diff --git a/packages/paperclip-runner/scripts/generate-semantic-contracts.mjs b/packages/paperclip-runner/scripts/generate-semantic-contracts.mjs
index 684e5a2bef..8721a1423c 100644
--- a/packages/paperclip-runner/scripts/generate-semantic-contracts.mjs
+++ b/packages/paperclip-runner/scripts/generate-semantic-contracts.mjs
@@ -3,10 +3,12 @@ import { fileURLToPath } from "node:url";
 import { dirname, resolve } from "node:path";
 import { serializeCapabilityGeneratedSemanticContracts } from "../dist/semantic-tools/provider-neutral.js";
 import { PAPERCLIP_RUNNER_BUILD_METADATA } from "../dist/evals/build-metadata.js";
+import { buildProtocolManifest } from "./generate-protocol-manifest.mjs";
 
 const packageRoot = resolve(dirname(fileURLToPath(import.meta.url)), "..");
 const outputPath = resolve(packageRoot, "generated/capability/semantic-tool-contracts.json");
 const generated = serializeCapabilityGeneratedSemanticContracts();
+const manifestPath = resolve(packageRoot, "protocol/manifest.json");
 // This is an explicitly seeded schema fixture, not retained live evidence.
 // Keep its advertised catalog identity synchronized with the shipped contracts.
 const fixturePath = resolve(packageRoot, "protocol/fixtures/evals/native-execution-seeded.json");
@@ -20,7 +22,12 @@ if (process.argv.includes("--check")) {
     process.exitCode = 1;
   }
   if (!fixtureCurrent) {
-    process.stderr.write("native-execution-seeded.json catalog is stale; run generate:semantic-contracts and generate:protocol-manifest\n");
+    process.stderr.write("native-execution-seeded.json catalog is stale; run generate:semantic-contracts\n");
+    process.exitCode = 1;
+  }
+  const manifest = `${JSON.stringify(await buildProtocolManifest(), null, 2)}\n`;
+  if (await readFile(manifestPath, "utf8").catch(() => "") !== manifest) {
+    process.stderr.write("protocol/manifest.json is stale; run generate:semantic-contracts\n");
     process.exitCode = 1;
   }
 } else {
@@ -29,5 +36,7 @@ if (process.argv.includes("--check")) {
     fixture.runner.catalogSha256 = PAPERCLIP_RUNNER_BUILD_METADATA.semanticCatalog.sha256;
     await writeFile(fixturePath, `${JSON.stringify(fixture, null, 2)}\n`);
   }
-  process.stdout.write(`wrote ${outputPath}\n`);
+  // The manifest hashes fixture bytes, so refresh it after the seeded catalog.
+  await writeFile(manifestPath, `${JSON.stringify(await buildProtocolManifest(), null, 2)}\n`);
+  process.stdout.write(`wrote ${outputPath} and ${manifestPath}\n`);
 }
diff --git a/packages/paperclip-runner/src/evals/native-execution.test.ts b/packages/paperclip-runner/src/evals/native-execution.test.ts
index e78760f63b..9700ae81b0 100644
--- a/packages/paperclip-runner/src/evals/native-execution.test.ts
+++ b/packages/paperclip-runner/src/evals/native-execution.test.ts
@@ -1,4 +1,9 @@
-import { readFile } from "node:fs/promises";
+import { execFile } from "node:child_process";
+import { cp, mkdir, mkdtemp, readFile, rm, symlink, writeFile } from "node:fs/promises";
+import { tmpdir } from "node:os";
+import { join } from "node:path";
+import { fileURLToPath } from "node:url";
+import { promisify } from "node:util";
 import Ajv2020 from "ajv/dist/2020.js";
 import { describe, expect, it } from "vitest";
 
@@ -10,8 +15,47 @@ import {
   parsePaperclipNativeExecution,
 } from "./native-execution.js";
 import { PAPERCLIP_RUNNER_BUILD_METADATA } from "./build-metadata.js";
+import { serializeCapabilityGeneratedSemanticContracts } from "../semantic-tools/provider-neutral.js";
 
 describe("paperclip-runner/native-execution/v1", () => {
+  it("refreshes a stale seeded catalog and its manifest with one semantic generator invocation", async () => {
+    const root = await mkdtemp(join(tmpdir(), "paperclip-semantic-generator-"));
+    const packageRoot = fileURLToPath(new URL("../../", import.meta.url));
+    const run = promisify(execFile);
+    try {
+      await cp(join(packageRoot, "protocol"), join(root, "protocol"), { recursive: true });
+      await mkdir(join(root, "scripts"));
+      for (const script of ["generate-semantic-contracts.mjs", "generate-protocol-manifest.mjs", "protocol-contract.mjs"]) {
+        await cp(join(packageRoot, "scripts", script), join(root, "scripts", script));
+      }
+      await symlink(join(packageRoot, "node_modules"), join(root, "node_modules"), "dir");
+      await writeFile(join(root, "package.json"), JSON.stringify({ type: "module" }));
+      await mkdir(join(root, "dist/semantic-tools"), { recursive: true });
+      await mkdir(join(root, "dist/evals"), { recursive: true });
+      await mkdir(join(root, "generated/capability"), { recursive: true });
+      // Materialize current source exports without requiring a previous package build.
+      await writeFile(join(root, "dist/semantic-tools/provider-neutral.js"),
+        `export const serializeCapabilityGeneratedSemanticContracts = () => ${JSON.stringify(serializeCapabilityGeneratedSemanticContracts())};`);
+      await writeFile(join(root, "dist/evals/build-metadata.js"),
+        `export const PAPERCLIP_RUNNER_BUILD_METADATA = ${JSON.stringify(PAPERCLIP_RUNNER_BUILD_METADATA)};`);
+      const fixturePath = join(root, "protocol/fixtures/evals/native-execution-seeded.json");
+      const fixture = JSON.parse(await readFile(fixturePath, "utf8"));
+      fixture.runner.catalogSha256 = `sha256:${"0".repeat(64)}`;
+      await writeFile(fixturePath, `${JSON.stringify(fixture, null, 2)}\n`);
+      // Leave a stale manifest even if the restored fixture bytes happen to match the original.
+      await writeFile(join(root, "protocol/manifest.json"), "{}\n");
+      const generator = join(root, "scripts/generate-semantic-contracts.mjs");
+      await expect(run(process.execPath, [generator, "--check"])).rejects.toThrow();
+      await run(process.execPath, [generator]);
+      expect(JSON.parse(await readFile(fixturePath, "utf8")).runner.catalogSha256)
+        .toBe(PAPERCLIP_RUNNER_BUILD_METADATA.semanticCatalog.sha256);
+      await run(process.execPath, [generator, "--check"]);
+      await run(process.execPath, [join(root, "scripts/generate-protocol-manifest.mjs"), "--check"]);
+    } finally {
+      await rm(root, { recursive: true, force: true });
+    }
+  });
+
   it("keeps the shipped seeded fixture valid against the published JSON Schema", async () => {
     const ajv = new Ajv2020({ allErrors: true, strict: false });
     for (const schema of Object.values(prpSchemaBundle)) ajv.addSchema(schema);