Fix apply_samples cross-repo subdirectory patch staging (#40086) (#40087)

* fix: stage cross-repo subdirectory sample patches in the right checkout (#40086)

apply_samples.cjs always created the sample branch and committed the patch
in the main workspace root. For a cross-repo checkout placed in a subdirectory
(path: github), the safe-outputs MCP handler resolves the target repo to the
subdirectory via the checkout manifest and looks for the branch there, so it
failed with 'fatal: Needed a single revision'.

Resolve the patch-staging directory using the same manifest-first
findRepoCheckout the MCP handler uses, driven by the sample's arguments.repo
override or the configured target-repo. Falls back to the workspace root when
no target repo is set or the checkout cannot be located.

* Potential fix for pull request finding

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

---------

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

Author: dsyme

.changeset/patch-apply-samples-cross-repo-subdir-staging.md

@@ -23,6 +23,8 @@
 //   GH_AW_SAMPLES        — JSON array of replay entries (required)
 //   GH_AW_AGENT_STDIO_LOG     — path where the synthetic stdio log is written
 //   GH_AW_SAFE_OUTPUTS_CONFIG_PATH — path to the MCP server's config.json
+//                               (also read to resolve the per-tool target-repo so
+//                               cross-repo patches are staged in the right checkout)
 //   GH_AW_SAFE_OUTPUTS        — path to the MCP server's outputs.jsonl
 //   GITHUB_WORKSPACE          — git working directory for pre-staging (optional;
 //                               falls back to cwd)
@@ -35,6 +37,7 @@ const path = require("path");
 const os = require("os");
 const { getErrorMessage } = require("./error_helpers.cjs");
 const { ERR_VALIDATION, ERR_PARSE, ERR_SYSTEM, ERR_API, ERR_CONFIG } = require("./error_codes.cjs");
+const { findRepoCheckout } = require("./find_repo_checkout.cjs");
 
 const DEFAULT_BASE_BRANCH = process.env.GH_AW_CUSTOM_BASE_BRANCH || process.env.GITHUB_BASE_REF || process.env.GITHUB_REF_NAME || "main";
 const PATCH_SIDECAR_TOOLS = new Set(["create_pull_request", "push_to_pull_request_branch"]);
@@ -243,6 +246,84 @@ async function derivePrHeadRef(entry) {
   return null;
 }
 
+/**
+ * Read the configured `target-repo` for a given safe-output tool from the
+ * safe-outputs config file (GH_AW_SAFE_OUTPUTS_CONFIG_PATH). Returns an empty
+ * string when no config is available or no target-repo is configured.
+ * @param {string} tool
+ * @returns {string}
+ */
+function readConfiguredTargetRepo(tool) {
+  const configPath = process.env.GH_AW_SAFE_OUTPUTS_CONFIG_PATH;
+  if (!configPath || !configPath.trim()) {
+    return "";
+  }
+
+  const toolKey = typeof tool === "string" ? tool.replace(/-/g, "_") : "";
+
+  try {
+    const raw = fs.readFileSync(configPath, "utf8");
+    const parsed = JSON.parse(raw);
+
+    // Mirror safe_outputs_config.cjs behavior: normalize top-level keys by replacing '-' with '_'.
+    const config = parsed && typeof parsed === "object" ? Object.fromEntries(Object.entries(parsed).map(([k, v]) => [String(k).replace(/-/g, "_"), v])) : {};
+
+    const toolConfig = toolKey && config && typeof config === "object" ? config[toolKey] : null;
+    const target = toolConfig && typeof toolConfig === "object" ? toolConfig["target-repo"] || toolConfig["target_repo"] : null;
+    if (typeof target === "string") {
+      return target.trim();
+    }
+  } catch (err) {
+    core.debug(`apply_samples: could not read target-repo from ${configPath}: ${getErrorMessage(err)}`);
+  }
+  return "";
+}
+
+/**
+ * Resolve the on-disk working directory in which a sample's patch should be
+ * staged (branch created + patch committed).
+ *
+ * For cross-repo checkouts placed in a subdirectory (e.g. `path: github`), the
+ * branch and commit must be created inside that subdirectory so the safe-outputs
+ * MCP handler — which resolves the same checkout via the checkout manifest — can
+ * find the branch. Staging in the main workspace root instead leaves the branch
+ * invisible to the MCP server, producing "fatal: Needed a single revision" when
+ * it tries to pin the branch (issue #40086).
+ *
+ * Resolution mirrors the MCP handler: the target repo comes from the sample's
+ * `arguments.repo` override or the configured `target-repo`, and the checkout
+ * directory is resolved via the manifest-first `findRepoCheckout`. Falls back to
+ * the workspace root when no target repo is set or the checkout cannot be located.
+ *
+ * @param {SampleEntry} entry
+ * @param {string} workspace
+ * @returns {string}
+ */
+function resolvePatchWorkspace(entry, workspace) {
+  let targetRepo = "";
+  if (entry.arguments && typeof entry.arguments.repo === "string" && entry.arguments.repo.trim()) {
+    targetRepo = entry.arguments.repo.trim();
+  } else {
+    targetRepo = readConfiguredTargetRepo(entry.tool);
+  }
+  if (!targetRepo) {
+    return workspace;
+  }
+  try {
+    const result = findRepoCheckout(targetRepo, workspace);
+    if (result && result.success && result.path) {
+      if (path.resolve(result.path) !== path.resolve(workspace)) {
+        core.info(`apply_samples: staging patch for ${targetRepo} in checkout subdirectory ${result.path}`);
+      }
+      return result.path;
+    }
+    core.debug(`apply_samples: findRepoCheckout(${targetRepo}) did not locate a checkout; using workspace root`);
+  } catch (err) {
+    core.debug(`apply_samples: findRepoCheckout(${targetRepo}) failed: ${getErrorMessage(err)}; using workspace root`);
+  }
+  return workspace;
+}
+
 /**
  * Pre-stage a branch + patch for samples whose tool reads the workspace diff.
  *
@@ -264,6 +345,11 @@ async function preStagePatch(entry, index, workspace) {
     return;
   }
 
+  // Resolve the directory in which to create the branch and commit the patch.
+  // For cross-repo checkouts in a subdirectory this is the checkout subdir, not
+  // the main workspace root (issue #40086).
+  const repoCwd = resolvePatchWorkspace(entry, workspace);
+
   let branch;
   if (entry.tool === "push_to_pull_request_branch") {
     // Source ref MUST match the PR's head ref so that
@@ -286,36 +372,36 @@ async function preStagePatch(entry, index, workspace) {
     entry.arguments.branch = branch;
   }
 
-  ensureGitIdentity(workspace);
+  ensureGitIdentity(repoCwd);
 
   // Start from the base branch so the diff is meaningful. Tolerate the case
   // where the base ref doesn't exist locally — fall back to HEAD.
   try {
-    runGit(["checkout", DEFAULT_BASE_BRANCH], workspace);
+    runGit(["checkout", DEFAULT_BASE_BRANCH], repoCwd);
   } catch (err) {
     core.warning(`apply_samples: could not check out base branch ${DEFAULT_BASE_BRANCH}: ${getErrorMessage(err)}; staying on current HEAD`);
   }
 
   // Create the branch (or check it out if it already exists from a previous sample).
   try {
-    runGit(["checkout", "-b", branch], workspace);
+    runGit(["checkout", "-b", branch], repoCwd);
   } catch {
-    runGit(["checkout", branch], workspace);
+    runGit(["checkout", branch], repoCwd);
   }
 
   // Write patch to a temp file and apply it.
   const tmpPatch = path.join(os.tmpdir(), `gh-aw-sample-${index + 1}.patch`);
   fs.writeFileSync(tmpPatch, patch.endsWith("\n") ? patch : patch + "\n");
   try {
-    runGit(["apply", "--whitespace=nowarn", tmpPatch], workspace);
+    runGit(["apply", "--whitespace=nowarn", tmpPatch], repoCwd);
   } catch (err) {
     // Fall back to --3way for patches that don't apply cleanly on top of an
     // empty working tree (uncommon but possible for synthetic samples).
-    runGit(["apply", "--3way", "--whitespace=nowarn", tmpPatch], workspace);
+    runGit(["apply", "--3way", "--whitespace=nowarn", tmpPatch], repoCwd);
   }
 
-  runGit(["add", "-A"], workspace);
-  runGit(["commit", "-m", `gh-aw sample ${index + 1}: ${entry.tool}`, "--allow-empty"], workspace);
+  runGit(["add", "-A"], repoCwd);
+  runGit(["commit", "-m", `gh-aw sample ${index + 1}: ${entry.tool}`, "--allow-empty"], repoCwd);
 }
 
 /**
@@ -561,6 +647,8 @@ module.exports = {
   main,
   loadSamples,
   preStagePatch,
+  resolvePatchWorkspace,
+  readConfiguredTargetRepo,
   resolveMcpServerPath,
   selectTokenForRepo,
   sendJsonRpc,

actions/setup/js/apply_samples.cjs

@@ -326,6 +326,79 @@ describe("apply_samples.cjs preStagePatch (create_pull_request / push_to_pull_re
     expect(diff).toContain("+hello from a deterministic sample");
   });
 
+  it("stages the patch in the cross-repo checkout subdirectory (path: github) (issue #40086)", async () => {
+    // Reproduce the failing layout: a main repo at the workspace root and a
+    // side-repo checked out into a `github/` subdirectory. The checkout manifest
+    // maps the target repo to path "github", so preStagePatch must create the
+    // branch + commit inside ${workspace}/github — not the main repo root —
+    // otherwise the safe-outputs MCP server cannot pin the branch.
+    const workspace = makeTempDir("gh-aw-prestage-subdir-");
+    initRepo(workspace, "main");
+
+    const subdir = path.join(workspace, "github");
+    fs.mkdirSync(subdir);
+    initRepo(subdir, "main");
+
+    const manifestPath = path.join(workspace, "checkout-manifest.json");
+    fs.writeFileSync(
+      manifestPath,
+      JSON.stringify({
+        "githubnext/gh-aw-side-repo": {
+          repository: "githubnext/gh-aw-side-repo",
+          path: "github",
+          default_branch: "main",
+        },
+      })
+    );
+
+    const configPath = path.join(workspace, "config.json");
+    fs.writeFileSync(
+      configPath,
+      JSON.stringify({
+        create_pull_request: { "target-repo": "githubnext/gh-aw-side-repo" },
+      })
+    );
+
+    const branchName = "gh-aw-sample-copilot-siderepo-subdir-pr";
+    const fileToAdd = "subdir-notes.md";
+    const entry = {
+      tool: "create_pull_request",
+      arguments: { title: "Subdir PR", body: "body", branch: branchName },
+      sidecars: { patch: newFileDiff(fileToAdd, "side repo content\n") },
+    };
+
+    // Reset the checkout-manifest module cache so our manifest is loaded fresh.
+    require("./checkout_manifest.cjs")._resetCache();
+
+    const prevBase = process.env.GH_AW_CUSTOM_BASE_BRANCH;
+    const prevManifest = process.env.GH_AW_CHECKOUT_MANIFEST;
+    const prevConfig = process.env.GH_AW_SAFE_OUTPUTS_CONFIG_PATH;
+    process.env.GH_AW_CUSTOM_BASE_BRANCH = "main";
+    process.env.GH_AW_CHECKOUT_MANIFEST = manifestPath;
+    process.env.GH_AW_SAFE_OUTPUTS_CONFIG_PATH = configPath;
+    try {
+      await preStagePatch(entry, 0, workspace);
+    } finally {
+      require("./checkout_manifest.cjs")._resetCache();
+      if (prevBase === undefined) delete process.env.GH_AW_CUSTOM_BASE_BRANCH;
+      else process.env.GH_AW_CUSTOM_BASE_BRANCH = prevBase;
+      if (prevManifest === undefined) delete process.env.GH_AW_CHECKOUT_MANIFEST;
+      else process.env.GH_AW_CHECKOUT_MANIFEST = prevManifest;
+      if (prevConfig === undefined) delete process.env.GH_AW_SAFE_OUTPUTS_CONFIG_PATH;
+      else process.env.GH_AW_SAFE_OUTPUTS_CONFIG_PATH = prevConfig;
+    }
+
+    // The branch + commit + file land in the side-repo subdirectory...
+    expect(git(["rev-parse", "--abbrev-ref", "HEAD"], subdir).trim()).toBe(branchName);
+    expect(git(["branch", "--list", branchName], subdir)).toContain(branchName);
+    expect(fs.existsSync(path.join(subdir, fileToAdd))).toBe(true);
+
+    // ...and NOT in the main repo root (which stays on its seed branch).
+    expect(git(["rev-parse", "--abbrev-ref", "HEAD"], workspace).trim()).toBe("main");
+    expect(git(["branch", "--list", branchName], workspace).trim()).toBe("");
+    expect(fs.existsSync(path.join(workspace, fileToAdd))).toBe(false);
+  });
+
   it("derives push_to_pull_request_branch branch from pull_request event payload", async () => {
     const workspace = makeTempDir("gh-aw-prestage-push-pr-");
     initRepo(workspace, "main");