutput(command, args = []) {
+      if (command !== "git") {
+        throw new Error(`unexpected command: ${command}`);
+      }
+      const result = execGit(args, { cwd, allowFailure: true });
+      if (result.status !== 0) {
+        throw new Error(result.stderr || result.stdout);
+      }
+      return { exitCode: result.status, stdout: result.stdout, stderr: result.stderr };
+    },
+  };
+}
+
+describe("create_pull_request bundle integration", () => {
+  const tempDirs = [];
+
+  afterEach(() => {
+    for (const tempDir of tempDirs.splice(0)) {
+      fs.rmSync(tempDir, { recursive: true, force: true });
+    }
+    vi.clearAllMocks();
+  });
+
+  it("applies a bundle when the target branch is currently checked out", async () => {
+    const branchName = "autoloop/perf-comparison";
+    const sourceRepo = createRepo("create-pr-bundle-source-");
+    const targetRepo = createRepo("create-pr-bundle-target-");
+    tempDirs.push(sourceRepo, targetRepo);
+
+    fs.writeFileSync(path.join(sourceRepo, "file.txt"), "base\n");
+    execGit(["add", "file.txt"], { cwd: sourceRepo });
+    execGit(["commit", "-m", "base"], { cwd: sourceRepo });
+    execGit(["branch", "-M", "main"], { cwd: sourceRepo });
+    execGit(["checkout", "-b", branchName], { cwd: sourceRepo });
+    fs.writeFileSync(path.join(sourceRepo, "file.txt"), "bundle tip\n");
+    execGit(["commit", "-am", "bundle tip"], { cwd: sourceRepo });
+    const expectedHead = execGit(["rev-parse", "HEAD"], { cwd: sourceRepo }).stdout.trim();
+    const bundlePath = path.join(sourceRepo, "change.bundle");
+    execGit(["bundle", "create", bundlePath, `refs/heads/${branchName}`], { cwd: sourceRepo });
+
+    fs.writeFileSync(path.join(targetRepo, "file.txt"), "checked out branch before bundle\n");
+    execGit(["add", "file.txt"], { cwd: targetRepo });
+    execGit(["commit", "-m", "old branch state"], { cwd: targetRepo });
+    execGit(["checkout", "-b", branchName], { cwd: targetRepo });
+
+    const directFetchResult = execGit(["fetch", bundlePath, `refs/heads/${branchName}:refs/heads/${branchName}`], { cwd: targetRepo, allowFailure: true });
+    expect(directFetchResult.status).not.toBe(0);
+    expect(directFetchResult.stderr).toContain("refusing to fetch into branch");
+
+    const { applyBundleToBranch } = require("./create_pull_request.cjs");
+    await applyBundleToBranch(bundlePath, branchName, "", createExecApi(targetRepo));
+
+    const actualHead = execGit(["rev-parse", "HEAD"], { cwd: targetRepo }).stdout.trim();
+    expect(actualHead).toBe(expectedHead);
+    expect(fs.readFileSync(path.join(targetRepo, "file.txt"), "utf8")).toBe("bundle tip\n");
+    expect(execGit(["show-ref", "--verify", "refs/bundles/create-pr-autoloop-perf-comparison"], { cwd: targetRepo, allowFailure: true }).status).not.toBe(0);
+  });
+});

From 083ed99ce825d6644dadad19b7500238d7dfe542 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 14 May 2026 11:39:28 +0000
Subject: [PATCH 04/10] Address integration validation feedback

Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>
---
 actions/setup/js/create_pull_request.cjs                    | 3 +--
 .../js/create_pull_request_bundle_integration.test.cjs      | 6 +++---
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/actions/setup/js/create_pull_request.cjs b/actions/setup/js/create_pull_request.cjs
index ad8d9044505..fdff946ce17 100644
--- a/actions/setup/js/create_pull_request.cjs
+++ b/actions/setup/js/create_pull_request.cjs
@@ -1321,7 +1321,6 @@ async function main(config = {}) {
       // This preserves merge commit topology and per-commit metadata (messages, authorship)
       // unlike git format-patch which flattens history and drops merge resolution content.
       core.info(`Applying changes from bundle: ${bundleFilePath}`);
-      const bundleSourceRef = `refs/heads/${originalAgentBranch || branchName}`;
       try {
         await applyBundleToBranch(bundleFilePath, branchName, originalAgentBranch, exec);
       } catch (bundleError) {
@@ -1383,7 +1382,7 @@ To create a pull request with the changes:
 gh run download ${runId} -n agent -D /tmp/agent-${runId}
 
 # Fetch the bundle into a local branch
-git fetch /tmp/agent-${runId}/${artifactFileName} ${bundleSourceRef}:refs/heads/${branchName}
+git fetch /tmp/agent-${runId}/${artifactFileName} refs/heads/${originalAgentBranch || branchName}:refs/heads/${branchName}
 git checkout ${branchName}
 
 # Push the branch to origin
diff --git a/actions/setup/js/create_pull_request_bundle_integration.test.cjs b/actions/setup/js/create_pull_request_bundle_integration.test.cjs
index 393c99a79fa..17ed5fb0a95 100644
--- a/actions/setup/js/create_pull_request_bundle_integration.test.cjs
+++ b/actions/setup/js/create_pull_request_bundle_integration.test.cjs
@@ -100,9 +100,9 @@ describe("create_pull_request bundle integration", () => {
     execGit(["commit", "-m", "old branch state"], { cwd: targetRepo });
     execGit(["checkout", "-b", branchName], { cwd: targetRepo });
 
-    const directFetchResult = execGit(["fetch", bundlePath, `refs/heads/${branchName}:refs/heads/${branchName}`], { cwd: targetRepo, allowFailure: true });
-    expect(directFetchResult.status).not.toBe(0);
-    expect(directFetchResult.stderr).toContain("refusing to fetch into branch");
+    const checkedOutBranchFetchResult = execGit(["fetch", bundlePath, `refs/heads/${branchName}:refs/heads/${branchName}`], { cwd: targetRepo, allowFailure: true });
+    expect(checkedOutBranchFetchResult.status).not.toBe(0);
+    expect(checkedOutBranchFetchResult.stderr).toContain("refusing to fetch into branch");
 
     const { applyBundleToBranch } = require("./create_pull_request.cjs");
     await applyBundleToBranch(bundlePath, branchName, "", createExecApi(targetRepo));

From 5513624ad4f6e42ae7058784379f0d4893b8faf3 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 14 May 2026 12:53:31 +0000
Subject: [PATCH 05/10] Update bundle fallback instructions

Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>
---
 actions/setup/js/create_pull_request.cjs      |  9 ++++-
 actions/setup/js/create_pull_request.test.cjs | 39 +++++++++++++++++++
 2 files changed, 46 insertions(+), 2 deletions(-)

diff --git a/actions/setup/js/create_pull_request.cjs b/actions/setup/js/create_pull_request.cjs
index fdff946ce17..6eb780534fb 100644
--- a/actions/setup/js/create_pull_request.cjs
+++ b/actions/setup/js/create_pull_request.cjs
@@ -1364,6 +1364,8 @@ async function main(config = {}) {
         const runId = context.runId;
 
         const artifactFileName = bundleFilePath ? bundleFilePath.replace("/tmp/gh-aw/", "") : "aw-unknown.bundle";
+        const fallbackBundleSourceRef = `refs/heads/${originalAgentBranch || branchName}`;
+        const fallbackBundleTempRef = `refs/bundles/create-pr-${branchName.replace(/[^a-zA-Z0-9-]/g, "-")}`;
         const fallbackBody = `${body}
 
 ---
@@ -1381,9 +1383,12 @@ To create a pull request with the changes:
 # Download the artifact from the workflow run
 gh run download ${runId} -n agent -D /tmp/agent-${runId}
 
-# Fetch the bundle into a local branch
-git fetch /tmp/agent-${runId}/${artifactFileName} refs/heads/${originalAgentBranch || branchName}:refs/heads/${branchName}
+# Fetch the bundle into a temporary ref, then update the local branch
+git fetch /tmp/agent-${runId}/${artifactFileName} ${fallbackBundleSourceRef}:${fallbackBundleTempRef}
+git update-ref refs/heads/${branchName} ${fallbackBundleTempRef}
 git checkout ${branchName}
+git reset --hard
+git update-ref -d ${fallbackBundleTempRef}
 
 # Push the branch to origin
 git push origin ${branchName}
diff --git a/actions/setup/js/create_pull_request.test.cjs b/actions/setup/js/create_pull_request.test.cjs
index 36e244dea75..e02b540c0c1 100644
--- a/actions/setup/js/create_pull_request.test.cjs
+++ b/actions/setup/js/create_pull_request.test.cjs
@@ -168,6 +168,7 @@ describe("create_pull_request - bundle transport shallow checkout", () => {
           get: vi.fn().mockResolvedValue({ data: { default_branch: "main" } }),
         },
         issues: {
+          create: vi.fn().mockResolvedValue({ data: { number: 99, html_url: "https://github.com/test-owner/test-repo/issues/99" } }),
           addLabels: vi.fn().mockResolvedValue({}),
         },
       },
@@ -351,6 +352,44 @@ index 0000000..abc1234
     expect(global.exec.exec).toHaveBeenCalledWith("git", ["fetch", bundlePath, "refs/heads/autoloop/perf-comparison:refs/bundles/create-pr-autoloop-perf-comparison"]);
     expect(global.exec.exec).toHaveBeenCalledWith("git", ["update-ref", "refs/heads/autoloop/perf-comparison", "refs/bundles/create-pr-autoloop-perf-comparison"]);
   });
+
+  it("should give fallback issue bundle instructions that avoid direct branch fetches", async () => {
+    const patchPath = path.join(tempDir, "test.patch");
+    fs.writeFileSync(
+      patchPath,
+      `From abc123 Mon Sep 17 00:00:00 2001
+From: Test Author <test@example.com>
+Date: Mon, 1 Jan 2024 00:00:00 +0000
+Subject: [PATCH] Test commit
+
+diff --git a/test.txt b/test.txt
+new file mode 100644
+index 0000000..abc1234
+--- /dev/null
++++ b/test.txt
+@@ -0,0 +1 @@
++Hello World
+--
+2.34.1
+`
+    );
+    const bundlePath = path.join(tempDir, "aw-test.bundle");
+    fs.writeFileSync(bundlePath, "bundle content");
+    pushSignedSpy.mockRejectedValueOnce(new Error("push rejected"));
+
+    const { main } = require("./create_pull_request.cjs");
+    const handler = await main({ base_branch: "main", preserve_branch_name: true });
+    const result = await handler({ title: "Test PR", body: "Test body", branch: "autoloop/perf-comparison", patch_path: patchPath, bundle_path: bundlePath }, {});
+
+    expect(result.success).toBe(true);
+    expect(result.fallback_used).toBe(true);
+
+    const fallbackIssueBody = global.github.rest.issues.create.mock.calls[0][0].body;
+    expect(fallbackIssueBody).toContain("refs/heads/autoloop/perf-comparison:refs/bundles/create-pr-autoloop-perf-comparison");
+    expect(fallbackIssueBody).toContain("git update-ref refs/heads/autoloop/perf-comparison refs/bundles/create-pr-autoloop-perf-comparison");
+    expect(fallbackIssueBody).toContain("git reset --hard");
+    expect(fallbackIssueBody).not.toContain("refs/heads/autoloop/perf-comparison:refs/heads/autoloop/perf-comparison");
+  });
 });
 
 describe("create_pull_request - fallback-as-issue configuration", () => {

From 3f18c9f4a02518ea88e72811359cfdb8a0735841 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 14 May 2026 12:56:20 +0000
Subject: [PATCH 06/10] Use unique bundle temp refs

Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>
---
 actions/setup/js/create_pull_request.cjs      | 14 +++++++++--
 actions/setup/js/create_pull_request.test.cjs | 24 ++++++++++++-------
 ...e_pull_request_bundle_integration.test.cjs |  2 +-
 3 files changed, 29 insertions(+), 11 deletions(-)

diff --git a/actions/setup/js/create_pull_request.cjs b/actions/setup/js/create_pull_request.cjs
index 6eb780534fb..ddbb739d366 100644
--- a/actions/setup/js/create_pull_request.cjs
+++ b/actions/setup/js/create_pull_request.cjs
@@ -69,6 +69,14 @@ const HANDLER_TYPE = "create_pull_request";
 /** @type {string} Label always added to fallback issues so the triage system can find them */
 const MANAGED_FALLBACK_ISSUE_LABEL = "agentic-workflows";
 
+/**
+ * @param {string} branchName
+ * @returns {string}
+ */
+function createBundleTempRef(branchName) {
+  return `refs/bundles/create-pr-${branchName.replace(/[^a-zA-Z0-9-]/g, "-")}-${crypto.randomBytes(4).toString("hex")}`;
+}
+
 /**
  * Apply a git bundle to a local branch without fetching directly into the branch ref.
  * Fetching directly into refs/heads/<branch> fails when that branch is currently checked out.
@@ -82,7 +90,7 @@ const MANAGED_FALLBACK_ISSUE_LABEL = "agentic-workflows";
 async function applyBundleToBranch(bundleFilePath, branchName, originalAgentBranch, execApi) {
   let bundleBranchRef = `refs/heads/${originalAgentBranch || branchName}`;
   const bundleTargetRef = `refs/heads/${branchName}`;
-  const bundleTempRef = `refs/bundles/create-pr-${branchName.replace(/[^a-zA-Z0-9-]/g, "-")}`;
+  const bundleTempRef = createBundleTempRef(branchName);
 
   try {
     await ensureFullHistoryForBundle(execApi);
@@ -1365,7 +1373,7 @@ async function main(config = {}) {
 
         const artifactFileName = bundleFilePath ? bundleFilePath.replace("/tmp/gh-aw/", "") : "aw-unknown.bundle";
         const fallbackBundleSourceRef = `refs/heads/${originalAgentBranch || branchName}`;
-        const fallbackBundleTempRef = `refs/bundles/create-pr-${branchName.replace(/[^a-zA-Z0-9-]/g, "-")}`;
+        const fallbackBundleTempRef = createBundleTempRef(branchName);
         const fallbackBody = `${body}
 
 ---
@@ -1387,7 +1395,9 @@ gh run download ${runId} -n agent -D /tmp/agent-${runId}
 git fetch /tmp/agent-${runId}/${artifactFileName} ${fallbackBundleSourceRef}:${fallbackBundleTempRef}
 git update-ref refs/heads/${branchName} ${fallbackBundleTempRef}
 git checkout ${branchName}
+# Ensure the working tree matches the updated branch
 git reset --hard
+# Remove the temporary bundle ref
 git update-ref -d ${fallbackBundleTempRef}
 
 # Push the branch to origin
diff --git a/actions/setup/js/create_pull_request.test.cjs b/actions/setup/js/create_pull_request.test.cjs
index e02b540c0c1..52f75deec11 100644
--- a/actions/setup/js/create_pull_request.test.cjs
+++ b/actions/setup/js/create_pull_request.test.cjs
@@ -252,8 +252,10 @@ index 0000000..abc1234
 
     expect(result.success).toBe(true);
     expect(global.exec.exec).toHaveBeenCalledWith("git", ["fetch", "--unshallow", "origin"], expect.any(Object));
-    expect(global.exec.exec).toHaveBeenCalledWith("git", ["fetch", bundlePath, "refs/heads/feature/test:refs/bundles/create-pr-feature-test"]);
-    expect(global.exec.exec).toHaveBeenCalledWith("git", ["update-ref", "refs/heads/feature/test", "refs/bundles/create-pr-feature-test"]);
+    const bundleFetchCall = global.exec.exec.mock.calls.find(([, args]) => Array.isArray(args) && args[0] === "fetch" && args[1] === bundlePath);
+    expect(bundleFetchCall[1][2]).toMatch(/^refs\/heads\/feature\/test:refs\/bundles\/create-pr-feature-test-[a-f0-9]{8}$/);
+    const bundleTempRef = bundleFetchCall[1][2].split(":")[1];
+    expect(global.exec.exec).toHaveBeenCalledWith("git", ["update-ref", "refs/heads/feature/test", bundleTempRef]);
     expect(global.exec.exec).toHaveBeenCalledWith("git", ["reset", "--hard"]);
     const unshallowCallIndex = global.exec.exec.mock.calls.findIndex(([, args]) => Array.isArray(args) && args[0] === "fetch" && args[1] === "--unshallow");
     const bundleFetchCallIndex = global.exec.exec.mock.calls.findIndex(([, args]) => Array.isArray(args) && args[0] === "fetch" && args[1] === bundlePath);
@@ -285,7 +287,7 @@ index 0000000..abc1234
     fs.writeFileSync(bundlePath, "bundle content");
 
     global.exec.exec.mockImplementation((cmd, args) => {
-      if (cmd === "git" && Array.isArray(args) && args[0] === "fetch" && args[1] === bundlePath && args[2] === "refs/heads/ops-review-may09-2026:refs/bundles/create-pr-ops-review-may09-2026") {
+      if (cmd === "git" && Array.isArray(args) && args[0] === "fetch" && args[1] === bundlePath && /^refs\/heads\/ops-review-may09-2026:refs\/bundles\/create-pr-ops-review-may09-2026-[a-f0-9]{8}$/.test(args[2])) {
         throw new Error("fatal: couldn't find remote ref refs/heads/ops-review-may09-2026");
       }
       return Promise.resolve(0);
@@ -317,7 +319,8 @@ index 0000000..abc1234
 
     expect(result.success).toBe(true);
     expect(global.exec.getExecOutput).toHaveBeenCalledWith("git", ["bundle", "list-heads", bundlePath]);
-    expect(global.exec.exec).toHaveBeenCalledWith("git", ["fetch", bundlePath, "refs/heads/main:refs/bundles/create-pr-ops-review-may09-2026"]);
+    const resolvedFetchCall = global.exec.exec.mock.calls.find(([, args]) => Array.isArray(args) && args[0] === "fetch" && args[1] === bundlePath && args[2].startsWith("refs/heads/main:"));
+    expect(resolvedFetchCall[1][2]).toMatch(/^refs\/heads\/main:refs\/bundles\/create-pr-ops-review-may09-2026-[a-f0-9]{8}$/);
   });
 
   it("should not fetch a bundle directly into the target branch", async () => {
@@ -349,8 +352,10 @@ index 0000000..abc1234
 
     expect(result.success).toBe(true);
     expect(global.exec.exec).not.toHaveBeenCalledWith("git", ["fetch", bundlePath, "refs/heads/autoloop/perf-comparison:refs/heads/autoloop/perf-comparison"]);
-    expect(global.exec.exec).toHaveBeenCalledWith("git", ["fetch", bundlePath, "refs/heads/autoloop/perf-comparison:refs/bundles/create-pr-autoloop-perf-comparison"]);
-    expect(global.exec.exec).toHaveBeenCalledWith("git", ["update-ref", "refs/heads/autoloop/perf-comparison", "refs/bundles/create-pr-autoloop-perf-comparison"]);
+    const bundleFetchCall = global.exec.exec.mock.calls.find(([, args]) => Array.isArray(args) && args[0] === "fetch" && args[1] === bundlePath);
+    expect(bundleFetchCall[1][2]).toMatch(/^refs\/heads\/autoloop\/perf-comparison:refs\/bundles\/create-pr-autoloop-perf-comparison-[a-f0-9]{8}$/);
+    const bundleTempRef = bundleFetchCall[1][2].split(":")[1];
+    expect(global.exec.exec).toHaveBeenCalledWith("git", ["update-ref", "refs/heads/autoloop/perf-comparison", bundleTempRef]);
   });
 
   it("should give fallback issue bundle instructions that avoid direct branch fetches", async () => {
@@ -385,9 +390,12 @@ index 0000000..abc1234
     expect(result.fallback_used).toBe(true);
 
     const fallbackIssueBody = global.github.rest.issues.create.mock.calls[0][0].body;
-    expect(fallbackIssueBody).toContain("refs/heads/autoloop/perf-comparison:refs/bundles/create-pr-autoloop-perf-comparison");
-    expect(fallbackIssueBody).toContain("git update-ref refs/heads/autoloop/perf-comparison refs/bundles/create-pr-autoloop-perf-comparison");
+    const tempRefMatch = fallbackIssueBody.match(/refs\/heads\/autoloop\/perf-comparison:(refs\/bundles\/create-pr-autoloop-perf-comparison-[a-f0-9]{8})/);
+    expect(tempRefMatch).not.toBeNull();
+    const fallbackBundleTempRef = tempRefMatch[1];
+    expect(fallbackIssueBody).toContain(`git update-ref refs/heads/autoloop/perf-comparison ${fallbackBundleTempRef}`);
     expect(fallbackIssueBody).toContain("git reset --hard");
+    expect(fallbackIssueBody).toContain(`git update-ref -d ${fallbackBundleTempRef}`);
     expect(fallbackIssueBody).not.toContain("refs/heads/autoloop/perf-comparison:refs/heads/autoloop/perf-comparison");
   });
 });
diff --git a/actions/setup/js/create_pull_request_bundle_integration.test.cjs b/actions/setup/js/create_pull_request_bundle_integration.test.cjs
index 17ed5fb0a95..839f77a5d02 100644
--- a/actions/setup/js/create_pull_request_bundle_integration.test.cjs
+++ b/actions/setup/js/create_pull_request_bundle_integration.test.cjs
@@ -110,6 +110,6 @@ describe("create_pull_request bundle integration", () => {
     const actualHead = execGit(["rev-parse", "HEAD"], { cwd: targetRepo }).stdout.trim();
     expect(actualHead).toBe(expectedHead);
     expect(fs.readFileSync(path.join(targetRepo, "file.txt"), "utf8")).toBe("bundle tip\n");
-    expect(execGit(["show-ref", "--verify", "refs/bundles/create-pr-autoloop-perf-comparison"], { cwd: targetRepo, allowFailure: true }).status).not.toBe(0);
+    expect(execGit(["for-each-ref", "--format=%(refname)", "refs/bundles/create-pr-autoloop-perf-comparison-"], { cwd: targetRepo }).stdout).toBe("");
   });
 });

From 5fea75206d79f2c4a211965e6802881bcbf3aa9a Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 14 May 2026 12:57:50 +0000
Subject: [PATCH 07/10] Address bundle temp ref review feedback

Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>
---
 actions/setup/js/create_pull_request.cjs      |  4 +++-
 actions/setup/js/create_pull_request.test.cjs | 13 ++++++++++++-
 2 files changed, 15 insertions(+), 2 deletions(-)

diff --git a/actions/setup/js/create_pull_request.cjs b/actions/setup/js/create_pull_request.cjs
index ddbb739d366..13c1c3cf937 100644
--- a/actions/setup/js/create_pull_request.cjs
+++ b/actions/setup/js/create_pull_request.cjs
@@ -74,7 +74,9 @@ const MANAGED_FALLBACK_ISSUE_LABEL = "agentic-workflows";
  * @returns {string}
  */
 function createBundleTempRef(branchName) {
-  return `refs/bundles/create-pr-${branchName.replace(/[^a-zA-Z0-9-]/g, "-")}-${crypto.randomBytes(4).toString("hex")}`;
+  // Avoid collisions between sanitized branch names such as foo/bar and foo-bar.
+  const suffix = crypto.randomBytes(4).toString("hex");
+  return `refs/bundles/create-pr-${branchName.replace(/[^a-zA-Z0-9-]/g, "-")}-${suffix}`;
 }
 
 /**
diff --git a/actions/setup/js/create_pull_request.test.cjs b/actions/setup/js/create_pull_request.test.cjs
index 52f75deec11..43bf942063a 100644
--- a/actions/setup/js/create_pull_request.test.cjs
+++ b/actions/setup/js/create_pull_request.test.cjs
@@ -253,6 +253,9 @@ index 0000000..abc1234
     expect(result.success).toBe(true);
     expect(global.exec.exec).toHaveBeenCalledWith("git", ["fetch", "--unshallow", "origin"], expect.any(Object));
     const bundleFetchCall = global.exec.exec.mock.calls.find(([, args]) => Array.isArray(args) && args[0] === "fetch" && args[1] === bundlePath);
+    if (!bundleFetchCall) {
+      throw new Error("expected bundle fetch call");
+    }
     expect(bundleFetchCall[1][2]).toMatch(/^refs\/heads\/feature\/test:refs\/bundles\/create-pr-feature-test-[a-f0-9]{8}$/);
     const bundleTempRef = bundleFetchCall[1][2].split(":")[1];
     expect(global.exec.exec).toHaveBeenCalledWith("git", ["update-ref", "refs/heads/feature/test", bundleTempRef]);
@@ -320,6 +323,9 @@ index 0000000..abc1234
     expect(result.success).toBe(true);
     expect(global.exec.getExecOutput).toHaveBeenCalledWith("git", ["bundle", "list-heads", bundlePath]);
     const resolvedFetchCall = global.exec.exec.mock.calls.find(([, args]) => Array.isArray(args) && args[0] === "fetch" && args[1] === bundlePath && args[2].startsWith("refs/heads/main:"));
+    if (!resolvedFetchCall) {
+      throw new Error("expected resolved bundle fetch call");
+    }
     expect(resolvedFetchCall[1][2]).toMatch(/^refs\/heads\/main:refs\/bundles\/create-pr-ops-review-may09-2026-[a-f0-9]{8}$/);
   });
 
@@ -353,6 +359,9 @@ index 0000000..abc1234
     expect(result.success).toBe(true);
     expect(global.exec.exec).not.toHaveBeenCalledWith("git", ["fetch", bundlePath, "refs/heads/autoloop/perf-comparison:refs/heads/autoloop/perf-comparison"]);
     const bundleFetchCall = global.exec.exec.mock.calls.find(([, args]) => Array.isArray(args) && args[0] === "fetch" && args[1] === bundlePath);
+    if (!bundleFetchCall) {
+      throw new Error("expected bundle fetch call");
+    }
     expect(bundleFetchCall[1][2]).toMatch(/^refs\/heads\/autoloop\/perf-comparison:refs\/bundles\/create-pr-autoloop-perf-comparison-[a-f0-9]{8}$/);
     const bundleTempRef = bundleFetchCall[1][2].split(":")[1];
     expect(global.exec.exec).toHaveBeenCalledWith("git", ["update-ref", "refs/heads/autoloop/perf-comparison", bundleTempRef]);
@@ -391,7 +400,9 @@ index 0000000..abc1234
 
     const fallbackIssueBody = global.github.rest.issues.create.mock.calls[0][0].body;
     const tempRefMatch = fallbackIssueBody.match(/refs\/heads\/autoloop\/perf-comparison:(refs\/bundles\/create-pr-autoloop-perf-comparison-[a-f0-9]{8})/);
-    expect(tempRefMatch).not.toBeNull();
+    if (!tempRefMatch?.[1]) {
+      throw new Error("expected fallback bundle temp ref");
+    }
     const fallbackBundleTempRef = tempRefMatch[1];
     expect(fallbackIssueBody).toContain(`git update-ref refs/heads/autoloop/perf-comparison ${fallbackBundleTempRef}`);
     expect(fallbackIssueBody).toContain("git reset --hard");

From fe85167a3d553ca703aec0ba8ab3950fcb001d9e Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 14 May 2026 12:59:02 +0000
Subject: [PATCH 08/10] Document bundle temp ref cleanup

Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>
---
 actions/setup/js/create_pull_request.cjs      |  9 +++++---
 ...e_pull_request_bundle_integration.test.cjs | 21 ++++++++++++++++---
 2 files changed, 24 insertions(+), 6 deletions(-)

diff --git a/actions/setup/js/create_pull_request.cjs b/actions/setup/js/create_pull_request.cjs
index 13c1c3cf937..0fff6aa65a4 100644
--- a/actions/setup/js/create_pull_request.cjs
+++ b/actions/setup/js/create_pull_request.cjs
@@ -70,11 +70,14 @@ const HANDLER_TYPE = "create_pull_request";
 const MANAGED_FALLBACK_ISSUE_LABEL = "agentic-workflows";
 
 /**
- * @param {string} branchName
- * @returns {string}
+ * Creates a temporary refs/bundles ref for applying create_pull_request bundles.
+ * Branch names are sanitized for ref compatibility, and a short crypto-random
+ * suffix avoids collisions between branches that sanitize to the same value.
+ *
+ * @param {string} branchName - Target branch name
+ * @returns {string} Temporary bundle ref name
  */
 function createBundleTempRef(branchName) {
-  // Avoid collisions between sanitized branch names such as foo/bar and foo-bar.
   const suffix = crypto.randomBytes(4).toString("hex");
   return `refs/bundles/create-pr-${branchName.replace(/[^a-zA-Z0-9-]/g, "-")}-${suffix}`;
 }
diff --git a/actions/setup/js/create_pull_request_bundle_integration.test.cjs b/actions/setup/js/create_pull_request_bundle_integration.test.cjs
index 839f77a5d02..50303997d91 100644
--- a/actions/setup/js/create_pull_request_bundle_integration.test.cjs
+++ b/actions/setup/js/create_pull_request_bundle_integration.test.cjs
@@ -43,7 +43,7 @@ function createRepo(prefix) {
   return repoDir;
 }
 
-function createExecApi(cwd) {
+function createExecApi(cwd, onExec) {
   return {
     async exec(command, args = []) {
       if (command !== "git") {
@@ -53,6 +53,9 @@ function createExecApi(cwd) {
       if (result.status !== 0) {
         throw new Error(result.stderr || result.stdout);
       }
+      if (onExec) {
+        onExec(args);
+      }
       return result.status;
     },
     async getExecOutput(command, args = []) {
@@ -104,12 +107,24 @@ describe("create_pull_request bundle integration", () => {
     expect(checkedOutBranchFetchResult.status).not.toBe(0);
     expect(checkedOutBranchFetchResult.stderr).toContain("refusing to fetch into branch");
 
+    let bundleTempRef = "";
     const { applyBundleToBranch } = require("./create_pull_request.cjs");
-    await applyBundleToBranch(bundlePath, branchName, "", createExecApi(targetRepo));
+    await applyBundleToBranch(
+      bundlePath,
+      branchName,
+      "",
+      createExecApi(targetRepo, args => {
+        if (args[0] === "fetch" && args[1] === bundlePath) {
+          bundleTempRef = args[2].split(":")[1];
+          expect(execGit(["show-ref", "--verify", bundleTempRef], { cwd: targetRepo }).status).toBe(0);
+        }
+      })
+    );
 
     const actualHead = execGit(["rev-parse", "HEAD"], { cwd: targetRepo }).stdout.trim();
     expect(actualHead).toBe(expectedHead);
     expect(fs.readFileSync(path.join(targetRepo, "file.txt"), "utf8")).toBe("bundle tip\n");
-    expect(execGit(["for-each-ref", "--format=%(refname)", "refs/bundles/create-pr-autoloop-perf-comparison-"], { cwd: targetRepo }).stdout).toBe("");
+    expect(bundleTempRef).toMatch(/^refs\/bundles\/create-pr-autoloop-perf-comparison-[a-f0-9]{8}$/);
+    expect(execGit(["show-ref", "--verify", bundleTempRef], { cwd: targetRepo, allowFailure: true }).status).not.toBe(0);
   });
 });

From afadfdd836af663be1d8756927ef9879592b93e8 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 14 May 2026 13:07:15 +0000
Subject: [PATCH 09/10] Address bundle review comments

Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>
---
 actions/setup/js/create_pull_request.cjs      |  1 +
 ...e_pull_request_bundle_integration.test.cjs | 47 +++++++++++++++++++
 2 files changed, 48 insertions(+)

diff --git a/actions/setup/js/create_pull_request.cjs b/actions/setup/js/create_pull_request.cjs
index 0fff6aa65a4..96a34c6d323 100644
--- a/actions/setup/js/create_pull_request.cjs
+++ b/actions/setup/js/create_pull_request.cjs
@@ -127,6 +127,7 @@ async function applyBundleToBranch(bundleFilePath, branchName, originalAgentBran
     await execApi.exec("git", ["update-ref", bundleTargetRef, bundleTempRef]);
     core.info(`Created local branch ${branchName} from bundle`);
     await execApi.exec("git", ["checkout", branchName]);
+    // Ensure the working tree matches the new HEAD in case checkout left any index/worktree drift.
     await execApi.exec("git", ["reset", "--hard"]);
     core.info(`Checked out branch ${branchName} from bundle`);
   } finally {
diff --git a/actions/setup/js/create_pull_request_bundle_integration.test.cjs b/actions/setup/js/create_pull_request_bundle_integration.test.cjs
index 50303997d91..9c37f784c2f 100644
--- a/actions/setup/js/create_pull_request_bundle_integration.test.cjs
+++ b/actions/setup/js/create_pull_request_bundle_integration.test.cjs
@@ -127,4 +127,51 @@ describe("create_pull_request bundle integration", () => {
     expect(bundleTempRef).toMatch(/^refs\/bundles\/create-pr-autoloop-perf-comparison-[a-f0-9]{8}$/);
     expect(execGit(["show-ref", "--verify", bundleTempRef], { cwd: targetRepo, allowFailure: true }).status).not.toBe(0);
   });
+
+  it("cleans up the temp ref when updating the target branch fails", async () => {
+    const branchName = "autoloop/perf-comparison";
+    const sourceRepo = createRepo("create-pr-bundle-source-");
+    const targetRepo = createRepo("create-pr-bundle-target-");
+    tempDirs.push(sourceRepo, targetRepo);
+
+    fs.writeFileSync(path.join(sourceRepo, "file.txt"), "base\n");
+    execGit(["add", "file.txt"], { cwd: sourceRepo });
+    execGit(["commit", "-m", "base"], { cwd: sourceRepo });
+    execGit(["branch", "-M", "main"], { cwd: sourceRepo });
+    execGit(["checkout", "-b", branchName], { cwd: sourceRepo });
+    fs.writeFileSync(path.join(sourceRepo, "file.txt"), "bundle tip\n");
+    execGit(["commit", "-am", "bundle tip"], { cwd: sourceRepo });
+    const bundlePath = path.join(sourceRepo, "change.bundle");
+    execGit(["bundle", "create", bundlePath, `refs/heads/${branchName}`], { cwd: sourceRepo });
+
+    fs.writeFileSync(path.join(targetRepo, "file.txt"), "old branch state\n");
+    execGit(["add", "file.txt"], { cwd: targetRepo });
+    execGit(["commit", "-m", "old branch state"], { cwd: targetRepo });
+    execGit(["checkout", "-b", branchName], { cwd: targetRepo });
+    const originalHead = execGit(["rev-parse", `refs/heads/${branchName}`], { cwd: targetRepo }).stdout.trim();
+
+    let bundleTempRef = "";
+    const execApi = createExecApi(targetRepo, args => {
+      if (args[0] === "fetch" && args[1] === bundlePath) {
+        bundleTempRef = args[2].split(":")[1];
+      }
+    });
+    const { applyBundleToBranch } = require("./create_pull_request.cjs");
+
+    await expect(
+      applyBundleToBranch(bundlePath, branchName, "", {
+        ...execApi,
+        async exec(command, args = []) {
+          if (command === "git" && args[0] === "update-ref" && args[1] === `refs/heads/${branchName}`) {
+            throw new Error("simulated update-ref failure");
+          }
+          return execApi.exec(command, args);
+        },
+      })
+    ).rejects.toThrow("simulated update-ref failure");
+
+    expect(bundleTempRef).toMatch(/^refs\/bundles\/create-pr-autoloop-perf-comparison-[a-f0-9]{8}$/);
+    expect(execGit(["show-ref", "--verify", bundleTempRef], { cwd: targetRepo, allowFailure: true }).status).not.toBe(0);
+    expect(execGit(["rev-parse", `refs/heads/${branchName}`], { cwd: targetRepo }).stdout.trim()).toBe(originalHead);
+  });
 });

From fcd70125cbb317192bf13aef10eb557f7cd21408 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Thu, 14 May 2026 13:07:56 +0000
Subject: [PATCH 10/10] Tweak bundle reset comment wording

Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>
---
 actions/setup/js/create_pull_request.cjs | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/actions/setup/js/create_pull_request.cjs b/actions/setup/js/create_pull_request.cjs
index 96a34c6d323..5dc2d97a1dc 100644
--- a/actions/setup/js/create_pull_request.cjs
+++ b/actions/setup/js/create_pull_request.cjs
@@ -127,7 +127,7 @@ async function applyBundleToBranch(bundleFilePath, branchName, originalAgentBran
     await execApi.exec("git", ["update-ref", bundleTargetRef, bundleTempRef]);
     core.info(`Created local branch ${branchName} from bundle`);
     await execApi.exec("git", ["checkout", branchName]);
-    // Ensure the working tree matches the new HEAD in case checkout left any index/worktree drift.
+    // Ensure the working tree matches the new HEAD in case checkout left any index/working tree drift.
     await execApi.exec("git", ["reset", "--hard"]);
     core.info(`Checked out branch ${branchName} from bundle`);
   } finally {