diff --git a/scripts/check-skill-frontmatter.mjs b/scripts/check-skill-frontmatter.mjs
index 883892c..83e7890 100644
--- a/scripts/check-skill-frontmatter.mjs
+++ b/scripts/check-skill-frontmatter.mjs
@@ -1,8 +1,16 @@
 #!/usr/bin/env node
-// Fails when any skills/*/SKILL.md has frontmatter that a strict YAML parser rejects,
-// or that lacks a non-empty `name` matching its folder or a non-empty `description`.
-// Agents parse the frontmatter with a real YAML parser and silently drop a skill that
-// fails, so this is the only place the defect becomes visible.
+// Fails when a skill's frontmatter is something a strict YAML parser rejects, or lacks a
+// non-empty `name` matching its folder or a non-empty `description`. Agents parse the
+// frontmatter with a real YAML parser and silently drop a skill that fails, so this is
+// the only place the defect becomes visible.
+//
+// The plugin ships the index shape: `skills/` holds one skill, `using-unity`, whose
+// SKILL.md lists every skill, and each skill is `skills/using-unity/references/<name>/<name>.md`
+// (renamed from SKILL.md so agents don't register it on its own). The publish job in
+// unity/skills writes that layout. When `skills/using-unity` exists this checks it: the
+// index skill's own frontmatter, each skill's file, that `skills/` holds nothing else, and
+// that the index lists exactly the skills in `references/`, each with its file. Without it,
+// every `skills/<name>/SKILL.md` is checked, as in the flat layout the plugin used before.
 //
 // Also enforces two checks from the Claude Code plugin directory's scan: no angle brackets
 // (like `<genre>`) in a skill description, and a root README.md of at least 40 words.
@@ -12,39 +20,45 @@ import { join } from 'node:path';
 import yaml from 'js-yaml';
 
 const root = process.argv[2] ?? 'skills';
+const indexSkill = 'using-unity';
 const readme = 'README.md';
 const minReadmeWords = 40;
 let checked = 0;
 const failures = [];
 
-for (const dir of readdirSync(root, { withFileTypes: true })) {
-  if (!dir.isDirectory()) continue;
-  const path = join(root, dir.name, 'SKILL.md');
+const dirs = (path) =>
+  readdirSync(path, { withFileTypes: true })
+    .filter((entry) => entry.isDirectory())
+    .map((entry) => entry.name)
+    .sort();
+
+/** Checks one skill file's frontmatter; returns its text, or undefined if it's missing. */
+function checkSkillFile(path, name) {
   if (!existsSync(path)) {
     failures.push(`${path}: missing`);
-    continue;
+    return undefined;
   }
   const text = readFileSync(path, 'utf8');
   const match = text.match(/^---\r?\n([\s\S]*?)\r?\n---(?:\r?\n|$)/);
   if (!match) {
     failures.push(`${path}: no YAML frontmatter block`);
-    continue;
+    return text;
   }
   let data;
   try {
     data = yaml.load(match[1]);
   } catch (error) {
     failures.push(`${path}: frontmatter is not valid YAML: ${error.message.split('\n')[0]}`);
-    continue;
+    return text;
   }
   if (typeof data !== 'object' || data === null) {
     failures.push(`${path}: frontmatter is not a mapping`);
-    continue;
+    return text;
   }
   if (typeof data.name !== 'string' || data.name.trim() === '') {
     failures.push(`${path}: missing or empty name`);
-  } else if (data.name !== dir.name) {
-    failures.push(`${path}: name "${data.name}" does not match folder "${dir.name}"`);
+  } else if (data.name !== name) {
+    failures.push(`${path}: name "${data.name}" does not match folder "${name}"`);
   }
   if (typeof data.description !== 'string' || data.description.trim() === '') {
     failures.push(`${path}: missing or empty description`);
@@ -52,6 +66,45 @@ for (const dir of readdirSync(root, { withFileTypes: true })) {
     failures.push(`${path}: description contains angle brackets; reword or use a plain placeholder`);
   }
   checked += 1;
+  return text;
+}
+
+if (existsSync(join(root, indexSkill))) {
+  for (const name of dirs(root).filter((name) => name !== indexSkill)) {
+    failures.push(`${join(root, name)}: only ${indexSkill} belongs in ${root}/; this folder loads as a separate skill`);
+  }
+  const indexPath = join(root, indexSkill, 'SKILL.md');
+  const index = checkSkillFile(indexPath, indexSkill) ?? '';
+  const referencesDir = join(root, indexSkill, 'references');
+  const skills = existsSync(referencesDir) ? dirs(referencesDir) : [];
+  if (skills.length === 0) {
+    failures.push(`${referencesDir}: no skills`);
+  }
+  for (const name of skills) {
+    checkSkillFile(join(referencesDir, name, `${name}.md`), name);
+  }
+  // Index lines: "- **<name>**: <description> File: `references/<name>/<name>.md`".
+  const listed = new Map();
+  for (const line of index.split(/\r?\n/)) {
+    const entry = line.match(/^- \*\*([^*]+)\*\*: .* File: `([^`]+)`$/);
+    if (entry) listed.set(entry[1], entry[2]);
+  }
+  for (const name of skills) {
+    if (!listed.has(name)) {
+      failures.push(`${indexPath}: doesn't list ${name}, so agents can't reach it`);
+    } else if (listed.get(name) !== `references/${name}/${name}.md`) {
+      failures.push(`${indexPath}: lists ${name} with file ${listed.get(name)}, expected references/${name}/${name}.md`);
+    }
+  }
+  for (const name of listed.keys()) {
+    if (!skills.includes(name)) {
+      failures.push(`${indexPath}: lists ${name}, which isn't in ${referencesDir}`);
+    }
+  }
+} else {
+  for (const name of dirs(root)) {
+    checkSkillFile(join(root, name, 'SKILL.md'), name);
+  }
 }
 
 if (!existsSync(readme)) {