fix(ci): resolve ubuntu check regressions

scripts/tests/generate-skills.test.mjs

@@ -9,7 +9,7 @@
  */
 
 import assert from "node:assert/strict";
-import { mkdtemp, mkdir, writeFile, rm } from "node:fs/promises";
+import { mkdtemp, mkdir, writeFile, rm, readFile } from "node:fs/promises";
 import crypto from "node:crypto";
 import { tmpdir } from "node:os";
 import path from "node:path";
@@ -25,6 +25,7 @@ const {
   makePackageJsonContent,
   getGeneratedRoots,
   buildManifest,
+  generateSkills,
 } = await import(`${SCRIPTS_DIR}/generate-skills.mjs`);
 
 // ── detectFileType ────────────────────────────────────────────────────────
@@ -348,3 +349,17 @@ test("buildManifest: sha256 matches actual file content", async () => {
     await rm(dir, { recursive: true, force: true });
   }
 });
+
+test("generateSkills: clears pre-existing empty generated directories without EISDIR", async () => {
+  const targetRoot = await mkdtemp(path.join(tmpdir(), "generate-skills-target-"));
+  try {
+    await mkdir(path.join(targetRoot, "skills", "create-plan", "claude-code", "templates"), { recursive: true });
+
+    await generateSkills(path.resolve(SCRIPTS_DIR, ".."), { targetRoot });
+
+    await readFile(path.join(targetRoot, "skills", "create-plan", "claude-code", "SKILL.md"), "utf8");
+    await readFile(path.join(targetRoot, "skills", "create-plan", "claude-code", "templates", "milestone-plan.md"), "utf8");
+  } finally {
+    await rm(targetRoot, { recursive: true, force: true });
+  }
+});