diff --git a/src/genie-commands/doctor.test.ts b/src/genie-commands/doctor.test.ts
new file mode 100644
index 000000000..cada023e0
--- /dev/null
+++ b/src/genie-commands/doctor.test.ts
@@ -0,0 +1,123 @@
+/**
+ * Tests for `checkLegacyAgentFrontmatter` — Group 6 of wish
+ * `dir-sync-frontmatter-refresh`.
+ *
+ * The check walks every agent directory under `agents/` and warns when an
+ * AGENTS.md starts with a `---` fence while an `agent.yaml` is also
+ * present — the configuration-in-wrong-file scenario that sync silently
+ * ignores post-migration.
+ */
+
+import { afterEach, beforeEach, describe, expect, test } from 'bun:test';
+import { mkdirSync, mkdtempSync, rmSync, writeFileSync } from 'node:fs';
+import { tmpdir } from 'node:os';
+import { join } from 'node:path';
+import { checkLegacyAgentFrontmatter } from './doctor.js';
+
+let workspaceRoot: string;
+
+beforeEach(() => {
+  workspaceRoot = mkdtempSync(join(tmpdir(), 'doctor-legacy-fm-'));
+});
+
+afterEach(() => {
+  try {
+    rmSync(workspaceRoot, { recursive: true, force: true });
+  } catch {
+    /* ignore */
+  }
+});
+
+function seedAgent(name: string, files: { agentYaml?: string; agentsMd?: string }): void {
+  const agentDir = join(workspaceRoot, 'agents', name);
+  mkdirSync(agentDir, { recursive: true });
+  if (files.agentYaml !== undefined) writeFileSync(join(agentDir, 'agent.yaml'), files.agentYaml);
+  if (files.agentsMd !== undefined) writeFileSync(join(agentDir, 'AGENTS.md'), files.agentsMd);
+}
+
+describe('checkLegacyAgentFrontmatter', () => {
+  test('warns when AGENTS.md has frontmatter AND agent.yaml exists', async () => {
+    seedAgent('drifted', {
+      agentYaml: 'promptMode: append\nmodel: opus\n',
+      agentsMd: '---\nmodel: sonnet\n---\n\n# body',
+    });
+
+    const results = checkLegacyAgentFrontmatter(workspaceRoot);
+    expect(results).toHaveLength(1);
+    expect(results[0].status).toBe('warn');
+    expect(results[0].name).toBe('agents/drifted/AGENTS.md');
+    expect(results[0].message).toMatch(/legacy frontmatter/i);
+    expect(results[0].suggestion).toMatch(/agent\.yaml/);
+  });
+
+  test('silent (pass) when agent.yaml absent — pre-migration state', async () => {
+    seedAgent('pre-migration', {
+      agentsMd: '---\nmodel: sonnet\n---\n\n# body',
+    });
+
+    const results = checkLegacyAgentFrontmatter(workspaceRoot);
+    expect(results).toHaveLength(1);
+    expect(results[0].status).toBe('pass');
+    expect(results[0].name).toMatch(/No legacy frontmatter/);
+  });
+
+  test('silent (pass) when AGENTS.md has no fence — clean post-migration', async () => {
+    seedAgent('clean', {
+      agentYaml: 'promptMode: append\n',
+      agentsMd: '# Agent: clean\n\nBody content.',
+    });
+
+    const results = checkLegacyAgentFrontmatter(workspaceRoot);
+    expect(results).toHaveLength(1);
+    expect(results[0].status).toBe('pass');
+  });
+
+  test('silent when agents/ directory does not exist', async () => {
+    // No seeding — workspace has no agents/ dir.
+    const results = checkLegacyAgentFrontmatter(workspaceRoot);
+    expect(results).toHaveLength(0);
+  });
+
+  test('flags multiple agents independently', async () => {
+    seedAgent('drifted-one', {
+      agentYaml: 'promptMode: append\n',
+      agentsMd: '---\nmodel: opus\n---\n# body',
+    });
+    seedAgent('clean', {
+      agentYaml: 'promptMode: append\n',
+      agentsMd: '# Agent: clean\n\nBody.',
+    });
+    seedAgent('drifted-two', {
+      agentYaml: 'promptMode: append\n',
+      agentsMd: '---\ncolor: red\n---\n# body',
+    });
+
+    const results = checkLegacyAgentFrontmatter(workspaceRoot);
+    // 2 warnings + 0 pass fillers (pass filler only emitted when zero warnings)
+    expect(results).toHaveLength(2);
+    const names = results.map((r) => r.name).sort();
+    expect(names).toEqual(['agents/drifted-one/AGENTS.md', 'agents/drifted-two/AGENTS.md']);
+  });
+
+  test('ignores non-directory entries in agents/', async () => {
+    // Seed one drifted agent so we get a warning to assert.
+    seedAgent('real', {
+      agentYaml: 'promptMode: append\n',
+      agentsMd: '---\nmodel: opus\n---\n',
+    });
+    // Drop a file inside agents/ — should be skipped, not crash.
+    writeFileSync(join(workspaceRoot, 'agents', 'README'), 'not an agent');
+
+    const results = checkLegacyAgentFrontmatter(workspaceRoot);
+    expect(results).toHaveLength(1);
+    expect(results[0].name).toBe('agents/real/AGENTS.md');
+  });
+
+  test('skips agent dirs that only have agent.yaml (no AGENTS.md)', async () => {
+    seedAgent('yaml-only', { agentYaml: 'promptMode: append\n' });
+
+    const results = checkLegacyAgentFrontmatter(workspaceRoot);
+    expect(results).toHaveLength(1);
+    expect(results[0].status).toBe('pass');
+  });
+});
diff --git a/src/genie-commands/doctor.ts b/src/genie-commands/doctor.ts
index 50cba4e25..bc382cb0e 100644
--- a/src/genie-commands/doctor.ts
+++ b/src/genie-commands/doctor.ts
@@ -5,7 +5,7 @@
  * Checks prerequisites, configuration, and tmux connectivity.
  */
 
-import { existsSync, unlinkSync } from 'node:fs';
+import { existsSync, readFileSync, readdirSync, statSync, unlinkSync } from 'node:fs';
 import { homedir } from 'node:os';
 import { join } from 'node:path';
 import { $ } from 'bun';
@@ -14,6 +14,7 @@ import { contractClaudePath, getClaudeSettingsPath } from '../lib/claude-setting
 import { tmuxBin } from '../lib/ensure-tmux.js';
 import { genieConfigExists, getGenieConfigPath, isSetupComplete, loadGenieConfig } from '../lib/genie-config.js';
 import { checkCommand } from '../lib/system-detect.js';
+import { findWorkspace } from '../lib/workspace.js';
 
 interface CheckResult {
   name: string;
@@ -395,6 +396,73 @@ async function checkBridge(): Promise<CheckResult[]> {
   return results;
 }
 
+/**
+ * Check that no agent has leftover `---` frontmatter in its `AGENTS.md`
+ * when `agent.yaml` is also present. Wish `dir-sync-frontmatter-refresh`
+ * (Group 6) eliminates frontmatter entirely post-migration — if a user
+ * pastes config back into AGENTS.md, sync silently ignores it, which is
+ * confusing. This check surfaces the drift loudly.
+ *
+ * Exported for unit tests and for callers that want to run this check
+ * outside `genie doctor` (e.g. a pre-sync lint).
+ */
+export function checkLegacyAgentFrontmatter(workspaceRoot?: string): CheckResult[] {
+  const results: CheckResult[] = [];
+  const root = workspaceRoot ?? findWorkspace()?.root;
+  if (!root) return [];
+
+  const agentsDir = join(root, 'agents');
+  if (!existsSync(agentsDir)) return [];
+
+  let entries: string[];
+  try {
+    entries = readdirSync(agentsDir);
+  } catch {
+    return [];
+  }
+
+  for (const name of entries) {
+    const agentDir = join(agentsDir, name);
+    try {
+      if (!statSync(agentDir).isDirectory()) continue;
+    } catch {
+      continue;
+    }
+
+    const yamlPath = join(agentDir, 'agent.yaml');
+    const agentsMdPath = join(agentDir, 'AGENTS.md');
+
+    // Only flag when both files exist AND AGENTS.md starts with a fence.
+    // Pre-migration state (no yaml, frontmatter present) is NOT a warning —
+    // sync will migrate it on the next run.
+    if (!existsSync(yamlPath) || !existsSync(agentsMdPath)) continue;
+
+    let headContent: string;
+    try {
+      // Read only the first handful of bytes to cheaply detect the fence.
+      headContent = readFileSync(agentsMdPath, 'utf-8').slice(0, 4);
+    } catch {
+      continue;
+    }
+
+    if (!headContent.startsWith('---')) continue;
+
+    results.push({
+      name: `agents/${name}/AGENTS.md`,
+      status: 'warn',
+      message: 'legacy frontmatter detected (ignored by sync)',
+      suggestion: `Move config into agents/${name}/agent.yaml — AGENTS.md is prompt-only post-migration.`,
+    });
+  }
+
+  // Single positive result when nothing drifted, so the section prints a
+  // clean "✓" row.
+  if (results.length === 0) {
+    results.push({ name: 'No legacy frontmatter in agents/*/AGENTS.md', status: 'pass' });
+  }
+  return results;
+}
+
 /**
  * Main doctor command
  */
@@ -424,6 +492,7 @@ export async function doctorCommand(options?: { fix?: boolean }): Promise<void>
   runCheckSection('Tmux', await checkTmux(), counts);
   runCheckSection('Worker Profiles', await checkWorkerProfiles(), counts);
   runCheckSection('Omni Bridge', await checkBridge(), counts);
+  runCheckSection('Agent Config', checkLegacyAgentFrontmatter(), counts);
 
   // Summary
   console.log();