diff --git a/package.json b/package.json
index 89ef88fd09..0a8ec3fb41 100644
--- a/package.json
+++ b/package.json
@@ -16,7 +16,7 @@
     "build-storybook": "pnpm --filter @paperclipai/ui build-storybook",
     "build": "pnpm run preflight:workspace-links && pnpm -r build",
     "typecheck": "pnpm run preflight:workspace-links && pnpm -r typecheck",
-    "typecheck:build-gaps": "pnpm run preflight:workspace-links && node scripts/run-typecheck-build-gaps.mjs",
+    "typecheck:build-gaps": "pnpm run preflight:workspace-links && pnpm --filter @paperclipai/plugin-sdk ensure-build-deps && pnpm --filter @paperclipai/server build && node scripts/run-typecheck-build-gaps.mjs",
     "test": "pnpm run test:run",
     "test:watch": "pnpm run preflight:workspace-links && vitest",
     "test:run": "pnpm run preflight:workspace-links && node scripts/run-vitest-stable.mjs",
diff --git a/scripts/__tests__/run-typecheck-build-gaps.test.mjs b/scripts/__tests__/run-typecheck-build-gaps.test.mjs
new file mode 100644
index 0000000000..f3d1bc0799
--- /dev/null
+++ b/scripts/__tests__/run-typecheck-build-gaps.test.mjs
@@ -0,0 +1,60 @@
+import assert from "node:assert/strict";
+import { spawnSync } from "node:child_process";
+import { mkdirSync, mkdtempSync, rmSync, writeFileSync } from "node:fs";
+import { tmpdir } from "node:os";
+import path from "node:path";
+import test from "node:test";
+
+const script = new URL("../run-typecheck-build-gaps.mjs", import.meta.url).pathname;
+
+function createFixtureRepo() {
+  return mkdtempSync(path.join(tmpdir(), "run-typecheck-build-gaps-test-"));
+}
+
+function writeFixtureFile(root, relativePath, body = "fixture") {
+  const filePath = path.join(root, relativePath);
+  mkdirSync(path.dirname(filePath), { recursive: true });
+  writeFileSync(filePath, body);
+}
+
+function runRuntimeAssetGuard(root) {
+  return spawnSync(process.execPath, [script, "--runtime-assets-only"], {
+    cwd: root,
+    encoding: "utf8",
+  });
+}
+
+test("passes when all source runtime assets are present in dist", () => {
+  const root = createFixtureRepo();
+  try {
+    writeFixtureFile(root, "server/src/built-ins/agents/default.md");
+    writeFixtureFile(root, "server/dist/built-ins/agents/default.md");
+    writeFixtureFile(root, "server/src/onboarding-assets/welcome.txt");
+    writeFixtureFile(root, "server/dist/onboarding-assets/welcome.txt");
+    writeFixtureFile(root, "server/src/built-ins/ignored.ts");
+
+    const result = runRuntimeAssetGuard(root);
+
+    assert.equal(result.status, 0, result.stderr);
+    assert.match(result.stdout, /server runtime assets present in dist: 2 file\(s\)/);
+    assert.equal(result.stderr, "");
+  } finally {
+    rmSync(root, { recursive: true, force: true });
+  }
+});
+
+test("fails with the missing source asset and expected dist path", () => {
+  const root = createFixtureRepo();
+  try {
+    writeFixtureFile(root, "server/src/built-ins/agents/default.md");
+
+    const result = runRuntimeAssetGuard(root);
+
+    assert.notEqual(result.status, 0);
+    assert.match(result.stderr, /Missing server runtime asset\(s\) in dist/);
+    assert.match(result.stderr, /source: server\/src\/built-ins\/agents\/default\.md/);
+    assert.match(result.stderr, /expected dist: server\/dist\/built-ins\/agents\/default\.md/);
+  } finally {
+    rmSync(root, { recursive: true, force: true });
+  }
+});
diff --git a/scripts/run-typecheck-build-gaps.mjs b/scripts/run-typecheck-build-gaps.mjs
index e149990bf6..9c2320969e 100644
--- a/scripts/run-typecheck-build-gaps.mjs
+++ b/scripts/run-typecheck-build-gaps.mjs
@@ -1,9 +1,17 @@
 #!/usr/bin/env node
-import { readFileSync } from "node:fs";
+import { existsSync, readFileSync, readdirSync, statSync } from "node:fs";
 import path from "node:path";
 import { spawnSync } from "node:child_process";
 
 const repoRoot = process.cwd();
+const args = new Set(process.argv.slice(2));
+const allowedArgs = new Set(["--runtime-assets-only"]);
+
+for (const arg of args) {
+  if (!allowedArgs.has(arg)) {
+    fail(`Unknown argument: ${arg}`);
+  }
+}
 
 function fail(message) {
   console.error(`[typecheck:build-gaps] ${message}`);
@@ -30,6 +38,91 @@ function readJson(filePath) {
   return JSON.parse(readFileSync(filePath, "utf8"));
 }
 
+function formatPath(filePath) {
+  return path.relative(repoRoot, filePath).split(path.sep).join("/");
+}
+
+function listFilesRecursive(rootDir) {
+  if (!existsSync(rootDir)) {
+    return [];
+  }
+
+  const files = [];
+  const entries = readdirSync(rootDir, { withFileTypes: true }).sort((left, right) =>
+    left.name.localeCompare(right.name),
+  );
+
+  for (const entry of entries) {
+    const entryPath = path.join(rootDir, entry.name);
+    if (entry.isDirectory()) {
+      files.push(...listFilesRecursive(entryPath));
+      continue;
+    }
+
+    if (entry.isFile()) {
+      files.push(entryPath);
+    }
+  }
+
+  return files;
+}
+
+function isRuntimeAsset(filePath) {
+  const ext = path.extname(filePath).toLowerCase();
+  return !new Set([".ts", ".tsx", ".mts", ".cts", ".js", ".jsx", ".mjs", ".cjs"]).has(ext);
+}
+
+function checkServerRuntimeAssets() {
+  const runtimeAssetTrees = [
+    {
+      sourceDir: path.join(repoRoot, "server", "src", "built-ins"),
+      distDir: path.join(repoRoot, "server", "dist", "built-ins"),
+    },
+    {
+      sourceDir: path.join(repoRoot, "server", "src", "onboarding-assets"),
+      distDir: path.join(repoRoot, "server", "dist", "onboarding-assets"),
+    },
+  ];
+  const missingAssets = [];
+  let checkedCount = 0;
+
+  for (const assetTree of runtimeAssetTrees) {
+    const sourceAssets = listFilesRecursive(assetTree.sourceDir).filter(isRuntimeAsset);
+    checkedCount += sourceAssets.length;
+
+    for (const sourcePath of sourceAssets) {
+      const relativeAssetPath = path.relative(assetTree.sourceDir, sourcePath);
+      const distPath = path.join(assetTree.distDir, relativeAssetPath);
+
+      if (!existsSync(distPath) || !statSync(distPath).isFile()) {
+        missingAssets.push({ sourcePath, distPath });
+      }
+    }
+  }
+
+  if (missingAssets.length > 0) {
+    const missingList = missingAssets
+      .map(
+        ({ sourcePath, distPath }) =>
+          `  - source: ${formatPath(sourcePath)}\n    expected dist: ${formatPath(distPath)}`,
+      )
+      .join("\n");
+
+    fail(
+      `Missing server runtime asset(s) in dist:\n${missingList}\nRun pnpm --filter @paperclipai/server build and ensure source runtime asset trees are copied into dist.`,
+    );
+  }
+
+  console.log(
+    `[typecheck:build-gaps] server runtime assets present in dist: ${checkedCount} file(s)`,
+  );
+}
+
+if (args.has("--runtime-assets-only")) {
+  checkServerRuntimeAssets();
+  process.exit(0);
+}
+
 function listWorkspacePackages() {
   const result = spawnSync("pnpm", ["ls", "-r", "--depth", "-1", "--json"], {
     cwd: repoRoot,
@@ -82,12 +175,12 @@ console.log(
   `[typecheck:build-gaps] typechecking ${buildGapPackages.length} workspace(s): ${buildGapPackages.map(({ name }) => name).join(", ") || "(none)"}`,
 );
 
-if (buildGapPackages.length === 0) {
-  process.exit(0);
+if (buildGapPackages.length > 0) {
+  run("pnpm", ["--filter", "@paperclipai/plugin-sdk", "ensure-build-deps"]);
+
+  for (const workspacePkg of buildGapPackages) {
+    run("pnpm", ["--filter", workspacePkg.name, "typecheck"]);
+  }
 }
 
-run("pnpm", ["--filter", "@paperclipai/plugin-sdk", "ensure-build-deps"]);
-
-for (const workspacePkg of buildGapPackages) {
-  run("pnpm", ["--filter", workspacePkg.name, "typecheck"]);
-}
+checkServerRuntimeAssets();