diff --git a/packages/paperclip-runner/package.json b/packages/paperclip-runner/package.json
index f850a302394..eae1c1610d1 100644
--- a/packages/paperclip-runner/package.json
+++ b/packages/paperclip-runner/package.json
@@ -80,7 +80,7 @@
     "typecheck:browser": "tsc -p tsconfig.browser.json --noEmit",
     "test": "pnpm run test:typescript && pnpm run test:rust",
     "test:typescript": "pnpm run test:typescript:prep && vitest run",
-    "test:typescript:prep": "pnpm run ensure:eval-build-deps && pnpm run build:rust && node --test test/protocol-contract.test.mjs test/acpx-sidecar-contract.test.mjs test/acpx-codex-package-contract.test.mjs test/acpx-message-boundaries-package-contract.test.mjs test/acpx-rich-extensions-package-contract.test.mjs test/acpx-pi-receipt-package-contract.test.mjs test/acpx-response-delivery-package-contract.test.mjs scripts/candidate-provider-pack.test.mjs scripts/aws-agentcore-provisioning.test.mjs scripts/build-verified-provider-entrypoints.test.mjs scripts/local-provider-smoke-environment.test.mjs scripts/materialize-opencode-binary.test.mjs scripts/installed-package-pack.test.mjs scripts/runner-package-executable.test.mjs",
+    "test:typescript:prep": "pnpm run ensure:eval-build-deps && pnpm run build:rust && node --test test/protocol-contract.test.mjs test/acpx-sidecar-contract.test.mjs test/acpx-codex-package-contract.test.mjs test/acpx-message-boundaries-package-contract.test.mjs test/acpx-rich-extensions-package-contract.test.mjs test/acpx-pi-receipt-package-contract.test.mjs test/acpx-response-delivery-package-contract.test.mjs scripts/candidate-provider-pack.test.mjs scripts/aws-agentcore-provisioning.test.mjs scripts/build-verified-provider-entrypoints.test.mjs scripts/local-provider-smoke-environment.test.mjs scripts/materialize-opencode-binary.test.mjs scripts/installed-package-pack.test.mjs scripts/runner-package-executable.test.mjs scripts/stage-runner-binary.test.mjs",
     "test:typescript:vitest": "node ./scripts/run-pr-vitest-lane.mjs",
     "test:rust": "cargo test --release --manifest-path runner/Cargo.toml --locked --workspace",
     "test:codex": "cargo test --manifest-path runner/Cargo.toml --locked -p paperclip-runner-core --test codex_provider",
diff --git a/packages/paperclip-runner/scripts/stage-runner-binary.mjs b/packages/paperclip-runner/scripts/stage-runner-binary.mjs
index d75f4bbb6de..48643ea7083 100644
--- a/packages/paperclip-runner/scripts/stage-runner-binary.mjs
+++ b/packages/paperclip-runner/scripts/stage-runner-binary.mjs
@@ -1,24 +1,38 @@
 import { execFile } from "node:child_process";
-import { chmod, copyFile, mkdir } from "node:fs/promises";
+import { constants } from "node:fs";
+import { chmod, copyFile, mkdir, mkdtemp, rename, rm } from "node:fs/promises";
 import path from "node:path";
 import { promisify } from "node:util";
 import { fileURLToPath } from "node:url";
 
 const execFileAsync = promisify(execFile);
 
-const packageRoot = path.resolve(path.dirname(fileURLToPath(import.meta.url)), "..");
-const executable = process.platform === "win32" ? "paperclip-runnerd.exe" : "paperclip-runnerd";
-const source = path.join(packageRoot, "runner", "target", "release", executable);
-const destinationDirectory = path.join(packageRoot, "dist", "bin");
-const destination = path.join(destinationDirectory, executable);
+export async function stageRunnerBinary(source, destination) {
+  const destinationDirectory = path.dirname(destination);
+  await mkdir(destinationDirectory, { recursive: true });
+  const stagingDirectory = await mkdtemp(path.join(destinationDirectory, ".runnerd-stage-"));
+  const staged = path.join(stagingDirectory, path.basename(destination));
+  try {
+    await copyFile(source, staged, constants.COPYFILE_EXCL);
+    if (process.platform !== "win32") await chmod(staged, 0o755);
+    // Sign the new inode before publication. Replacing the pathname atomically
+    // preserves a running old executable instead of truncating its live inode.
+    if (process.platform === "darwin") {
+      await execFileAsync("codesign", ["--force", "--sign", "-", staged], { timeout: 30_000 });
+      await execFileAsync("codesign", ["--verify", "--strict", staged], { timeout: 30_000 });
+    }
+    await rename(staged, destination);
+  } finally {
+    // This fresh directory is the only cleanup target, never the destination.
+    await rm(stagingDirectory, { recursive: true, force: true });
+  }
+}
 
-await mkdir(destinationDirectory, { recursive: true });
-await copyFile(source, destination);
-if (process.platform !== "win32") await chmod(destination, 0o755);
-// Rust's linker emits an ad-hoc Mach-O signature. Copying that executable to
-// its package location preserves the bytes but can leave the kernel rejecting
-// the new inode with SIGKILL. Re-sign the staged inode so local packaged-runner
-// evals execute the same artifact that was just built.
-if (process.platform === "darwin") {
-  await execFileAsync("codesign", ["--force", "--sign", "-", destination]);
+if (process.argv[1] && path.resolve(process.argv[1]) === fileURLToPath(import.meta.url)) {
+  const packageRoot = path.resolve(path.dirname(fileURLToPath(import.meta.url)), "..");
+  const executable = process.platform === "win32" ? "paperclip-runnerd.exe" : "paperclip-runnerd";
+  await stageRunnerBinary(
+    path.join(packageRoot, "runner", "target", "release", executable),
+    path.join(packageRoot, "dist", "bin", executable),
+  );
 }
diff --git a/packages/paperclip-runner/scripts/stage-runner-binary.test.mjs b/packages/paperclip-runner/scripts/stage-runner-binary.test.mjs
new file mode 100644
index 00000000000..81696b8ba65
--- /dev/null
+++ b/packages/paperclip-runner/scripts/stage-runner-binary.test.mjs
@@ -0,0 +1,83 @@
+import assert from "node:assert/strict";
+import { spawn } from "node:child_process";
+import { once } from "node:events";
+import { mkdtemp, readFile, readdir, rm, stat, writeFile } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import path from "node:path";
+import { test } from "node:test";
+import { stageRunnerBinary } from "./stage-runner-binary.mjs";
+
+async function withOwnedChildren(root, action) {
+  const owned = [];
+  const start = (command, args) => {
+    const child = spawn(command, args, { env: { PATH: "/usr/bin:/bin" }, stdio: "ignore" });
+    // close follows both exit and spawn error. A failed second spawn must not
+    // interrupt retirement of the first still-running executable.
+    const closed = new Promise(resolve => child.once("close", resolve));
+    const spawned = once(child, "spawn");
+    void spawned.catch(() => {});
+    owned.push({ child, closed });
+    return { child, spawned, closed };
+  };
+  try { return await action(start); }
+  finally {
+    try {
+      const results = await Promise.allSettled(owned.map(async ({ child, closed }) => {
+        if (child.pid && child.exitCode === null && child.signalCode === null) child.kill("SIGKILL");
+        await closed;
+      }));
+      const failures = results.filter(result => result.status === "rejected");
+      if (failures.length) throw new AggregateError(failures.map(result => result.reason), "Owned test child cleanup failed");
+    } finally { await rm(root, { recursive: true, force: true }); }
+  }
+}
+
+test("atomically publishes while the previous executable is running", { skip: process.platform === "win32", timeout: 15_000 }, async () => {
+  const root = await mkdtemp(path.join(tmpdir(), "runnerd-stage-test-"));
+  const destination = path.join(root, "paperclip-runnerd");
+  await withOwnedChildren(root, async start => {
+    await stageRunnerBinary("/bin/sleep", destination);
+    const previous = await stat(destination);
+    const old = start(destination, ["30"]);
+    await old.spawned;
+    await stageRunnerBinary("/bin/sleep", destination);
+    const published = await stat(destination);
+    assert.notEqual(published.ino, previous.ino);
+    assert.equal(published.mode & 0o777, 0o755);
+    assert.equal(old.child.exitCode, null);
+    assert.equal(old.child.signalCode, null);
+    assert.deepEqual(await readdir(root), ["paperclip-runnerd"]);
+    const next = start(destination, ["0"]);
+    await next.spawned; await next.closed;
+    assert.equal(next.child.exitCode, 0);
+  });
+});
+
+test("a second spawn error still retires the live old child and removes its fixture", { skip: process.platform === "win32", timeout: 15_000 }, async () => {
+  const root = await mkdtemp(path.join(tmpdir(), "runnerd-stage-spawn-failure-"));
+  let old;
+  await assert.rejects(withOwnedChildren(root, async start => {
+    old = start("/bin/sleep", ["30"]); await old.spawned;
+    const failed = start(path.join(root, "missing-executable"), []);
+    await failed.spawned;
+  }), { code: "ENOENT" });
+  assert.notEqual(old.child.signalCode, null);
+  await assert.rejects(stat(root), { code: "ENOENT" });
+});
+
+test("failed preparation preserves the published bytes and mode", async () => {
+  const root = await mkdtemp(path.join(tmpdir(), "runnerd-stage-failure-"));
+  const destination = path.join(root, "paperclip-runnerd");
+  try {
+    await writeFile(destination, "previous build", { mode: 0o755 });
+    const before = await stat(destination);
+    await assert.rejects(stageRunnerBinary(path.join(root, "absent-source"), destination), { code: "ENOENT" });
+    assert.equal(await readFile(destination, "utf8"), "previous build");
+    const after = await stat(destination);
+    assert.equal(after.ino, before.ino);
+    assert.equal(after.mode, before.mode);
+    assert.deepEqual(await readdir(root), ["paperclip-runnerd"]);
+  } finally {
+    await rm(root, { recursive: true, force: true });
+  }
+});