From 576941f66fed4430a395f86c8d78924ae1631392 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 25 Apr 2026 00:43:51 +0000
Subject: [PATCH 1/6] Initial plan


From c9ba089da58b7e1645e5e2c9d07a6a46667fff10 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 25 Apr 2026 01:03:54 +0000
Subject: [PATCH 2/6] fix: use target-repo config to find checkout path in
 pushToPullRequestBranchHandler

When a workflow configures `target-repo` for `push_to_pull_request_branch`,
call `findRepoCheckout` to resolve the subdirectory checkout path, ensuring
patch generation runs from the correct directory rather than always using
GITHUB_WORKSPACE root.

Closes #21307

Agent-Logs-Url: https://github.com/github/gh-aw/sessions/b40b9f06-4916-453b-a852-db2c1a780448

Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>
---
 actions/setup/js/safe_outputs_handlers.cjs    | 19 +++----
 .../setup/js/safe_outputs_handlers.test.cjs   | 50 ++++++++++++++++++-
 2 files changed, 58 insertions(+), 11 deletions(-)

diff --git a/actions/setup/js/safe_outputs_handlers.cjs b/actions/setup/js/safe_outputs_handlers.cjs
index 02bba1a83d8..ed3b499848c 100644
--- a/actions/setup/js/safe_outputs_handlers.cjs
+++ b/actions/setup/js/safe_outputs_handlers.cjs
@@ -486,12 +486,15 @@ function createHandlers(server, appendSafeOutput, config = {}) {
     // Get base branch for the resolved target repository
     const baseBranch = await getBaseBranch(repoParts);
 
-    // Determine the working directory for git operations
-    // If repo is specified, find where it's checked out
+    // Determine the working directory for git operations.
+    // Look up the checkout path when the target repo is explicitly provided by the agent
+    // or explicitly configured via target-repo in the workflow config — this ensures patch
+    // generation runs from the correct directory when the target repo is checked out in a subdirectory.
     let repoCwd = null;
-    if (entry.repo && entry.repo.trim()) {
-      const repoSlug = repoResult.repo;
-      const checkoutResult = findRepoCheckout(repoSlug);
+    const itemRepo = repoResult.repo;
+    if ((entry.repo && entry.repo.trim()) || pushConfig["target-repo"]) {
+      server.debug(`Looking for checkout of target repo: ${itemRepo}`);
+      const checkoutResult = findRepoCheckout(itemRepo);
       if (!checkoutResult.success) {
         return {
           content: [
@@ -499,9 +502,7 @@ function createHandlers(server, appendSafeOutput, config = {}) {
               type: "text",
               text: JSON.stringify({
                 result: "error",
-                error:
-                  `Repository checkout not found for ${repoSlug}. Ensure the repository is checked out in this workflow using actions/checkout. ` +
-                  "If checking out multiple repositories, use the 'path' input so the checkout can be located.",
+                error: `Repository '${itemRepo}' not found in workspace. Check out the target repo with a path in checkout. ` + "If checking out multiple repositories, use the 'path' input so the checkout can be located.",
               }),
             },
           ],
@@ -510,7 +511,7 @@ function createHandlers(server, appendSafeOutput, config = {}) {
       }
       repoCwd = checkoutResult.path;
       entry.repo_cwd = repoCwd;
-      server.debug(`Selected checkout folder for ${repoSlug}: ${repoCwd}`);
+      server.debug(`Selected checkout folder for ${itemRepo}: ${repoCwd}`);
     }
 
     // If branch is not provided, is empty, or equals the base branch, use the current branch from git
diff --git a/actions/setup/js/safe_outputs_handlers.test.cjs b/actions/setup/js/safe_outputs_handlers.test.cjs
index 8a055023362..9c547b5f832 100644
--- a/actions/setup/js/safe_outputs_handlers.test.cjs
+++ b/actions/setup/js/safe_outputs_handlers.test.cjs
@@ -675,11 +675,57 @@ describe("safe_outputs_handlers", () => {
       expect(result.isError).toBe(true);
       const responseData = JSON.parse(result.content[0].text);
       expect(responseData.result).toBe("error");
-      expect(responseData.error).toContain("Repository checkout not found for test-owner/test-repo");
-      expect(responseData.error).toContain("actions/checkout");
+      expect(responseData.error).toContain("Repository 'test-owner/test-repo' not found in workspace");
+      expect(responseData.error).toContain("path in checkout");
       expect(responseData.error).toContain("'path' input");
     });
 
+    it("should return error when defaultTargetRepo checkout is not found and entry.repo is not set", async () => {
+      const configWithTarget = {
+        push_to_pull_request_branch: { "target-repo": "test-owner/test-repo" },
+      };
+      const handlersWithTarget = createHandlers(mockServer, mockAppendSafeOutput, configWithTarget);
+
+      const result = await handlersWithTarget.pushToPullRequestBranchHandler({
+        branch: "feature/test-change",
+      });
+
+      expect(result.isError).toBe(true);
+      const responseData = JSON.parse(result.content[0].text);
+      expect(responseData.result).toBe("error");
+      expect(responseData.error).toContain("Repository 'test-owner/test-repo' not found in workspace");
+      expect(responseData.error).toContain("path in checkout");
+    });
+
+    it("should detect branch from defaultTargetRepo checkout when entry.repo is not provided", async () => {
+      const { targetRepoDir } = createSideRepoWithTrackedAndLocalCommits();
+
+      const configWithTarget = {
+        push_to_pull_request_branch: { "target-repo": "test-owner/test-repo" },
+      };
+      const handlersWithTarget = createHandlers(mockServer, mockAppendSafeOutput, configWithTarget);
+
+      process.env.GITHUB_BASE_REF = "main";
+      try {
+        const result = await handlersWithTarget.pushToPullRequestBranchHandler({
+          branch: "main",
+        });
+
+        expect(result.isError).toBeFalsy();
+        expect(mockServer.debug).toHaveBeenCalledWith(expect.stringContaining(`Selected checkout folder for test-owner/test-repo: ${targetRepoDir}`));
+        expect(mockServer.debug).toHaveBeenCalledWith(expect.stringContaining("detecting actual working branch: feature/test-change"));
+        expect(mockAppendSafeOutput).toHaveBeenCalledWith(
+          expect.objectContaining({
+            type: "push_to_pull_request_branch",
+            branch: "feature/test-change",
+            repo_cwd: targetRepoDir,
+          })
+        );
+      } finally {
+        delete process.env.GITHUB_BASE_REF;
+      }
+    });
+
     it("should detect branch from the checked out target repo when repo is provided", async () => {
       const { targetRepoDir } = createSideRepoWithTrackedAndLocalCommits();
 

From 3dd08ad5ad73538a670aa101eadc240af5202177 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 25 Apr 2026 01:05:18 +0000
Subject: [PATCH 3/6] refactor: use template literal for error message and add
 debug assertion to test

Agent-Logs-Url: https://github.com/github/gh-aw/sessions/b40b9f06-4916-453b-a852-db2c1a780448

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

diff --git a/actions/setup/js/safe_outputs_handlers.cjs b/actions/setup/js/safe_outputs_handlers.cjs
index ed3b499848c..329ff135c1e 100644
--- a/actions/setup/js/safe_outputs_handlers.cjs
+++ b/actions/setup/js/safe_outputs_handlers.cjs
@@ -502,7 +502,7 @@ function createHandlers(server, appendSafeOutput, config = {}) {
               type: "text",
               text: JSON.stringify({
                 result: "error",
-                error: `Repository '${itemRepo}' not found in workspace. Check out the target repo with a path in checkout. ` + "If checking out multiple repositories, use the 'path' input so the checkout can be located.",
+                error: `Repository '${itemRepo}' not found in workspace. Check out the target repo with a path in checkout. If checking out multiple repositories, use the 'path' input so the checkout can be located.`,
               }),
             },
           ],
diff --git a/actions/setup/js/safe_outputs_handlers.test.cjs b/actions/setup/js/safe_outputs_handlers.test.cjs
index 9c547b5f832..c7aff922310 100644
--- a/actions/setup/js/safe_outputs_handlers.test.cjs
+++ b/actions/setup/js/safe_outputs_handlers.test.cjs
@@ -712,6 +712,7 @@ describe("safe_outputs_handlers", () => {
         });
 
         expect(result.isError).toBeFalsy();
+        expect(mockServer.debug).toHaveBeenCalledWith(expect.stringContaining("Looking for checkout of target repo: test-owner/test-repo"));
         expect(mockServer.debug).toHaveBeenCalledWith(expect.stringContaining(`Selected checkout folder for test-owner/test-repo: ${targetRepoDir}`));
         expect(mockServer.debug).toHaveBeenCalledWith(expect.stringContaining("detecting actual working branch: feature/test-change"));
         expect(mockAppendSafeOutput).toHaveBeenCalledWith(

From b853ca79794c5e794f9fbd6f7bbcf207224390ac Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 25 Apr 2026 01:14:58 +0000
Subject: [PATCH 4/6] fix: pass repoCwd to all git ops in
 push_to_pull_request_branch conclusion handler

Resolves #28374. When the target repo differs from the workflow repo,
find its checkout directory using findRepoCheckout and pass cwd to every
git exec call (fetch, checkout, am, push, ls-remote, rev-parse, rev-list,
review-branch, fallback-branch, bundle ops, and pushSignedCommits).

Agent-Logs-Url: https://github.com/github/gh-aw/sessions/3b1d2ad5-2971-4fdf-a11c-1bb150651885

Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>
---
 .../setup/js/push_to_pull_request_branch.cjs  | 61 ++++++++++----
 .../js/push_to_pull_request_branch.test.cjs   | 83 +++++++++++++++++++
 2 files changed, 126 insertions(+), 18 deletions(-)

diff --git a/actions/setup/js/push_to_pull_request_branch.cjs b/actions/setup/js/push_to_pull_request_branch.cjs
index 41f19229181..44f39f583df 100644
--- a/actions/setup/js/push_to_pull_request_branch.cjs
+++ b/actions/setup/js/push_to_pull_request_branch.cjs
@@ -17,6 +17,7 @@ const { checkFileProtection } = require("./manifest_file_helpers.cjs");
 const { buildWorkflowRunUrl } = require("./workflow_metadata_helpers.cjs");
 const { renderTemplateFromFile, buildProtectedFileList } = require("./messages_core.cjs");
 const { getGitAuthEnv } = require("./git_helpers.cjs");
+const { findRepoCheckout } = require("./find_repo_checkout.cjs");
 
 /**
  * @typedef {import('./types/handler-factory').HandlerFactoryFunction} HandlerFactoryFunction
@@ -353,6 +354,25 @@ async function main(config = {}) {
 
     core.info(`Target repository: ${itemRepo}`);
 
+    // Resolve the checkout directory for the target repo.
+    // When the target repo differs from the workflow repo, it may be checked out
+    // into a subdirectory of GITHUB_WORKSPACE (e.g. via actions/checkout path:).
+    // All git operations must run from that directory, not from GITHUB_WORKSPACE.
+    let repoCwd = undefined;
+    const workflowRepo = process.env.GITHUB_REPOSITORY || "";
+    if (itemRepo.toLowerCase() !== workflowRepo.toLowerCase()) {
+      core.info(`Cross-repo push: looking for checkout of ${itemRepo}`);
+      const checkoutResult = findRepoCheckout(itemRepo, process.env.GITHUB_WORKSPACE, { allowedRepos });
+      if (!checkoutResult.success) {
+        return {
+          success: false,
+          error: `Repository '${itemRepo}' not found in workspace. Check out the target repo with a path in checkout. If checking out multiple repositories, use the 'path' input so the checkout can be located.`,
+        };
+      }
+      repoCwd = checkoutResult.path;
+      core.info(`Found checkout for ${itemRepo} at: ${repoCwd}`);
+    }
+
     // Fetch the specific PR to get its head branch, title, and labels
     let pullRequest;
     try {
@@ -490,6 +510,7 @@ async function main(config = {}) {
     {
       const lsRemoteResult = await exec.getExecOutput("git", ["ls-remote", "--exit-code", "--heads", "origin", branchName], {
         env: { ...process.env, ...gitAuthEnv },
+        ...(repoCwd ? { cwd: repoCwd } : {}),
         ignoreReturnCode: true,
       });
 
@@ -525,6 +546,7 @@ async function main(config = {}) {
       core.info(`Fetching branch: ${branchName}`);
       await exec.exec("git", ["fetch", "origin", `${branchName}:refs/remotes/origin/${branchName}`], {
         env: { ...process.env, ...gitAuthEnv },
+        ...(repoCwd ? { cwd: repoCwd } : {}),
       });
     } catch (fetchError) {
       const fetchErrorMessage = fetchError instanceof Error ? fetchError.message : String(fetchError);
@@ -538,7 +560,7 @@ async function main(config = {}) {
 
     // Check if branch exists on origin
     try {
-      await exec.exec(`git rev-parse --verify origin/${branchName}`);
+      await exec.exec(`git rev-parse --verify origin/${branchName}`, [], ...(repoCwd ? [{ cwd: repoCwd }] : []));
     } catch (verifyError) {
       const missingBranchError = MISSING_BRANCH_ERROR_TEMPLATE(branchName);
       if (ignoreMissingBranchFailure) {
@@ -550,7 +572,7 @@ async function main(config = {}) {
 
     // Checkout the branch from origin
     try {
-      await exec.exec(`git checkout -B ${branchName} origin/${branchName}`);
+      await exec.exec(`git checkout -B ${branchName} origin/${branchName}`, [], ...(repoCwd ? [{ cwd: repoCwd }] : []));
       core.info(`Checked out existing branch from origin: ${branchName}`);
     } catch (checkoutError) {
       return { success: false, error: `Failed to checkout branch ${branchName}: ${checkoutError instanceof Error ? checkoutError.message : String(checkoutError)}` };
@@ -566,7 +588,7 @@ async function main(config = {}) {
     if (hasChanges) {
       // Capture HEAD before applying changes to compute new-commit count later
       try {
-        const { stdout } = await exec.getExecOutput("git", ["rev-parse", "HEAD"]);
+        const { stdout } = await exec.getExecOutput("git", ["rev-parse", "HEAD"], ...(repoCwd ? [{ cwd: repoCwd }] : []));
         remoteHeadBeforePatch = stdout.trim();
       } catch {
         // Non-fatal - extra empty commit will be skipped
@@ -579,16 +601,16 @@ async function main(config = {}) {
         const bundleRef = `refs/bundles/push-${branchName.replace(/[^a-zA-Z0-9-]/g, "-")}`;
         try {
           // Fetch from bundle into a temporary ref
-          await exec.exec("git", ["fetch", bundleFilePath, `refs/heads/${message.branch}:${bundleRef}`]);
+          await exec.exec("git", ["fetch", bundleFilePath, `refs/heads/${message.branch}:${bundleRef}`], ...(repoCwd ? [{ cwd: repoCwd }] : []));
           core.info(`Fetched bundle to ${bundleRef}`);
 
           // Fast-forward the current branch to the bundle tip
-          await exec.exec("git", ["merge", "--ff-only", bundleRef]);
+          await exec.exec("git", ["merge", "--ff-only", bundleRef], ...(repoCwd ? [{ cwd: repoCwd }] : []));
           core.info("Fast-forwarded branch to bundle tip");
 
           // Clean up the temporary ref
           try {
-            await exec.exec("git", ["update-ref", "-d", bundleRef]);
+            await exec.exec("git", ["update-ref", "-d", bundleRef], ...(repoCwd ? [{ cwd: repoCwd }] : []));
           } catch {
             // Non-fatal cleanup
           }
@@ -596,7 +618,7 @@ async function main(config = {}) {
           core.error(`Failed to apply bundle: ${bundleError instanceof Error ? bundleError.message : String(bundleError)}`);
           // Clean up temp ref if it exists
           try {
-            await exec.exec("git", ["update-ref", "-d", bundleRef]);
+            await exec.exec("git", ["update-ref", "-d", bundleRef], ...(repoCwd ? [{ cwd: repoCwd }] : []));
           } catch {
             // Ignore
           }
@@ -631,7 +653,7 @@ async function main(config = {}) {
 
           // Use --3way to handle cross-repo patches where the patch base may differ from target repo
           // This allows git to resolve create-vs-modify mismatches when a file exists in target but not source
-          await exec.exec(`git am --3way ${patchFilePath}`);
+          await exec.exec(`git am --3way ${patchFilePath}`, [], ...(repoCwd ? [{ cwd: repoCwd }] : []));
           core.info("Patch applied successfully");
         } catch (error) {
           core.error(`Failed to apply patch: ${getErrorMessage(error)}`);
@@ -640,23 +662,23 @@ async function main(config = {}) {
           try {
             core.info("Investigating patch failure...");
 
-            const statusResult = await exec.getExecOutput("git", ["status"]);
+            const statusResult = await exec.getExecOutput("git", ["status"], ...(repoCwd ? [{ cwd: repoCwd }] : []));
             core.info("Git status output:");
             core.info(statusResult.stdout);
 
-            const logResult = await exec.getExecOutput("git", ["log", "--oneline", "-5"]);
+            const logResult = await exec.getExecOutput("git", ["log", "--oneline", "-5"], ...(repoCwd ? [{ cwd: repoCwd }] : []));
             core.info("Recent commits (last 5):");
             core.info(logResult.stdout);
 
-            const diffResult = await exec.getExecOutput("git", ["diff", "HEAD"]);
+            const diffResult = await exec.getExecOutput("git", ["diff", "HEAD"], ...(repoCwd ? [{ cwd: repoCwd }] : []));
             core.info("Uncommitted changes:");
             core.info(diffResult.stdout && diffResult.stdout.trim() ? diffResult.stdout : "(no uncommitted changes)");
 
-            const patchDiffResult = await exec.getExecOutput("git", ["am", "--show-current-patch=diff"]);
+            const patchDiffResult = await exec.getExecOutput("git", ["am", "--show-current-patch=diff"], ...(repoCwd ? [{ cwd: repoCwd }] : []));
             core.info("Failed patch diff:");
             core.info(patchDiffResult.stdout);
 
-            const patchFullResult = await exec.getExecOutput("git", ["am", "--show-current-patch"]);
+            const patchFullResult = await exec.getExecOutput("git", ["am", "--show-current-patch"], ...(repoCwd ? [{ cwd: repoCwd }] : []));
             core.info("Failed patch (full):");
             core.info(patchFullResult.stdout);
           } catch (investigateError) {
@@ -679,12 +701,13 @@ async function main(config = {}) {
         const reviewBranchName = normalizeBranchName(`${branchName}-review`, String(Date.now()));
         try {
           // Rename current local branch to review branch
-          await exec.exec("git", ["checkout", "-b", reviewBranchName]);
+          await exec.exec("git", ["checkout", "-b", reviewBranchName], ...(repoCwd ? [{ cwd: repoCwd }] : []));
           core.info(`Created review branch: ${reviewBranchName}`);
 
           // Push the review branch
           await exec.exec("git", ["push", "origin", reviewBranchName], {
             env: { ...process.env, ...gitAuthEnv },
+            ...(repoCwd ? { cwd: repoCwd } : {}),
           });
           core.info(`Pushed review branch: ${reviewBranchName}`);
 
@@ -750,7 +773,7 @@ async function main(config = {}) {
           repo: repoParts.repo,
           branch: branchName,
           baseRef: remoteHeadBeforePatch || `origin/${branchName}`,
-          cwd: process.cwd(),
+          cwd: repoCwd || process.cwd(),
           gitAuthEnv,
         });
         if (pushedSha) {
@@ -771,6 +794,7 @@ async function main(config = {}) {
         try {
           const lsRemoteAfterPushResult = await exec.getExecOutput("git", ["ls-remote", "--exit-code", "--heads", "origin", branchName], {
             env: { ...process.env, ...gitAuthEnv },
+            ...(repoCwd ? { cwd: repoCwd } : {}),
             ignoreReturnCode: true,
           });
 
@@ -790,9 +814,10 @@ async function main(config = {}) {
           const fallbackBranchName = normalizeBranchName(`${branchName}-fallback`, String(Date.now()));
           core.warning(`Non-fast-forward push detected; creating fallback pull request from '${fallbackBranchName}' to '${branchName}'`);
           try {
-            await exec.exec("git", ["checkout", "-b", fallbackBranchName]);
+            await exec.exec("git", ["checkout", "-b", fallbackBranchName], ...(repoCwd ? [{ cwd: repoCwd }] : []));
             await exec.exec("git", ["push", "origin", fallbackBranchName], {
               env: { ...process.env, ...gitAuthEnv },
+              ...(repoCwd ? { cwd: repoCwd } : {}),
             });
 
             const fallbackBody = [
@@ -842,7 +867,7 @@ async function main(config = {}) {
       // Count new commits pushed for the CI trigger decision
       if (remoteHeadBeforePatch) {
         try {
-          const { stdout: countStr } = await exec.getExecOutput("git", ["rev-list", "--count", `${remoteHeadBeforePatch}..HEAD`]);
+          const { stdout: countStr } = await exec.getExecOutput("git", ["rev-list", "--count", `${remoteHeadBeforePatch}..HEAD`], ...(repoCwd ? [{ cwd: repoCwd }] : []));
           newCommitCount = parseInt(countStr.trim(), 10);
           core.info(`${newCommitCount} new commit(s) pushed to branch`);
         } catch {
@@ -872,7 +897,7 @@ async function main(config = {}) {
     // Fall back to local HEAD only if the helper did not return one.
     let commitSha = pushedCommitSha;
     if (!commitSha) {
-      const commitShaRes = await exec.getExecOutput("git", ["rev-parse", "HEAD"]);
+      const commitShaRes = await exec.getExecOutput("git", ["rev-parse", "HEAD"], ...(repoCwd ? [{ cwd: repoCwd }] : []));
       if (commitShaRes.exitCode !== 0) {
         return { success: false, error: "Failed to get commit SHA" };
       }
diff --git a/actions/setup/js/push_to_pull_request_branch.test.cjs b/actions/setup/js/push_to_pull_request_branch.test.cjs
index 4d5ea8fa604..369c304a88e 100644
--- a/actions/setup/js/push_to_pull_request_branch.test.cjs
+++ b/actions/setup/js/push_to_pull_request_branch.test.cjs
@@ -1666,6 +1666,89 @@ ${diffs}
       expect(result.error || "").not.toContain("outside the allowed-files list");
     });
   });
+
+  // ──────────────────────────────────────────────────────
+  // Cross-Repo Checkout Scenarios
+  // ──────────────────────────────────────────────────────
+
+  describe("cross-repo checkout", () => {
+    it("should return error when target repo differs from workflow repo and is not found in workspace", async () => {
+      // GITHUB_REPOSITORY is set to "test-owner/test-repo" in beforeEach
+      // Targeting "other-owner/other-repo" - different repo, not checked out
+      mockGithub.rest.pulls.get = vi.fn().mockResolvedValue({
+        data: {
+          head: {
+            ref: "feature-branch",
+            repo: { full_name: "other-owner/other-repo", fork: false, owner: { login: "other-owner" } },
+          },
+          base: {
+            repo: { full_name: "other-owner/other-repo", owner: { login: "other-owner" } },
+          },
+          title: "Cross-repo PR",
+          labels: [],
+        },
+      });
+
+      const patchPath = createPatchFile();
+      const module = await loadModule();
+      const handler = await module.main({ "target-repo": "other-owner/other-repo" });
+
+      const result = await handler({ patch_path: patchPath, pull_request_number: 42 }, {});
+
+      expect(result.success).toBe(false);
+      expect(result.error).toContain("other-owner/other-repo");
+      expect(result.error).toContain("not found in workspace");
+    });
+
+    it("should pass cwd to git commands when target repo is checked out in a subdirectory", async () => {
+      // Create a subdirectory checkout with a remote that matches "other-owner/other-repo"
+      const subRepoDir = path.join(tempDir, "other-repo");
+      fs.mkdirSync(subRepoDir, { recursive: true });
+      const { execSync } = await import("child_process");
+      execSync("git init -b main", { cwd: subRepoDir, stdio: "pipe" });
+      execSync("git config user.email 'test@example.com'", { cwd: subRepoDir, stdio: "pipe" });
+      execSync("git config user.name 'Test User'", { cwd: subRepoDir, stdio: "pipe" });
+      execSync("git remote add origin https://github.com/other-owner/other-repo.git", { cwd: subRepoDir, stdio: "pipe" });
+
+      // Set workspace to tempDir so findRepoCheckout scans it
+      process.env.GITHUB_WORKSPACE = tempDir;
+
+      mockGithub.rest.pulls.get = vi.fn().mockResolvedValue({
+        data: {
+          head: {
+            ref: "feature-branch",
+            repo: { full_name: "other-owner/other-repo", fork: false, owner: { login: "other-owner" } },
+          },
+          base: {
+            repo: { full_name: "other-owner/other-repo", owner: { login: "other-owner" } },
+          },
+          title: "Cross-repo PR",
+          labels: [],
+        },
+      });
+      mockGithub.rest.repos.get = vi.fn().mockResolvedValue({ data: { default_branch: "main" } });
+      mockGithub.rest.repos.getBranchProtection = vi.fn().mockRejectedValue(Object.assign(new Error("not protected"), { status: 404 }));
+
+      mockExec.getExecOutput.mockResolvedValue({ exitCode: 0, stdout: "abc123\n", stderr: "" });
+
+      const patchPath = createPatchFile();
+      const module = await loadModule();
+      const handler = await module.main({ "target-repo": "other-owner/other-repo" });
+
+      await handler({ patch_path: patchPath, pull_request_number: 42 }, {});
+
+      // Verify git ls-remote was called with cwd pointing at the subdirectory
+      expect(mockCore.info).toHaveBeenCalledWith(expect.stringContaining(`Found checkout for other-owner/other-repo at: ${subRepoDir}`));
+
+      // Verify at least one exec call received cwd pointing at the subdirectory
+      const allExecCalls = [...mockExec.exec.mock.calls, ...mockExec.getExecOutput.mock.calls];
+      const cwdCalls = allExecCalls.filter(call => {
+        const opts = call.find(arg => arg && typeof arg === "object" && !Array.isArray(arg) && "cwd" in arg);
+        return opts && opts.cwd === subRepoDir;
+      });
+      expect(cwdCalls.length).toBeGreaterThan(0);
+    });
+  });
 });
 
 // ──────────────────────────────────────────────────────

From 82ecb333eebf0ed6083896b1d1626e7873c8e4c8 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 25 Apr 2026 01:18:10 +0000
Subject: [PATCH 5/6] refactor: use baseGitOpts helper for consistent cwd
 passing in git exec calls

Agent-Logs-Url: https://github.com/github/gh-aw/sessions/3b1d2ad5-2971-4fdf-a11c-1bb150651885

Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>
---
 .../setup/js/push_to_pull_request_branch.cjs  | 49 ++++++++++---------
 1 file changed, 25 insertions(+), 24 deletions(-)

diff --git a/actions/setup/js/push_to_pull_request_branch.cjs b/actions/setup/js/push_to_pull_request_branch.cjs
index 44f39f583df..5266db3f9fd 100644
--- a/actions/setup/js/push_to_pull_request_branch.cjs
+++ b/actions/setup/js/push_to_pull_request_branch.cjs
@@ -373,7 +373,8 @@ async function main(config = {}) {
       core.info(`Found checkout for ${itemRepo} at: ${repoCwd}`);
     }
 
-    // Fetch the specific PR to get its head branch, title, and labels
+    // Base options for all git exec calls - includes cwd when running in a subdirectory checkout
+    const baseGitOpts = repoCwd ? { cwd: repoCwd } : {};
     let pullRequest;
     try {
       const response = await githubClient.rest.pulls.get({
@@ -510,7 +511,7 @@ async function main(config = {}) {
     {
       const lsRemoteResult = await exec.getExecOutput("git", ["ls-remote", "--exit-code", "--heads", "origin", branchName], {
         env: { ...process.env, ...gitAuthEnv },
-        ...(repoCwd ? { cwd: repoCwd } : {}),
+        ...baseGitOpts,
         ignoreReturnCode: true,
       });
 
@@ -546,7 +547,7 @@ async function main(config = {}) {
       core.info(`Fetching branch: ${branchName}`);
       await exec.exec("git", ["fetch", "origin", `${branchName}:refs/remotes/origin/${branchName}`], {
         env: { ...process.env, ...gitAuthEnv },
-        ...(repoCwd ? { cwd: repoCwd } : {}),
+        ...baseGitOpts,
       });
     } catch (fetchError) {
       const fetchErrorMessage = fetchError instanceof Error ? fetchError.message : String(fetchError);
@@ -560,7 +561,7 @@ async function main(config = {}) {
 
     // Check if branch exists on origin
     try {
-      await exec.exec(`git rev-parse --verify origin/${branchName}`, [], ...(repoCwd ? [{ cwd: repoCwd }] : []));
+      await exec.exec(`git rev-parse --verify origin/${branchName}`, [], baseGitOpts);
     } catch (verifyError) {
       const missingBranchError = MISSING_BRANCH_ERROR_TEMPLATE(branchName);
       if (ignoreMissingBranchFailure) {
@@ -572,7 +573,7 @@ async function main(config = {}) {
 
     // Checkout the branch from origin
     try {
-      await exec.exec(`git checkout -B ${branchName} origin/${branchName}`, [], ...(repoCwd ? [{ cwd: repoCwd }] : []));
+      await exec.exec(`git checkout -B ${branchName} origin/${branchName}`, [], baseGitOpts);
       core.info(`Checked out existing branch from origin: ${branchName}`);
     } catch (checkoutError) {
       return { success: false, error: `Failed to checkout branch ${branchName}: ${checkoutError instanceof Error ? checkoutError.message : String(checkoutError)}` };
@@ -588,7 +589,7 @@ async function main(config = {}) {
     if (hasChanges) {
       // Capture HEAD before applying changes to compute new-commit count later
       try {
-        const { stdout } = await exec.getExecOutput("git", ["rev-parse", "HEAD"], ...(repoCwd ? [{ cwd: repoCwd }] : []));
+        const { stdout } = await exec.getExecOutput("git", ["rev-parse", "HEAD"], baseGitOpts);
         remoteHeadBeforePatch = stdout.trim();
       } catch {
         // Non-fatal - extra empty commit will be skipped
@@ -601,16 +602,16 @@ async function main(config = {}) {
         const bundleRef = `refs/bundles/push-${branchName.replace(/[^a-zA-Z0-9-]/g, "-")}`;
         try {
           // Fetch from bundle into a temporary ref
-          await exec.exec("git", ["fetch", bundleFilePath, `refs/heads/${message.branch}:${bundleRef}`], ...(repoCwd ? [{ cwd: repoCwd }] : []));
+          await exec.exec("git", ["fetch", bundleFilePath, `refs/heads/${message.branch}:${bundleRef}`], baseGitOpts);
           core.info(`Fetched bundle to ${bundleRef}`);
 
           // Fast-forward the current branch to the bundle tip
-          await exec.exec("git", ["merge", "--ff-only", bundleRef], ...(repoCwd ? [{ cwd: repoCwd }] : []));
+          await exec.exec("git", ["merge", "--ff-only", bundleRef], baseGitOpts);
           core.info("Fast-forwarded branch to bundle tip");
 
           // Clean up the temporary ref
           try {
-            await exec.exec("git", ["update-ref", "-d", bundleRef], ...(repoCwd ? [{ cwd: repoCwd }] : []));
+            await exec.exec("git", ["update-ref", "-d", bundleRef], baseGitOpts);
           } catch {
             // Non-fatal cleanup
           }
@@ -618,7 +619,7 @@ async function main(config = {}) {
           core.error(`Failed to apply bundle: ${bundleError instanceof Error ? bundleError.message : String(bundleError)}`);
           // Clean up temp ref if it exists
           try {
-            await exec.exec("git", ["update-ref", "-d", bundleRef], ...(repoCwd ? [{ cwd: repoCwd }] : []));
+            await exec.exec("git", ["update-ref", "-d", bundleRef], baseGitOpts);
           } catch {
             // Ignore
           }
@@ -653,7 +654,7 @@ async function main(config = {}) {
 
           // Use --3way to handle cross-repo patches where the patch base may differ from target repo
           // This allows git to resolve create-vs-modify mismatches when a file exists in target but not source
-          await exec.exec(`git am --3way ${patchFilePath}`, [], ...(repoCwd ? [{ cwd: repoCwd }] : []));
+          await exec.exec(`git am --3way ${patchFilePath}`, [], baseGitOpts);
           core.info("Patch applied successfully");
         } catch (error) {
           core.error(`Failed to apply patch: ${getErrorMessage(error)}`);
@@ -662,23 +663,23 @@ async function main(config = {}) {
           try {
             core.info("Investigating patch failure...");
 
-            const statusResult = await exec.getExecOutput("git", ["status"], ...(repoCwd ? [{ cwd: repoCwd }] : []));
+            const statusResult = await exec.getExecOutput("git", ["status"], baseGitOpts);
             core.info("Git status output:");
             core.info(statusResult.stdout);
 
-            const logResult = await exec.getExecOutput("git", ["log", "--oneline", "-5"], ...(repoCwd ? [{ cwd: repoCwd }] : []));
+            const logResult = await exec.getExecOutput("git", ["log", "--oneline", "-5"], baseGitOpts);
             core.info("Recent commits (last 5):");
             core.info(logResult.stdout);
 
-            const diffResult = await exec.getExecOutput("git", ["diff", "HEAD"], ...(repoCwd ? [{ cwd: repoCwd }] : []));
+            const diffResult = await exec.getExecOutput("git", ["diff", "HEAD"], baseGitOpts);
             core.info("Uncommitted changes:");
             core.info(diffResult.stdout && diffResult.stdout.trim() ? diffResult.stdout : "(no uncommitted changes)");
 
-            const patchDiffResult = await exec.getExecOutput("git", ["am", "--show-current-patch=diff"], ...(repoCwd ? [{ cwd: repoCwd }] : []));
+            const patchDiffResult = await exec.getExecOutput("git", ["am", "--show-current-patch=diff"], baseGitOpts);
             core.info("Failed patch diff:");
             core.info(patchDiffResult.stdout);
 
-            const patchFullResult = await exec.getExecOutput("git", ["am", "--show-current-patch"], ...(repoCwd ? [{ cwd: repoCwd }] : []));
+            const patchFullResult = await exec.getExecOutput("git", ["am", "--show-current-patch"], baseGitOpts);
             core.info("Failed patch (full):");
             core.info(patchFullResult.stdout);
           } catch (investigateError) {
@@ -701,13 +702,13 @@ async function main(config = {}) {
         const reviewBranchName = normalizeBranchName(`${branchName}-review`, String(Date.now()));
         try {
           // Rename current local branch to review branch
-          await exec.exec("git", ["checkout", "-b", reviewBranchName], ...(repoCwd ? [{ cwd: repoCwd }] : []));
+          await exec.exec("git", ["checkout", "-b", reviewBranchName], baseGitOpts);
           core.info(`Created review branch: ${reviewBranchName}`);
 
           // Push the review branch
           await exec.exec("git", ["push", "origin", reviewBranchName], {
             env: { ...process.env, ...gitAuthEnv },
-            ...(repoCwd ? { cwd: repoCwd } : {}),
+            ...baseGitOpts,
           });
           core.info(`Pushed review branch: ${reviewBranchName}`);
 
@@ -773,7 +774,7 @@ async function main(config = {}) {
           repo: repoParts.repo,
           branch: branchName,
           baseRef: remoteHeadBeforePatch || `origin/${branchName}`,
-          cwd: repoCwd || process.cwd(),
+          ...baseGitOpts,
           gitAuthEnv,
         });
         if (pushedSha) {
@@ -794,7 +795,7 @@ async function main(config = {}) {
         try {
           const lsRemoteAfterPushResult = await exec.getExecOutput("git", ["ls-remote", "--exit-code", "--heads", "origin", branchName], {
             env: { ...process.env, ...gitAuthEnv },
-            ...(repoCwd ? { cwd: repoCwd } : {}),
+            ...baseGitOpts,
             ignoreReturnCode: true,
           });
 
@@ -814,10 +815,10 @@ async function main(config = {}) {
           const fallbackBranchName = normalizeBranchName(`${branchName}-fallback`, String(Date.now()));
           core.warning(`Non-fast-forward push detected; creating fallback pull request from '${fallbackBranchName}' to '${branchName}'`);
           try {
-            await exec.exec("git", ["checkout", "-b", fallbackBranchName], ...(repoCwd ? [{ cwd: repoCwd }] : []));
+            await exec.exec("git", ["checkout", "-b", fallbackBranchName], baseGitOpts);
             await exec.exec("git", ["push", "origin", fallbackBranchName], {
               env: { ...process.env, ...gitAuthEnv },
-              ...(repoCwd ? { cwd: repoCwd } : {}),
+              ...baseGitOpts,
             });
 
             const fallbackBody = [
@@ -867,7 +868,7 @@ async function main(config = {}) {
       // Count new commits pushed for the CI trigger decision
       if (remoteHeadBeforePatch) {
         try {
-          const { stdout: countStr } = await exec.getExecOutput("git", ["rev-list", "--count", `${remoteHeadBeforePatch}..HEAD`], ...(repoCwd ? [{ cwd: repoCwd }] : []));
+          const { stdout: countStr } = await exec.getExecOutput("git", ["rev-list", "--count", `${remoteHeadBeforePatch}..HEAD`], baseGitOpts);
           newCommitCount = parseInt(countStr.trim(), 10);
           core.info(`${newCommitCount} new commit(s) pushed to branch`);
         } catch {
@@ -897,7 +898,7 @@ async function main(config = {}) {
     // Fall back to local HEAD only if the helper did not return one.
     let commitSha = pushedCommitSha;
     if (!commitSha) {
-      const commitShaRes = await exec.getExecOutput("git", ["rev-parse", "HEAD"], ...(repoCwd ? [{ cwd: repoCwd }] : []));
+      const commitShaRes = await exec.getExecOutput("git", ["rev-parse", "HEAD"], baseGitOpts);
       if (commitShaRes.exitCode !== 0) {
         return { success: false, error: "Failed to get commit SHA" };
       }

From 47c722f40621c58fc3fa04976813b4a02cf0f3c8 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 25 Apr 2026 02:15:45 +0000
Subject: [PATCH 6/6] fix: address review comments - improve error messages and
 test name clarity

Agent-Logs-Url: https://github.com/github/gh-aw/sessions/af16cbe6-1871-4390-9b68-5737f98974e0

Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>
---
 actions/setup/js/push_to_pull_request_branch.cjs | 2 +-
 actions/setup/js/safe_outputs_handlers.cjs       | 2 +-
 actions/setup/js/safe_outputs_handlers.test.cjs  | 7 ++++---
 3 files changed, 6 insertions(+), 5 deletions(-)

diff --git a/actions/setup/js/push_to_pull_request_branch.cjs b/actions/setup/js/push_to_pull_request_branch.cjs
index 5266db3f9fd..91b2550238f 100644
--- a/actions/setup/js/push_to_pull_request_branch.cjs
+++ b/actions/setup/js/push_to_pull_request_branch.cjs
@@ -366,7 +366,7 @@ async function main(config = {}) {
       if (!checkoutResult.success) {
         return {
           success: false,
-          error: `Repository '${itemRepo}' not found in workspace. Check out the target repo with a path in checkout. If checking out multiple repositories, use the 'path' input so the checkout can be located.`,
+          error: `Repository '${itemRepo}' not found in workspace. Check out the target repo with actions/checkout and set its 'path' input so the checkout can be located. If checking out multiple repositories, ensure each actions/checkout step uses the appropriate 'path' input.`,
         };
       }
       repoCwd = checkoutResult.path;
diff --git a/actions/setup/js/safe_outputs_handlers.cjs b/actions/setup/js/safe_outputs_handlers.cjs
index 329ff135c1e..897c676d15d 100644
--- a/actions/setup/js/safe_outputs_handlers.cjs
+++ b/actions/setup/js/safe_outputs_handlers.cjs
@@ -502,7 +502,7 @@ function createHandlers(server, appendSafeOutput, config = {}) {
               type: "text",
               text: JSON.stringify({
                 result: "error",
-                error: `Repository '${itemRepo}' not found in workspace. Check out the target repo with a path in checkout. If checking out multiple repositories, use the 'path' input so the checkout can be located.`,
+                error: `Repository '${itemRepo}' not found in workspace. Check out the target repo with actions/checkout and set its 'path' input so the checkout can be located. If checking out multiple repositories, ensure each actions/checkout step uses the appropriate 'path' input.`,
               }),
             },
           ],
diff --git a/actions/setup/js/safe_outputs_handlers.test.cjs b/actions/setup/js/safe_outputs_handlers.test.cjs
index c7aff922310..09332830b67 100644
--- a/actions/setup/js/safe_outputs_handlers.test.cjs
+++ b/actions/setup/js/safe_outputs_handlers.test.cjs
@@ -676,11 +676,11 @@ describe("safe_outputs_handlers", () => {
       const responseData = JSON.parse(result.content[0].text);
       expect(responseData.result).toBe("error");
       expect(responseData.error).toContain("Repository 'test-owner/test-repo' not found in workspace");
-      expect(responseData.error).toContain("path in checkout");
+      expect(responseData.error).toContain("actions/checkout");
       expect(responseData.error).toContain("'path' input");
     });
 
-    it("should return error when defaultTargetRepo checkout is not found and entry.repo is not set", async () => {
+    it("should return error when configured target-repo checkout is not found and entry.repo is not set", async () => {
       const configWithTarget = {
         push_to_pull_request_branch: { "target-repo": "test-owner/test-repo" },
       };
@@ -694,7 +694,8 @@ describe("safe_outputs_handlers", () => {
       const responseData = JSON.parse(result.content[0].text);
       expect(responseData.result).toBe("error");
       expect(responseData.error).toContain("Repository 'test-owner/test-repo' not found in workspace");
-      expect(responseData.error).toContain("path in checkout");
+      expect(responseData.error).toContain("actions/checkout");
+      expect(responseData.error).toContain("'path' input");
     });
 
     it("should detect branch from defaultTargetRepo checkout when entry.repo is not provided", async () => {