msd-core/tests/agent-install-validation.test.cjs

/**
 * MSD Agent Installation Validation Tests (#1371)
 *
 * Validates that MSD detects missing or incomplete agent installations and
 * surfaces warnings through init commands and health checks. When agents are
 * not installed, Task(subagent_type="msd-*") silently falls back to
 * general-purpose, losing specialized instructions.
 */

const { test, describe, beforeEach, afterEach } = require('node:test');
const assert = require('node:assert/strict');
const fs = require('fs');
const os = require('os');
const path = require('path');
const { runMsdTools, createTempProject, cleanup } = require('./helpers.cjs');

const AGENTS_DIR_NAME = 'agents';
const MODEL_PROFILES = require('../msd-core/bin/lib/model-profiles.cjs').MODEL_PROFILES;
const EXPECTED_AGENTS = Object.keys(MODEL_PROFILES);

/**
 * Create a fake MSD install directory structure that mirrors what the installer
 * produces. msd-tools.cjs lives at <configDir>/msd-core/bin/msd-tools.cjs,
 * so the agents dir is at <configDir>/agents/.
 *
 * We use --cwd to point at the project, and MSD_INSTALL_DIR env to override
 * the agents directory location for testing.
 */
function _createAgentsDir(configDir, agentNames = []) {
  const agentsDir = path.join(configDir, AGENTS_DIR_NAME);
  fs.mkdirSync(agentsDir, { recursive: true });
  for (const name of agentNames) {
    fs.writeFileSync(
      path.join(agentsDir, `${name}.md`),
      `---\nname: ${name}\ndescription: Test agent\ntools: Read, Bash\ncolor: cyan\n---\nAgent content.\n`
    );
  }
  return agentsDir;
}

function createCompleteCodexAgents(configDir) {
  const agentsDir = path.join(configDir, '.codex', AGENTS_DIR_NAME);
  fs.mkdirSync(agentsDir, { recursive: true });
  const files = {};
  for (const name of EXPECTED_AGENTS) {
    fs.writeFileSync(path.join(agentsDir, `${name}.md`), `# ${name}\n`);
    fs.writeFileSync(path.join(agentsDir, `${name}.toml`), `name = "${name}"\n`);
    files[`agents/${name}.md`] = {};
    files[`agents/${name}.toml`] = {};
  }
  fs.writeFileSync(
    path.join(configDir, '.codex', 'msd-file-manifest.json'),
    JSON.stringify({ files }),
  );
  return agentsDir;
}

// ─── Init command agent validation ──────────────────────────────────────────

describe('init commands: agents_installed field (#1371)', () => {
  let tmpDir;

  beforeEach(() => {
    tmpDir = createTempProject();
  });

  afterEach(() => {
    cleanup(tmpDir);
  });

  // Point the SDK at the repo's agents/ dir (sibling of msd-core/) via the
  // MSD_AGENTS_DIR override. The SDK side of init resolves agents from
  // MSD_AGENTS_DIR or the runtime config dir (~/.claude/agents for Claude); it
  // does NOT walk up from cwd like the CJS-era code did. Without this override
  // these tests would only pass on a dev machine with ~/.claude/agents/
  // populated — which masked the divergence on Linux CI where that path is
  // absent. See sdk/src/query/QUERY-HANDLERS.md ("subprocess vs in-process
  // path resolution") and sdk/src/query/helpers.ts:resolveAgentsDir.
  const REPO_AGENTS_DIR = path.resolve(__dirname, '..', 'agents');

  test('init execute-phase includes agents_installed=true when agents exist', () => {
    const phaseDir = path.join(tmpDir, '.planning', 'phases', '01-setup');
    fs.mkdirSync(phaseDir, { recursive: true });

    const result = runMsdTools('init execute-phase 1 --raw', tmpDir, { MSD_AGENTS_DIR: REPO_AGENTS_DIR });
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.strictEqual(typeof output.agents_installed, 'boolean',
      'init execute-phase must include agents_installed field');
    assert.strictEqual(output.agents_installed, true,
      'agents_installed should be true when MSD_AGENTS_DIR has msd-*.md files');
  });

  test('init plan-phase includes agents_installed=true when agents exist', () => {
    const phaseDir = path.join(tmpDir, '.planning', 'phases', '01-setup');
    fs.mkdirSync(phaseDir, { recursive: true });

    const result = runMsdTools('init plan-phase 1 --raw', tmpDir, { MSD_AGENTS_DIR: REPO_AGENTS_DIR });
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.strictEqual(typeof output.agents_installed, 'boolean',
      'init plan-phase must include agents_installed field');
    assert.strictEqual(output.agents_installed, true);
  });

  test('init plan-phase reports the complete project-local Codex installation', () => {
    const phaseDir = path.join(tmpDir, '.planning', 'phases', '01-setup');
    const globalHome = path.join(tmpDir, 'global-codex');
    fs.mkdirSync(phaseDir, { recursive: true });
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'config.json'),
      JSON.stringify({ runtime: 'codex' }),
    );
    createCompleteCodexAgents(tmpDir);
    const canonicalRoot = fs.realpathSync(tmpDir);
    const localAgentsDir = path.join(canonicalRoot, '.codex', AGENTS_DIR_NAME);
    _createAgentsDir(globalHome, EXPECTED_AGENTS);

    const result = runMsdTools('init plan-phase 1 --raw', tmpDir, { CODEX_HOME: globalHome });
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.strictEqual(output.project_root, canonicalRoot);
    assert.strictEqual(output.agent_runtime, 'codex');
    assert.strictEqual(output.agents_dir, localAgentsDir);
    assert.strictEqual(output.agents_installed, true);
    assert.deepStrictEqual(output.missing_agents, []);
  });

  test('init reports codex when the session signal is present', () => {
    const phaseDir = path.join(tmpDir, '.planning', 'phases', '01-setup');
    fs.mkdirSync(phaseDir, { recursive: true });

    const result = runMsdTools('init plan-phase 1 --raw', tmpDir, { CODEX_SANDBOX: 'seatbelt' });
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.strictEqual(output.agent_runtime, 'codex');
  });

  test('init honors explicit config runtime over detection', () => {
    const phaseDir = path.join(tmpDir, '.planning', 'phases', '01-setup');
    fs.mkdirSync(phaseDir, { recursive: true });
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'config.json'),
      JSON.stringify({ runtime: 'claude' }),
    );

    const result = runMsdTools('init plan-phase 1 --raw', tmpDir, { CODEX_SANDBOX: 'seatbelt' });
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.strictEqual(output.agent_runtime, 'claude');
  });

  test('init is unaffected in a non-codex session', () => {
    const phaseDir = path.join(tmpDir, '.planning', 'phases', '01-setup');
    fs.mkdirSync(phaseDir, { recursive: true });

    const result = runMsdTools('init plan-phase 1 --raw', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.strictEqual(output.agent_runtime, 'claude');
  });

  test('init honors MSD_RUNTIME over detection', () => {
    const phaseDir = path.join(tmpDir, '.planning', 'phases', '01-setup');
    fs.mkdirSync(phaseDir, { recursive: true });

    const result = runMsdTools('init plan-phase 1 --raw', tmpDir, {
      MSD_RUNTIME: 'opencode',
      CODEX_SANDBOX: 'seatbelt',
    });
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.strictEqual(output.agent_runtime, 'opencode');
  });

  test('init execute-phase includes missing_agents list when agents are missing', () => {
    const phaseDir = path.join(tmpDir, '.planning', 'phases', '01-setup');
    fs.mkdirSync(phaseDir, { recursive: true });

    const result = runMsdTools('init execute-phase 1 --raw', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(Array.isArray(output.missing_agents),
      'init execute-phase must include missing_agents array');
  });

  test('init quick includes agents_installed field', () => {
    const result = runMsdTools(['init', 'quick', 'test description', '--raw'], tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.strictEqual(typeof output.agents_installed, 'boolean',
      'init quick must include agents_installed field');
  });
});

// ─── Health check: agent installation ───────────────────────────────────────

describe('validate health: agent installation check W010 (#1371)', () => {
  let tmpDir;

  beforeEach(() => {
    tmpDir = createTempProject();
    // Write minimal project files so health check doesn't fail on E001-E005
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'PROJECT.md'),
      '# Project\n\n## What This Is\nTest\n\n## Core Value\nTest\n\n## Requirements\nTest\n'
    );
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'ROADMAP.md'),
      '# Roadmap\n\n### Phase 1: Setup\n'
    );
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'STATE.md'),
      '# Session State\n\n## Current Position\n\nPhase: 1\n'
    );
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'config.json'),
      JSON.stringify({
        model_profile: 'balanced',
        commit_docs: true,
        workflow: { nyquist_validation: true },
      }, null, 2)
    );
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-setup'), { recursive: true });
  });

  afterEach(() => {
    cleanup(tmpDir);
  });

  test('health check reports healthy when agents are installed (repo layout)', () => {
    // In the repo, agents/ exists as a sibling of msd-core/, so the
    // health check should find them via the msd-tools.cjs path resolution
    const result = runMsdTools('validate health --raw', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    // Should not have W010 warning about missing agents
    const w010 = (output.warnings || []).find(w => w.code === 'W010');
    assert.ok(!w010, 'Should not warn about missing agents when agents/ dir exists with files');
  });
});

// ─── Codex project-local validation status ──────────────────────────────────

describe('Codex project-local validation status', () => {
  let tmpDir;
  let globalHome;

  beforeEach(() => {
    tmpDir = createTempProject();
    globalHome = path.join(tmpDir, 'global-codex');
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'config.json'),
      JSON.stringify({ runtime: 'codex' }),
    );
    _createAgentsDir(globalHome, EXPECTED_AGENTS);
  });

  afterEach(() => {
    cleanup(tmpDir);
  });

  test('validate agents and health use a complete project-local Codex installation', () => {
    createCompleteCodexAgents(tmpDir);
    const localAgentsDir = path.join(fs.realpathSync(tmpDir), '.codex', AGENTS_DIR_NAME);
    const env = { CODEX_HOME: globalHome };

    const validateResult = runMsdTools('validate agents --raw', tmpDir, env);
    assert.ok(validateResult.success, `validate agents failed: ${validateResult.error}`);
    const validateOutput = JSON.parse(validateResult.output);
    assert.strictEqual(validateOutput.agents_dir, localAgentsDir);
    assert.strictEqual(validateOutput.agents_found, true);
    assert.deepStrictEqual(validateOutput.missing, []);
    assert.deepStrictEqual(validateOutput.incomplete, []);

    const healthResult = runMsdTools('validate health --raw', tmpDir, env);
    assert.ok(healthResult.success, `validate health failed: ${healthResult.error}`);
    const healthOutput = JSON.parse(healthResult.output);
    assert.ok(!(healthOutput.warnings || []).some(warning => warning.code === 'W010'));
  });

  test('an empty project-local Codex directory remains authoritative for validate agents and health', () => {
    fs.mkdirSync(path.join(tmpDir, '.codex', AGENTS_DIR_NAME), { recursive: true });
    fs.writeFileSync(path.join(tmpDir, '.codex', 'msd-file-manifest.json'), JSON.stringify({ files: {} }));
    const localAgentsDir = path.join(fs.realpathSync(tmpDir), '.codex', AGENTS_DIR_NAME);
    const env = { CODEX_HOME: globalHome };

    const validateResult = runMsdTools('validate agents --raw', tmpDir, env);
    assert.ok(validateResult.success, `validate agents failed: ${validateResult.error}`);
    const validateOutput = JSON.parse(validateResult.output);
    assert.strictEqual(validateOutput.agents_dir, localAgentsDir);
    assert.strictEqual(validateOutput.agents_found, false);
    assert.deepStrictEqual(validateOutput.installed, []);
    assert.deepStrictEqual(validateOutput.incomplete, []);
    assert.deepStrictEqual(validateOutput.missing, EXPECTED_AGENTS);

    const healthResult = runMsdTools('validate health --raw', tmpDir, env);
    assert.ok(healthResult.success, `validate health failed: ${healthResult.error}`);
    const healthOutput = JSON.parse(healthResult.output);
    assert.ok((healthOutput.warnings || []).some(warning => warning.code === 'W010'));
  });
});

// ─── Agent file format detection (.toml / MSD_AGENTS_DIR) ────────────────────────────────────

describe('checkAgentsInstalled: agent file formats and MSD_AGENTS_DIR', () => {
  let tmpDir;

  beforeEach(() => {
    tmpDir = createTempProject();
  });

  afterEach(() => {
    cleanup(tmpDir);
  });

  test('agents_installed=true when agents exist as .toml (Codex format) (#278)', () => {
    const agentsDir = path.join(tmpDir, 'codex-agents');
    fs.mkdirSync(agentsDir, { recursive: true });
    for (const name of EXPECTED_AGENTS) {
      fs.writeFileSync(
        path.join(agentsDir, `${name}.toml`),
        `name = "${name}"\ndescription = "Test agent"\n`
      );
    }

    const result = runMsdTools('validate agents --raw', tmpDir, { MSD_AGENTS_DIR: agentsDir });
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.strictEqual(output.agents_found, true,
      'agents_found must be true when agents exist as .toml (Codex format)');
    assert.deepStrictEqual(output.missing, [],
      'missing must be empty when all agents exist as .toml');
  });

  test('MSD_AGENTS_DIR env var overrides default agents directory', () => {
    // Create a custom agents dir in a subdirectory
    const customAgentsDir = path.join(tmpDir, 'custom-agents');
    fs.mkdirSync(customAgentsDir, { recursive: true });
    // Put one agent there as .md (standard format)
    fs.writeFileSync(
      path.join(customAgentsDir, `${EXPECTED_AGENTS[0]}.md`),
      `---\nname: ${EXPECTED_AGENTS[0]}\ndescription: Test agent\n---\nAgent content.\n`
    );

    const result = runMsdTools('validate agents --raw', tmpDir, { MSD_AGENTS_DIR: customAgentsDir });
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    // The custom dir path should be reported
    assert.strictEqual(output.agents_dir, customAgentsDir,
      'agents_dir must reflect MSD_AGENTS_DIR override');
  });
});

describe('validate agents subcommand (#1371)', () => {
  let tmpDir;

  beforeEach(() => {
    tmpDir = createTempProject();
  });

  afterEach(() => {
    cleanup(tmpDir);
  });

  test('validate agents returns status with agent list', () => {
    const result = runMsdTools('validate agents --raw', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok('agents_dir' in output, 'Must include agents_dir path');
    assert.ok('installed' in output, 'Must include installed array');
    assert.ok('missing' in output, 'Must include missing array');
    assert.ok('agents_found' in output, 'Must include agents_found boolean');
  });

  test('validate agents lists all expected agent types', () => {
    const result = runMsdTools('validate agents --raw', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    // The expected agents come from MODEL_PROFILES keys
    assert.ok(output.expected.length > 0, 'Must have expected agents');
  });
});

// ─── Sandbox posture drift, at the COMMAND (#3897 rung 3, ADR-3473 §8.3) ─────
//
// tests/agent-install-check.test.cjs's T28 already proves checkCodexSandboxPosture
// itself detects a drifted sandbox_mode. That is a UNIT row — it drives the
// helper directly. Before verify.cts wired the helper into cmdValidateAgents,
// T28 stayed green while `msd-tools validate agents` (the actual command a
// user/CI runs) never surfaced the drift at all — the ADR-3180 Decision 4(b)
// failure shape ("asserting at a helper's return, not at the consumer's
// output"). This row drives the real CLI end to end and asserts on ITS JSON,
// so a future regression that leaves the helper correct but un-wired from the
// command fails here even if T28 stays green.
describe('validate agents surfaces sandbox posture drift at the command (#3897 rung 3)', () => {
  let tmpDir;
  let agentsDir;

  beforeEach(() => {
    tmpDir = createTempProject();
    agentsDir = path.join(tmpDir, 'codex-agents');
    fs.mkdirSync(agentsDir, { recursive: true });
  });

  afterEach(() => {
    cleanup(tmpDir);
  });

  test('validateAgentsSurfacesSandboxDriftAtTheCommand_3897: `validate agents` reports the drifted agent/expected/found via sandbox_posture', () => {
    // agents/msd-executor.md (the real repo role source — checkCodexSandboxPosture
    // reads it directly, it is not fixture-overridable) declares tools that derive
    // workspace-write. Install a drifted TOML claiming read-only instead.
    fs.writeFileSync(
      path.join(agentsDir, 'msd-executor.toml'),
      'name = "msd-executor"\ndescription = "Executes plans"\nsandbox_mode = "read-only"\n'
      + "developer_instructions = '''\nExecute.\n'''\n",
    );

    const env = { MSD_AGENTS_DIR: agentsDir, MSD_RUNTIME: 'codex' };
    const result = runMsdTools('validate agents --raw', tmpDir, env);
    assert.ok(result.success, `validate agents failed: ${result.error}`);
    assert.strictEqual(result.exitCode, 0, 'model-posture drift is report-only, not fatal — sandbox posture must match that precedent');

    const output = JSON.parse(result.output);
    assert.ok(
      output.sandbox_posture,
      `expected \`validate agents\` output to carry a sandbox_posture key, got keys: ${Object.keys(output).join(', ')}`,
    );
    assert.strictEqual(output.sandbox_posture.ok, false);
    const violation = output.sandbox_posture.violations.find((v) => v.agent === 'msd-executor');
    assert.ok(violation, 'the command output must name the drifted agent');
    assert.strictEqual(violation.expected, 'workspace-write');
    assert.strictEqual(violation.found, 'read-only');
  });
});

// ─── Bug #1058: validate agents detects manifest-backed .md/.toml pair drift ──

describe('bug #1058: validate agents detects manifest-backed .md/.toml pair drift', () => {
  // All real agents/msd-*.md files in the repo (used to populate fixtures)
  const REPO_AGENTS_DIR_1058 = path.resolve(__dirname, '..', 'agents');

  /**
   * Copy all msd-*.md files from the repo agents dir into destDir.
   */
  function copyAgentMdFiles(destDir) {
    const files = fs.readdirSync(REPO_AGENTS_DIR_1058).filter(f => /^msd-.*\.md$/.test(f));
    for (const file of files) {
      const src = path.join(REPO_AGENTS_DIR_1058, file);
      const dst = path.join(destDir, file);
      fs.copyFileSync(src, dst);
    }
  }

  /**
   * Build a msd-file-manifest.json whose files map includes both .md and .toml
   * entries for every EXPECTED_AGENTS entry.
   */
  function buildManifestBothPairs(agents) {
    const files = {};
    for (const name of agents) {
      files[`agents/${name}.md`] = 'deadbeef';
      files[`agents/${name}.toml`] = 'deadbeef';
    }
    return { version: '1.0.0', files };
  }

  let tmpDir;

  afterEach(() => {
    if (tmpDir) {
      cleanup(tmpDir);
      tmpDir = null;
    }
  });

  test('agents_found=false and incomplete non-empty when .toml files are absent but manifest expects them', () => {
    // Arrange: all .md files present, manifest says both .md and .toml are expected,
    // but NO .toml files are created on disk.
    tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'msd-bug-1058-missing-toml-'));
    const agentsDir = path.join(tmpDir, 'agents');
    fs.mkdirSync(agentsDir, { recursive: true });

    // Copy real .md files
    copyAgentMdFiles(agentsDir);

    // Write manifest with both .md and .toml entries but no .toml files on disk
    fs.writeFileSync(
      path.join(tmpDir, 'msd-file-manifest.json'),
      JSON.stringify(buildManifestBothPairs(EXPECTED_AGENTS), null, 2),
    );

    // Act
    const result = runMsdTools('validate agents --raw', tmpDir, {
      MSD_RUNTIME: 'codex',
      MSD_AGENTS_DIR: agentsDir,
    });
    assert.ok(result.success, `Command failed: ${result.error}`);
    const output = JSON.parse(result.output);

    // Assert: the completeness check must catch the missing .toml files
    assert.strictEqual(
      output.agents_found,
      false,
      `Expected agents_found=false when manifest-tracked .toml files are absent, got agents_found=${output.agents_found}`,
    );
    assert.ok(
      Array.isArray(output.incomplete),
      'Expected output.incomplete to be an array',
    );
    // Every agent whose .toml is absent must appear in incomplete (sorted deep-equal)
    assert.deepStrictEqual(
      [...output.incomplete].sort(),
      [...EXPECTED_AGENTS].sort(),
      `Expected incomplete to equal full EXPECTED_AGENTS set; got ${JSON.stringify(output.incomplete)}`,
    );
    // missing (entirely-absent .md) must be empty — these agents are not missing, only incomplete
    assert.deepStrictEqual(
      output.missing,
      [],
      `Expected missing=[] when all .md files are present; got ${JSON.stringify(output.missing)}`,
    );
  });

  test('agents_found=false and incomplete non-empty when .md files are absent but manifest expects them', () => {
    // Arrange: only .toml files present on disk, manifest says both .md and .toml are expected,
    // but NO .md files exist. This is the opposite-side pair-drift case.
    tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'msd-bug-1058-missing-md-'));
    const agentsDir = path.join(tmpDir, 'agents');
    fs.mkdirSync(agentsDir, { recursive: true });

    // Create ONLY .toml files — deliberately skip .md files
    for (const name of EXPECTED_AGENTS) {
      fs.writeFileSync(path.join(agentsDir, `${name}.toml`), `name = "${name}"
`);
    }

    // Write manifest with both .md and .toml entries
    fs.writeFileSync(
      path.join(tmpDir, 'msd-file-manifest.json'),
      JSON.stringify(buildManifestBothPairs(EXPECTED_AGENTS), null, 2),
    );

    // Act
    const result = runMsdTools('validate agents --raw', tmpDir, {
      MSD_RUNTIME: 'codex',
      MSD_AGENTS_DIR: agentsDir,
    });
    assert.ok(result.success, `Command failed: ${result.error}`);
    const output = JSON.parse(result.output);

    // Assert: missing .md files must surface as incomplete (pair-drift detected symmetrically)
    assert.strictEqual(
      output.agents_found,
      false,
      `Expected agents_found=false when manifest-tracked .md files are absent, got agents_found=${output.agents_found}`,
    );
    assert.ok(
      Array.isArray(output.incomplete),
      'Expected output.incomplete to be an array',
    );
    assert.ok(
      output.incomplete.length > 0,
      `Expected incomplete to be non-empty when .md files are absent; got ${JSON.stringify(output.incomplete)}`,
    );
  });

  test('agents_found=true and incomplete=[] when both .md and .toml files are present', () => {
    // Arrange: all .md AND .toml present, manifest says both expected
    tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'msd-bug-1058-complete-pair-'));
    const agentsDir = path.join(tmpDir, 'agents');
    fs.mkdirSync(agentsDir, { recursive: true });

    // Copy real .md files
    copyAgentMdFiles(agentsDir);

    // Create .toml files for each expected agent
    for (const name of EXPECTED_AGENTS) {
      fs.writeFileSync(path.join(agentsDir, `${name}.toml`), `name = "${name}"\n`);
    }

    // Write manifest with both .md and .toml entries
    fs.writeFileSync(
      path.join(tmpDir, 'msd-file-manifest.json'),
      JSON.stringify(buildManifestBothPairs(EXPECTED_AGENTS), null, 2),
    );

    // Act
    const result = runMsdTools('validate agents --raw', tmpDir, {
      MSD_RUNTIME: 'codex',
      MSD_AGENTS_DIR: agentsDir,
    });
    assert.ok(result.success, `Command failed: ${result.error}`);
    const output = JSON.parse(result.output);

    // Assert: complete pair => no false positive
    assert.strictEqual(
      output.agents_found,
      true,
      `Expected agents_found=true when both .md and .toml files are present; got ${output.agents_found}`,
    );
    assert.deepStrictEqual(
      output.incomplete,
      [],
      `Expected incomplete=[] when all manifest-tracked files are present; got ${JSON.stringify(output.incomplete)}`,
    );
  });

  test('no spurious incomplete flags when no manifest is present (protects claude/bundled installs)', () => {
    // Arrange: all .md files present, NO manifest file at all
    tmpDir = fs.mkdtempSync(path.join(os.tmpdir(), 'msd-bug-1058-no-manifest-'));
    const agentsDir = path.join(tmpDir, 'agents');
    fs.mkdirSync(agentsDir, { recursive: true });

    // Copy real .md files
    copyAgentMdFiles(agentsDir);

    // Explicitly do NOT write msd-file-manifest.json

    // Act
    const result = runMsdTools('validate agents --raw', tmpDir, {
      MSD_RUNTIME: 'codex',
      MSD_AGENTS_DIR: agentsDir,
    });
    assert.ok(result.success, `Command failed: ${result.error}`);
    const output = JSON.parse(result.output);

    // Assert: without a manifest, completeness check must no-op (incomplete empty)
    assert.deepStrictEqual(
      output.incomplete,
      [],
      `Expected incomplete=[] when no manifest present; got ${JSON.stringify(output.incomplete)}`,
    );
    // agents_found should reflect plain file presence (all .md files copied => true)
    assert.strictEqual(
      output.agents_found,
      true,
      `Expected agents_found=true when all .md files are present and no manifest; got ${output.agents_found}`,
    );
  });
});