@howlil/ez-agents 3.4.2 → 4.0.0

package/bin/lib/verify.cjs

@@ -0,0 +1,863 @@
+/**
+ * Verify — Verification suite, consistency, and health validation
+ */
+
+const fs = require('fs');
+const path = require('path');
+const { safeReadFile, normalizePhaseName, execGit, findPhaseInternal, getMilestoneInfo, output, error } = require('./core.cjs');
+const { extractFrontmatter, parseMustHavesBlock } = require('./frontmatter.cjs');
+const { writeStateMd } = require('./state.cjs');
+const { defaultLogger: logger } = require('./logger.cjs');
+
+async function cmdVerifySummary(cwd, summaryPath, checkFileCount, raw) {
+  if (!summaryPath) {
+    error('summary-path required');
+  }
+
+  const fullPath = path.join(cwd, summaryPath);
+  const checkCount = checkFileCount || 2;
+
+  // Check 1: Summary exists
+  if (!fs.existsSync(fullPath)) {
+    const result = {
+      passed: false,
+      checks: {
+        summary_exists: false,
+        files_created: { checked: 0, found: 0, missing: [] },
+        commits_exist: false,
+        self_check: 'not_found',
+      },
+      errors: ['SUMMARY.md not found'],
+    };
+    output(result, raw, 'failed');
+    return;
+  }
+
+  const content = fs.readFileSync(fullPath, 'utf-8');
+  const errors = [];
+
+  // Check 2: Spot-check files mentioned in summary
+  const mentionedFiles = new Set();
+  const patterns = [
+    /`([^`]+\.[a-zA-Z]+)`/g,
+    /(?:Created|Modified|Added|Updated|Edited):\s*`?([^\s`]+\.[a-zA-Z]+)`?/gi,
+  ];
+
+  for (const pattern of patterns) {
+    let m;
+    while ((m = pattern.exec(content)) !== null) {
+      const filePath = m[1];
+      if (filePath && !filePath.startsWith('http') && filePath.includes('/')) {
+        mentionedFiles.add(filePath);
+      }
+    }
+  }
+
+  const filesToCheck = Array.from(mentionedFiles).slice(0, checkCount);
+  const missing = [];
+  for (const file of filesToCheck) {
+    if (!fs.existsSync(path.join(cwd, file))) {
+      missing.push(file);
+    }
+  }
+
+  // Check 3: Commits exist
+  const commitHashPattern = /\b[0-9a-f]{7,40}\b/g;
+  const hashes = content.match(commitHashPattern) || [];
+  let commitsExist = false;
+  if (hashes.length > 0) {
+    for (const hash of hashes.slice(0, 3)) {
+      const result = await execGit(cwd, ['cat-file', '-t', hash]);
+      if (result.exitCode === 0 && result.stdout === 'commit') {
+        commitsExist = true;
+        break;
+      }
+    }
+  }
+
+  // Check 4: Self-check section
+  let selfCheck = 'not_found';
+  const selfCheckPattern = /##\s*(?:Self[- ]?Check|Verification|Quality Check)/i;
+  if (selfCheckPattern.test(content)) {
+    const passPattern = /(?:all\s+)?(?:pass|✓|✅|complete|succeeded)/i;
+    const failPattern = /(?:fail|✗|❌|incomplete|blocked)/i;
+    const checkSection = content.slice(content.search(selfCheckPattern));
+    if (failPattern.test(checkSection)) {
+      selfCheck = 'failed';
+    } else if (passPattern.test(checkSection)) {
+      selfCheck = 'passed';
+    }
+  }
+
+  if (missing.length > 0) errors.push('Missing files: ' + missing.join(', '));
+  if (!commitsExist && hashes.length > 0) errors.push('Referenced commit hashes not found in git history');
+  if (selfCheck === 'failed') errors.push('Self-check section indicates failure');
+
+  const checks = {
+    summary_exists: true,
+    files_created: { checked: filesToCheck.length, found: filesToCheck.length - missing.length, missing },
+    commits_exist: commitsExist,
+    self_check: selfCheck,
+  };
+
+  const passed = missing.length === 0 && selfCheck !== 'failed';
+  const result = { passed, checks, errors };
+  output(result, raw, passed ? 'passed' : 'failed');
+}
+
+function cmdVerifyPlanStructure(cwd, filePath, raw) {
+  if (!filePath) { error('file path required'); }
+  const fullPath = path.isAbsolute(filePath) ? filePath : path.join(cwd, filePath);
+  const content = safeReadFile(fullPath);
+  if (!content) { output({ error: 'File not found', path: filePath }, raw); return; }
+
+  const fm = extractFrontmatter(content);
+  const errors = [];
+  const warnings = [];
+
+  // Check required frontmatter fields
+  const required = ['phase', 'plan', 'type', 'wave', 'depends_on', 'files_modified', 'autonomous', 'must_haves'];
+  for (const field of required) {
+    if (fm[field] === undefined) errors.push(`Missing required frontmatter field: ${field}`);
+  }
+
+  // Parse and check task elements
+  const taskPattern = /<task[^>]*>([\s\S]*?)<\/task>/g;
+  const tasks = [];
+  let taskMatch;
+  while ((taskMatch = taskPattern.exec(content)) !== null) {
+    const taskContent = taskMatch[1];
+    const nameMatch = taskContent.match(/<name>([\s\S]*?)<\/name>/);
+    const taskName = nameMatch ? nameMatch[1].trim() : 'unnamed';
+    const hasFiles = /<files>/.test(taskContent);
+    const hasAction = /<action>/.test(taskContent);
+    const hasVerify = /<verify>/.test(taskContent);
+    const hasDone = /<done>/.test(taskContent);
+
+    if (!nameMatch) errors.push('Task missing <name> element');
+    if (!hasAction) errors.push(`Task '${taskName}' missing <action>`);
+    if (!hasVerify) warnings.push(`Task '${taskName}' missing <verify>`);
+    if (!hasDone) warnings.push(`Task '${taskName}' missing <done>`);
+    if (!hasFiles) warnings.push(`Task '${taskName}' missing <files>`);
+
+    tasks.push({ name: taskName, hasFiles, hasAction, hasVerify, hasDone });
+  }
+
+  if (tasks.length === 0) warnings.push('No <task> elements found');
+
+  // Wave/depends_on consistency
+  if (fm.wave && parseInt(fm.wave) > 1 && (!fm.depends_on || (Array.isArray(fm.depends_on) && fm.depends_on.length === 0))) {
+    warnings.push('Wave > 1 but depends_on is empty');
+  }
+
+  // Autonomous/checkpoint consistency
+  const hasCheckpoints = /<task\s+type=["']?checkpoint/.test(content);
+  if (hasCheckpoints && fm.autonomous !== 'false' && fm.autonomous !== false) {
+    errors.push('Has checkpoint tasks but autonomous is not false');
+  }
+
+  output({
+    valid: errors.length === 0,
+    errors,
+    warnings,
+    task_count: tasks.length,
+    tasks,
+    frontmatter_fields: Object.keys(fm),
+  }, raw, errors.length === 0 ? 'valid' : 'invalid');
+}
+
+function cmdVerifyPhaseCompleteness(cwd, phase, raw) {
+  if (!phase) { error('phase required'); }
+  const phaseInfo = findPhaseInternal(cwd, phase);
+  if (!phaseInfo || !phaseInfo.found) {
+    output({ error: 'Phase not found', phase }, raw);
+    return;
+  }
+
+  const errors = [];
+  const warnings = [];
+  const phaseDir = path.join(cwd, phaseInfo.directory);
+
+  // List plans and summaries
+  let files;
+  try {
+    files = fs.readdirSync(phaseDir);
+  } catch (err) {
+    logger.warn('Failed to read phase directory in cmdVerifyPhaseCompleteness', { phaseDir, error: err.message });
+    output({ error: 'Cannot read phase directory' }, raw);
+    return;
+  }
+
+  const plans = files.filter(f => f.match(/-PLAN\.md$/i));
+  const summaries = files.filter(f => f.match(/-SUMMARY\.md$/i));
+
+  // Extract plan IDs (everything before -PLAN.md)
+  const planIds = new Set(plans.map(p => p.replace(/-PLAN\.md$/i, '')));
+  const summaryIds = new Set(summaries.map(s => s.replace(/-SUMMARY\.md$/i, '')));
+
+  // Plans without summaries
+  const incompletePlans = [...planIds].filter(id => !summaryIds.has(id));
+  if (incompletePlans.length > 0) {
+    errors.push(`Plans without summaries: ${incompletePlans.join(', ')}`);
+  }
+
+  // Summaries without plans (orphans)
+  const orphanSummaries = [...summaryIds].filter(id => !planIds.has(id));
+  if (orphanSummaries.length > 0) {
+    warnings.push(`Summaries without plans: ${orphanSummaries.join(', ')}`);
+  }
+
+  output({
+    complete: errors.length === 0,
+    phase: phaseInfo.phase_number,
+    plan_count: plans.length,
+    summary_count: summaries.length,
+    incomplete_plans: incompletePlans,
+    orphan_summaries: orphanSummaries,
+    errors,
+    warnings,
+  }, raw, errors.length === 0 ? 'complete' : 'incomplete');
+}
+
+function cmdVerifyReferences(cwd, filePath, raw) {
+  if (!filePath) { error('file path required'); }
+  const fullPath = path.isAbsolute(filePath) ? filePath : path.join(cwd, filePath);
+  const content = safeReadFile(fullPath);
+  if (!content) { output({ error: 'File not found', path: filePath }, raw); return; }
+
+  const found = [];
+  const missing = [];
+
+  // Find @-references: @path/to/file (must contain / to be a file path)
+  const atRefs = content.match(/@([^\s\n,)]+\/[^\s\n,)]+)/g) || [];
+  for (const ref of atRefs) {
+    const cleanRef = ref.slice(1); // remove @
+    const resolved = cleanRef.startsWith('~/')
+      ? path.join(process.env.HOME || '', cleanRef.slice(2))
+      : path.join(cwd, cleanRef);
+    if (fs.existsSync(resolved)) {
+      found.push(cleanRef);
+    } else {
+      missing.push(cleanRef);
+    }
+  }
+
+  // Find backtick file paths that look like real paths (contain / and have extension)
+  const backtickRefs = content.match(/`([^`]+\/[^`]+\.[a-zA-Z]{1,10})`/g) || [];
+  for (const ref of backtickRefs) {
+    const cleanRef = ref.slice(1, -1); // remove backticks
+    if (cleanRef.startsWith('http') || cleanRef.includes('${') || cleanRef.includes('{{')) continue;
+    if (found.includes(cleanRef) || missing.includes(cleanRef)) continue; // dedup
+    const resolved = path.join(cwd, cleanRef);
+    if (fs.existsSync(resolved)) {
+      found.push(cleanRef);
+    } else {
+      missing.push(cleanRef);
+    }
+  }
+
+  output({
+    valid: missing.length === 0,
+    found: found.length,
+    missing,
+    total: found.length + missing.length,
+  }, raw, missing.length === 0 ? 'valid' : 'invalid');
+}
+
+async function cmdVerifyCommits(cwd, hashes, raw) {
+  if (!hashes || hashes.length === 0) { error('At least one commit hash required'); }
+
+  const valid = [];
+  const invalid = [];
+  for (const hash of hashes) {
+    // Use git cat-file -t which supports both short and full hashes
+    // First try with the hash as-is (works for both short and full)
+    const result = await execGit(cwd, ['cat-file', '-t', hash]);
+    if (result.exitCode === 0 && result.stdout.trim() === 'commit') {
+      valid.push(hash);
+    } else {
+      // If that fails, try to resolve to full hash first
+      const resolveResult = await execGit(cwd, ['rev-parse', hash]);
+      if (resolveResult.exitCode === 0) {
+        const fullHash = resolveResult.stdout.trim();
+        const result2 = await execGit(cwd, ['cat-file', '-t', fullHash]);
+        if (result2.exitCode === 0 && result2.stdout.trim() === 'commit') {
+          valid.push(hash);
+        } else {
+          invalid.push(hash);
+        }
+      } else {
+        invalid.push(hash);
+      }
+    }
+  }
+
+  output({
+    all_valid: invalid.length === 0,
+    valid,
+    invalid,
+    total: hashes.length,
+  }, raw, invalid.length === 0 ? 'valid' : 'invalid');
+}
+
+function cmdVerifyArtifacts(cwd, planFilePath, raw) {
+  if (!planFilePath) { error('plan file path required'); }
+  const fullPath = path.isAbsolute(planFilePath) ? planFilePath : path.join(cwd, planFilePath);
+  const content = safeReadFile(fullPath);
+  if (!content) { output({ error: 'File not found', path: planFilePath }, raw); return; }
+
+  const artifacts = parseMustHavesBlock(content, 'artifacts');
+  if (artifacts.length === 0) {
+    output({ error: 'No must_haves.artifacts found in frontmatter', path: planFilePath }, raw);
+    return;
+  }
+
+  const results = [];
+  for (const artifact of artifacts) {
+    if (typeof artifact === 'string') continue; // skip simple string items
+    const artPath = artifact.path;
+    if (!artPath) continue;
+
+    const artFullPath = path.join(cwd, artPath);
+    const exists = fs.existsSync(artFullPath);
+    const check = { path: artPath, exists, issues: [], passed: false };
+
+    if (exists) {
+      const fileContent = safeReadFile(artFullPath) || '';
+      const lineCount = fileContent.split('\n').length;
+
+      if (artifact.min_lines && lineCount < artifact.min_lines) {
+        check.issues.push(`Only ${lineCount} lines, need ${artifact.min_lines}`);
+      }
+      if (artifact.contains && !fileContent.includes(artifact.contains)) {
+        check.issues.push(`Missing pattern: ${artifact.contains}`);
+      }
+      if (artifact.exports) {
+        const exports = Array.isArray(artifact.exports) ? artifact.exports : [artifact.exports];
+        for (const exp of exports) {
+          if (!fileContent.includes(exp)) check.issues.push(`Missing export: ${exp}`);
+        }
+      }
+      check.passed = check.issues.length === 0;
+    } else {
+      check.issues.push('File not found');
+    }
+
+    results.push(check);
+  }
+
+  const passed = results.filter(r => r.passed).length;
+  output({
+    all_passed: passed === results.length,
+    passed,
+    total: results.length,
+    artifacts: results,
+  }, raw, passed === results.length ? 'valid' : 'invalid');
+}
+
+function cmdVerifyKeyLinks(cwd, planFilePath, raw) {
+  if (!planFilePath) { error('plan file path required'); }
+  const fullPath = path.isAbsolute(planFilePath) ? planFilePath : path.join(cwd, planFilePath);
+  const content = safeReadFile(fullPath);
+  if (!content) { output({ error: 'File not found', path: planFilePath }, raw); return; }
+
+  const keyLinks = parseMustHavesBlock(content, 'key_links');
+  if (keyLinks.length === 0) {
+    output({ error: 'No must_haves.key_links found in frontmatter', path: planFilePath }, raw);
+    return;
+  }
+
+  const results = [];
+  for (const link of keyLinks) {
+    if (typeof link === 'string') continue;
+    const check = { from: link.from, to: link.to, via: link.via || '', verified: false, detail: '' };
+
+    const sourceContent = safeReadFile(path.join(cwd, link.from || ''));
+    if (!sourceContent) {
+      check.detail = 'Source file not found';
+    } else if (link.pattern) {
+      try {
+        const regex = new RegExp(link.pattern);
+        if (regex.test(sourceContent)) {
+          check.verified = true;
+          check.detail = 'Pattern found in source';
+        } else {
+          const targetContent = safeReadFile(path.join(cwd, link.to || ''));
+          if (targetContent && regex.test(targetContent)) {
+            check.verified = true;
+            check.detail = 'Pattern found in target';
+          } else {
+            check.detail = `Pattern "${link.pattern}" not found in source or target`;
+          }
+        }
+      } catch (err) {
+        logger.warn('Invalid regex while verifying key links', { pattern: link.pattern, error: err.message });
+        check.detail = `Invalid regex pattern: ${link.pattern}`;
+      }
+    } else {
+      // No pattern: just check source references target
+      if (sourceContent.includes(link.to || '')) {
+        check.verified = true;
+        check.detail = 'Target referenced in source';
+      } else {
+        check.detail = 'Target not referenced in source';
+      }
+    }
+
+    results.push(check);
+  }
+
+  const verified = results.filter(r => r.verified).length;
+  output({
+    all_verified: verified === results.length,
+    verified,
+    total: results.length,
+    links: results,
+  }, raw, verified === results.length ? 'valid' : 'invalid');
+}
+
+function cmdValidateConsistency(cwd, raw) {
+  const roadmapPath = path.join(cwd, '.planning', 'ROADMAP.md');
+  const phasesDir = path.join(cwd, '.planning', 'phases');
+  const errors = [];
+  const warnings = [];
+
+  // Check for ROADMAP
+  if (!fs.existsSync(roadmapPath)) {
+    errors.push('ROADMAP.md not found');
+    output({ passed: false, errors, warnings }, raw, 'failed');
+    return;
+  }
+
+  const roadmapContent = fs.readFileSync(roadmapPath, 'utf-8');
+
+  // Extract phases from ROADMAP
+  const roadmapPhases = new Set();
+  const phasePattern = /#{2,4}\s*Phase\s+(\d+[A-Z]?(?:\.\d+)*)\s*:/gi;
+  let m;
+  while ((m = phasePattern.exec(roadmapContent)) !== null) {
+    roadmapPhases.add(m[1]);
+  }
+
+  // Get phases on disk
+  const diskPhases = new Set();
+  try {
+    const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
+    const dirs = entries.filter(e => e.isDirectory()).map(e => e.name);
+    for (const dir of dirs) {
+      const dm = dir.match(/^(\d+[A-Z]?(?:\.\d+)*)/i);
+      if (dm) diskPhases.add(dm[1]);
+    }
+  } catch (err) {
+    logger.warn('Failed to enumerate phase directories while validating consistency', { phasesDir, error: err.message });
+  }
+
+  // Check: phases in ROADMAP but not on disk
+  for (const p of roadmapPhases) {
+    if (!diskPhases.has(p) && !diskPhases.has(normalizePhaseName(p))) {
+      warnings.push(`Phase ${p} in ROADMAP.md but no directory on disk`);
+    }
+  }
+
+  // Check: phases on disk but not in ROADMAP
+  for (const p of diskPhases) {
+    const unpadded = String(parseInt(p, 10));
+    if (!roadmapPhases.has(p) && !roadmapPhases.has(unpadded)) {
+      warnings.push(`Phase ${p} exists on disk but not in ROADMAP.md`);
+    }
+  }
+
+  // Check: sequential phase numbers (integers only)
+  const integerPhases = [...diskPhases]
+    .filter(p => !p.includes('.'))
+    .map(p => parseInt(p, 10))
+    .sort((a, b) => a - b);
+
+  for (let i = 1; i < integerPhases.length; i++) {
+    if (integerPhases[i] !== integerPhases[i - 1] + 1) {
+      warnings.push(`Gap in phase numbering: ${integerPhases[i - 1]} → ${integerPhases[i]}`);
+    }
+  }
+
+  // Check: plan numbering within phases
+  try {
+    const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
+    const dirs = entries.filter(e => e.isDirectory()).map(e => e.name).sort();
+
+    for (const dir of dirs) {
+      const phaseFiles = fs.readdirSync(path.join(phasesDir, dir));
+      const plans = phaseFiles.filter(f => f.endsWith('-PLAN.md')).sort();
+
+      // Extract plan numbers
+      const planNums = plans.map(p => {
+        const pm = p.match(/-(\d{2})-PLAN\.md$/);
+        return pm ? parseInt(pm[1], 10) : null;
+      }).filter(n => n !== null);
+
+      for (let i = 1; i < planNums.length; i++) {
+        if (planNums[i] !== planNums[i - 1] + 1) {
+          warnings.push(`Gap in plan numbering in ${dir}: plan ${planNums[i - 1]} → ${planNums[i]}`);
+        }
+      }
+
+      // Check: plans without summaries (completed plans)
+      const summaries = phaseFiles.filter(f => f.endsWith('-SUMMARY.md'));
+      const planIds = new Set(plans.map(p => p.replace('-PLAN.md', '')));
+      const summaryIds = new Set(summaries.map(s => s.replace('-SUMMARY.md', '')));
+
+      // Summary without matching plan is suspicious
+      for (const sid of summaryIds) {
+        if (!planIds.has(sid)) {
+          warnings.push(`Summary ${sid}-SUMMARY.md in ${dir} has no matching PLAN.md`);
+        }
+      }
+    }
+  } catch (err) {
+    logger.warn('Failed to validate plan numbering while validating consistency', { phasesDir, error: err.message });
+  }
+
+  // Check: frontmatter in plans has required fields
+  try {
+    const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
+    const dirs = entries.filter(e => e.isDirectory()).map(e => e.name);
+
+    for (const dir of dirs) {
+      const phaseFiles = fs.readdirSync(path.join(phasesDir, dir));
+      const plans = phaseFiles.filter(f => f.endsWith('-PLAN.md'));
+
+      for (const plan of plans) {
+        const content = fs.readFileSync(path.join(phasesDir, dir, plan), 'utf-8');
+        const fm = extractFrontmatter(content);
+
+        if (!fm.wave) {
+          warnings.push(`${dir}/${plan}: missing 'wave' in frontmatter`);
+        }
+      }
+    }
+  } catch (err) {
+    logger.warn('Failed to validate plan frontmatter while validating consistency', { phasesDir, error: err.message });
+  }
+
+  const passed = errors.length === 0;
+  output({ passed, errors, warnings, warning_count: warnings.length }, raw, passed ? 'passed' : 'failed');
+}
+
+function cmdValidateHealth(cwd, options, raw) {
+  const planningDir = path.join(cwd, '.planning');
+  const projectPath = path.join(planningDir, 'PROJECT.md');
+  const roadmapPath = path.join(planningDir, 'ROADMAP.md');
+  const statePath = path.join(planningDir, 'STATE.md');
+  const configPath = path.join(planningDir, 'config.json');
+  const phasesDir = path.join(planningDir, 'phases');
+
+  const errors = [];
+  const warnings = [];
+  const info = [];
+  const repairs = [];
+
+  // Helper to add issue
+  const addIssue = (severity, code, message, fix, repairable = false) => {
+    const issue = { code, message, fix, repairable };
+    if (severity === 'error') errors.push(issue);
+    else if (severity === 'warning') warnings.push(issue);
+    else info.push(issue);
+  };
+
+  // ─── Check 1: .planning/ exists ───────────────────────────────────────────
+  if (!fs.existsSync(planningDir)) {
+    addIssue('error', 'E001', '.planning/ directory not found', 'Run /ez:new-project to initialize');
+    output({
+      status: 'broken',
+      errors,
+      warnings,
+      info,
+      repairable_count: 0,
+    }, raw);
+    return;
+  }
+
+  // ─── Check 2: PROJECT.md exists and has required sections ─────────────────
+  if (!fs.existsSync(projectPath)) {
+    addIssue('error', 'E002', 'PROJECT.md not found', 'Run /ez:new-project to create');
+  } else {
+    const content = fs.readFileSync(projectPath, 'utf-8');
+    const requiredSections = ['## What This Is', '## Core Value', '## Requirements'];
+    for (const section of requiredSections) {
+      if (!content.includes(section)) {
+        addIssue('warning', 'W001', `PROJECT.md missing section: ${section}`, 'Add section manually');
+      }
+    }
+  }
+
+  // ─── Check 3: ROADMAP.md exists ───────────────────────────────────────────
+  if (!fs.existsSync(roadmapPath)) {
+    addIssue('error', 'E003', 'ROADMAP.md not found', 'Run /ez:new-milestone to create roadmap');
+  }
+
+  // ─── Check 4: STATE.md exists and references valid phases ─────────────────
+  if (!fs.existsSync(statePath)) {
+    addIssue('error', 'E004', 'STATE.md not found', 'Run /ez:health --repair to regenerate', true);
+    repairs.push('regenerateState');
+  } else {
+    const stateContent = fs.readFileSync(statePath, 'utf-8');
+    // Extract phase references from STATE.md
+    const phaseRefs = [...stateContent.matchAll(/[Pp]hase\s+(\d+(?:\.\d+)*)/g)].map(m => m[1]);
+    // Get disk phases
+    const diskPhases = new Set();
+    try {
+      const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
+      for (const e of entries) {
+        if (e.isDirectory()) {
+          const m = e.name.match(/^(\d+(?:\.\d+)*)/);
+          if (m) diskPhases.add(m[1]);
+        }
+      }
+    } catch (err) {
+      logger.warn('Failed to read phase directories while validating STATE references', { phasesDir, error: err.message });
+    }
+    // Check for invalid references
+    for (const ref of phaseRefs) {
+      const normalizedRef = String(parseInt(ref, 10)).padStart(2, '0');
+      if (!diskPhases.has(ref) && !diskPhases.has(normalizedRef) && !diskPhases.has(String(parseInt(ref, 10)))) {
+        // Only warn if phases dir has any content (not just an empty project)
+        if (diskPhases.size > 0) {
+          addIssue('warning', 'W002', `STATE.md references phase ${ref}, but only phases ${[...diskPhases].sort().join(', ')} exist`, 'Run /ez:health --repair to regenerate STATE.md', true);
+          if (!repairs.includes('regenerateState')) repairs.push('regenerateState');
+        }
+      }
+    }
+  }
+
+  // ─── Check 5: config.json valid JSON + valid schema ───────────────────────
+  if (!fs.existsSync(configPath)) {
+    addIssue('warning', 'W003', 'config.json not found', 'Run /ez:health --repair to create with defaults', true);
+    repairs.push('createConfig');
+  } else {
+    try {
+      const raw = fs.readFileSync(configPath, 'utf-8');
+      const parsed = JSON.parse(raw);
+      // Validate known fields
+      const validProfiles = ['quality', 'balanced', 'budget'];
+      if (parsed.model_profile && !validProfiles.includes(parsed.model_profile)) {
+        addIssue('warning', 'W004', `config.json: invalid model_profile "${parsed.model_profile}"`, `Valid values: ${validProfiles.join(', ')}`);
+      }
+    } catch (err) {
+      logger.warn('Failed to parse config.json in cmdValidateHealth', { configPath, error: err.message });
+      addIssue('error', 'E005', `config.json: JSON parse error - ${err.message}`, 'Run /ez:health --repair to reset to defaults', true);
+      repairs.push('resetConfig');
+    }
+  }
+
+  // ─── Check 5b: Nyquist validation key presence ──────────────────────────
+  if (fs.existsSync(configPath)) {
+    try {
+      const configRaw = fs.readFileSync(configPath, 'utf-8');
+      const configParsed = JSON.parse(configRaw);
+      if (configParsed.workflow && configParsed.workflow.nyquist_validation === undefined) {
+        addIssue('warning', 'W008', 'config.json: workflow.nyquist_validation absent (defaults to enabled but agents may skip)', 'Run /ez:health --repair to add key', true);
+        if (!repairs.includes('addNyquistKey')) repairs.push('addNyquistKey');
+      }
+    } catch (err) {
+      logger.warn('Failed to parse config for nyquist key check', { configPath, error: err.message });
+    }
+  }
+
+  // ─── Check 6: Phase directory naming (NN-name format) ─────────────────────
+  try {
+    const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
+    for (const e of entries) {
+      if (e.isDirectory() && !e.name.match(/^\d{2}(?:\.\d+)*-[\w-]+$/)) {
+        addIssue('warning', 'W005', `Phase directory "${e.name}" doesn't follow NN-name format`, 'Rename to match pattern (e.g., 01-setup)');
+      }
+    }
+  } catch (err) {
+    logger.warn('Failed to inspect phase directory naming in health validation', { phasesDir, error: err.message });
+  }
+
+  // ─── Check 7: Orphaned plans (PLAN without SUMMARY) ───────────────────────
+  try {
+    const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
+    for (const e of entries) {
+      if (!e.isDirectory()) continue;
+      const phaseFiles = fs.readdirSync(path.join(phasesDir, e.name));
+      const plans = phaseFiles.filter(f => f.endsWith('-PLAN.md') || f === 'PLAN.md');
+      const summaries = phaseFiles.filter(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md');
+      const summaryBases = new Set(summaries.map(s => s.replace('-SUMMARY.md', '').replace('SUMMARY.md', '')));
+
+      for (const plan of plans) {
+        const planBase = plan.replace('-PLAN.md', '').replace('PLAN.md', '');
+        if (!summaryBases.has(planBase)) {
+          addIssue('info', 'I001', `${e.name}/${plan} has no SUMMARY.md`, 'May be in progress');
+        }
+      }
+    }
+  } catch (err) {
+    logger.warn('Failed to inspect orphaned plans in health validation', { phasesDir, error: err.message });
+  }
+
+  // ─── Check 7b: Nyquist VALIDATION.md consistency ────────────────────────
+  try {
+    const phaseEntries = fs.readdirSync(phasesDir, { withFileTypes: true });
+    for (const e of phaseEntries) {
+      if (!e.isDirectory()) continue;
+      const phaseFiles = fs.readdirSync(path.join(phasesDir, e.name));
+      const hasResearch = phaseFiles.some(f => f.endsWith('-RESEARCH.md'));
+      const hasValidation = phaseFiles.some(f => f.endsWith('-VALIDATION.md'));
+      if (hasResearch && !hasValidation) {
+        const researchFile = phaseFiles.find(f => f.endsWith('-RESEARCH.md'));
+        const researchContent = fs.readFileSync(path.join(phasesDir, e.name, researchFile), 'utf-8');
+        if (researchContent.includes('## Validation Architecture')) {
+          addIssue('warning', 'W009', `Phase ${e.name}: has Validation Architecture in RESEARCH.md but no VALIDATION.md`, 'Re-run /ez-plan-phase with --research to regenerate');
+        }
+      }
+    }
+  } catch (err) {
+    logger.warn('Failed to inspect validation architecture consistency in health validation', { phasesDir, error: err.message });
+  }
+
+  // ─── Check 8: Run existing consistency checks ─────────────────────────────
+  // Inline subset of cmdValidateConsistency
+  if (fs.existsSync(roadmapPath)) {
+    const roadmapContent = fs.readFileSync(roadmapPath, 'utf-8');
+    const roadmapPhases = new Set();
+    const phasePattern = /#{2,4}\s*Phase\s+(\d+[A-Z]?(?:\.\d+)*)\s*:/gi;
+    let m;
+    while ((m = phasePattern.exec(roadmapContent)) !== null) {
+      roadmapPhases.add(m[1]);
+    }
+
+    const diskPhases = new Set();
+    try {
+      const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
+      for (const e of entries) {
+        if (e.isDirectory()) {
+          const dm = e.name.match(/^(\d+[A-Z]?(?:\.\d+)*)/i);
+          if (dm) diskPhases.add(dm[1]);
+        }
+      }
+    } catch (err) {
+      logger.warn('Failed to run roadmap/disk consistency checks in health validation', { roadmapPath, phasesDir, error: err.message });
+    }
+
+    // Phases in ROADMAP but not on disk
+    for (const p of roadmapPhases) {
+      const padded = String(parseInt(p, 10)).padStart(2, '0');
+      if (!diskPhases.has(p) && !diskPhases.has(padded)) {
+        addIssue('warning', 'W006', `Phase ${p} in ROADMAP.md but no directory on disk`, 'Create phase directory or remove from roadmap');
+      }
+    }
+
+    // Phases on disk but not in ROADMAP
+    for (const p of diskPhases) {
+      const unpadded = String(parseInt(p, 10));
+      if (!roadmapPhases.has(p) && !roadmapPhases.has(unpadded)) {
+        addIssue('warning', 'W007', `Phase ${p} exists on disk but not in ROADMAP.md`, 'Add to roadmap or remove directory');
+      }
+    }
+  }
+
+  // ─── Perform repairs if requested ─────────────────────────────────────────
+  const repairActions = [];
+  if (options.repair && repairs.length > 0) {
+    for (const repair of repairs) {
+      try {
+        switch (repair) {
+          case 'createConfig':
+          case 'resetConfig': {
+            const defaults = {
+              model_profile: 'balanced',
+              commit_docs: true,
+              search_gitignored: false,
+              branching_strategy: 'none',
+              research: true,
+              plan_checker: true,
+              verifier: true,
+              parallelization: true,
+            };
+            fs.writeFileSync(configPath, JSON.stringify(defaults, null, 2), 'utf-8');
+            repairActions.push({ action: repair, success: true, path: 'config.json' });
+            break;
+          }
+          case 'regenerateState': {
+            // Create timestamped backup before overwriting
+            if (fs.existsSync(statePath)) {
+              const timestamp = new Date().toISOString().replace(/[:.]/g, '-').slice(0, 19);
+              const backupPath = `${statePath}.bak-${timestamp}`;
+              fs.copyFileSync(statePath, backupPath);
+              repairActions.push({ action: 'backupState', success: true, path: backupPath });
+            }
+            // Generate minimal STATE.md from ROADMAP.md structure
+            const milestone = getMilestoneInfo(cwd);
+            let stateContent = `# Session State\n\n`;
+            stateContent += `## Project Reference\n\n`;
+            stateContent += `See: .planning/PROJECT.md\n\n`;
+            stateContent += `## Position\n\n`;
+            stateContent += `**Milestone:** ${milestone.version} ${milestone.name}\n`;
+            stateContent += `**Current phase:** (determining...)\n`;
+            stateContent += `**Status:** Resuming\n\n`;
+            stateContent += `## Session Log\n\n`;
+            stateContent += `- ${new Date().toISOString().split('T')[0]}: STATE.md regenerated by /ez:health --repair\n`;
+            writeStateMd(statePath, stateContent, cwd);
+            repairActions.push({ action: repair, success: true, path: 'STATE.md' });
+            break;
+          }
+          case 'addNyquistKey': {
+            if (fs.existsSync(configPath)) {
+              try {
+                const configRaw = fs.readFileSync(configPath, 'utf-8');
+                const configParsed = JSON.parse(configRaw);
+                if (!configParsed.workflow) configParsed.workflow = {};
+                if (configParsed.workflow.nyquist_validation === undefined) {
+                  configParsed.workflow.nyquist_validation = true;
+                  fs.writeFileSync(configPath, JSON.stringify(configParsed, null, 2), 'utf-8');
+                }
+                repairActions.push({ action: repair, success: true, path: 'config.json' });
+              } catch (err) {
+                logger.error('Failed to repair nyquist key', { error: err.message });
+                repairActions.push({ action: repair, success: false, error: err.message });
+              }
+            }
+            break;
+          }
+        }
+      } catch (err) {
+        logger.error('Failed to perform repair action', { action: repair, error: err.message });
+        repairActions.push({ action: repair, success: false, error: err.message });
+      }
+    }
+  }
+
+  // ─── Determine overall status ─────────────────────────────────────────────
+  let status;
+  if (errors.length > 0) {
+    status = 'broken';
+  } else if (warnings.length > 0) {
+    status = 'degraded';
+  } else {
+    status = 'healthy';
+  }
+
+  const repairableCount = errors.filter(e => e.repairable).length +
+                         warnings.filter(w => w.repairable).length;
+
+  output({
+    status,
+    errors,
+    warnings,
+    info,
+    repairable_count: repairableCount,
+    repairs_performed: repairActions.length > 0 ? repairActions : undefined,
+  }, raw);
+}
+
+module.exports = {
+  cmdVerifySummary,
+  cmdVerifyPlanStructure,
+  cmdVerifyPhaseCompleteness,
+  cmdVerifyReferences,
+  cmdVerifyCommits,
+  cmdVerifyArtifacts,
+  cmdVerifyKeyLinks,
+  cmdValidateConsistency,
+  cmdValidateHealth,
+};