fix(acr): enumerateAgents counts only CC-registered agents — recurse + frontmatter filter + HOME dedup (M-BUG-3/4/5)

enumerateAgents previously counted every .md in an agents dir as an
always-loaded agent. Per the official CC subagents docs, CC registers a
subagent only when its frontmatter declares both name and description, scans
agents dirs recursively, and (at a HOME self-scan) must not count
~/.claude/agents twice.

- M-BUG-5: require valid name+description frontmatter; frontmatter-less files
  are registration no-ops costing 0 always-loaded tokens. Fixes the user-agent
  over-count (this machine: 13 -> 0).
- M-BUG-3: listMarkdownFiles gains opt-in recursion; enumerateAgents recurses
  so agents in subfolders (agents/review/x.md) are counted, matching CC.
- M-BUG-4: configDirs dedupes project==user paths, so a `manifest --global`
  self-scan (repoPath===$HOME) counts ~/.claude once (user scope), killing the
  spurious "project 13" double-count. Benefits rules/agents/output-styles.

TDD: 4 failing tests -> green. Full suite 1305/0; --json/--raw byte-stable,
frozen v5.0.0 + SC-5 + default-output snapshots untouched (no snapshot records
agent enumeration rows).

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EnUvKEqyEa1m9gy6Aqhdqq

scanners/lib/active-config-reader.mjs

@@ -572,14 +572,20 @@ async function countPluginItems(pluginRoot) {
   return counts;
 }
 
-async function listMarkdownFiles(dir) {
+async function listMarkdownFiles(dir, recursive = false) {
   const out = [];
   let entries;
   try { entries = await readdir(dir, { withFileTypes: true }); } catch { return out; }
   for (const e of entries) {
+    const full = join(dir, e.name);
+    if (e.isDirectory()) {
+      // Opt-in recursion (M-BUG-3): CC scans agents dirs recursively, so agents
+      // organized into subfolders must be enumerated too. Other callers stay flat.
+      if (recursive) out.push(...await listMarkdownFiles(full, true));
+      continue;
+    }
     if (!e.isFile()) continue;
     if (!e.name.endsWith('.md')) continue;
-    const full = join(dir, e.name);
     try {
       const s = await stat(full);
       out.push({ path: full, size: s.size });
@@ -662,6 +668,11 @@ export async function enumerateSkills(pluginList = []) {
 // Rules, agents, output styles (v5.6 Foundation enumeration)
 // ─────────────────────────────────────────────────────────────────────────
 
+/** True when `v` is a non-empty, non-whitespace string (a usable frontmatter field). */
+function hasText(v) {
+  return typeof v === 'string' && v.trim().length > 0;
+}
+
 /**
  * Build the project/user/plugin directory list for a per-kind enumerator.
  * Project + user dirs live under `.claude/<dir>`; plugins under each of the
@@ -669,8 +680,16 @@ export async function enumerateSkills(pluginList = []) {
  */
 function configDirs(repoPath, pluginList, subdir, pluginSubdirs = [subdir]) {
   const home = process.env.HOME || process.env.USERPROFILE || '';
-  const dirs = [{ dir: join(repoPath, '.claude', subdir), source: 'project', pluginName: null }];
-  if (home) dirs.push({ dir: join(home, '.claude', subdir), source: 'user', pluginName: null });
+  const projectDir = join(repoPath, '.claude', subdir);
+  const userDir = home ? join(home, '.claude', subdir) : null;
+  const dirs = [];
+  // M-BUG-4: when repoPath === $HOME (the `manifest --global` self-scan), the
+  // project dir resolves to the same path as the user dir. Count it once, as
+  // user scope, instead of enumerating the same directory twice.
+  if (!(userDir && userDir === projectDir)) {
+    dirs.push({ dir: projectDir, source: 'project', pluginName: null });
+  }
+  if (userDir) dirs.push({ dir: userDir, source: 'user', pluginName: null });
   for (const p of pluginList) {
     for (const sub of pluginSubdirs) {
       dirs.push({ dir: join(p.path, sub), source: 'plugin', pluginName: p.name });
@@ -730,8 +749,17 @@ export async function enumerateAgents(repoPath, pluginList = []) {
   const lp = deriveLoadPattern('agent');
   const dirs = configDirs(repoPath, pluginList, 'agents');
   for (const { dir, source, pluginName } of dirs) {
-    const files = await listMarkdownFiles(dir);
+    const files = await listMarkdownFiles(dir, true); // M-BUG-3: CC scans agents dirs recursively
     for (const f of files) {
+      // M-BUG-5: CC registers a subagent only when its frontmatter declares both
+      // `name` and `description` (docs: identity comes only from `name`; both are
+      // required). Frontmatter-less / incomplete files are registration no-ops
+      // that cost zero always-loaded tokens — don't count them as agents.
+      let frontmatter;
+      try {
+        ({ frontmatter } = parseFrontmatter(await readFile(f.path, 'utf-8')));
+      } catch { continue; }
+      if (!hasText(frontmatter && frontmatter.name) || !hasText(frontmatter && frontmatter.description)) continue;
       out.push({
         name: basename(f.path).replace(/\.md$/, ''),
         source,