@sienklogic/plan-build-run 2.21.1 → 2.21.2

package/plugins/pbr/scripts/pbr-tools.js

@@ -3,1376 +3,491 @@
 /**
  * pbr-tools.js — Structured JSON state operations for Plan-Build-Run skills.
  *
- * Provides read-only commands that return JSON, replacing LLM-based text parsing
- * of STATE.md, ROADMAP.md, and config.json. Skills call this via:
- *   node ${CLAUDE_PLUGIN_ROOT}/scripts/pbr-tools.js <command> [args]
+ * Thin router that delegates CLI commands to handler modules in commands/.
+ * Core logic lives in lib/ modules. Wrapper functions here provide backward
+ * compatibility for hook scripts and tests that require('./pbr-tools').
  *
- * Commands:
- *   state load              — Full project state as JSON
- *   state check-progress    — Recalculate progress from filesystem
- *   state update <f> <v>    — Atomically update a STATE.md field
- *   config validate          — Validate config.json against schema
- *   plan-index <phase>      — Plan inventory for a phase, grouped by wave
- *   frontmatter <filepath>  — Parse .md file's YAML frontmatter → JSON
- *   must-haves <phase>      — Collect all must-haves from phase plans → JSON
- *   phase-info <phase>      — Comprehensive single-phase status → JSON
- *   roadmap update-status <phase> <status>      — Update phase status in ROADMAP.md
- *   roadmap update-plans <phase> <complete> <total> — Update phase plans in ROADMAP.md
- *   history append <type> <title> [body] — Append record to HISTORY.md
- *   history load                         — Load all HISTORY.md records as JSON
- */
-
-const fs = require('fs');
-const path = require('path');
-
-const cwd = process.cwd();
-const planningDir = path.join(cwd, '.planning');
-
-// --- Phase status transition state machine ---
-
-/**
- * Valid phase status transitions. Each key is a current status, and its value
- * is an array of statuses that are legal to transition to. This is advisory —
- * invalid transitions produce a stderr warning but are not blocked, to avoid
- * breaking existing workflows.
+ * Command modules:
+ *   commands/state.js   — state, state-bundle
+ *   commands/config.js  — config, validate
+ *   commands/roadmap.js — roadmap
+ *   commands/phase.js   — phase, compound, init, plan-index, frontmatter, must-haves, phase-info, milestone-stats
+ *   commands/verify.js  — verify, spot-check, staleness-check, summary-gate, checkpoint, seeds
+ *   commands/todo.js    — todo, history, auto-cleanup
+ *   commands/misc.js    — all remaining (intel, learnings, session, claim, spec, help, etc.)
  *
- * State machine:
- *   pending -> planned, skipped
- *   planned -> building
- *   building -> built, partial, needs_fixes
- *   built -> verified, needs_fixes
- *   partial -> building, needs_fixes
- *   verified -> building (re-execution)
- *   needs_fixes -> planned, building
- *   skipped -> pending (unskip)
- */
-const VALID_STATUS_TRANSITIONS = {
-  pending:     ['planned', 'skipped'],
-  planned:     ['building'],
-  building:    ['built', 'partial', 'needs_fixes'],
-  built:       ['verified', 'needs_fixes'],
-  partial:     ['building', 'needs_fixes'],
-  verified:    ['building'],
-  needs_fixes: ['planned', 'building'],
-  skipped:     ['pending']
-};
-
-/**
- * Check whether a phase status transition is valid according to the state machine.
- * Returns { valid, warning? } — never blocks, only advises.
+ * Usage: node ${CLAUDE_PLUGIN_ROOT}/scripts/pbr-tools.js <command> [args]
+ * Run `pbr-tools.js help` for full command listing.
  *
- * @param {string} oldStatus - Current phase status
- * @param {string} newStatus - Desired phase status
- * @returns {{ valid: boolean, warning?: string }}
+ * Environment: PBR_PROJECT_ROOT — Override project root directory
  */
-function validateStatusTransition(oldStatus, newStatus) {
-  const from = (oldStatus || '').trim().toLowerCase();
-  const to = (newStatus || '').trim().toLowerCase();
 
-  // If the status isn't changing, that's always fine
-  if (from === to) {
-    return { valid: true };
-  }
-
-  // If the old status is unknown to our map, we can't validate — allow it
-  if (!VALID_STATUS_TRANSITIONS[from]) {
-    return { valid: true };
-  }
-
-  const allowed = VALID_STATUS_TRANSITIONS[from];
-  if (allowed.includes(to)) {
-    return { valid: true };
-  }
-
-  return {
-    valid: false,
-    warning: `Suspicious status transition: "${from}" -> "${to}". Expected one of: [${allowed.join(', ')}]. Proceeding anyway (advisory).`
-  };
-}
-
-// --- Cached config loader ---
+const fs = require('fs');
+const path = require('path');
 
-let _configCache = null;
-let _configMtime = 0;
-let _configPath = null;
+// --- Import lib modules (used by wrapper functions for backward-compat exports) ---
+const { KNOWN_AGENTS, VALID_STATUS_TRANSITIONS, validateStatusTransition, output, error,
+  parseYamlFrontmatter, parseMustHaves, findFiles, tailLines, countMustHaves,
+  determinePhaseStatus, atomicWrite, lockedFileUpdate, writeActiveSkill,
+  sessionLoad, sessionSave, SESSION_ALLOWED_KEYS, acquireClaim, releaseClaim,
+  listClaims: _listClaims } = require('./lib/core');
+const { configLoad: _configLoad, configClearCache: _configClearCache,
+  configValidate: _configValidate, resolveDepthProfile, DEPTH_PROFILE_DEFAULTS,
+  loadUserDefaults, saveUserDefaults, mergeUserDefaults, USER_DEFAULTS_PATH } = require('./lib/config');
+const { parseStateMd, updateFrontmatterField, stateLoad: _stateLoad,
+  stateCheckProgress: _stateCheckProgress, stateUpdate: _stateUpdate,
+  statePatch: _statePatch, stateAdvancePlan: _stateAdvancePlan,
+  stateRecordMetric: _stateRecordMetric, stateRecordActivity: _stateRecordActivity,
+  stateUpdateProgress: _stateUpdateProgress, stateReconcile: _stateReconcile,
+  stateBackup: _stateBackup } = require('./lib/state');
+const { parseRoadmapMd, findRoadmapRow, updateTableRow,
+  roadmapUpdateStatus: _roadmapUpdateStatus, roadmapUpdatePlans: _roadmapUpdatePlans,
+  roadmapAnalyze: _roadmapAnalyze } = require('./lib/roadmap');
+const { frontmatter: _frontmatter, planIndex: _planIndex,
+  mustHavesCollect: _mustHavesCollect, phaseInfo: _phaseInfo, phaseAdd: _phaseAdd,
+  phaseRemove: _phaseRemove, phaseList: _phaseList, milestoneStats: _milestoneStats,
+  phaseComplete: _phaseComplete, phaseInsert: _phaseInsert,
+  phaseNextNumber: _phaseNextNumber } = require('./lib/phase');
+const { compoundInitPhase: _compoundInitPhase, compoundCompletePhase: _compoundCompletePhase,
+  compoundInitMilestone: _compoundInitMilestone } = require('./lib/compound');
+const { initExecutePhase: _initExecutePhase, initPlanPhase: _initPlanPhase,
+  initQuick: _initQuick, initVerifyWork: _initVerifyWork, initResume: _initResume,
+  initProgress: _initProgress, initStateBundle: _initStateBundle,
+  initContinue: _initContinue, initMilestone: _initMilestone, initBegin: _initBegin,
+  initStatus: _initStatus, initMapCodebase: _initMapCodebase } = require('./lib/init');
+const { historyAppend: _historyAppend, historyLoad: _historyLoad } = require('./lib/history');
+const { todoList: _todoList, todoGet: _todoGet, todoAdd: _todoAdd, todoDone: _todoDone } = require('./lib/todo');
+const { autoCloseTodos: _autoCloseTodos, autoArchiveNotes: _autoArchiveNotes } = require('./lib/auto-cleanup');
+const { applyMigrations: _applyMigrations } = require('./lib/migrate');
+const { verifySpotCheck: _verifySpotCheck } = require('./lib/spot-check');
+const { referenceGet: _referenceGet } = require('./lib/reference');
+const { skillSection: _skillSection, listAvailableSkills: _listAvailableSkills } = require('./lib/skill-section');
+const { helpList: _helpList, skillMetadata: _skillMetadata } = require('./lib/help');
+const { stepVerify: _stepVerify } = require('./lib/step-verify');
+const { contextTriage: _contextTriage } = require('./lib/context');
+const { phaseAlternatives: _phaseAlternatives, prerequisiteAlternatives: _prereqAlternatives,
+  configAlternatives: _configAlternatives } = require('./lib/alternatives');
+const { stalenessCheck: _stalenessCheck, summaryGate: _summaryGate,
+  checkpointInit: _checkpointInit, checkpointUpdate: _checkpointUpdate,
+  seedsMatch: _seedsMatch, ciPoll: _ciPoll, rollback: _rollback } = require('./lib/build');
+const { parseJestOutput: _parseJestOutput, parseLintOutput: _parseLintOutput,
+  autoFixLint: _autoFixLint, runCiFixLoop: _runCiFixLoop } = require('./lib/ci-fix-loop');
+const { quickStatus: _quickStatus } = require('./quick-status');
+
+// --- Command modules (CLI dispatch handlers) ---
+const { handleState, handleStateBundle } = require('./commands/state');
+const { handleConfig } = require('./commands/config');
+const { handleRoadmap } = require('./commands/roadmap');
+const { handlePhase, handleCompound, handleInit, handlePhaseDirect } = require('./commands/phase');
+const { handleVerify, handleSpotCheckDirect, handleStalenessCheck, handleSummaryGate, handleCheckpoint, handleSeeds } = require('./commands/verify');
+const { handleTodo, handleHistory, handleAutoCleanup } = require('./commands/todo');
+const { handleMisc } = require('./commands/misc');
+const { handleBenchmarks } = require('./commands/benchmarks');
+const { handleCalibrate } = require('./commands/calibrate');
+const { handleStressTest } = require('./commands/stress-test');
+const { normalizeMsysPath } = require('./lib/msys-path');
+
+// --- Module-level state (for backwards compatibility) ---
+
+let cwd = process.env.PBR_PROJECT_ROOT || process.cwd();
+cwd = normalizeMsysPath(cwd);
+let planningDir = path.join(cwd, '.planning');
+
+// --- Wrapper functions that pass planningDir to lib modules ---
+// These preserve the original function signatures (no planningDir param)
+// so existing callers (hook scripts, tests) continue to work.
 
-/**
- * Load config.json with in-process mtime-based caching.
- * Returns the parsed config object, or null if not found / parse error.
- * Cache invalidates when file mtime changes or path differs.
- *
- * @param {string} [dir] - Path to .planning directory (defaults to cwd/.planning)
- * @returns {object|null} Parsed config or null
- */
 function configLoad(dir) {
-  const configPath = path.join(dir || planningDir, 'config.json');
-  try {
-    if (!fs.existsSync(configPath)) return null;
-    const stat = fs.statSync(configPath);
-    const mtime = stat.mtimeMs;
-    if (_configCache && mtime === _configMtime && configPath === _configPath) {
-      return _configCache;
-    }
-    _configCache = JSON.parse(fs.readFileSync(configPath, 'utf8'));
-    _configMtime = mtime;
-    _configPath = configPath;
-    return _configCache;
-  } catch (_e) {
-    return null;
-  }
+  return _configLoad(dir || planningDir);
 }
 
-/**
- * Clear the configLoad() in-process cache.
- * Useful in tests where multiple temp directories are used in rapid succession.
- */
 function configClearCache() {
-  _configCache = null;
-  _configMtime = 0;
-  _configPath = null;
+  _configClearCache();
+  cwd = process.env.PBR_PROJECT_ROOT || process.cwd();
+  cwd = normalizeMsysPath(cwd);
+  planningDir = path.join(cwd, '.planning');
 }
 
-/**
- * Read the last N lines from a file efficiently.
- * Reads the entire file but only parses (JSON.parse) the trailing entries.
- * For JSONL files where full parsing is expensive, this avoids parsing
- * all lines when you only need recent entries.
- *
- * @param {string} filePath - Absolute path to the file
- * @param {number} n - Number of trailing lines to return
- * @returns {string[]} Array of raw line strings (last n lines)
- */
-function tailLines(filePath, n) {
-  try {
-    if (!fs.existsSync(filePath)) return [];
-    const content = fs.readFileSync(filePath, 'utf8').trim();
-    if (!content) return [];
-    const lines = content.split('\n');
-    if (lines.length <= n) return lines;
-    return lines.slice(lines.length - n);
-  } catch (_e) {
-    return [];
-  }
+function configValidate(preloadedConfig) {
+  return _configValidate(preloadedConfig, planningDir);
 }
 
-/**
- * Built-in depth profile defaults. These define the effective settings
- * for each depth level. User config.depth_profiles overrides these.
- */
-const DEPTH_PROFILE_DEFAULTS = {
-  quick: {
-    'features.research_phase': false,
-    'features.plan_checking': false,
-    'features.goal_verification': false,
-    'features.inline_verify': false,
-    'scan.mapper_count': 2,
-    'scan.mapper_areas': ['tech', 'arch'],
-    'debug.max_hypothesis_rounds': 3
-  },
-  standard: {
-    'features.research_phase': true,
-    'features.plan_checking': true,
-    'features.goal_verification': true,
-    'features.inline_verify': false,
-    'scan.mapper_count': 4,
-    'scan.mapper_areas': ['tech', 'arch', 'quality', 'concerns'],
-    'debug.max_hypothesis_rounds': 5
-  },
-  comprehensive: {
-    'features.research_phase': true,
-    'features.plan_checking': true,
-    'features.goal_verification': true,
-    'features.inline_verify': true,
-    'scan.mapper_count': 4,
-    'scan.mapper_areas': ['tech', 'arch', 'quality', 'concerns'],
-    'debug.max_hypothesis_rounds': 10
-  }
-};
-
-/**
- * Resolve the effective depth profile for the current config.
- * Merges built-in defaults with any user overrides from config.depth_profiles.
- *
- * @param {object|null} config - Parsed config.json (from configLoad). If null, returns 'standard' defaults.
- * @returns {{ depth: string, profile: object }} The resolved depth name and flattened profile settings.
- */
-function resolveDepthProfile(config) {
-  const depth = (config && config.depth) || 'standard';
-  const defaults = DEPTH_PROFILE_DEFAULTS[depth] || DEPTH_PROFILE_DEFAULTS.standard;
-
-  // Merge user overrides if present
-  const userOverrides = (config && config.depth_profiles && config.depth_profiles[depth]) || {};
-  const profile = { ...defaults, ...userOverrides };
+function stateLoad() {
+  return _stateLoad(planningDir);
+}
 
-  return { depth, profile };
+function stateCheckProgress() {
+  return _stateCheckProgress(planningDir);
 }
 
-function main() {
-  const args = process.argv.slice(2);
-  const command = args[0];
-  const subcommand = args[1];
+function stateUpdate(field, value) {
+  return _stateUpdate(field, value, planningDir);
+}
 
-  try {
-    if (command === 'state' && subcommand === 'load') {
-      output(stateLoad());
-    } else if (command === 'state' && subcommand === 'check-progress') {
-      output(stateCheckProgress());
-    } else if (command === 'state' && subcommand === 'update') {
-      const field = args[2];
-      const value = args[3];
-      if (!field || value === undefined) {
-        error('Usage: pbr-tools.js state update <field> <value>\nFields: current_phase, status, plans_complete, last_activity');
-      }
-      output(stateUpdate(field, value));
-    } else if (command === 'config' && subcommand === 'validate') {
-      output(configValidate());
-    } else if (command === 'config' && subcommand === 'resolve-depth') {
-      const dir = args[2] || undefined;
-      const config = configLoad(dir);
-      output(resolveDepthProfile(config));
-    } else if (command === 'plan-index') {
-      const phase = args[1];
-      if (!phase) {
-        error('Usage: pbr-tools.js plan-index <phase-number>');
-      }
-      output(planIndex(phase));
-    } else if (command === 'frontmatter') {
-      const filePath = args[1];
-      if (!filePath) {
-        error('Usage: pbr-tools.js frontmatter <filepath>');
-      }
-      output(frontmatter(filePath));
-    } else if (command === 'must-haves') {
-      const phase = args[1];
-      if (!phase) {
-        error('Usage: pbr-tools.js must-haves <phase-number>');
-      }
-      output(mustHavesCollect(phase));
-    } else if (command === 'phase-info') {
-      const phase = args[1];
-      if (!phase) {
-        error('Usage: pbr-tools.js phase-info <phase-number>');
-      }
-      output(phaseInfo(phase));
-    } else if (command === 'roadmap' && subcommand === 'update-status') {
-      const phase = args[2];
-      const status = args[3];
-      if (!phase || !status) {
-        error('Usage: pbr-tools.js roadmap update-status <phase-number> <status>');
-      }
-      output(roadmapUpdateStatus(phase, status));
-    } else if (command === 'roadmap' && subcommand === 'update-plans') {
-      const phase = args[2];
-      const complete = args[3];
-      const total = args[4];
-      if (!phase || complete === undefined || total === undefined) {
-        error('Usage: pbr-tools.js roadmap update-plans <phase-number> <complete> <total>');
-      }
-      output(roadmapUpdatePlans(phase, complete, total));
-    } else if (command === 'history' && subcommand === 'append') {
-      const type = args[2];   // 'milestone' or 'phase'
-      const title = args[3];
-      const body = args[4] || '';
-      if (!type || !title) {
-        error('Usage: pbr-tools.js history append <milestone|phase> <title> [body]');
-      }
-      output(historyAppend({ type, title, body }));
-    } else if (command === 'history' && subcommand === 'load') {
-      output(historyLoad());
-    } else if (command === 'event') {
-      const category = args[1];
-      const event = args[2];
-      let details = {};
-      if (args[3]) {
-        try { details = JSON.parse(args[3]); } catch (_e) { details = { raw: args[3] }; }
-      }
-      if (!category || !event) {
-        error('Usage: pbr-tools.js event <category> <event> [JSON-details]');
-      }
-      const { logEvent } = require('./event-logger');
-      logEvent(category, event, details);
-      output({ logged: true, category, event });
-    } else {
-      error(`Unknown command: ${args.join(' ')}\nCommands: state load|check-progress|update, config validate, plan-index, frontmatter, must-haves, phase-info, roadmap update-status|update-plans, history append|load, event`);
-    }
-  } catch (e) {
-    error(e.message);
-  }
+function statePatch(jsonStr) {
+  return _statePatch(jsonStr, planningDir);
 }
 
-// --- Commands ---
+function stateAdvancePlan() {
+  return _stateAdvancePlan(planningDir);
+}
 
-function stateLoad() {
-  const result = {
-    exists: false,
-    config: null,
-    state: null,
-    roadmap: null,
-    phase_count: 0,
-    current_phase: null,
-    progress: null
-  };
-
-  if (!fs.existsSync(planningDir)) {
-    return result;
-  }
-  result.exists = true;
+function stateRecordMetric(metricArgs) {
+  return _stateRecordMetric(metricArgs, planningDir);
+}
 
-  // Load config.json
-  const configPath = path.join(planningDir, 'config.json');
-  if (fs.existsSync(configPath)) {
-    try {
-      result.config = JSON.parse(fs.readFileSync(configPath, 'utf8'));
-    } catch (_) {
-      result.config = { _error: 'Failed to parse config.json' };
-    }
-  }
+function stateRecordActivity(description) {
+  return _stateRecordActivity(description, planningDir);
+}
 
-  // Load STATE.md
-  const statePath = path.join(planningDir, 'STATE.md');
-  if (fs.existsSync(statePath)) {
-    const content = fs.readFileSync(statePath, 'utf8');
-    result.state = parseStateMd(content);
-  }
+function stateUpdateProgress() {
+  return _stateUpdateProgress(planningDir);
+}
 
-  // Load ROADMAP.md
-  const roadmapPath = path.join(planningDir, 'ROADMAP.md');
-  if (fs.existsSync(roadmapPath)) {
-    const content = fs.readFileSync(roadmapPath, 'utf8');
-    result.roadmap = parseRoadmapMd(content);
-    result.phase_count = result.roadmap.phases.length;
-  }
+function stateReconcile() {
+  return _stateReconcile(planningDir);
+}
 
-  // Extract current phase
-  if (result.state && result.state.current_phase) {
-    result.current_phase = result.state.current_phase;
-  }
+function stateBackup() {
+  return _stateBackup(planningDir);
+}
 
-  // Calculate progress
-  result.progress = calculateProgress();
+function roadmapAnalyze() {
+  return _roadmapAnalyze(planningDir);
+}
 
-  return result;
+function roadmapUpdateStatus(phaseNum, newStatus) {
+  return _roadmapUpdateStatus(phaseNum, newStatus, planningDir);
 }
 
-function stateCheckProgress() {
-  const phasesDir = path.join(planningDir, 'phases');
-  if (!fs.existsSync(phasesDir)) {
-    return { phases: [], total_plans: 0, completed_plans: 0, percentage: 0 };
-  }
+function roadmapUpdatePlans(phaseNum, complete, total) {
+  return _roadmapUpdatePlans(phaseNum, complete, total, planningDir);
+}
 
-  const phases = [];
-  let totalPlans = 0;
-  let completedPlans = 0;
-
-  const entries = fs.readdirSync(phasesDir, { withFileTypes: true })
-    .filter(e => e.isDirectory())
-    .sort((a, b) => a.name.localeCompare(b.name));
-
-  for (const entry of entries) {
-    const phaseDir = path.join(phasesDir, entry.name);
-    const plans = findFiles(phaseDir, /-PLAN\.md$/);
-    const summaries = findFiles(phaseDir, /^SUMMARY-.*\.md$/);
-    const verification = fs.existsSync(path.join(phaseDir, 'VERIFICATION.md'));
-
-    const completedSummaries = summaries.filter(s => {
-      const content = fs.readFileSync(path.join(phaseDir, s), 'utf8');
-      return /status:\s*["']?complete/i.test(content);
-    });
-
-    const phaseInfo = {
-      directory: entry.name,
-      plans: plans.length,
-      summaries: summaries.length,
-      completed: completedSummaries.length,
-      has_verification: verification,
-      status: determinePhaseStatus(plans.length, completedSummaries.length, summaries.length, verification, phaseDir)
-    };
-
-    phases.push(phaseInfo);
-    totalPlans += plans.length;
-    completedPlans += completedSummaries.length;
-  }
 
-  return {
-    phases,
-    total_plans: totalPlans,
-    completed_plans: completedPlans,
-    percentage: totalPlans > 0 ? Math.round((completedPlans / totalPlans) * 100) : 0
-  };
+function frontmatter(filePath) {
+  return _frontmatter(filePath);
 }
 
 function planIndex(phaseNum) {
-  const phasesDir = path.join(planningDir, 'phases');
-  if (!fs.existsSync(phasesDir)) {
-    return { error: 'No phases directory found' };
-  }
-
-  // Find phase directory matching the number
-  const entries = fs.readdirSync(phasesDir, { withFileTypes: true })
-    .filter(e => e.isDirectory());
-
-  const phaseDir = entries.find(e => e.name.startsWith(phaseNum.padStart(2, '0') + '-'));
-  if (!phaseDir) {
-    return { error: `No phase directory found matching phase ${phaseNum}` };
-  }
-
-  const fullDir = path.join(phasesDir, phaseDir.name);
-  const planFiles = findFiles(fullDir, /-PLAN\.md$/);
-
-  const plans = [];
-  const waves = {};
-
-  for (const file of planFiles) {
-    const content = fs.readFileSync(path.join(fullDir, file), 'utf8');
-    const frontmatter = parseYamlFrontmatter(content);
-
-    const plan = {
-      file,
-      plan_id: frontmatter.plan || file.replace(/-PLAN\.md$/, ''),
-      wave: parseInt(frontmatter.wave, 10) || 1,
-      type: frontmatter.type || 'unknown',
-      autonomous: frontmatter.autonomous !== false,
-      depends_on: frontmatter.depends_on || [],
-      gap_closure: frontmatter.gap_closure || false,
-      has_summary: fs.existsSync(path.join(fullDir, `SUMMARY-${frontmatter.plan || ''}.md`)),
-      must_haves_count: countMustHaves(frontmatter.must_haves)
-    };
-
-    plans.push(plan);
-
-    const waveKey = `wave_${plan.wave}`;
-    if (!waves[waveKey]) waves[waveKey] = [];
-    waves[waveKey].push(plan.plan_id);
-  }
-
-  return {
-    phase: phaseDir.name,
-    total_plans: plans.length,
-    plans,
-    waves
-  };
+  return _planIndex(phaseNum, planningDir);
 }
 
-function configValidate(preloadedConfig) {
-  let config;
-  if (preloadedConfig) {
-    config = preloadedConfig;
-  } else {
-    const configPath = path.join(planningDir, 'config.json');
-    if (!fs.existsSync(configPath)) {
-      return { valid: false, errors: ['config.json not found'], warnings: [] };
-    }
-
-    try {
-      config = JSON.parse(fs.readFileSync(configPath, 'utf8'));
-    } catch (e) {
-      return { valid: false, errors: [`config.json is not valid JSON: ${e.message}`], warnings: [] };
-    }
-  }
-
-  const schema = JSON.parse(fs.readFileSync(path.join(__dirname, 'config-schema.json'), 'utf8'));
-  const warnings = [];
-  const errors = [];
-
-  validateObject(config, schema, '', errors, warnings);
-
-  // Semantic conflict detection — logical contradictions that pass schema validation
-  // Clear contradictions → errors; ambiguous/preference issues → warnings
-  if (config.mode === 'autonomous' && config.gates) {
-    const activeGates = Object.entries(config.gates || {}).filter(([, v]) => v === true).map(([k]) => k);
-    if (activeGates.length > 0) {
-      errors.push(`mode=autonomous with active gates (${activeGates.join(', ')}): gates are unreachable in autonomous mode`);
-    }
-  }
-  if (config.features && config.features.auto_continue && config.mode === 'interactive') {
-    warnings.push('features.auto_continue=true with mode=interactive: auto_continue only fires in autonomous mode');
-  }
-  if (config.parallelization) {
-    if (config.parallelization.enabled === false && config.parallelization.plan_level === true) {
-      warnings.push('parallelization.enabled=false with plan_level=true: plan_level is ignored when parallelization is disabled');
-    }
-    if (config.parallelization.max_concurrent_agents === 1 && config.teams && config.teams.coordination) {
-      errors.push('parallelization.max_concurrent_agents=1 with teams.coordination set: teams require concurrent agents to be useful');
-    }
-  }
+function mustHavesCollect(phaseNum) {
+  return _mustHavesCollect(phaseNum, planningDir);
+}
 
-  return {
-    valid: errors.length === 0,
-    errors,
-    warnings
-  };
+function phaseInfo(phaseNum) {
+  return _phaseInfo(phaseNum, planningDir);
 }
 
-// --- New read-only commands ---
+function phaseAdd(slug, afterPhase, options) {
+  return _phaseAdd(slug, afterPhase, planningDir, options);
+}
 
-/**
- * Parse a markdown file's YAML frontmatter and return as JSON.
- * Wraps parseYamlFrontmatter() + parseMustHaves().
- */
-function frontmatter(filePath) {
-  const resolved = path.resolve(filePath);
-  if (!fs.existsSync(resolved)) {
-    return { error: `File not found: ${resolved}` };
-  }
-  const content = fs.readFileSync(resolved, 'utf8');
-  return parseYamlFrontmatter(content);
+function phaseRemove(phaseNum) {
+  return _phaseRemove(phaseNum, planningDir);
 }
 
-/**
- * Collect all must-haves from all PLAN.md files in a phase.
- * Returns per-plan grouping + flat deduplicated list + total count.
- */
-function mustHavesCollect(phaseNum) {
-  const phasesDir = path.join(planningDir, 'phases');
-  if (!fs.existsSync(phasesDir)) {
-    return { error: 'No phases directory found' };
-  }
+function phaseList(opts) {
+  return _phaseList(planningDir, opts);
+}
 
-  const entries = fs.readdirSync(phasesDir, { withFileTypes: true })
-    .filter(e => e.isDirectory());
-  const phaseDir = entries.find(e => e.name.startsWith(phaseNum.padStart(2, '0') + '-'));
-  if (!phaseDir) {
-    return { error: `No phase directory found matching phase ${phaseNum}` };
-  }
+function phaseNextNumber() {
+  return _phaseNextNumber(planningDir);
+}
 
-  const fullDir = path.join(phasesDir, phaseDir.name);
-  const planFiles = findFiles(fullDir, /-PLAN\.md$/);
+function phaseComplete(phaseNum) {
+  return _phaseComplete(phaseNum, planningDir);
+}
 
-  const perPlan = {};
-  const allTruths = new Set();
-  const allArtifacts = new Set();
-  const allKeyLinks = new Set();
+function phaseInsert(position, slug, options) {
+  return _phaseInsert(position, slug, planningDir, options);
+}
 
-  for (const file of planFiles) {
-    const content = fs.readFileSync(path.join(fullDir, file), 'utf8');
-    const fm = parseYamlFrontmatter(content);
-    const planId = fm.plan || file.replace(/-PLAN\.md$/, '');
-    const mh = fm.must_haves || { truths: [], artifacts: [], key_links: [] };
+function milestoneStats(version) {
+  return _milestoneStats(version, planningDir);
+}
 
-    perPlan[planId] = mh;
-    (mh.truths || []).forEach(t => allTruths.add(t));
-    (mh.artifacts || []).forEach(a => allArtifacts.add(a));
-    (mh.key_links || []).forEach(k => allKeyLinks.add(k));
-  }
+function compoundInitPhase(phaseNum, slug, opts) {
+  return _compoundInitPhase(phaseNum, slug, planningDir, opts);
+}
 
-  const all = {
-    truths: [...allTruths],
-    artifacts: [...allArtifacts],
-    key_links: [...allKeyLinks]
-  };
+function compoundCompletePhase(phaseNum) {
+  return _compoundCompletePhase(phaseNum, planningDir);
+}
 
-  return {
-    phase: phaseDir.name,
-    plans: perPlan,
-    all,
-    total: all.truths.length + all.artifacts.length + all.key_links.length
-  };
+function compoundInitMilestone(version, opts) {
+  return _compoundInitMilestone(version, planningDir, opts);
 }
 
-/**
- * Comprehensive single-phase status combining roadmap, filesystem, and plan data.
- */
-function phaseInfo(phaseNum) {
-  const phasesDir = path.join(planningDir, 'phases');
-  if (!fs.existsSync(phasesDir)) {
-    return { error: 'No phases directory found' };
-  }
+function initExecutePhase(phaseNum, overridePlanningDir, overrideModel) {
+  return _initExecutePhase(phaseNum, overridePlanningDir || planningDir, overrideModel);
+}
 
-  const entries = fs.readdirSync(phasesDir, { withFileTypes: true })
-    .filter(e => e.isDirectory());
-  const phaseDir = entries.find(e => e.name.startsWith(phaseNum.padStart(2, '0') + '-'));
-  if (!phaseDir) {
-    return { error: `No phase directory found matching phase ${phaseNum}` };
-  }
+function initPlanPhase(phaseNum, overridePlanningDir, overrideModel) {
+  return _initPlanPhase(phaseNum, overridePlanningDir || planningDir, overrideModel);
+}
 
-  const fullDir = path.join(phasesDir, phaseDir.name);
+function initQuick(description) {
+  return _initQuick(description, planningDir);
+}
 
-  // Get roadmap info
-  let roadmapInfo = null;
-  const roadmapPath = path.join(planningDir, 'ROADMAP.md');
-  if (fs.existsSync(roadmapPath)) {
-    const roadmapContent = fs.readFileSync(roadmapPath, 'utf8');
-    const roadmap = parseRoadmapMd(roadmapContent);
-    roadmapInfo = roadmap.phases.find(p => p.number === phaseNum.padStart(2, '0')) || null;
-  }
+function initVerifyWork(phaseNum, overridePlanningDir, overrideModel) {
+  return _initVerifyWork(phaseNum, overridePlanningDir || planningDir, overrideModel);
+}
 
-  // Get plan index
-  const plans = planIndex(phaseNum);
+function initResume() {
+  return _initResume(planningDir);
+}
 
-  // Check for verification
-  const verificationPath = path.join(fullDir, 'VERIFICATION.md');
-  let verification = null;
-  if (fs.existsSync(verificationPath)) {
-    const vContent = fs.readFileSync(verificationPath, 'utf8');
-    verification = parseYamlFrontmatter(vContent);
-  }
+function initProgress() {
+  return _initProgress(planningDir);
+}
 
-  // Check summaries
-  const summaryFiles = findFiles(fullDir, /^SUMMARY-.*\.md$/);
-  const summaries = summaryFiles.map(f => {
-    const content = fs.readFileSync(path.join(fullDir, f), 'utf8');
-    const fm = parseYamlFrontmatter(content);
-    return { file: f, plan: fm.plan || f.replace(/^SUMMARY-|\.md$/g, ''), status: fm.status || 'unknown' };
-  });
-
-  // Determine filesystem status
-  const planCount = plans.total_plans || 0;
-  const completedCount = summaries.filter(s => s.status === 'complete').length;
-  const hasVerification = fs.existsSync(verificationPath);
-  const fsStatus = determinePhaseStatus(planCount, completedCount, summaryFiles.length, hasVerification, fullDir);
-
-  return {
-    phase: phaseDir.name,
-    name: roadmapInfo ? roadmapInfo.name : phaseDir.name.replace(/^\d+-/, ''),
-    goal: roadmapInfo ? roadmapInfo.goal : null,
-    roadmap_status: roadmapInfo ? roadmapInfo.status : null,
-    filesystem_status: fsStatus,
-    plans: plans.plans || [],
-    plan_count: planCount,
-    summaries,
-    completed: completedCount,
-    verification,
-    has_context: fs.existsSync(path.join(fullDir, 'CONTEXT.md'))
-  };
-}
-
-// --- Mutation commands ---
+function initContinue() {
+  return _initContinue(planningDir);
+}
 
-/**
- * Atomically update a field in STATE.md using lockedFileUpdate.
- * Supports both legacy and frontmatter (v2) formats.
- *
- * @param {string} field - One of: current_phase, status, plans_complete, last_activity
- * @param {string} value - New value (use 'now' for last_activity to auto-timestamp)
- */
-function stateUpdate(field, value) {
-  const statePath = path.join(planningDir, 'STATE.md');
-  if (!fs.existsSync(statePath)) {
-    return { success: false, error: 'STATE.md not found' };
-  }
+function initMilestone() {
+  return _initMilestone(planningDir);
+}
 
-  const validFields = ['current_phase', 'status', 'plans_complete', 'last_activity'];
-  if (!validFields.includes(field)) {
-    return { success: false, error: `Invalid field: ${field}. Valid fields: ${validFields.join(', ')}` };
-  }
+function initBegin() {
+  return _initBegin(planningDir);
+}
 
-  // Auto-timestamp
-  if (field === 'last_activity' && value === 'now') {
-    value = new Date().toISOString().slice(0, 19).replace('T', ' ');
-  }
+function initStatus() {
+  return _initStatus(planningDir);
+}
 
-  const result = lockedFileUpdate(statePath, (content) => {
-    const fm = parseYamlFrontmatter(content);
-    if (fm.version === 2 || fm.current_phase !== undefined) {
-      return updateFrontmatterField(content, field, value);
-    }
-    return updateLegacyStateField(content, field, value);
-  });
+function initMapCodebase() {
+  return _initMapCodebase(planningDir);
+}
 
-  if (result.success) {
-    return { success: true, field, value };
-  }
-  return { success: false, error: result.error };
+function stateBundle(phaseNum) {
+  return _initStateBundle(phaseNum, planningDir);
 }
 
-/**
- * Append a record to HISTORY.md. Creates the file if it doesn't exist.
- * Each entry is a markdown section appended at the end.
- *
- * @param {object} entry - { type: 'milestone'|'phase', title: string, body: string }
- * @param {string} [dir] - Path to .planning directory (defaults to cwd/.planning)
- * @returns {{success: boolean, error?: string}}
- */
 function historyAppend(entry, dir) {
-  const historyPath = path.join(dir || planningDir, 'HISTORY.md');
-  const timestamp = new Date().toISOString().slice(0, 10);
-
-  let header = '';
-  if (!fs.existsSync(historyPath)) {
-    header = '# Project History\n\nCompleted milestones and phase records. This file is append-only.\n\n';
-  }
-
-  const section = `${header}## ${entry.type === 'milestone' ? 'Milestone' : 'Phase'}: ${entry.title}\n_Completed: ${timestamp}_\n\n${entry.body.trim()}\n\n---\n\n`;
-
-  try {
-    fs.appendFileSync(historyPath, section, 'utf8');
-    return { success: true };
-  } catch (e) {
-    return { success: false, error: e.message };
-  }
+  return _historyAppend(entry, dir || planningDir);
 }
 
-/**
- * Load HISTORY.md and parse it into structured records.
- * Returns null if HISTORY.md doesn't exist.
- *
- * @param {string} [dir] - Path to .planning directory
- * @returns {object|null} { records: [{type, title, date, body}], line_count }
- */
 function historyLoad(dir) {
-  const historyPath = path.join(dir || planningDir, 'HISTORY.md');
-  if (!fs.existsSync(historyPath)) return null;
-
-  const content = fs.readFileSync(historyPath, 'utf8');
-  const records = [];
-  const sectionRegex = /^## (Milestone|Phase): (.+)\n_Completed: (\d{4}-\d{2}-\d{2})_\n\n([\s\S]*?)(?=\n---|\s*$)/gm;
-
-  let match;
-  while ((match = sectionRegex.exec(content)) !== null) {
-    records.push({
-      type: match[1].toLowerCase(),
-      title: match[2].trim(),
-      date: match[3],
-      body: match[4].trim()
-    });
-  }
-
-  return {
-    records,
-    line_count: content.split('\n').length
-  };
+  return _historyLoad(dir || planningDir);
 }
 
-/**
- * Update the Status column for a phase in ROADMAP.md's Phase Overview table.
- */
-function roadmapUpdateStatus(phaseNum, newStatus) {
-  const roadmapPath = path.join(planningDir, 'ROADMAP.md');
-  if (!fs.existsSync(roadmapPath)) {
-    return { success: false, error: 'ROADMAP.md not found' };
-  }
-
-  let oldStatus = null;
-
-  const result = lockedFileUpdate(roadmapPath, (content) => {
-    const lines = content.split('\n');
-    const rowIdx = findRoadmapRow(lines, phaseNum);
-    if (rowIdx === -1) {
-      return content; // No matching row found
-    }
-    const parts = lines[rowIdx].split('|');
-    oldStatus = parts[6] ? parts[6].trim() : 'unknown';
-    lines[rowIdx] = updateTableRow(lines[rowIdx], 5, newStatus);
-    return lines.join('\n');
-  });
-
-  if (!oldStatus) {
-    return { success: false, error: `Phase ${phaseNum} not found in ROADMAP.md table` };
-  }
-
-  // Advisory transition validation — warn on suspicious transitions but don't block
-  const transition = validateStatusTransition(oldStatus, newStatus);
-  if (!transition.valid && transition.warning) {
-    process.stderr.write(`[pbr-tools] WARNING: ${transition.warning}\n`);
-  }
-
-  if (result.success) {
-    const response = { success: true, old_status: oldStatus, new_status: newStatus };
-    if (!transition.valid) {
-      response.transition_warning = transition.warning;
-    }
-    return response;
-  }
-  return { success: false, error: result.error };
+function todoList(opts) {
+  return _todoList(planningDir, opts);
 }
 
-/**
- * Update the Plans column for a phase in ROADMAP.md's Phase Overview table.
- */
-function roadmapUpdatePlans(phaseNum, complete, total) {
-  const roadmapPath = path.join(planningDir, 'ROADMAP.md');
-  if (!fs.existsSync(roadmapPath)) {
-    return { success: false, error: 'ROADMAP.md not found' };
-  }
-
-  let oldPlans = null;
-  const newPlans = `${complete}/${total}`;
-
-  const result = lockedFileUpdate(roadmapPath, (content) => {
-    const lines = content.split('\n');
-    const rowIdx = findRoadmapRow(lines, phaseNum);
-    if (rowIdx === -1) {
-      return content;
-    }
-    const parts = lines[rowIdx].split('|');
-    oldPlans = parts[4] ? parts[4].trim() : 'unknown';
-    lines[rowIdx] = updateTableRow(lines[rowIdx], 3, newPlans);
-    return lines.join('\n');
-  });
-
-  if (!oldPlans) {
-    return { success: false, error: `Phase ${phaseNum} not found in ROADMAP.md table` };
-  }
-
-  if (result.success) {
-    return { success: true, old_plans: oldPlans, new_plans: newPlans };
-  }
-  return { success: false, error: result.error };
+function todoGet(num) {
+  return _todoGet(planningDir, num);
 }
 
-// --- Mutation helpers ---
-
-/**
- * Update a field in legacy (non-frontmatter) STATE.md content.
- * Pure function: content in, content out.
- */
-function updateLegacyStateField(content, field, value) {
-  const lines = content.split('\n');
-
-  switch (field) {
-    case 'current_phase': {
-      const idx = lines.findIndex(l => /Phase:\s*\d+\s+of\s+\d+/.test(l));
-      if (idx !== -1) {
-        lines[idx] = lines[idx].replace(/(Phase:\s*)\d+/, (_, prefix) => `${prefix}${value}`);
-      }
-      break;
-    }
-    case 'status': {
-      const idx = lines.findIndex(l => /^Status:/i.test(l));
-      if (idx !== -1) {
-        lines[idx] = `Status: ${value}`;
-      } else {
-        const phaseIdx = lines.findIndex(l => /Phase:/.test(l));
-        if (phaseIdx !== -1) {
-          lines.splice(phaseIdx + 1, 0, `Status: ${value}`);
-        } else {
-          lines.push(`Status: ${value}`);
-        }
-      }
-      break;
-    }
-    case 'plans_complete': {
-      const idx = lines.findIndex(l => /Plan:\s*\d+\s+of\s+\d+/.test(l));
-      if (idx !== -1) {
-        lines[idx] = lines[idx].replace(/(Plan:\s*)\d+/, (_, prefix) => `${prefix}${value}`);
-      }
-      break;
-    }
-    case 'last_activity': {
-      const idx = lines.findIndex(l => /^Last Activity:/i.test(l));
-      if (idx !== -1) {
-        lines[idx] = `Last Activity: ${value}`;
-      } else {
-        const statusIdx = lines.findIndex(l => /^Status:/i.test(l));
-        if (statusIdx !== -1) {
-          lines.splice(statusIdx + 1, 0, `Last Activity: ${value}`);
-        } else {
-          lines.push(`Last Activity: ${value}`);
-        }
-      }
-      break;
-    }
-  }
-
-  return lines.join('\n');
+function todoAdd(title, opts) {
+  return _todoAdd(planningDir, title, opts);
 }
 
-/**
- * Update a field in YAML frontmatter content.
- * Pure function: content in, content out.
- */
-function updateFrontmatterField(content, field, value) {
-  const match = content.match(/^(---\s*\n)([\s\S]*?)(\n---)/);
-  if (!match) return content;
-
-  const before = match[1];
-  let yaml = match[2];
-  const after = match[3];
-  const rest = content.slice(match[0].length);
-
-  // Format value: integers stay bare, strings get quotes
-  const isNum = /^\d+$/.test(String(value));
-  const formatted = isNum ? value : `"${value}"`;
-
-  const fieldRegex = new RegExp(`^(${field})\\s*:.*$`, 'm');
-  if (fieldRegex.test(yaml)) {
-    yaml = yaml.replace(fieldRegex, () => `${field}: ${formatted}`);
-  } else {
-    yaml = yaml + `\n${field}: ${formatted}`;
-  }
-
-  return before + yaml + after + rest;
+function todoDone(num) {
+  return _todoDone(planningDir, num);
 }
 
-/**
- * Find the row index of a phase in a ROADMAP.md table.
- * @returns {number} Line index or -1 if not found
- */
-function findRoadmapRow(lines, phaseNum) {
-  const paddedPhase = phaseNum.padStart(2, '0');
-  for (let i = 0; i < lines.length; i++) {
-    if (!lines[i].includes('|')) continue;
-    const parts = lines[i].split('|');
-    if (parts.length < 3) continue;
-    const phaseCol = parts[1] ? parts[1].trim() : '';
-    if (phaseCol === paddedPhase) {
-      return i;
-    }
-  }
-  return -1;
+function autoCloseTodos(context) {
+  return _autoCloseTodos(planningDir, context);
 }
 
-/**
- * Update a specific column in a markdown table row.
- * @param {string} row - The full table row string (e.g., "| 01 | Setup | ... |")
- * @param {number} columnIndex - 0-based column index (Phase=0, Name=1, ..., Status=5)
- * @param {string} newValue - New cell value
- * @returns {string} Updated row
- */
-function updateTableRow(row, columnIndex, newValue) {
-  const parts = row.split('|');
-  // parts[0] is empty (before first |), data starts at parts[1]
-  const partIndex = columnIndex + 1;
-  if (partIndex < parts.length) {
-    parts[partIndex] = ` ${newValue} `;
-  }
-  return parts.join('|');
+function autoArchiveNotes(context) {
+  return _autoArchiveNotes(planningDir, context);
 }
 
-/**
- * Lightweight JSON Schema validator — supports type, enum, properties,
- * additionalProperties, minimum, maximum for the config schema.
- */
-function validateObject(value, schema, prefix, errors, warnings) {
-  if (schema.type && typeof value !== schema.type) {
-    if (!(schema.type === 'integer' && typeof value === 'number' && Number.isInteger(value))) {
-      errors.push(`${prefix || 'root'}: expected ${schema.type}, got ${typeof value}`);
-      return;
-    }
-  }
-
-  if (schema.enum && !schema.enum.includes(value)) {
-    errors.push(`${prefix || 'root'}: value "${value}" not in allowed values [${schema.enum.join(', ')}]`);
-    return;
-  }
-
-  if (schema.minimum !== undefined && value < schema.minimum) {
-    errors.push(`${prefix || 'root'}: value ${value} is below minimum ${schema.minimum}`);
-  }
-  if (schema.maximum !== undefined && value > schema.maximum) {
-    errors.push(`${prefix || 'root'}: value ${value} is above maximum ${schema.maximum}`);
-  }
-
-  if (schema.type === 'object' && schema.properties) {
-    const knownKeys = new Set(Object.keys(schema.properties));
 
-    for (const key of Object.keys(value)) {
-      const fullKey = prefix ? `${prefix}.${key}` : key;
-      if (!knownKeys.has(key)) {
-        if (schema.additionalProperties === false) {
-          warnings.push(`${fullKey}: unrecognized key (possible typo?)`);
-        }
-        continue;
-      }
-      validateObject(value[key], schema.properties[key], fullKey, errors, warnings);
-    }
-  }
+function migrate(options) {
+  return _applyMigrations(planningDir, options);
 }
 
-/**
- * Locked file update: read-modify-write with exclusive lockfile.
- * Prevents concurrent writes to STATE.md and ROADMAP.md.
- *
- * @param {string} filePath - Absolute path to the file to update
- * @param {function} updateFn - Receives current content, returns new content
- * @param {object} opts - Options: { retries: 3, retryDelayMs: 100, timeoutMs: 5000 }
- * @returns {object} { success, content?, error? }
- */
-function lockedFileUpdate(filePath, updateFn, opts = {}) {
-  const retries = opts.retries || 3;
-  const retryDelayMs = opts.retryDelayMs || 100;
-  const timeoutMs = opts.timeoutMs || 5000;
-  const lockPath = filePath + '.lock';
-
-  let lockFd = null;
-  let lockAcquired = false;
-
-  try {
-    // Acquire lock with retries
-    for (let attempt = 0; attempt < retries; attempt++) {
-      try {
-        lockFd = fs.openSync(lockPath, 'wx');
-        lockAcquired = true;
-        break;
-      } catch (e) {
-        if (e.code === 'EEXIST') {
-          // Lock exists — check if stale (older than timeoutMs)
-          try {
-            const stats = fs.statSync(lockPath);
-            if (Date.now() - stats.mtimeMs > timeoutMs) {
-              // Stale lock — remove and retry
-              fs.unlinkSync(lockPath);
-              continue;
-            }
-          } catch (_statErr) {
-            // Lock disappeared between check — retry
-            continue;
-          }
-
-          if (attempt < retries - 1) {
-            // Wait and retry
-            const waitMs = retryDelayMs * (attempt + 1);
-            const start = Date.now();
-            while (Date.now() - start < waitMs) {
-              // Busy wait (synchronous context)
-            }
-            continue;
-          }
-          return { success: false, error: `Could not acquire lock for ${path.basename(filePath)} after ${retries} attempts` };
-        }
-        throw e;
-      }
-    }
-
-    if (!lockAcquired) {
-      return { success: false, error: `Could not acquire lock for ${path.basename(filePath)}` };
-    }
-
-    // Write PID to lock file for debugging
-    fs.writeSync(lockFd, `${process.pid}`);
-    fs.closeSync(lockFd);
-    lockFd = null;
-
-    // Read current content
-    let content = '';
-    if (fs.existsSync(filePath)) {
-      content = fs.readFileSync(filePath, 'utf8');
-    }
-
-    // Apply update
-    const newContent = updateFn(content);
-
-    // Write back atomically
-    const writeResult = atomicWrite(filePath, newContent);
-    if (!writeResult.success) {
-      return { success: false, error: writeResult.error };
-    }
 
-    return { success: true, content: newContent };
-  } catch (e) {
-    return { success: false, error: e.message };
-  } finally {
-    // Close fd if still open
-    try {
-      if (lockFd !== null) fs.closeSync(lockFd);
-    } catch (_e) { /* ignore */ }
-    // Only release lock if we acquired it
-    if (lockAcquired) {
-      try {
-        fs.unlinkSync(lockPath);
-      } catch (_e) { /* ignore — may already be cleaned up */ }
-    }
-  }
+function verifySpotCheck(type, dirPath) {
+  return _verifySpotCheck(type, dirPath);
 }
 
-// --- Parsers ---
-
-function parseStateMd(content) {
-  const result = {
-    current_phase: null,
-    phase_name: null,
-    progress: null,
-    status: null,
-    line_count: content.split('\n').length,
-    format: 'legacy' // 'legacy' or 'frontmatter'
-  };
-
-  // Check for YAML frontmatter (version 2 format)
-  const frontmatter = parseYamlFrontmatter(content);
-  if (frontmatter.version === 2 || frontmatter.current_phase !== undefined) {
-    result.format = 'frontmatter';
-    result.current_phase = frontmatter.current_phase || null;
-    result.total_phases = frontmatter.total_phases || null;
-    result.phase_name = frontmatter.phase_slug || frontmatter.phase_name || null;
-    result.status = frontmatter.status || null;
-    result.progress = frontmatter.progress_percent !== undefined ? frontmatter.progress_percent : null;
-    result.plans_total = frontmatter.plans_total || null;
-    result.plans_complete = frontmatter.plans_complete || null;
-    result.last_activity = frontmatter.last_activity || null;
-    result.last_command = frontmatter.last_command || null;
-    result.blockers = frontmatter.blockers || [];
-    return result;
-  }
-
-  // Legacy regex-based parsing (version 1 format, no frontmatter)
-  // DEPRECATED (2026-02): v1 STATE.md format (no YAML frontmatter) is deprecated.
-  // New projects should use v2 (frontmatter) format, generated by /pbr:setup.
-  // v1 support will be removed in a future major version.
-  process.stderr.write('[pbr] WARNING: STATE.md uses legacy v1 format. Run /pbr:setup to migrate to v2 format.\n');
-  // Extract "Phase: N of M"
-  const phaseMatch = content.match(/Phase:\s*(\d+)\s+of\s+(\d+)/);
-  if (phaseMatch) {
-    result.current_phase = parseInt(phaseMatch[1], 10);
-    result.total_phases = parseInt(phaseMatch[2], 10);
-  }
+function referenceGet(name, options) {
+  // Resolve plugin root — try CLAUDE_PLUGIN_ROOT env, then walk up from __dirname
+  const pluginRoot = process.env.CLAUDE_PLUGIN_ROOT || path.resolve(__dirname, '..');
+  let root = normalizeMsysPath(pluginRoot);
+  return _referenceGet(name, options, root);
+}
 
-  // Extract phase name (line after "Phase:")
-  const nameMatch = content.match(/--\s+(.+?)(?:\n|$)/);
-  if (nameMatch) {
-    result.phase_name = nameMatch[1].trim();
-  }
+function resolvePluginRoot() {
+  // Resolve plugin root — try CLAUDE_PLUGIN_ROOT env, then walk up from __dirname
+  const pluginRoot = process.env.CLAUDE_PLUGIN_ROOT || path.resolve(__dirname, '..');
+  return normalizeMsysPath(pluginRoot);
+}
 
-  // Extract progress percentage
-  const progressMatch = content.match(/(\d+)%/);
-  if (progressMatch) {
-    result.progress = parseInt(progressMatch[1], 10);
-  }
+function skillSectionGet(skillName, sectionQuery) {
+  return _skillSection(skillName, sectionQuery, resolvePluginRoot());
+}
 
-  // Extract plan status
-  const statusMatch = content.match(/Status:\s*(.+?)(?:\n|$)/i);
-  if (statusMatch) {
-    result.status = statusMatch[1].trim();
+function listSkillHeadings(skillName) {
+  const { listHeadings } = require('./lib/reference');
+  const root = resolvePluginRoot();
+  const skillPath = require('path').join(root, 'skills', skillName, 'SKILL.md');
+  if (!require('fs').existsSync(skillPath)) {
+    return { error: `Skill not found: ${skillName}`, available: _listAvailableSkills(root) };
   }
+  const content = require('fs').readFileSync(skillPath, 'utf8');
+  return { skill: skillName, headings: listHeadings(content) };
+}
 
-  return result;
-}
-
-function parseRoadmapMd(content) {
-  const result = { phases: [], has_progress_table: false };
-
-  // Find Phase Overview table
-  const overviewMatch = content.match(/## Phase Overview[\s\S]*?\|[\s\S]*?(?=\n##|\s*$)/);
-  if (overviewMatch) {
-    const rows = overviewMatch[0].split('\n').filter(r => r.includes('|'));
-    // Skip header and separator rows
-    for (let i = 2; i < rows.length; i++) {
-      const cols = rows[i].split('|').map(c => c.trim()).filter(Boolean);
-      if (cols.length >= 3) {
-        result.phases.push({
-          number: cols[0],
-          name: cols[1],
-          goal: cols[2],
-          plans: cols[3] || '',
-          wave: cols[4] || '',
-          status: cols[5] || 'pending'
-        });
-      }
-    }
-  }
+function contextTriage(options) {
+  return _contextTriage(options, planningDir);
+}
 
-  // Check for Progress table
-  result.has_progress_table = /## Progress/.test(content);
+function stalenessCheck(phaseSlug) { return _stalenessCheck(phaseSlug, planningDir); }
+function summaryGate(phaseSlug, planId) { return _summaryGate(phaseSlug, planId, planningDir); }
+function checkpointInit(phaseSlug, plans) { return _checkpointInit(phaseSlug, plans, planningDir); }
+function checkpointUpdate(phaseSlug, opts) { return _checkpointUpdate(phaseSlug, opts, planningDir); }
+function seedsMatch(phaseSlug, phaseNum) { return _seedsMatch(phaseSlug, phaseNum, planningDir); }
+function ciPoll(runId, timeoutSecs) { return _ciPoll(runId, timeoutSecs, planningDir); }
+function ciFix(options) { return _runCiFixLoop({ ...options, cwd: path.resolve('.') }); }
+function rollbackPlan(manifestPath) { return _rollback(manifestPath, planningDir); }
 
-  return result;
+function helpListCmd() {
+  const root = resolvePluginRoot();
+  return _helpList(root);
+}
+function skillMetadataCmd(skillName) {
+  const root = resolvePluginRoot();
+  return _skillMetadata(skillName, root);
 }
 
-function parseYamlFrontmatter(content) {
-  const match = content.match(/^---\s*\n([\s\S]*?)\n---/);
-  if (!match) return {};
-
-  const yaml = match[1];
-  const result = {};
+function quickStatus() { return _quickStatus(planningDir); }
 
-  // Simple YAML parser for flat and basic nested values
-  const lines = yaml.split('\n');
-  let currentKey = null;
+/**
+ * Build cleanup context from phase SUMMARY files and git log.
+ * @param {string} phaseNum - Phase number (e.g. "38")
+ * @returns {{ phaseName: string, phaseNum: string, keyFiles: string[], commitMessages: string[], summaryDescriptions: string[] }}
+ */
+function buildCleanupContext(phaseNum) {
+  const padded = String(phaseNum).padStart(2, '0');
+  const phasesDir = path.join(planningDir, 'phases');
+  if (!fs.existsSync(phasesDir)) throw new Error('No phases directory found');
 
-  for (const line of lines) {
-    // Array item
-    if (/^\s+-\s+/.test(line) && currentKey) {
-      const val = line.replace(/^\s+-\s+/, '').trim().replace(/^["']|["']$/g, '');
-      if (!result[currentKey]) result[currentKey] = [];
-      if (Array.isArray(result[currentKey])) {
-        result[currentKey].push(val);
-      }
-      continue;
-    }
+  const phaseDir = fs.readdirSync(phasesDir).find(d => d.startsWith(padded + '-'));
+  if (!phaseDir) throw new Error(`Phase ${phaseNum} directory not found`);
 
-    // Key-value pair
-    const kvMatch = line.match(/^(\w[\w_]*)\s*:\s*(.*)/);
-    if (kvMatch) {
-      currentKey = kvMatch[1];
-      let val = kvMatch[2].trim();
+  const phaseName = phaseDir.replace(/^\d+-/, '').replace(/-/g, ' ');
+  const phaseDirPath = path.join(phasesDir, phaseDir);
 
-      if (val === '' || val === '|') {
-        // Possible array or block follows
-        continue;
+  // Collect key_files and descriptions from all SUMMARY files
+  const keyFiles = [];
+  const summaryDescriptions = [];
+  const summaryFiles = fs.readdirSync(phaseDirPath).filter(f => /^SUMMARY/i.test(f) && f.endsWith('.md'));
+  for (const sf of summaryFiles) {
+    try {
+      const content = fs.readFileSync(path.join(phaseDirPath, sf), 'utf8');
+      const fm = parseYamlFrontmatter(content);
+      if (fm.key_files && Array.isArray(fm.key_files)) {
+        keyFiles.push(...fm.key_files.map(kf => typeof kf === 'string' ? kf.split(':')[0].trim() : ''));
       }
-
-      // Handle arrays on same line: [a, b, c]
-      if (val.startsWith('[') && val.endsWith(']')) {
-        result[currentKey] = val.slice(1, -1).split(',')
-          .map(v => v.trim().replace(/^["']|["']$/g, ''))
-          .filter(Boolean);
-        continue;
+      if (fm.provides && Array.isArray(fm.provides)) {
+        summaryDescriptions.push(...fm.provides);
       }
-
-      // Clean quotes
-      val = val.replace(/^["']|["']$/g, '');
-
-      // Type coercion
-      if (val === 'true') val = true;
-      else if (val === 'false') val = false;
-      else if (/^\d+$/.test(val)) val = parseInt(val, 10);
-
-      result[currentKey] = val;
-    }
+    } catch (_e) { /* skip unreadable summaries */ }
   }
 
-  // Handle must_haves as a nested object
-  if (yaml.includes('must_haves:')) {
-    result.must_haves = parseMustHaves(yaml);
-  }
-
-  return result;
-}
-
-function parseMustHaves(yaml) {
-  const result = { truths: [], artifacts: [], key_links: [] };
-  let section = null;
-
-  const inMustHaves = yaml.split('\n');
-  let collecting = false;
-
-  for (const line of inMustHaves) {
-    if (/^\s*must_haves:/.test(line)) {
-      collecting = true;
-      continue;
-    }
-    if (collecting) {
-      if (/^\s{2}truths:/.test(line)) { section = 'truths'; continue; }
-      if (/^\s{2}artifacts:/.test(line)) { section = 'artifacts'; continue; }
-      if (/^\s{2}key_links:/.test(line)) { section = 'key_links'; continue; }
-      if (/^\w/.test(line)) break; // New top-level key, stop
-
-      if (section && /^\s+-\s+/.test(line)) {
-        result[section].push(line.replace(/^\s+-\s+/, '').trim().replace(/^["']|["']$/g, ''));
-      }
-    }
-  }
+  // Get recent commit messages
+  let commitMessages = [];
+  try {
+    const { execSync } = require('child_process');
+    const log = execSync('git log --oneline -20', { encoding: 'utf8', cwd: path.join(planningDir, '..') });
+    commitMessages = log.split('\n').filter(l => l.trim()).map(l => {
+      const parts = l.match(/^[0-9a-f]+\s+(.*)/);
+      return parts ? parts[1] : '';
+    }).filter(Boolean);
+  } catch (_e) { /* git not available */ }
 
-  return result;
+  return { phaseName, phaseNum: String(phaseNum), keyFiles, commitMessages, summaryDescriptions };
 }
 
-// --- Helpers ---
+// --- Claim wrapper functions ---
 
-function findFiles(dir, pattern) {
-  try {
-    return fs.readdirSync(dir).filter(f => pattern.test(f)).sort();
-  } catch (_) {
-    return [];
-  }
+function claimAcquire(phaseSlug, sessionId, skill) {
+  const phaseDir = path.join(planningDir, 'phases', phaseSlug);
+  if (!fs.existsSync(phaseDir)) return { error: `Phase directory not found: ${phaseSlug}` };
+  return acquireClaim(planningDir, phaseDir, sessionId, skill);
 }
 
-function determinePhaseStatus(planCount, completedCount, summaryCount, hasVerification, phaseDir) {
-  if (planCount === 0) {
-    // Check for CONTEXT.md (discussed only)
-    if (fs.existsSync(path.join(phaseDir, 'CONTEXT.md'))) return 'discussed';
-    return 'not_started';
-  }
-  if (completedCount === 0 && summaryCount === 0) return 'planned';
-  if (completedCount < planCount) return 'building';
-  if (!hasVerification) return 'built';
-  // Check verification status
-  try {
-    const vContent = fs.readFileSync(path.join(phaseDir, 'VERIFICATION.md'), 'utf8');
-    if (/status:\s*["']?passed/i.test(vContent)) return 'verified';
-    if (/status:\s*["']?gaps_found/i.test(vContent)) return 'needs_fixes';
-    return 'reviewed';
-  } catch (_) {
-    return 'built';
-  }
+function claimRelease(phaseSlug, sessionId) {
+  const phaseDir = path.join(planningDir, 'phases', phaseSlug);
+  if (!fs.existsSync(phaseDir)) return { error: `Phase directory not found: ${phaseSlug}` };
+  return releaseClaim(planningDir, phaseDir, sessionId);
 }
 
-function countMustHaves(mustHaves) {
-  if (!mustHaves) return 0;
-  return (mustHaves.truths || []).length +
-    (mustHaves.artifacts || []).length +
-    (mustHaves.key_links || []).length;
+function claimList() {
+  return _listClaims(planningDir);
 }
 
-function calculateProgress() {
-  const phasesDir = path.join(planningDir, 'phases');
-  if (!fs.existsSync(phasesDir)) {
-    return { total: 0, completed: 0, percentage: 0 };
-  }
-
-  let total = 0;
-  let completed = 0;
-
-  const entries = fs.readdirSync(phasesDir, { withFileTypes: true })
-    .filter(e => e.isDirectory());
-
-  for (const entry of entries) {
-    const dir = path.join(phasesDir, entry.name);
-    const plans = findFiles(dir, /-PLAN\.md$/);
-    total += plans.length;
 
-    const summaries = findFiles(dir, /^SUMMARY-.*\.md$/);
-    for (const s of summaries) {
-      const content = fs.readFileSync(path.join(dir, s), 'utf8');
-      if (/status:\s*["']?complete/i.test(content)) completed++;
-    }
-  }
+// --- CLI entry point (thin router — delegates to command modules) ---
 
-  return {
-    total,
-    completed,
-    percentage: total > 0 ? Math.round((completed / total) * 100) : 0
-  };
-}
-
-function output(data) {
-  process.stdout.write(JSON.stringify(data, null, 2));
-  process.exit(0);
-}
-
-function error(msg) {
-  process.stdout.write(JSON.stringify({ error: msg }));
-  process.exit(1);
-}
-
-/**
- * Write content to a file atomically: write to .tmp, backup original to .bak,
- * rename .tmp over original. On failure, restore from .bak if available.
- *
- * @param {string} filePath - Target file path
- * @param {string} content - Content to write
- * @returns {{success: boolean, error?: string}} Result
- */
-function atomicWrite(filePath, content) {
-  const tmpPath = filePath + '.tmp';
-  const bakPath = filePath + '.bak';
+async function main() {
+  const args = process.argv.slice(2);
+  const command = args[0];
+  const ctx = { planningDir, cwd, output, error };
 
   try {
-    // 1. Write to temp file
-    fs.writeFileSync(tmpPath, content, 'utf8');
-
-    // 2. Backup original if it exists
-    if (fs.existsSync(filePath)) {
-      try {
-        fs.copyFileSync(filePath, bakPath);
-      } catch (_e) {
-        // Backup failure is non-fatal — proceed with rename
+    if (command === 'state') {
+      await handleState(args, ctx);
+    } else if (command === 'state-bundle') {
+      handleStateBundle(args, ctx);
+    } else if (command === 'config' || command === 'validate') {
+      await handleConfig(args, ctx);
+    } else if (command === 'roadmap') {
+      await handleRoadmap(args, ctx);
+    } else if (command === 'phase') {
+      await handlePhase(args, ctx);
+    } else if (command === 'compound') {
+      await handleCompound(args, ctx);
+    } else if (command === 'init') {
+      await handleInit(args, ctx);
+    } else if (['plan-index', 'frontmatter', 'must-haves', 'phase-info', 'milestone-stats'].includes(command)) {
+      handlePhaseDirect(args, ctx);
+    } else if (command === 'verify') {
+      handleVerify(args, ctx);
+    } else if (command === 'spot-check') {
+      handleSpotCheckDirect(args, ctx);
+    } else if (command === 'staleness-check') {
+      handleStalenessCheck(args, ctx);
+    } else if (command === 'summary-gate') {
+      handleSummaryGate(args, ctx);
+    } else if (command === 'checkpoint') {
+      handleCheckpoint(args, ctx);
+    } else if (command === 'seeds') {
+      handleSeeds(args, ctx);
+    } else if (command === 'todo') {
+      handleTodo(args, ctx);
+    } else if (command === 'history') {
+      handleHistory(args, ctx);
+    } else if (command === 'auto-cleanup') {
+      handleAutoCleanup(args, ctx);
+    } else if (command === 'benchmarks') {
+      await handleBenchmarks(args, ctx);
+    } else if (command === 'calibrate') {
+      handleCalibrate(args, ctx);
+    } else if (command === 'stress-test') {
+      await handleStressTest(args, ctx);
+    } else {
+      // Delegate to misc handler for all remaining commands
+      const result = await handleMisc(args, ctx);
+      if (result === 'NOT_HANDLED') {
+        error(`Unknown command: ${args.join(' ')}\nRun: pbr-tools.js help`);
       }
     }
-
-    // 3. Rename temp over original (atomic on most filesystems)
-    fs.renameSync(tmpPath, filePath);
-
-    return { success: true };
   } catch (e) {
-    // Rename failed — try to restore from backup
-    try {
-      if (fs.existsSync(bakPath)) {
-        fs.copyFileSync(bakPath, filePath);
-      }
-    } catch (_restoreErr) {
-      // Restore also failed — nothing more we can do
-    }
-
-    // Clean up temp file if it still exists
-    try {
-      if (fs.existsSync(tmpPath)) {
-        fs.unlinkSync(tmpPath);
-      }
-    } catch (_cleanupErr) {
-      // Best-effort cleanup
-    }
-
-    return { success: false, error: e.message };
+    error(e.message);
   }
 }
 
-if (require.main === module || process.argv[1] === __filename) { main(); }
-module.exports = { parseStateMd, parseRoadmapMd, parseYamlFrontmatter, parseMustHaves, countMustHaves, stateLoad, stateCheckProgress, configLoad, configClearCache, configValidate, lockedFileUpdate, planIndex, determinePhaseStatus, findFiles, atomicWrite, tailLines, frontmatter, mustHavesCollect, phaseInfo, stateUpdate, roadmapUpdateStatus, roadmapUpdatePlans, updateLegacyStateField, updateFrontmatterField, updateTableRow, findRoadmapRow, resolveDepthProfile, DEPTH_PROFILE_DEFAULTS, historyAppend, historyLoad, VALID_STATUS_TRANSITIONS, validateStatusTransition };
+if (require.main === module || process.argv[1] === __filename) { main().catch(err => { process.stderr.write(err.message + '\n'); process.exit(1); }); }
+module.exports = { KNOWN_AGENTS, initExecutePhase, initPlanPhase, initQuick, initVerifyWork, initResume, initProgress, initStateBundle: stateBundle, stateBundle, statePatch, stateAdvancePlan, stateRecordMetric, stateRecordActivity, stateUpdateProgress, parseStateMd, parseRoadmapMd, parseYamlFrontmatter, parseMustHaves, countMustHaves, stateLoad, stateCheckProgress, configLoad, configClearCache, configValidate, lockedFileUpdate, planIndex, determinePhaseStatus, findFiles, atomicWrite, tailLines, frontmatter, mustHavesCollect, phaseInfo, stateUpdate, roadmapUpdateStatus, roadmapUpdatePlans, roadmapAnalyze, updateFrontmatterField, updateTableRow, findRoadmapRow, resolveDepthProfile, DEPTH_PROFILE_DEFAULTS, historyAppend, historyLoad, VALID_STATUS_TRANSITIONS, validateStatusTransition, writeActiveSkill, phaseAdd, phaseRemove, phaseList, loadUserDefaults, saveUserDefaults, mergeUserDefaults, USER_DEFAULTS_PATH, todoList, todoGet, todoAdd, todoDone, migrate, verifySpotCheck, referenceGet, milestoneStats, contextTriage, stalenessCheck, summaryGate, checkpointInit, checkpointUpdate, seedsMatch, ciPoll, ciFix, parseJestOutput: _parseJestOutput, parseLintOutput: _parseLintOutput, autoFixLint: _autoFixLint, runCiFixLoop: _runCiFixLoop, rollbackPlan, sessionLoad, sessionSave, SESSION_ALLOWED_KEYS, claimAcquire, claimRelease, claimList, skillSectionGet, listSkillHeadings, stepVerify: _stepVerify, phaseAlternatives: _phaseAlternatives, prerequisiteAlternatives: _prereqAlternatives, configAlternatives: _configAlternatives, phaseComplete, phaseInsert, quickStatus, autoCloseTodos, autoArchiveNotes, buildCleanupContext, helpListCmd, skillMetadataCmd, initMapCodebase };