Prevent stale-base signed replay from synthesizing unrelated changes; enforce policy on GraphQL payload

.github/skills/agentic-workflows/SKILL.md

@@ -12,6 +12,7 @@ This skill is a dispatcher: identify the task type, load the matching workflow p
 Read only the files you need:
 Load these files from `github/gh-aw` (they are not available locally).
 - `.github/aw/agentic-chat.md`
+- `.github/aw/agentic-workflows-mcp.md`
 - `.github/aw/asciicharts.md`
 - `.github/aw/campaign.md`
 - `.github/aw/charts-trending.md`
@@ -27,6 +28,7 @@ Load these files from `github/gh-aw` (they are not available locally).
 - `.github/aw/github-agentic-workflows.md`
 - `.github/aw/github-mcp-server.md`
 - `.github/aw/llms.md`
+- `.github/aw/mcp-clis.md`
 - `.github/aw/memory.md`
 - `.github/aw/messages.md`
 - `.github/aw/network.md`

actions/setup/js/create_pull_request.cjs

@@ -182,15 +182,16 @@ async function tryRecoverGitAmAddAddConflict(execApi) {
  * @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
+ * @param {string} [baseBranch] - Base branch name (used for iterative shallow-clone deepening)
  * @returns {Promise<void>}
  */
-async function applyBundleToBranch(bundleFilePath, branchName, originalAgentBranch, execApi) {
+async function applyBundleToBranch(bundleFilePath, branchName, originalAgentBranch, execApi, baseBranch) {
   let bundleBranchRef = `refs/heads/${originalAgentBranch || branchName}`;
   const bundleTargetRef = `refs/heads/${branchName}`;
   const bundleTempRef = createBundleTempRef(branchName);
 
   try {
-    await ensureFullHistoryForBundle(execApi);
+    await ensureFullHistoryForBundle(execApi, {}, { baseRef: baseBranch, bundleFilePath });
     core.info(`Applying bundle ${bundleFilePath} to ${bundleTargetRef} using temp ref ${bundleTempRef} from ${bundleBranchRef}`);
 
     // Fetch from bundle into a temporary ref, then update the target branch.
@@ -1478,7 +1479,7 @@ async function main(config = {}) {
         // unlike git format-patch which flattens history and drops merge resolution content.
         core.info(`Applying changes from bundle: ${bundleFilePath}`);
         try {
-          await applyBundleToBranch(bundleFilePath, branchName, originalAgentBranch, exec);
+          await applyBundleToBranch(bundleFilePath, branchName, originalAgentBranch, exec, baseBranch);
         } catch (bundleError) {
           core.error(`Failed to apply bundle: ${bundleError instanceof Error ? bundleError.message : String(bundleError)}`);
           return { success: false, error: "Failed to apply bundle" };
@@ -1502,6 +1503,7 @@ async function main(config = {}) {
               signedCommits,
               resolvedTemporaryIds,
               currentRepo: itemRepo,
+              validationConfig: config,
             });
             core.info("Changes pushed to branch (from bundle)");
 
@@ -1534,6 +1536,7 @@ async function main(config = {}) {
                   signedCommits,
                   resolvedTemporaryIds,
                   currentRepo: itemRepo,
+                  validationConfig: config,
                 });
                 core.info("Changes pushed to branch after bundle rewrite retry");
 
@@ -1865,6 +1868,7 @@ gh pr create --title '${title}' --base ${baseBranch} --head ${branchName} --repo
                 signedCommits,
                 resolvedTemporaryIds,
                 currentRepo: itemRepo,
+                validationConfig: config,
               });
               core.info("Changes pushed to branch");
 
@@ -2013,6 +2017,7 @@ ${patchPreview}`;
                 signedCommits,
                 resolvedTemporaryIds,
                 currentRepo: itemRepo,
+                validationConfig: config,
               });
               core.info("Empty branch pushed successfully");
 

actions/setup/js/create_pull_request.test.cjs

@@ -187,6 +187,17 @@ describe("create_pull_request - bundle transport shallow checkout", () => {
         if (cmd === "git" && args[0] === "rev-parse" && args[1] === "--is-shallow-repository") {
           return Promise.resolve({ exitCode: 0, stdout: "true\n", stderr: "" });
         }
+        if (cmd === "git" && args[0] === "bundle" && args[1] === "verify") {
+          // Declare a fake prerequisite so ensureFullHistoryForBundle proceeds to deepen.
+          return Promise.resolve({ exitCode: 1, stdout: "", stderr: `The bundle requires this ref:\n${"a".repeat(40)}\n` });
+        }
+        if (cmd === "git" && args[0] === "merge-base" && args[1] === "--is-ancestor") {
+          // Report prereq missing initially → iterative deepen kicks in; after the
+          // first deepen fetch we still report missing so the fallback --unshallow
+          // path is exercised. The default mock for exec() resolves successfully,
+          // so all 7 deepen steps complete instantly before the fallback fires.
+          return Promise.resolve({ exitCode: 1, stdout: "", stderr: "" });
+        }
         if (cmd === "git" && args[0] === "rev-list") {
           return Promise.resolve({ exitCode: 0, stdout: "1\n", stderr: "" });
         }
@@ -225,7 +236,7 @@ describe("create_pull_request - bundle transport shallow checkout", () => {
     vi.clearAllMocks();
   });
 
-  it("should fetch bundle without forcing an unshallow fetch", async () => {
+  it("should deepen origin/<base> before fetching bundle in shallow repositories", async () => {
     const patchPath = path.join(tempDir, "test.patch");
     fs.writeFileSync(
       patchPath,
@@ -264,8 +275,9 @@ index 0000000..abc1234
     expect(global.exec.exec).toHaveBeenCalledWith("git", ["update-ref", "refs/heads/feature/test", bundleTempRef]);
     expect(global.exec.exec).toHaveBeenCalledWith("git", ["reset", "--hard"]);
     const bundleFetchCallIndex = global.exec.getExecOutput.mock.calls.findIndex(([, args]) => Array.isArray(args) && args[0] === "fetch" && args[1] === bundlePath);
-    const unshallowCallIndex = global.exec.exec.mock.calls.findIndex(([, args]) => Array.isArray(args) && args[0] === "fetch" && args[1] === "--unshallow");
-    expect(unshallowCallIndex).toBe(-1);
+    // Iterative deepen replaces a single --unshallow: assert the first --deepen step ran.
+    const deepenCallIndex = global.exec.exec.mock.calls.findIndex(([, args]) => Array.isArray(args) && args[0] === "fetch" && typeof args[1] === "string" && args[1].startsWith("--deepen="));
+    expect(deepenCallIndex).toBeGreaterThanOrEqual(0);
     expect(bundleFetchCallIndex).toBeGreaterThanOrEqual(0);
   });
 

actions/setup/js/git_helpers.cjs

@@ -152,21 +152,108 @@ function hasMergeCommitsInRange(baseRef, headRef, options = {}) {
 }
 
 /**
- * Probe shallow-repository status before fetching a git bundle.
+ * Deepen sequence (per call to `git fetch --deepen=N`). Each value adds N
+ * commits to the existing shallow history. Total reachable depth after the
+ * final step is the sum of these values (~7850 commits).
+ */
+const BUNDLE_DEEPEN_STEPS = [50, 100, 200, 500, 1000, 2000, 4000];
+
+/**
+ * Extract prerequisite commit SHAs declared in a git bundle file.
+ *
+ * Runs `git bundle verify <file>` (with `ignoreReturnCode`) and parses the
+ * "The bundle requires this ref:" section as well as the
+ * "Repository lacks these prerequisite commits:" error block. Both formats
+ * list the prerequisite commit SHAs.
+ *
+ * @param {{ getExecOutput: Function }} execApi
+ * @param {string} bundleFilePath
+ * @param {Object} [options]
+ * @returns {Promise<string[]>} Deduplicated lowercase 40-char SHAs, or [] on failure.
+ */
+async function getBundlePrerequisites(execApi, bundleFilePath, options = {}) {
+  try {
+    const { stdout, stderr } = await execApi.getExecOutput("git", ["bundle", "verify", bundleFilePath], { ...options, ignoreReturnCode: true, silent: true });
+    const combined = `${stdout || ""}\n${stderr || ""}`;
+    const prereqs = new Set();
+    const lines = combined.split(/\r?\n/);
+    let inRequires = false;
+    for (const line of lines) {
+      if (/the bundle (requires|records) (this|these)/i.test(line)) {
+        inRequires = true;
+        continue;
+      }
+      if (/the bundle contains/i.test(line)) {
+        inRequires = false;
+        continue;
+      }
+      if (inRequires) {
+        const match = line.match(/\b([0-9a-f]{40})\b/i);
+        if (match) {
+          prereqs.add(match[1].toLowerCase());
+          continue;
+        }
+        if (line.trim() === "") {
+          inRequires = false;
+        }
+      }
+    }
+    // Also pick up "Repository lacks these prerequisite commits:" block.
+    for (const sha of extractBundlePrerequisiteCommits(combined)) {
+      prereqs.add(sha);
+    }
+    return [...prereqs];
+  } catch (error) {
+    core.debug(`getBundlePrerequisites failed: ${getErrorMessage(error)}`);
+    return [];
+  }
+}
+
+/**
+ * Check which of the given SHAs are NOT yet ancestors of `targetRef`.
+ *
+ * @param {{ getExecOutput: Function }} execApi
+ * @param {string[]} shas
+ * @param {string} targetRef
+ * @param {Object} [options]
+ * @returns {Promise<string[]>} SHAs still missing (not ancestors / not present).
+ */
+async function findMissingAncestors(execApi, shas, targetRef, options = {}) {
+  const missing = [];
+  for (const sha of shas) {
+    const { exitCode } = await execApi.getExecOutput("git", ["merge-base", "--is-ancestor", sha, targetRef], { ...options, ignoreReturnCode: true, silent: true });
+    if (exitCode !== 0) {
+      missing.push(sha);
+    }
+  }
+  return missing;
+}
+
+/**
+ * Probe shallow-repository status before fetching a git bundle, and deepen
+ * the local clone as needed so the bundle's prerequisite commits become
+ * reachable from `origin/<baseRef>`.
  *
  * Bundles generated from a commit range can declare prerequisite commits. A
- * depth-1 checkout may not contain those prerequisites, and `git fetch <bundle>`
- * can reject the bundle before the caller can update refs.
+ * shallow checkout (e.g. `fetch-depth: 20`) may not contain those prerequisites,
+ * and `git fetch <bundle>` will reject the bundle before the caller can update
+ * refs. On a high-churn monorepo, `git fetch --unshallow` is catastrophic — it
+ * downloads the entire history. Instead we iterate `git fetch origin <baseRef>
+ * --deepen=<N>` with progressively larger N until every declared prerequisite
+ * satisfies `git merge-base --is-ancestor <prereq> origin/<baseRef>`.
  *
- * IMPORTANT: Do not unshallow here. Full-history fetches are prohibitively
- * expensive for large monorepos. Callers recover from prerequisite failures by
- * fetching only the missing commit objects from origin and retrying.
+ * When `deepenOptions.baseRef` or `deepenOptions.bundleFilePath` is missing
+ * (legacy callers), the function falls back to the previous behavior of a
+ * single `git fetch --unshallow origin`.
  *
  * @param {{ getExecOutput: Function, exec: Function }} execApi - Exec API to run git commands.
  * @param {Object} [options] - Options passed through to exec calls.
+ * @param {Object} [deepenOptions]
+ * @param {string} [deepenOptions.baseRef] - Remote branch name to deepen (no `origin/` prefix).
+ * @param {string} [deepenOptions.bundleFilePath] - Path to the bundle file whose prerequisites must become reachable.
  * @returns {Promise<void>}
  */
-async function ensureFullHistoryForBundle(execApi, options = {}) {
+async function ensureFullHistoryForBundle(execApi, options = {}, deepenOptions = {}) {
   let stdout;
   try {
     ({ stdout } = await execApi.getExecOutput("git", ["rev-parse", "--is-shallow-repository"], options));
@@ -175,8 +262,56 @@ async function ensureFullHistoryForBundle(execApi, options = {}) {
     core.warning(`Could not determine shallow repository status; skipping full-history fetch probe: ${message}`);
     return;
   }
-  if (stdout.trim() === "true") {
-    core.info("Repository is shallow; skipping full-history fetch and relying on prerequisite recovery");
+  if (stdout.trim() !== "true") {
+    return;
+  }
+
+  const { baseRef, bundleFilePath } = deepenOptions || {};
+
+  // Legacy path: no base ref / bundle info known — fall back to a single
+  // unshallow. Callers in monorepos should always supply baseRef + bundleFilePath
+  // to get incremental deepening instead.
+  if (!baseRef || !bundleFilePath) {
+    core.info("Repository is shallow; fetching full history before bundle processing (no baseRef/bundle info; using --unshallow)");
+    await execApi.exec("git", ["fetch", "--unshallow", "origin"], options);
+    return;
+  }
+
+  const prereqs = await getBundlePrerequisites(execApi, bundleFilePath, options);
+  if (prereqs.length === 0) {
+    core.info("Bundle declares no prerequisites; no deepen required");
+    return;
+  }
+
+  const targetRef = `origin/${baseRef}`;
+  const alreadyMissing = await findMissingAncestors(execApi, prereqs, targetRef, options);
+  if (alreadyMissing.length === 0) {
+    core.info(`Bundle prerequisites already reachable from ${targetRef}; no deepen required`);
+    return;
+  }
+
+  core.info(`Repository is shallow; iteratively deepening ${targetRef} to satisfy ${alreadyMissing.length} bundle prerequisite commit(s)`);
+  let missing = alreadyMissing;
+  for (const depth of BUNDLE_DEEPEN_STEPS) {
+    core.info(`Fetching origin ${baseRef} with --deepen=${depth} (${missing.length} prerequisite(s) still missing)`);
+    try {
+      await execApi.exec("git", ["fetch", `--deepen=${depth}`, "origin", baseRef], options);
+    } catch (fetchError) {
+      core.warning(`git fetch --deepen=${depth} origin ${baseRef} failed: ${getErrorMessage(fetchError)}; aborting iterative deepen`);
+      break;
+    }
+    missing = await findMissingAncestors(execApi, prereqs, targetRef, options);
+    if (missing.length === 0) {
+      core.info(`Bundle prerequisites reachable after --deepen=${depth}`);
+      return;
+    }
+  }
+
+  core.warning(`Bundle prerequisites still not reachable after iterative deepen (${missing.length} remaining); attempting --unshallow as a last resort`);
+  try {
+    await execApi.exec("git", ["fetch", "--unshallow", "origin", baseRef], options);
+  } catch (unshallowError) {
+    core.warning(`Fallback --unshallow fetch failed: ${getErrorMessage(unshallowError)}; bundle apply may still fail`);
   }
 }
 

actions/setup/js/git_helpers.test.cjs

@@ -283,7 +283,7 @@ describe("git_helpers.cjs", () => {
   });
 
   describe("ensureFullHistoryForBundle", () => {
-    it("should not fetch full history when the repository is shallow", async () => {
+    it("should unshallow the repository when the repository is shallow", async () => {
       const { ensureFullHistoryForBundle } = await import("./git_helpers.cjs");
       const execApi = {
         getExecOutput: vi.fn().mockResolvedValue({ stdout: "true\n" }),
@@ -294,7 +294,7 @@ describe("git_helpers.cjs", () => {
       await ensureFullHistoryForBundle(execApi, options);
 
       expect(execApi.getExecOutput).toHaveBeenCalledWith("git", ["rev-parse", "--is-shallow-repository"], options);
-      expect(execApi.exec).not.toHaveBeenCalled();
+      expect(execApi.exec).toHaveBeenCalledWith("git", ["fetch", "--unshallow", "origin"], options);
     });
 
     it("should not fetch full history when the repository is not shallow", async () => {
@@ -338,6 +338,86 @@ describe("git_helpers.cjs", () => {
       expect(warning).toHaveBeenCalledTimes(1);
       expect(warning).toHaveBeenCalledWith("Could not determine shallow repository status; skipping full-history fetch probe: unknown failure");
     });
+
+    it("should iteratively deepen origin/<base> when bundle prereqs are known and shallow", async () => {
+      const { ensureFullHistoryForBundle } = await import("./git_helpers.cjs");
+      const prereq = "a".repeat(40);
+      let deepenCalls = 0;
+      const execApi = {
+        getExecOutput: vi.fn().mockImplementation((cmd, args) => {
+          if (args[0] === "rev-parse" && args[1] === "--is-shallow-repository") {
+            return Promise.resolve({ stdout: "true\n" });
+          }
+          if (args[0] === "bundle" && args[1] === "verify") {
+            return Promise.resolve({
+              stdout: "",
+              stderr: `The bundle requires this ref:\n${prereq}\n`,
+              exitCode: 1,
+            });
+          }
+          if (args[0] === "merge-base" && args[1] === "--is-ancestor") {
+            // Become reachable only after the second deepen fetch.
+            return Promise.resolve({ exitCode: deepenCalls >= 2 ? 0 : 1, stdout: "", stderr: "" });
+          }
+          return Promise.resolve({ exitCode: 0, stdout: "", stderr: "" });
+        }),
+        exec: vi.fn().mockImplementation((cmd, args) => {
+          if (args && args[0] === "fetch" && args[1] && args[1].startsWith("--deepen=")) {
+            deepenCalls++;
+          }
+          return Promise.resolve(0);
+        }),
+      };
+
+      await ensureFullHistoryForBundle(execApi, {}, { baseRef: "main", bundleFilePath: "/tmp/test.bundle" });
+
+      // Two deepen fetches before ancestry succeeds; no --unshallow.
+      const fetchCalls = execApi.exec.mock.calls.filter(c => c[1] && c[1][0] === "fetch");
+      expect(fetchCalls.length).toBe(2);
+      expect(fetchCalls[0][1]).toEqual(["fetch", "--deepen=50", "origin", "main"]);
+      expect(fetchCalls[1][1]).toEqual(["fetch", "--deepen=100", "origin", "main"]);
+      expect(execApi.exec).not.toHaveBeenCalledWith("git", ["fetch", "--unshallow", "origin"], expect.anything());
+    });
+
+    it("should skip deepening when bundle declares no prerequisites", async () => {
+      const { ensureFullHistoryForBundle } = await import("./git_helpers.cjs");
+      const execApi = {
+        getExecOutput: vi.fn().mockImplementation((cmd, args) => {
+          if (args[0] === "rev-parse") return Promise.resolve({ stdout: "true\n" });
+          if (args[0] === "bundle" && args[1] === "verify") {
+            return Promise.resolve({ stdout: "The bundle contains this ref:\ndeadbeef refs/heads/x\n", stderr: "", exitCode: 0 });
+          }
+          return Promise.resolve({ exitCode: 0, stdout: "", stderr: "" });
+        }),
+        exec: vi.fn().mockResolvedValue(0),
+      };
+
+      await ensureFullHistoryForBundle(execApi, {}, { baseRef: "main", bundleFilePath: "/tmp/test.bundle" });
+
+      expect(execApi.exec).not.toHaveBeenCalled();
+    });
+
+    it("should skip deepening when prereqs are already reachable from origin/<base>", async () => {
+      const { ensureFullHistoryForBundle } = await import("./git_helpers.cjs");
+      const prereq = "b".repeat(40);
+      const execApi = {
+        getExecOutput: vi.fn().mockImplementation((cmd, args) => {
+          if (args[0] === "rev-parse") return Promise.resolve({ stdout: "true\n" });
+          if (args[0] === "bundle" && args[1] === "verify") {
+            return Promise.resolve({ stdout: `The bundle requires this ref:\n${prereq}\n`, stderr: "", exitCode: 0 });
+          }
+          if (args[0] === "merge-base" && args[1] === "--is-ancestor") {
+            return Promise.resolve({ exitCode: 0, stdout: "", stderr: "" });
+          }
+          return Promise.resolve({ exitCode: 0, stdout: "", stderr: "" });
+        }),
+        exec: vi.fn().mockResolvedValue(0),
+      };
+
+      await ensureFullHistoryForBundle(execApi, {}, { baseRef: "main", bundleFilePath: "/tmp/test.bundle" });
+
+      expect(execApi.exec).not.toHaveBeenCalled();
+    });
   });
 
   describe("isShallowOrSparseCheckout", () => {