diff --git a/scripts/generate-skills.mjs b/scripts/generate-skills.mjs
index a808062..fcf6697 100644
--- a/scripts/generate-skills.mjs
+++ b/scripts/generate-skills.mjs
@@ -512,7 +512,7 @@ async function clearGeneratedRoot(rootDir) {
       // Remove the directory only if nothing protected remains inside it.
       const remaining = await readdir(fullPath).catch(() => []);
       if (remaining.length === 0) {
-        await rm(fullPath, { force: true });
+        await rm(fullPath, { recursive: true, force: true });
       }
     } else {
       await rm(fullPath, { force: true });
diff --git a/scripts/manage-skills.mjs b/scripts/manage-skills.mjs
index c63bcf2..511588a 100755
--- a/scripts/manage-skills.mjs
+++ b/scripts/manage-skills.mjs
@@ -203,6 +203,15 @@ async function interactiveAnswers({ dryRun = false } = {}) {
   }
 }
 
+async function readAnswers(source) {
+  if (source === "-") {
+    let content = "";
+    for await (const chunk of input) content += chunk;
+    return JSON.parse(content);
+  }
+  return JSON.parse(await readFile(path.resolve(source), "utf8"));
+}
+
 async function main() {
   const args = parseArgs(process.argv.slice(2));
   if (args.help) {
@@ -216,7 +225,7 @@ async function main() {
 
   let answers;
   if (args.answers) {
-    answers = JSON.parse(await readFile(path.resolve(args.answers), "utf8"));
+    answers = await readAnswers(args.answers);
   } else {
     answers = await buildCliSelection(args);
   }
diff --git a/scripts/tests/generate-skills.test.mjs b/scripts/tests/generate-skills.test.mjs
index 90aa27a..1628adf 100644
--- a/scripts/tests/generate-skills.test.mjs
+++ b/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 });
+  }
+});
diff --git a/scripts/tests/skill-manager-core.test.mjs b/scripts/tests/skill-manager-core.test.mjs
index b25e82a..199273d 100644
--- a/scripts/tests/skill-manager-core.test.mjs
+++ b/scripts/tests/skill-manager-core.test.mjs
@@ -404,7 +404,7 @@ test("cli exits without confirmation when no operations are planned", () => {
   const output = execFileSync(process.execPath, [
     path.join(REPO_ROOT, "scripts", "manage-skills.mjs"),
     "--answers",
-    "/dev/stdin",
+    "-",
   ], {
     cwd: REPO_ROOT,
     encoding: "utf8",
diff --git a/skills/reviewer-runtime/pi/.generated-manifest.json b/skills/reviewer-runtime/pi/.generated-manifest.json
index 765b757..cb54e6f 100644
--- a/skills/reviewer-runtime/pi/.generated-manifest.json
+++ b/skills/reviewer-runtime/pi/.generated-manifest.json
@@ -13,7 +13,7 @@
       "path": "run-review.sh",
       "kind": "file",
       "mode": "755",
-      "sha256": "c5e4fd082ee1a14059183d2cd2c45653e16d63821edf9cf82e548c9307d29e75"
+      "sha256": "1af5076f0e4451c0870109216ee5780553ef7d402ec1359f38afefdaf53627c1"
     }
   ]
 }
diff --git a/skills/reviewer-runtime/pi/run-review.sh b/skills/reviewer-runtime/pi/run-review.sh
index 853b653..27a88cb 100755
--- a/skills/reviewer-runtime/pi/run-review.sh
+++ b/skills/reviewer-runtime/pi/run-review.sh
@@ -145,7 +145,7 @@ kill_child_process_group() {
   fi
 }
 
-# shellcheck disable=SC2329
+# shellcheck disable=SC2317,SC2329
 handle_signal() {
   local signal_name=$1
   INTERRUPTED=1
diff --git a/skills/reviewer-runtime/run-review.sh b/skills/reviewer-runtime/run-review.sh
index 40f102b..8bdafc6 100755
--- a/skills/reviewer-runtime/run-review.sh
+++ b/skills/reviewer-runtime/run-review.sh
@@ -144,7 +144,7 @@ kill_child_process_group() {
   fi
 }
 
-# shellcheck disable=SC2329
+# shellcheck disable=SC2317,SC2329
 handle_signal() {
   local signal_name=$1
   INTERRUPTED=1