// allow-test-rule: source-text-is-the-product
// Workflow .md / agent .md / command .md / reference .md files — their text
// IS what the runtime loads. Testing text content tests the deployed contract.
// Per CONTRIBUTING.md exception matrix.
// Migrated (#455): tests parse JSON output and assert on typed fields
// (output.status, error/warning/info codes). The single message.includes()
// at W001 checks the canonical section name '## Core Value' which is the
// product contract for PROJECT.md; stateContent.includes('# Session State')
// checks the canonical header of a generated file — both are
// source-text-is-the-product assertions, not output-grep violations.

/**
 * MSD Tools Tests - Validate Health Command
 *
 * Comprehensive tests for validate-health covering all 8 health checks
 * and the repair path.
 */

const { test, describe, beforeEach, afterEach } = require('node:test');
const assert = require('node:assert/strict');
const fs = require('fs');
const path = require('path');
const { runMsdTools, createTempProject, cleanup } = require('./helpers.cjs');
const { VALID_PROFILES } = require('../msd-core/bin/lib/model-catalog.cjs');
const { gitOrThrow } = require('./helpers/git-fixture.cjs');

// ─── Helpers for setting up minimal valid projects ────────────────────────────

function writeMinimalRoadmap(tmpDir, phases = ['1']) {
  const lines = phases.map(n => `### Phase ${n}: Phase ${n} Description`).join('\n');
  fs.writeFileSync(
    path.join(tmpDir, '.planning', 'ROADMAP.md'),
    `# Roadmap\n\n${lines}\n`
  );
}

function writeMinimalProjectMd(tmpDir, sections = ['## What This Is', '## Core Value', '## Requirements']) {
  const content = sections.map(s => `${s}\n\nContent here.\n`).join('\n');
  fs.writeFileSync(
    path.join(tmpDir, '.planning', 'PROJECT.md'),
    `# Project\n\n${content}`
  );
}

function writeMinimalStateMd(tmpDir, content) {
  const defaultContent = content || `# Session State\n\n## Current Position\n\nPhase: 1\n`;
  fs.writeFileSync(
    path.join(tmpDir, '.planning', 'STATE.md'),
    defaultContent
  );
}

function writeValidConfigJson(tmpDir) {
  fs.writeFileSync(
    path.join(tmpDir, '.planning', 'config.json'),
    JSON.stringify({ model_profile: 'balanced', commit_docs: true }, null, 2)
  );
}

// ─────────────────────────────────────────────────────────────────────────────
// validate health command — all 8 checks
// ─────────────────────────────────────────────────────────────────────────────

describe('validate health command', () => {
  let tmpDir;

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

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

  // ─── Check 1: .planning/ exists ───────────────────────────────────────────

  test("returns 'broken' when .planning directory is missing", () => {
    // createTempProject creates .planning/phases — remove it entirely
    // eslint-disable-next-line local/no-raw-rmsync-in-tests -- mid-test SUT setup: removes .planning/ to simulate missing dir condition
    fs.rmSync(path.join(tmpDir, '.planning'), { recursive: true, force: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.strictEqual(output.status, 'broken', 'should be broken');
    assert.ok(
      output.errors.some(e => e.code === 'E001'),
      `Expected E001 in errors: ${JSON.stringify(output.errors)}`
    );
  });

  // ─── Check 2: PROJECT.md exists and has required sections ─────────────────

  test('warns when PROJECT.md is missing', () => {
    // No PROJECT.md in .planning
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    writeValidConfigJson(tmpDir);
    // Create valid phase dir so no W007
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      output.errors.some(e => e.code === 'E002'),
      `Expected E002 in errors: ${JSON.stringify(output.errors)}`
    );
  });

  test('warns when PROJECT.md missing required sections', () => {
    // PROJECT.md missing "## Core Value" section
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'PROJECT.md'),
      '# Project\n\n## What This Is\n\nFoo\n\n## Requirements\n\nBar\n'
    );
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    writeValidConfigJson(tmpDir);
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    const w001s = output.warnings.filter(w => w.code === 'W001');
    assert.ok(w001s.length > 0, `Expected W001 warnings: ${JSON.stringify(output.warnings)}`);
    assert.ok(
      w001s.some(w => w.message.includes('## Core Value')),
      `Expected W001 mentioning "## Core Value": ${JSON.stringify(w001s)}`
    );
  });

  test('passes when PROJECT.md has all required sections', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    writeValidConfigJson(tmpDir);
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      !output.errors.some(e => e.code === 'E002'),
      `Should not have E002: ${JSON.stringify(output.errors)}`
    );
    assert.ok(
      !output.warnings.some(w => w.code === 'W001'),
      `Should not have W001: ${JSON.stringify(output.warnings)}`
    );
  });

  // ─── Check 3: ROADMAP.md exists ───────────────────────────────────────────

  test('errors when ROADMAP.md is missing', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalStateMd(tmpDir);
    writeValidConfigJson(tmpDir);
    // No ROADMAP.md

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      output.errors.some(e => e.code === 'E003'),
      `Expected E003 in errors: ${JSON.stringify(output.errors)}`
    );
  });

  // ─── Check 4: STATE.md exists and references valid phases ─────────────────

  test('errors when STATE.md is missing with repairable false (DESTRUCTIVE remedy is never auto-applied)', () => {
    // Phase 11 (#3309): E004's remedy (regenerateState) is DESTRUCTIVE, and
    // `--repair` refuses to auto-apply a DESTRUCTIVE remedy (design doc,
    // "--repair behavior change" section) — a disclosed breaking change from
    // the pre-migration `repairable: true`. `repairable` now means "an
    // automatic repair will actually run", not merely "a remedy exists to
    // describe".
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeValidConfigJson(tmpDir);
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });
    // No STATE.md

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    const e004 = output.errors.find(e => e.code === 'E004');
    assert.ok(e004, `Expected E004 in errors: ${JSON.stringify(output.errors)}`);
    assert.strictEqual(e004.repairable, false, 'E004 (DESTRUCTIVE remedy) should not be marked repairable');
  });

  test('warns when STATE.md references nonexistent phase', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeValidConfigJson(tmpDir);
    // STATE.md mentions Phase 99 but only 01-a dir exists
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'STATE.md'),
      '# Session State\n\nPhase 99 is the current phase.\n'
    );
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    const w002 = output.warnings.find(w => w.code === 'W002');
    assert.ok(w002, `Expected W002 in warnings: ${JSON.stringify(output.warnings)}`);
    assert.strictEqual(w002.repairable, false, 'W002 should not be auto-repairable');
  });

  // Regression: #3652 — after /msd:complete-milestone, phase dirs move into
  // milestones/vX.Y-phases/ and their `#### Phase N:` headings in ROADMAP.md
  // get collapsed inside <details> blocks. The heading-scan regex misses
  // collapsed phases and collectDiskPhases() only walks the active archive,
  // so W002 used to fire for every historical phase number mentioned in
  // STATE.md's narrative body. Cross-referencing every milestone archive
  // suppresses the false positive.
  test('does not warn W002 for phase refs that live in any milestones archive (#3652)', () => {
    writeMinimalProjectMd(tmpDir);
    writeValidConfigJson(tmpDir);
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '23-current'), { recursive: true });
    fs.mkdirSync(path.join(tmpDir, '.planning', 'milestones', 'v1.3a-phases', '12-old-phase'), { recursive: true });
    for (const n of ['19-alpha', '20-beta', '21-gamma', '22-delta']) {
      fs.mkdirSync(path.join(tmpDir, '.planning', 'milestones', 'v1.3b-phases', n), { recursive: true });
    }
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'ROADMAP.md'),
      [
        '# Roadmap', '',
        '<details><summary>v1.3a: Shipped</summary>', '',
        '- Phase 12: archived', '',
        '</details>', '',
        '<details><summary>v1.3b: Shipped</summary>', '',
        '- Phase 19, 20, 21, 22: archived', '',
        '</details>', '',
        '## v1.4: Current', '',
        '### Phase 23: Current work', '',
      ].join('\n')
    );
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'STATE.md'),
      [
        '---', 'milestone: v1.4', 'milestone_name: Current', 'status: executing', '---', '',
        '# State', '',
        '**Current Phase:** 23', '',
        '## Recent', '- Phase 19 shipped', '- Phase 20 shipped', '- Phase 21 shipped', '- Phase 22 shipped',
        '', '## Decisions', '- Decision from Phase 12 still applies',
      ].join('\n')
    );

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    const w002s = (output.warnings || []).filter(w => w.code === 'W002');
    assert.strictEqual(w002s.length, 0, `Did not expect W002s for archived phases: ${JSON.stringify(w002s)}`);
    // Also no W006 for the archived phases — extractCurrentMilestone strips
    // shipped milestones before the Check 8 heading scan in the CJS path,
    // so archived phase numbers never reach `roadmapPhases`. Pins the
    // assumption that drove the decision NOT to mirror the W002 archive
    // union into Check 8 on the CJS side.
    const w006s = (output.warnings || []).filter(w =>
      w.code === 'W006' && /Phase (?:12|19|20|21|22)\b/.test(String(w.message)),
    );
    assert.strictEqual(w006s.length, 0, `Did not expect W006s for archived phases: ${JSON.stringify(w006s)}`);
  });

  // ─── Check 5: config.json valid JSON + valid schema ───────────────────────

  test('warns when config.json is missing with repairable true', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });
    // No config.json

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    const w003 = output.warnings.find(w => w.code === 'W003');
    assert.ok(w003, `Expected W003 in warnings: ${JSON.stringify(output.warnings)}`);
    assert.strictEqual(w003.repairable, true, 'W003 should be repairable');
  });

  test('errors when config.json has invalid JSON', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'config.json'),
      '{broken json'
    );
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      output.errors.some(e => e.code === 'E005'),
      `Expected E005 in errors: ${JSON.stringify(output.errors)}`
    );
  });

  test('warns when config.json has invalid model_profile', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'config.json'),
      JSON.stringify({ model_profile: 'invalid' })
    );
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      output.warnings.some(w => w.code === 'W004'),
      `Expected W004 in warnings: ${JSON.stringify(output.warnings)}`
    );
  });

  test('accepts inherit model_profile as valid', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'config.json'),
      JSON.stringify({
        model_profile: 'inherit',
        workflow: {
          research: true,
          plan_check: true,
          verifier: true,
          nyquist_validation: true,
        },
      })
    );
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      !output.warnings.some(w => w.code === 'W004'),
      `Should not warn for inherit model_profile: ${JSON.stringify(output.warnings)}`
    );
  });

  // ─── Check 5c: model_profile "adaptive" + per-phase-type tier validation
  // (W022, #2070) ──────────────────────────────────────────────────────────
  // W004 must be sourced from the catalog's VALID_PROFILES (so "adaptive"
  // is accepted), and a new W022 must fire for any `models.<phase_type>`
  // entry whose value is not a valid tier (opus/sonnet/haiku/inherit),
  // including non-string values, and for keys that are not valid phase types.

  test('accepts adaptive model_profile as valid (no W004)', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'config.json'),
      JSON.stringify({ model_profile: 'adaptive' })
    );
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      !output.warnings.some(w => w.code === 'W004'),
      `Should not warn W004 for adaptive model_profile: ${JSON.stringify(output.warnings)}`
    );
  });

  test('every catalog profile is accepted without W004', () => {
    // Loop over VALID_PROFILES so this can never drift from the catalog.
    for (const profile of VALID_PROFILES) {
      const dir = createTempProject();
      try {
        writeMinimalProjectMd(dir);
        writeMinimalRoadmap(dir, ['1']);
        writeMinimalStateMd(dir);
        fs.writeFileSync(
          path.join(dir, '.planning', 'config.json'),
          JSON.stringify({ model_profile: profile })
        );
        fs.mkdirSync(path.join(dir, '.planning', 'phases', '01-a'), { recursive: true });

        const result = runMsdTools('validate health', dir);
        assert.ok(result.success, `Command failed for profile "${profile}": ${result.error}`);

        const output = JSON.parse(result.output);
        assert.ok(
          !output.warnings.some(w => w.code === 'W004'),
          `Should not warn W004 for catalog profile "${profile}": ${JSON.stringify(output.warnings)}`
        );
      } finally {
        cleanup(dir);
      }
    }
  });

  test('still warns W004 for a genuinely invalid model_profile (regression guard)', () => {
    // Don't let the adaptive-profile fix over-broaden into accepting everything.
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'config.json'),
      JSON.stringify({ model_profile: 'bogus' })
    );
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      output.warnings.some(w => w.code === 'W004'),
      `Expected W004 to still fire for a bogus model_profile: ${JSON.stringify(output.warnings)}`
    );
  });

  test('warns W022 for an invalid tier value under models.<phase_type>', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'config.json'),
      JSON.stringify({ model_profile: 'balanced', models: { planning: 'opuss' } })
    );
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    const w022 = output.warnings.find(w => w.code === 'W022');
    assert.ok(w022, `Expected W022 in warnings: ${JSON.stringify(output.warnings)}`);
    const fullText = `${w022.message} ${w022.fix || ''}`;
    assert.ok(fullText.includes('planning'), `Expected W022 message to name "planning": ${JSON.stringify(w022)}`);
    assert.ok(fullText.includes('opuss'), `Expected W022 message to name "opuss": ${JSON.stringify(w022)}`);
    assert.ok(
      /ignor/i.test(fullText),
      `Expected W022 message to indicate the value will be ignored: ${JSON.stringify(w022)}`
    );
  });

  test('does not warn W022 or W004 for a valid tier value under models.<phase_type>', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'config.json'),
      JSON.stringify({ model_profile: 'balanced', models: { planning: 'opus' } })
    );
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      !output.warnings.some(w => w.code === 'W022'),
      `Should not have W022 for valid tier "opus": ${JSON.stringify(output.warnings)}`
    );
    assert.ok(
      !output.warnings.some(w => w.code === 'W004'),
      `Should not have W004: ${JSON.stringify(output.warnings)}`
    );
  });

  for (const tier of ['sonnet', 'haiku', 'inherit']) {
    test(`does not warn W022 for the valid tier value "${tier}" under models.<phase_type>`, () => {
      writeMinimalProjectMd(tmpDir);
      writeMinimalRoadmap(tmpDir, ['1']);
      writeMinimalStateMd(tmpDir);
      fs.writeFileSync(
        path.join(tmpDir, '.planning', 'config.json'),
        JSON.stringify({ model_profile: 'balanced', models: { planning: tier } })
      );
      fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

      const result = runMsdTools('validate health', tmpDir);
      assert.ok(result.success, `Command failed: ${result.error}`);

      const output = JSON.parse(result.output);
      assert.ok(
        !output.warnings.some(w => w.code === 'W022'),
        `Should not have W022 for valid tier "${tier}": ${JSON.stringify(output.warnings)}`
      );
    });
  }

  test('warns W022 for a numeric (non-string) models.<phase_type> value', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'config.json'),
      JSON.stringify({ model_profile: 'balanced', models: { planning: 5 } })
    );
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      output.warnings.some(w => w.code === 'W022'),
      `Expected W022 for numeric models.planning value: ${JSON.stringify(output.warnings)}`
    );
  });

  test('warns W022 for a null models.<phase_type> value', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'config.json'),
      JSON.stringify({ model_profile: 'balanced', models: { planning: null } })
    );
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      output.warnings.some(w => w.code === 'W022'),
      `Expected W022 for null models.planning value: ${JSON.stringify(output.warnings)}`
    );
  });

  test('warns W022 for an empty-string models.<phase_type> value', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'config.json'),
      JSON.stringify({ model_profile: 'balanced', models: { planning: '' } })
    );
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      output.warnings.some(w => w.code === 'W022'),
      `Expected W022 for empty-string models.planning value: ${JSON.stringify(output.warnings)}`
    );
  });

  test('warns W022 for a mistyped models phase-type key, naming the unknown key', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'config.json'),
      JSON.stringify({ model_profile: 'balanced', models: { plannning: 'opus' } })
    );
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    const w022 = output.warnings.find(w => w.code === 'W022');
    assert.ok(w022, `Expected W022 in warnings: ${JSON.stringify(output.warnings)}`);
    const fullText = `${w022.message} ${w022.fix || ''}`;
    assert.ok(
      fullText.includes('plannning'),
      `Expected W022 message to name the unknown key "plannning": ${JSON.stringify(w022)}`
    );
  });

  // ─── #2070 review finding 3: malformed top-level `models` is silently
  // skipped today (src/verify.cts guards `typeof === 'object' && !Array`
  // with no else branch, so an array/string/number/boolean `models` value
  // produces ZERO diagnostics — the same undiagnosable-no-op class #2070
  // targets). `models` absent or explicitly `null` must stay silent. ────────

  for (const [label, malformedModels] of [
    ['an array', []],
    ['a string', 'opus'],
    ['a number', 5],
    ['a boolean', true],
  ]) {
    test(`warns W022 for a top-level models value that is ${label} (not a plain object)`, () => {
      writeMinimalProjectMd(tmpDir);
      writeMinimalRoadmap(tmpDir, ['1']);
      writeMinimalStateMd(tmpDir);
      fs.writeFileSync(
        path.join(tmpDir, '.planning', 'config.json'),
        JSON.stringify({ model_profile: 'balanced', models: malformedModels })
      );
      fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

      const result = runMsdTools('validate health', tmpDir);
      assert.ok(result.success, `Command failed: ${result.error}`);

      const output = JSON.parse(result.output);
      const w022 = output.warnings.find(w => w.code === 'W022');
      assert.ok(
        w022,
        `Expected W022 when top-level models is ${label} (${JSON.stringify(malformedModels)}): ${JSON.stringify(output.warnings)}`
      );
      const fullText = `${w022.message} ${w022.fix || ''}`;
      assert.ok(fullText.includes('models'), `Expected W022 message to mention "models": ${JSON.stringify(w022)}`);
      assert.ok(/object/i.test(fullText), `Expected W022 message to indicate models must be an object: ${JSON.stringify(w022)}`);
      assert.ok(/ignor/i.test(fullText), `Expected W022 message to indicate the value will be ignored: ${JSON.stringify(w022)}`);
    });
  }

  test('does not warn W022 for an empty-object top-level models value (valid, just empty)', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'config.json'),
      JSON.stringify({ model_profile: 'balanced', models: {} })
    );
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      !output.warnings.some(w => w.code === 'W022'),
      `Should not warn W022 for an empty models object: ${JSON.stringify(output.warnings)}`
    );
  });

  test('does not warn W022 for a top-level models value of null (explicit unset)', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'config.json'),
      JSON.stringify({ model_profile: 'balanced', models: null })
    );
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      !output.warnings.some(w => w.code === 'W022'),
      `Should not warn W022 for models: null: ${JSON.stringify(output.warnings)}`
    );
  });

  test('does not warn W022 when the models key is absent entirely', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'config.json'),
      JSON.stringify({ model_profile: 'balanced' })
    );
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      !output.warnings.some(w => w.code === 'W022'),
      `Should not warn W022 when models is absent: ${JSON.stringify(output.warnings)}`
    );
  });

  // ─── Check 6: Phase directory naming (NN-name format) ─────────────────────

  test('warns about incorrectly named phase directories', () => {
    writeMinimalProjectMd(tmpDir);
    // Roadmap with no phases to avoid W006
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'ROADMAP.md'),
      '# Roadmap\n\nNo phases yet.\n'
    );
    writeMinimalStateMd(tmpDir, '# Session State\n\nNo phase references.\n');
    writeValidConfigJson(tmpDir);
    // Create a badly named dir
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', 'bad_name'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      output.warnings.some(w => w.code === 'W005'),
      `Expected W005 in warnings: ${JSON.stringify(output.warnings)}`
    );
  });

  // ─── Check 7: Orphaned plans (PLAN without SUMMARY) ───────────────────────

  test('reports orphaned plans (PLAN without SUMMARY) as info', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    writeValidConfigJson(tmpDir);
    // Create 01-test phase dir with a PLAN but no matching SUMMARY
    const phaseDir = path.join(tmpDir, '.planning', 'phases', '01-test');
    fs.mkdirSync(phaseDir, { recursive: true });
    fs.writeFileSync(path.join(phaseDir, '01-01-PLAN.md'), '# Plan\n');
    // No 01-01-SUMMARY.md

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      output.info.some(i => i.code === 'I001'),
      `Expected I001 in info: ${JSON.stringify(output.info)}`
    );
  });

  // ─── Check 8: Consistency (roadmap/disk sync) ─────────────────────────────

  test('warns about phase in ROADMAP but not on disk', () => {
    writeMinimalProjectMd(tmpDir);
    // ROADMAP mentions Phase 5 but no 05-xxx dir
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'ROADMAP.md'),
      '# Roadmap\n\n### Phase 5: Future Phase\n'
    );
    writeMinimalStateMd(tmpDir, '# Session State\n\nNo phase refs.\n');
    writeValidConfigJson(tmpDir);
    // No phase dirs

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      output.warnings.some(w => w.code === 'W006'),
      `Expected W006 in warnings: ${JSON.stringify(output.warnings)}`
    );
  });

  test('warns about phase on disk but not in ROADMAP', () => {
    writeMinimalProjectMd(tmpDir);
    // ROADMAP has no phases
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'ROADMAP.md'),
      '# Roadmap\n\nNo phases listed.\n'
    );
    writeMinimalStateMd(tmpDir, '# Session State\n\nNo phase refs.\n');
    writeValidConfigJson(tmpDir);
    // Orphan phase dir not in ROADMAP
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '99-orphan'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      output.warnings.some(w => w.code === 'W007'),
      `Expected W007 in warnings: ${JSON.stringify(output.warnings)}`
    );
  });

  // ─── Check 5b: Nyquist validation key presence (W008) ─────────────────────

  test('detects W008 when workflow.nyquist_validation absent from config', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir, '# Session State\n\nPhase 1 in progress.\n');
    // Config with workflow section but WITHOUT nyquist_validation key
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'config.json'),
      JSON.stringify({ model_profile: 'balanced', workflow: { research: true } }, null, 2)
    );
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      output.warnings.some(w => w.code === 'W008'),
      `Expected W008 in warnings: ${JSON.stringify(output.warnings)}`
    );
  });

  test('does not emit W008 when nyquist_validation is explicitly set', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir, '# Session State\n\nPhase 1 in progress.\n');
    // Config with workflow.nyquist_validation explicitly set
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'config.json'),
      JSON.stringify({ model_profile: 'balanced', workflow: { research: true, nyquist_validation: true } }, null, 2)
    );
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      !output.warnings.some(w => w.code === 'W008'),
      `Should not have W008: ${JSON.stringify(output.warnings)}`
    );
  });

  // ─── Check 8b: W006 false-positives for not-yet-started phases (#2009) ──────

  test('does not emit W006 for phases listed in ROADMAP summary as unchecked (not started)', () => {
    // A ROADMAP with Phase 1 started (has disk dir) and Phase 2 listed but
    // unchecked (- [ ]) — phase 2 has no directory because it hasn't started.
    // W006 must NOT fire for phase 2.
    writeMinimalProjectMd(tmpDir);
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'ROADMAP.md'),
      [
        '# Roadmap',
        '',
        '## v1.0.0',
        '',
        '- [x] **Phase 1: Setup** - First phase',
        '- [ ] **Phase 2: Build** - Not yet started',
        '',
        '### Phase 1: Setup',
        '',
        '### Phase 2: Build',
        '',
      ].join('\n')
    );
    writeMinimalStateMd(tmpDir, '# Session State\n\nPhase 1 in progress.\n');
    writeValidConfigJson(tmpDir);
    // Only phase 1 dir exists; phase 2 dir does not (not started yet)
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-setup'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    const w006s = output.warnings.filter(w => w.code === 'W006');
    assert.ok(
      w006s.length === 0,
      'W006 must not fire for phases with an unchecked summary checkbox (not yet started), got: ' +
        JSON.stringify(w006s)
    );
  });

  test('still emits W006 for a phase that was started (checked) but has no directory', () => {
    // Phase 1 is marked complete ([x]) in ROADMAP summary but has no directory
    // on disk — that IS a genuine inconsistency and should still trigger W006.
    writeMinimalProjectMd(tmpDir);
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'ROADMAP.md'),
      [
        '# Roadmap',
        '',
        '- [x] **Phase 1: Setup** - Completed',
        '',
        '### Phase 1: Setup',
        '',
      ].join('\n')
    );
    writeMinimalStateMd(tmpDir, '# Session State\n\nPhase 1 done.\n');
    writeValidConfigJson(tmpDir);
    // No phase 1 directory — even though roadmap says it's complete

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      output.warnings.some(w => w.code === 'W006'),
      'W006 must still fire when a completed phase has no directory, warnings: ' +
        JSON.stringify(output.warnings)
    );
  });

  // ─── Check 7b: Nyquist VALIDATION.md consistency (W009) ──────────────────

  test('detects W009 when RESEARCH.md has Validation Architecture but no VALIDATION.md', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir, '# Session State\n\nPhase 1 in progress.\n');
    writeValidConfigJson(tmpDir);
    // Create phase dir with RESEARCH.md containing Validation Architecture
    const phaseDir = path.join(tmpDir, '.planning', 'phases', '01-setup');
    fs.mkdirSync(phaseDir, { recursive: true });
    fs.writeFileSync(
      path.join(phaseDir, '01-RESEARCH.md'),
      '# Research\n\n## Validation Architecture\n\nSome validation content.\n'
    );
    // No VALIDATION.md

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      output.warnings.some(w => w.code === 'W009'),
      `Expected W009 in warnings: ${JSON.stringify(output.warnings)}`
    );
  });

  test('does not emit W009 when VALIDATION.md exists alongside RESEARCH.md', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir, '# Session State\n\nPhase 1 in progress.\n');
    writeValidConfigJson(tmpDir);
    // Create phase dir with both RESEARCH.md and VALIDATION.md
    const phaseDir = path.join(tmpDir, '.planning', 'phases', '01-setup');
    fs.mkdirSync(phaseDir, { recursive: true });
    fs.writeFileSync(
      path.join(phaseDir, '01-RESEARCH.md'),
      '# Research\n\n## Validation Architecture\n\nSome validation content.\n'
    );
    fs.writeFileSync(
      path.join(phaseDir, '01-VALIDATION.md'),
      '# Validation\n\nValidation content.\n'
    );

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      !output.warnings.some(w => w.code === 'W009'),
      `Should not have W009: ${JSON.stringify(output.warnings)}`
    );
  });

  // ─── Overall status ────────────────────────────────────────────────────────

  test("returns 'healthy' when all checks pass", () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir, '# Session State\n\nPhase 1 in progress.\n');
    writeValidConfigJson(tmpDir);
    // Create valid phase dir matching ROADMAP
    const phaseDir = path.join(tmpDir, '.planning', 'phases', '01-a');
    fs.mkdirSync(phaseDir, { recursive: true });
    // Add PLAN+SUMMARY so no I001
    fs.writeFileSync(path.join(phaseDir, '01-01-PLAN.md'), '# Plan\n');
    fs.writeFileSync(path.join(phaseDir, '01-01-SUMMARY.md'), '# Summary\n');

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.strictEqual(output.status, 'healthy', `Expected healthy, got ${output.status}. Errors: ${JSON.stringify(output.errors)}, Warnings: ${JSON.stringify(output.warnings)}`);
    assert.deepStrictEqual(output.errors, [], 'should have no errors');
    assert.deepStrictEqual(output.warnings, [], 'should have no warnings');
  });

  test("returns 'degraded' when only warnings exist", () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    // No config.json → W003 (warning, not error)
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.strictEqual(output.status, 'degraded', `Expected degraded, got ${output.status}`);
    assert.strictEqual(output.errors.length, 0, 'should have no errors');
    assert.ok(output.warnings.length > 0, 'should have warnings');
  });

  // #3225: sentinel phase dirs (999.x backlog/interim, 0.x drafts) are defined as
  // never-on-roadmap (SENTINEL_RANGES=[0,999]). The W006/W007 disk↔roadmap loops
  // never had the isSentinelPhaseId guard that phase.cts has, so every sentinel dir
  // produced a spurious W007 with wrong fix advice ("Add to roadmap or remove
  // directory"). Sentinels must be excluded; a real (non-sentinel) orphan must still warn.
  test('#3225: sentinel phase dirs (999/0) do not trigger W007; real orphans still do', () => {
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    writeValidConfigJson(tmpDir);
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });
    // Sentinel dirs — never-on-roadmap by convention.
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '999-interim'), { recursive: true });
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '0-drafts'), { recursive: true });
    // A real orphan (non-sentinel) that SHOULD still trigger W007.
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '77-orphan'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);
    const output = JSON.parse(result.output);

    const sentinelW007s = output.warnings.filter(
      w => w.code === 'W007' && /\b(0|999)\b/.test(w.message)
    );
    assert.strictEqual(
      sentinelW007s.length, 0,
      `sentinel phase dirs must not trigger W007; got: ${JSON.stringify(sentinelW007s)}`
    );

    // Negative space: the non-sentinel orphan must still be flagged.
    assert.ok(
      output.warnings.some(w => w.code === 'W007' && /77\b/.test(w.message)),
      `expected W007 for the real orphan 77; got: ${JSON.stringify(output.warnings.filter(w => w.code === 'W007'))}`
    );
  });
});

// ─────────────────────────────────────────────────────────────────────────────
// validate health --repair command
// ─────────────────────────────────────────────────────────────────────────────

describe('validate health --repair command', () => {
  let tmpDir;

  beforeEach(() => {
    tmpDir = createTempProject();
    // Set up base project with ROADMAP and PROJECT.md so repairs are triggered
    // (E001, E003 are not repairable so we always need .planning/ and ROADMAP.md)
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-a'), { recursive: true });
  });

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

  test('creates config.json with defaults when missing', () => {
    // STATE.md present so no STATE repair; no config.json
    writeMinimalStateMd(tmpDir, '# Session State\n\nPhase 1 in progress.\n');
    // Ensure no config.json
    const configPath = path.join(tmpDir, '.planning', 'config.json');
    if (fs.existsSync(configPath)) fs.unlinkSync(configPath);

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

    const output = JSON.parse(result.output);
    assert.ok(
      Array.isArray(output.repairs_performed),
      `Expected repairs_performed array: ${JSON.stringify(output)}`
    );
    const createAction = output.repairs_performed.find(r => r.action === 'createConfig');
    assert.ok(createAction, `Expected createConfig action: ${JSON.stringify(output.repairs_performed)}`);
    assert.strictEqual(createAction.success, true, 'createConfig should succeed');

    // Verify config.json now exists on disk with valid JSON and balanced profile
    assert.ok(fs.existsSync(configPath), 'config.json should now exist on disk');
    const diskConfig = JSON.parse(fs.readFileSync(configPath, 'utf-8'));
    assert.strictEqual(diskConfig.model_profile, 'balanced', 'default model_profile should be balanced');
    // Verify nested workflow structure matches config.cjs canonical format
    assert.ok(diskConfig.workflow, 'config should have nested workflow object');
    assert.strictEqual(diskConfig.workflow.research, true, 'workflow.research should default to true');
    assert.strictEqual(diskConfig.workflow.plan_check, true, 'workflow.plan_check should default to true');
    assert.strictEqual(diskConfig.workflow.verifier, true, 'workflow.verifier should default to true');
    assert.strictEqual(diskConfig.workflow.nyquist_validation, true, 'workflow.nyquist_validation should default to true');
    // Verify branch templates are present
    assert.strictEqual(diskConfig.phase_branch_template, 'msd/phase-{phase}-{slug}');
    assert.strictEqual(diskConfig.milestone_branch_template, 'msd/{milestone}-{slug}');
  });

  test('Phase 11 (#3309): refuses to reset config.json when JSON is invalid — resetConfig is DESTRUCTIVE, --repair leaves it untouched', () => {
    // Pre-migration this repair action applied unconditionally; the design
    // doc's "--repair behavior change" section makes this a disclosed
    // breaking change: a DESTRUCTIVE remedy is reported (still visible in
    // repairs_performed, as a refusal) but never executed by --repair.
    writeMinimalStateMd(tmpDir, '# Session State\n\nPhase 1 in progress.\n');
    const configPath = path.join(tmpDir, '.planning', 'config.json');
    const originalContent = '{broken json';
    fs.writeFileSync(configPath, originalContent);

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

    const output = JSON.parse(result.output);
    assert.ok(
      Array.isArray(output.repairs_performed),
      `Expected repairs_performed: ${JSON.stringify(output)}`
    );
    const resetAction = output.repairs_performed.find(r => r.action === 'resetConfig');
    assert.ok(resetAction, `Expected a resetConfig refusal entry: ${JSON.stringify(output.repairs_performed)}`);
    assert.strictEqual(resetAction.success, false, 'resetConfig must be refused, not applied');
    assert.match(resetAction.error || '', /destructive/i, 'refusal must explain WHY it was not applied');

    // config.json must remain exactly as it was — untouched.
    assert.strictEqual(fs.readFileSync(configPath, 'utf-8'), originalContent, 'config.json must not be modified by a refused repair');
  });

  test('Phase 11 (#3309): refuses to regenerate STATE.md when missing — regenerateState is DESTRUCTIVE, --repair leaves it absent', () => {
    writeValidConfigJson(tmpDir);
    // No STATE.md
    const statePath = path.join(tmpDir, '.planning', 'STATE.md');
    if (fs.existsSync(statePath)) fs.unlinkSync(statePath);

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

    const output = JSON.parse(result.output);
    assert.ok(
      Array.isArray(output.repairs_performed),
      `Expected repairs_performed: ${JSON.stringify(output)}`
    );
    const regenerateAction = output.repairs_performed.find(r => r.action === 'regenerateState');
    assert.ok(regenerateAction, `Expected a regenerateState refusal entry: ${JSON.stringify(output.repairs_performed)}`);
    assert.strictEqual(regenerateAction.success, false, 'regenerateState must be refused, not applied');
    assert.match(regenerateAction.error || '', /destructive/i, 'refusal must explain WHY it was not applied');

    // STATE.md must remain absent, and no backup file should have been created.
    assert.strictEqual(fs.existsSync(statePath), false, 'STATE.md must remain absent — the DESTRUCTIVE remedy is refused');
    const planningFiles = fs.readdirSync(path.join(tmpDir, '.planning'));
    assert.strictEqual(
      planningFiles.some(f => f.startsWith('STATE.md.bak-')),
      false,
      'no backup file should be created for a refused repair',
    );
  });

  test('does not rewrite existing STATE.md for invalid phase references', () => {
    writeValidConfigJson(tmpDir);
    const statePath = path.join(tmpDir, '.planning', 'STATE.md');
    const originalContent = '# Session State\n\nPhase 99 is current.\n';
    fs.writeFileSync(
      statePath,
      originalContent
    );

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

    const output = JSON.parse(result.output);
    assert.ok(
      !Array.isArray(output.repairs_performed) || !output.repairs_performed.some(r => r.action === 'regenerateState'),
      `Did not expect regenerateState for W002: ${JSON.stringify(output)}`
    );

    const stateContent = fs.readFileSync(statePath, 'utf-8');
    assert.strictEqual(stateContent, originalContent, 'existing STATE.md should be preserved');

    const planningDir = path.join(tmpDir, '.planning');
    const planningFiles = fs.readdirSync(planningDir);
    const backupFile = planningFiles.find(f => f.startsWith('STATE.md.bak-'));
    assert.strictEqual(backupFile, undefined, `Did not expect backup file for non-destructive repair. Found: ${planningFiles.join(', ')}`);
  });

  test('adds nyquist_validation key to config.json via addNyquistKey repair', () => {
    writeMinimalStateMd(tmpDir, '# Session State\n\nPhase 1 in progress.\n');
    // Config with workflow section but missing nyquist_validation
    const configPath = path.join(tmpDir, '.planning', 'config.json');
    fs.writeFileSync(
      configPath,
      JSON.stringify({ model_profile: 'balanced', workflow: { research: true } }, null, 2)
    );

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

    const output = JSON.parse(result.output);
    assert.ok(
      Array.isArray(output.repairs_performed),
      `Expected repairs_performed array: ${JSON.stringify(output)}`
    );
    const addKeyAction = output.repairs_performed.find(r => r.action === 'addNyquistKey');
    assert.ok(addKeyAction, `Expected addNyquistKey action: ${JSON.stringify(output.repairs_performed)}`);
    assert.strictEqual(addKeyAction.success, true, 'addNyquistKey should succeed');

    // Read config.json and verify workflow.nyquist_validation is true
    const diskConfig = JSON.parse(fs.readFileSync(configPath, 'utf-8'));
    assert.strictEqual(diskConfig.workflow.nyquist_validation, true, 'nyquist_validation should be true');
  });

  test('reports repairable_count correctly — counts NONE-risk findings only, not the DESTRUCTIVE E004', () => {
    // No config.json (W003, createConfig, NONE risk -> repairable=true) and no
    // STATE.md (E004, regenerateState, DESTRUCTIVE risk -> repairable=false,
    // Phase 11 #3309: --repair never auto-applies a DESTRUCTIVE remedy, so it
    // is deliberately excluded from this count — see the `diagnosticToIssueEntry`
    // comment in src/verify.cts for the full reasoning).
    const configPath = path.join(tmpDir, '.planning', 'config.json');
    if (fs.existsSync(configPath)) fs.unlinkSync(configPath);
    const statePath = path.join(tmpDir, '.planning', 'STATE.md');
    if (fs.existsSync(statePath)) fs.unlinkSync(statePath);

    // Run WITHOUT --repair to just check repairable_count
    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    const w003 = output.warnings.find(w => w.code === 'W003');
    const e004 = output.errors.find(e => e.code === 'E004');
    assert.ok(w003, `Expected W003 in warnings: ${JSON.stringify(output.warnings)}`);
    assert.ok(e004, `Expected E004 in errors: ${JSON.stringify(output.errors)}`);
    assert.strictEqual(w003.repairable, true, 'W003 (createConfig, NONE risk) should be repairable');
    assert.strictEqual(e004.repairable, false, 'E004 (regenerateState, DESTRUCTIVE risk) should not be repairable');
    assert.strictEqual(
      output.repairable_count, 1,
      `Expected repairable_count 1 (W003 only), got ${output.repairable_count}. Full output: ${JSON.stringify(output)}`
    );
  });

  test('phase mismatch warnings do not count as repairable issues', () => {
    writeValidConfigJson(tmpDir);
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'STATE.md'),
      '# Session State\n\nPhase 99 is the current phase.\n'
    );

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.strictEqual(output.repairable_count, 0, `Expected no repairable issues for W002: ${JSON.stringify(output)}`);
  });
});

// ─────────────────────────────────────────────────────────────────────────────
// Regression: CJS bundle drift — W005/W006/I001 false positives (#3806)
// PR #3479 fixed these in sdk/src/query/validate.ts but never propagated to
// msd-core/bin/lib/verify.cjs. These tests fail on old verify.cjs and
// pass on the fixed version.
// ─────────────────────────────────────────────────────────────────────────────

describe('validate health — #3806 CJS bundle drift regressions', () => {
  let tmpDir;

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

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

  // W005 regression: \d{2} → \d{2,} so 999.1-foo is accepted (#3806)
  test('does not emit W005 for a phase directory with a 3-digit prefix (999.1-foo)', () => {
    writeMinimalProjectMd(tmpDir);
    // Roadmap with no phases to avoid spurious W006
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'ROADMAP.md'),
      '# Roadmap\n\nNo phases yet.\n'
    );
    writeMinimalStateMd(tmpDir, '# Session State\n\nNo phase refs.\n');
    writeValidConfigJson(tmpDir);
    // 999.1-foo should be valid under the widened \d{2,} pattern
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '999.1-foo'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    const w005s = output.warnings.filter(w => w.code === 'W005');
    assert.strictEqual(
      w005s.length, 0,
      `W005 must not fire for "999.1-foo" (3-digit prefix is valid under \\d{2,}), got: ${JSON.stringify(w005s)}`
    );
  });

  // W005 regression: additional multi-digit variants
  test('does not emit W005 for phase directories with 4-digit and 2-digit prefixes', () => {
    writeMinimalProjectMd(tmpDir);
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'ROADMAP.md'),
      '# Roadmap\n\nNo phases yet.\n'
    );
    writeMinimalStateMd(tmpDir, '# Session State\n\nNo phase refs.\n');
    writeValidConfigJson(tmpDir);
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '1000-backlog'), { recursive: true });
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '99-done'), { recursive: true });
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '100.2-feature'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    const w005s = output.warnings.filter(w => w.code === 'W005');
    assert.strictEqual(
      w005s.length, 0,
      `W005 must not fire for multi-digit prefix dirs (\\d{2,} pattern), got: ${JSON.stringify(w005s)}`
    );
  });

  // W006 regression: archived phases in milestones/*-phases/ must not trigger W006 (#3806)
  test('does not emit W006 for a ROADMAP phase whose directory lives in a milestone archive', () => {
    writeMinimalProjectMd(tmpDir);
    // ROADMAP references Phase 1 in the current section
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'ROADMAP.md'),
      [
        '# Roadmap',
        '',
        '## v1.0.0',
        '',
        '### Phase 1: Setup',
        '',
      ].join('\n')
    );
    writeMinimalStateMd(tmpDir, '# Session State\n\nPhase 1 complete.\n');
    writeValidConfigJson(tmpDir);
    // Phase 1 directory is in a milestone archive, NOT in the flat phases/ dir
    const archiveDir = path.join(tmpDir, '.planning', 'milestones', 'v1.0.0-phases');
    fs.mkdirSync(path.join(archiveDir, '01-setup'), { recursive: true });
    // Ensure flat phases dir exists but does NOT contain phase 1
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    const w006s = output.warnings.filter(w => w.code === 'W006');
    assert.strictEqual(
      w006s.length, 0,
      `W006 must not fire for Phase 1 when its directory is in a milestone archive, got: ${JSON.stringify(w006s)}`
    );
  });

  // I001 regression: FOO-PLAN.md + FOO-SUMMARY.md must match via canonicalPlanStem (#3806)
  // e.g. 68-01-scaffolding-PLAN.md should match 68-01-SUMMARY.md (canonical stem = "68-01")
  test('does not emit I001 when PLAN name has a descriptor suffix but SUMMARY uses canonical stem', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir, '# Session State\n\nPhase 1 in progress.\n');
    writeValidConfigJson(tmpDir);
    // Create phase dir with descriptor-named PLAN and canonical-named SUMMARY
    const phaseDir = path.join(tmpDir, '.planning', 'phases', '01-setup');
    fs.mkdirSync(phaseDir, { recursive: true });
    // PLAN has a descriptor suffix; SUMMARY uses the canonical stem only
    fs.writeFileSync(path.join(phaseDir, '01-01-scaffolding-PLAN.md'), '# Plan\n');
    fs.writeFileSync(path.join(phaseDir, '01-01-SUMMARY.md'), '# Summary\n');

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    const i001s = output.info.filter(i => i.code === 'I001');
    assert.strictEqual(
      i001s.length, 0,
      `I001 must not fire when SUMMARY stem (01-01) matches the canonical base of PLAN (01-01-scaffolding → 01-01), got: ${JSON.stringify(i001s)}`
    );
  });

  // Confirm I001 still fires for a genuinely orphaned plan (no summary at all)
  test('still emits I001 for a PLAN with no matching SUMMARY at all', () => {
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir, '# Session State\n\nPhase 1 in progress.\n');
    writeValidConfigJson(tmpDir);
    const phaseDir = path.join(tmpDir, '.planning', 'phases', '01-setup');
    fs.mkdirSync(phaseDir, { recursive: true });
    fs.writeFileSync(path.join(phaseDir, '01-01-PLAN.md'), '# Plan\n');
    // No SUMMARY file at all

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      output.info.some(i => i.code === 'I001'),
      `I001 must still fire for an orphaned PLAN (no SUMMARY exists), got: ${JSON.stringify(output.info)}`
    );
  });
});

// ─────────────────────────────────────────────────────────────────────────────
// Graceful degradation when phasesDir is missing (#1973)
// ─────────────────────────────────────────────────────────────────────────────

describe('validate health — missing phasesDir', () => {
  let tmpDir;

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

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

  test('completes without throwing and emits zero phase-directory warnings when phasesDir does not exist', () => {
    // Setup: valid PROJECT, ROADMAP, STATE, config but NO phases directory
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1', '2']);
    writeMinimalStateMd(tmpDir);
    writeValidConfigJson(tmpDir);

    // Remove the phases directory if it exists
    const phasesDir = path.join(tmpDir, '.planning', 'phases');
    if (fs.existsSync(phasesDir)) {
      // eslint-disable-next-line local/no-raw-rmsync-in-tests -- mid-test SUT setup: removes phases/ to simulate missing phasesDir condition
      fs.rmSync(phasesDir, { recursive: true, force: true });
    }

    // Should complete without throwing
    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command should succeed when phasesDir is missing: ${result.error}`);

    const output = JSON.parse(result.output);

    // Assert no phase-directory warnings fired
    const phaseDirCodes = ['W005', 'W006', 'W007', 'W009', 'I001'];
    const issues = output.issues || [];
    for (const code of phaseDirCodes) {
      const matches = issues.filter(i => i.code === code);
      assert.strictEqual(matches.length, 0, `Expected no ${code} issues when phasesDir is missing, got: ${JSON.stringify(matches)}`);
    }
  });
});

// ─────────────────────────────────────────────────────────────────────────────
// #1472 regression — workstream-aware paths
// ─────────────────────────────────────────────────────────────────────────────

describe('validate health — #1472 workstream-aware path resolution', () => {
  let tmpDir;

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

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

  test('reports healthy when MSD_WORKSTREAM is set and files are in the correct workstream layout', () => {
    // Shared-root files at .planning/
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'PROJECT.md'),
      '# Project\n\n## What This Is\n\nTest project.\n\n## Core Value\n\nCore value here.\n\n## Requirements\n\nRequirements here.\n'
    );
    fs.writeFileSync(
      path.join(tmpDir, '.planning', 'config.json'),
      JSON.stringify({ model_profile: 'balanced', commit_docs: true, workflow: { nyquist_validation: true, ai_integration_phase: true } }, null, 2)
    );

    // Workstream-scoped files at .planning/workstreams/ws-a/
    const wsDir = path.join(tmpDir, '.planning', 'workstreams', 'ws-a');
    fs.mkdirSync(wsDir, { recursive: true });
    fs.writeFileSync(
      path.join(wsDir, 'ROADMAP.md'),
      '# Roadmap\n\n### Phase 1: Setup\n'
    );
    fs.writeFileSync(
      path.join(wsDir, 'STATE.md'),
      '# Session State\n\n## Current Position\n\nPhase: 1\n'
    );
    const wsPhaseDir = path.join(wsDir, 'phases', '01-setup');
    fs.mkdirSync(wsPhaseDir, { recursive: true });

    const result = runMsdTools('validate health', tmpDir, { MSD_WORKSTREAM: 'ws-a' });
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    // PROJECT.md and config.json must NOT be reported missing (E002/W003)
    assert.ok(
      !output.errors.some(e => e.code === 'E002'),
      `E002 (PROJECT.md missing) should not fire with workstream layout: ${JSON.stringify(output.errors)}`
    );
    assert.ok(
      !output.errors.some(e => e.code === 'E003'),
      `E003 (ROADMAP.md missing) should not fire with workstream layout: ${JSON.stringify(output.errors)}`
    );
    assert.ok(
      !output.errors.some(e => e.code === 'E004'),
      `E004 (STATE.md missing) should not fire with workstream layout: ${JSON.stringify(output.errors)}`
    );
    assert.ok(
      !output.warnings.some(w => w.code === 'W003'),
      `W003 (config.json missing) should not fire with workstream layout: ${JSON.stringify(output.warnings)}`
    );
    // Status should not be 'broken' due to path misrouting
    assert.notStrictEqual(
      output.status, 'broken',
      `Status should not be broken when files exist in the correct workstream layout: ${JSON.stringify(output)}`
    );
  });

  test('without MSD_WORKSTREAM, shared-root files are found at .planning/ root', () => {
    // All files at .planning/ root (no workstream sub-path)
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    writeValidConfigJson(tmpDir);
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-setup'), { recursive: true });

    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      !output.errors.some(e => ['E002', 'E003', 'E004'].includes(e.code)),
      `No E002/E003/E004 should fire in standard non-workstream layout: ${JSON.stringify(output.errors)}`
    );
  });
});

// ─────────────────────────────────────────────────────────────────────────────
// #1454 regression — W017 must not fire for the active worktree
// ─────────────────────────────────────────────────────────────────────────────

describe('validate health — #1454 W017 excludes active worktree', () => {
  let tmpDir;

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

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

  // The active-worktree exclusion guard in the SUT (src/verify.cts) compares
  // process.cwd() against each stale-finding path at runtime. The integration
  // scenario below covers the observable CLI contract; the unit-level injection
  // path is omitted here because bin/lib/verify.cjs is a gitignored tsc artifact
  // not present in a fresh worktree.

  test('validate health completes without W017 for the cwd itself when inspected as worktree root', () => {
    // Set up a minimal healthy project at tmpDir
    writeMinimalProjectMd(tmpDir);
    writeMinimalRoadmap(tmpDir, ['1']);
    writeMinimalStateMd(tmpDir);
    writeValidConfigJson(tmpDir);
    fs.mkdirSync(path.join(tmpDir, '.planning', 'phases', '01-setup'), { recursive: true });

    // Run with cwd = tmpDir. The SUT will call process.cwd() which is the test runner's cwd,
    // not tmpDir, so any stale worktree that matches tmpDir (as a non-cwd) CAN legitimately
    // be flagged. The guard only protects the CURRENT process.cwd().
    // What we assert: when there is no real git repo at tmpDir, no W017 fires (git worktree
    // list will fail / return empty — the try/catch swallows it silently).
    const result = runMsdTools('validate health', tmpDir);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      !output.warnings.some(w => w.code === 'W017'),
      `W017 should not fire for a non-git project dir: ${JSON.stringify(output.warnings)}`
    );
  });
});

// ─────────────────────────────────────────────────────────────────────────────
// W029 — .planning/ tracked-and-gitignored (#3586, epic #2292)
//
// Test matrix: .msd/phase/fix-3586-tracked-gitignored-planning/50-test-matrix.md
// section C (C1/C2) — CLI-LEVEL integration, through the real `msd-tools
// validate health` dispatch path (unlike tests/health-diagnostic-rules/
// config-validation.test.cjs's B-group, which drives `ruleFor('W029').check`
// directly against a hand-built snapshot). These two prove W029 is actually
// REACHABLE end-to-end — registered in RULES is not the same claim as wired
// into `cmdValidateHealth`'s JSON output.
//
// Asserted on the parsed JSON's `code` field only (never rendered text, per
// CONTRIBUTING's ban on raw-text output matching) — the real CLI response
// shape carries no per-diagnostic `severity` field; severity is expressed
// structurally by which top-level array (`errors` vs `warnings`) an entry
// lands in, so "W029 is in `warnings`" already encodes SEVERITY.WARNING.
// ─────────────────────────────────────────────────────────────────────────────

describe('validate health — W029 .planning/ tracked-and-gitignored (#3586)', () => {
  function initGitRepo(cwd) {
    gitOrThrow(['init'], { cwd });
    gitOrThrow(['config', 'user.email', 'test@test.com'], { cwd });
    gitOrThrow(['config', 'user.name', 'Test'], { cwd });
    gitOrThrow(['config', 'commit.gpgsign', 'false'], { cwd });
  }

  function commitAll(cwd, message) {
    gitOrThrow(['add', '-A'], { cwd });
    gitOrThrow(['commit', '-m', message], { cwd });
  }

  test('C1: healthReportsTrackedIgnoredState — a temp git project with .planning/ committed then gitignored reports W029', () => {
    const cwd = createTempProject();
    // createTempProject() writes only an EMPTY .planning/phases/ dir — git
    // never tracks an empty directory, so without a real file under
    // .planning/ the initial commit would track nothing and this fixture
    // could never reach the "tracked" half of the contradiction.
    fs.writeFileSync(path.join(cwd, '.planning', 'PROJECT.md'), '# Project\n');
    initGitRepo(cwd);
    commitAll(cwd, 'initial commit — .planning/ tracked');
    fs.writeFileSync(path.join(cwd, '.gitignore'), '.planning/\n');
    commitAll(cwd, 'add gitignore — .planning/ now contradictorily ignored-but-tracked');

    const result = runMsdTools('validate health', cwd);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    const w029 = output.warnings.find(w => w.code === 'W029');
    assert.ok(w029, `Expected W029 in warnings: ${JSON.stringify(output.warnings)}`);
    assert.strictEqual(w029.code, 'W029');
  });

  test('C2: healthSilentOnHealthyProject — the same project layout with .planning/ tracked and NOT ignored reports no W029', () => {
    const cwd = createTempProject();
    fs.writeFileSync(path.join(cwd, '.planning', 'PROJECT.md'), '# Project\n');
    initGitRepo(cwd);
    commitAll(cwd, 'initial commit — .planning/ tracked, no .gitignore at all');
    // No .gitignore written — the default, healthy state of essentially
    // every MSD project (mirrors the B2a/A3 fixture convention).

    const result = runMsdTools('validate health', cwd);
    assert.ok(result.success, `Command failed: ${result.error}`);

    const output = JSON.parse(result.output);
    assert.ok(
      !output.warnings.some(w => w.code === 'W029'),
      `Should not have W029 on a healthy tracked-not-ignored project: ${JSON.stringify(output.warnings)}`
    );
  });
});