msd-core/src/roadmap.cts

/**
 * Roadmap — Roadmap parsing and update operations
 *
 * ADR-457 build-at-publish: the hand-written bin/lib/roadmap.cjs collapsed
 * to a TypeScript source of truth. Behaviour is preserved byte-for-behaviour
 * from the prior hand-written .cjs; only strict types are added.
 */

import fs from 'node:fs';
import path from 'node:path';
// eslint-disable-next-line @typescript-eslint/no-require-imports
import core = require('./core.cjs');
const { escapeRegex, normalizePhaseName, phaseMarkdownRegexSource, phaseMarkdownRegexSourceExact, output, error, findPhaseInternal, stripShippedMilestones, extractCurrentMilestone, replaceInCurrentMilestone, phaseTokenMatches } = core;
import { platformWriteSync } from './shell-command-projection.cjs';
// eslint-disable-next-line @typescript-eslint/no-require-imports
import planningWorkspace = require('./planning-workspace.cjs');
const { planningPaths, withPlanningLock, findContextMdIn } = planningWorkspace;
// eslint-disable-next-line @typescript-eslint/no-require-imports
import scanPhasePlans = require('./plan-scan.cjs');
// eslint-disable-next-line @typescript-eslint/no-require-imports
import frontmatter = require('./frontmatter.cjs');
const { extractFrontmatter, parseMustHavesBlock } = frontmatter;

// ─── Types ────────────────────────────────────────────────────────────────────

interface PhasePlansAndSummaries {
  planCount: number;
  summaryCount: number;
  hasContext: boolean;
  hasResearch: boolean;
}

interface PhaseSearchResult {
  found: boolean;
  phase_number: string;
  phase_name: string;
  goal?: string | null;
  mode?: string | null;
  success_criteria?: string[];
  section?: string;
  error?: string;
  message?: string;
}

interface TruthValue {
  count: number;
  text: string;
}

// ─── coerceTruthToString ──────────────────────────────────────────────────────

/**
 * Coerce an arbitrary YAML scalar/object into a string for cross-cutting
 * truth aggregation. Handles:
 *   - strings (passthrough)
 *   - numbers / booleans (String() coercion — issue #2770: bare YAML ints
 *     like `- 3` must be surfaced, not silently skipped)
 *   - kv-shaped objects from parseMustHavesBlock continuation kv (issue
 *     #2757) — extract the first meaningful string field
 *
 * Returns the empty string when no usable text can be derived; callers should
 * skip empty results.
 */
function coerceTruthToString(t: unknown): string {
  if (t === null || t === undefined) return '';
  if (typeof t === 'string') return t;
  if (typeof t === 'number' || typeof t === 'boolean' || typeof t === 'bigint') {
    return String(t);
  }
  if (typeof t === 'object') {
    // Prefer common title-bearing keys produced by parseMustHavesBlock
    for (const k of ['title', 'text', 'name', 'rule', 'path', 'provides']) {
      const v = (t as Record<string, unknown>)[k];
      if (typeof v === 'string' && v.trim()) return v;
      if (typeof v === 'number' || typeof v === 'boolean') return String(v);
    }
  }
  return '';
}

// ─── countPhasePlansAndSummaries ──────────────────────────────────────────────

function countPhasePlansAndSummaries(phaseDir: string): PhasePlansAndSummaries {
  const { planCount, summaryCount } = scanPhasePlans(phaseDir);
  // hasContext and hasResearch are not plan-scan concerns — read the directory
  // once and share the listing for all non-plan metadata that cmdRoadmapAnalyze needs.
  let phaseFiles: string[] = [];
  try { phaseFiles = fs.readdirSync(phaseDir); } catch { /* empty */ }
  return {
    planCount,
    summaryCount,
    hasContext: findContextMdIn(phaseFiles) !== null,
    hasResearch: phaseFiles.some(f => f.endsWith('-RESEARCH.md') || f === 'RESEARCH.md'),
  };
}

// `phaseMarkdownRegexSource` moved to core.cjs (#3537) so phase.cjs and
// core.cjs itself can consume it without circular deps. Imported above.

// ─── searchPhaseInContent ─────────────────────────────────────────────────────

/**
 * Search for a phase header (and its section) within the given content string.
 * Returns a result object if found (either a full match or a malformed_roadmap
 * checklist-only match), or null if the phase is not present at all.
 */
function searchPhaseInContent(content: string, escapedPhase: string, phaseNum: string): PhaseSearchResult | null {
  // Match "## Phase X:", "### Phase X:", or "#### Phase X:" with optional name
  const phasePattern = new RegExp(
    `#{2,4}\\s*(?:\\[[^\\]]+\\]\\s*)?Phase\\s+${escapedPhase}:\\s*([^\\n]+)`,
    'i'
  );
  const headerMatch = content.match(phasePattern);

  if (!headerMatch) {
    // Fallback: check if phase exists in summary list but missing detail section
    const checklistPattern = new RegExp(
      `-\\s*\\[[ x]\\]\\s*\\*\\*Phase\\s+${escapedPhase}:\\s*([^*]+)\\*\\*`,
      'i'
    );
    const checklistMatch = content.match(checklistPattern);

    if (checklistMatch) {
      return {
        found: false,
        phase_number: phaseNum,
        phase_name: checklistMatch[1].trim(),
        error: 'malformed_roadmap',
        message: `Phase ${phaseNum} exists in summary list but missing "### Phase ${phaseNum}:" detail section. ROADMAP.md needs both formats.`
      };
    }

    return null;
  }

  const phaseName = headerMatch[1].trim();
  const headerIndex = headerMatch.index!;

  // Find the end of this section (next ## or ### phase header, or end of file).
  // Also matches bracket-prefixed headings like ### [GSD] Phase 2-01:.
  const restOfContent = content.slice(headerIndex);
  const nextHeaderMatch = restOfContent.match(/\n#{2,4}\s+(?:\[[^\]]+\]\s*)?Phase\s+[\w][\w.-]*/i);
  const sectionEnd = nextHeaderMatch
    ? headerIndex + nextHeaderMatch.index!
    : content.length;

  const section = content.slice(headerIndex, sectionEnd).trim();

  // Extract goal if present (supports both **Goal:** and **Goal**: formats)
  const goalMatch = section.match(/\*\*Goal(?::\*\*|\*\*:)\s*([^\n]+)/i);
  const goal = goalMatch ? goalMatch[1].trim() : null;

  // Mode: vertical-MVP slice mode flag. Lowercased + trimmed for canonical
  // comparison; unrecognized values are preserved verbatim for forward-compat.
  const modeMatch = section.match(/\*\*Mode(?::\*\*|\*\*:)\s*([^\n]+)/i);
  const mode = modeMatch ? modeMatch[1].trim().toLowerCase() : null;

  // Extract success criteria as structured array
  const criteriaMatch = section.match(/\*\*Success Criteria\*\*[^\n]*:\s*\n((?:\s*\d+\.\s*[^\n]+\n?)+)/i);
  const success_criteria = criteriaMatch
    ? criteriaMatch[1].trim().split('\n').map(line => line.replace(/^\s*\d+\.\s*/, '').trim()).filter(Boolean)
    : [];

  return {
    found: true,
    phase_number: phaseNum,
    phase_name: phaseName,
    goal,
    mode,
    success_criteria,
    section,
  };
}

// ─── cmdRoadmapGetPhase ───────────────────────────────────────────────────────

function cmdRoadmapGetPhase(cwd: string, phaseNum: string, raw: boolean): void {
  const roadmapPath = planningPaths(cwd).roadmap;

  if (!fs.existsSync(roadmapPath)) {
    output({ found: false, error: 'ROADMAP.md not found' }, raw, '');
    return;
  }

  try {
    const rawContent = fs.readFileSync(roadmapPath, 'utf-8');
    const milestoneContent = extractCurrentMilestone(rawContent, cwd);

    // #3599 two-pass: when the caller passes a project-code-prefixed ID like
    // `PROJ-42`, try the exact-prefixed heading first (`### Phase PROJ-42:`).
    // If no match, fall back to the #3537 padding-tolerant numeric form so
    // a `CK-01` query still resolves to `### Phase 1:`. Doing this at the
    // call site (instead of inside phaseMarkdownRegexSource) avoids the
    // alternation-order ambiguity where a bare `### Phase 42:` heading in
    // the same document would intercept the match for a `PROJ-42` query.
    const fullContent = stripShippedMilestones(rawContent);

    const exactSource = phaseMarkdownRegexSourceExact(phaseNum);
    if (exactSource) {
      const exactMilestone = searchPhaseInContent(milestoneContent, exactSource, phaseNum);
      if (exactMilestone && !exactMilestone.error) {
        output(exactMilestone, raw, exactMilestone.section);
        return;
      }
      const exactFull = searchPhaseInContent(fullContent, exactSource, phaseNum);
      if (exactFull && !exactFull.error) {
        output(exactFull, raw, exactFull.section);
        return;
      }
    }

    // #3537: padding-tolerant fragment so callers passing `02.7` still match
    // un-padded ROADMAP prose (`### Phase 2.7:`).
    const escapedPhase = phaseMarkdownRegexSource(phaseNum);

    // Search the current milestone slice first, then fall back to full roadmap.
    // A malformed_roadmap result (checklist-only) from the milestone should not
    // block finding a full header match in the wider roadmap content.
    const milestoneResult = searchPhaseInContent(milestoneContent, escapedPhase, phaseNum);
    const result = (milestoneResult && !milestoneResult.error)
      ? milestoneResult
      : searchPhaseInContent(fullContent, escapedPhase, phaseNum) || milestoneResult;

    if (!result) {
      output({ found: false, phase_number: phaseNum }, raw, '');
      return;
    }

    if (result.error) {
      output(result, raw, '');
      return;
    }

    output(result, raw, result.section);
  } catch (e) {
    error('Failed to read ROADMAP.md: ' + (e as Error).message);
  }
}

// ─── cmdRoadmapAnalyze ────────────────────────────────────────────────────────

function cmdRoadmapAnalyze(cwd: string, raw: boolean): void {
  const roadmapPath = planningPaths(cwd).roadmap;

  if (!fs.existsSync(roadmapPath)) {
    output({ error: 'ROADMAP.md not found', milestones: [], phases: [], current_phase: null }, raw, undefined);
    return;
  }

  const rawContent = fs.readFileSync(roadmapPath, 'utf-8');
  const content = extractCurrentMilestone(rawContent, cwd);
  const phasesDir = planningPaths(cwd).phases;

  // Extract all phase headings: ## Phase N: Name or ### Phase N: Name
  const phasePattern = /#{2,4}\s*(?:\[[^\]]+\]\s*)?Phase\s+(\d+[A-Z]?(?:[.-]\d+)*)\s*:\s*([^\n]+)/gi;
  const phases: Array<{
    number: string;
    name: string;
    goal: string | null;
    mode: string | null;
    depends_on: string | null;
    plan_count: number;
    summary_count: number;
    has_context: boolean;
    has_research: boolean;
    disk_status: string;
    roadmap_complete: boolean;
  }> = [];
  let match: RegExpExecArray | null;

  // Build phase directory lookup once (O(1) readdir instead of O(N) per phase)
  const _phaseDirNames = (() => {
    try {
      return fs.readdirSync(phasesDir, { withFileTypes: true })
        .filter(e => e.isDirectory())
        .map(e => e.name);
    } catch { return []; }
  })();

  while ((match = phasePattern.exec(content)) !== null) {
    const phaseNum = match[1];
    const phaseName = match[2].replace(/\(INSERTED\)/i, '').trim();

    // Extract goal from the section
    const sectionStart = match.index;
    const restOfContent = content.slice(sectionStart);
    // #3691: `\d` → `\d[\d.]*` so decimal phase headings (e.g. `### Phase 02.3:`) are
    // recognised as section boundaries.
    const nextHeader = restOfContent.match(/\n#{2,4}\s+(?:\[[^\]]+\]\s*)?Phase\s+\d[\d.-]*/i);
    const sectionEnd = nextHeader ? sectionStart + nextHeader.index! : content.length;
    const section = content.slice(sectionStart, sectionEnd);

    const goalMatch = section.match(/\*\*Goal(?::\*\*|\*\*:)\s*([^\n]+)/i);
    const goal = goalMatch ? goalMatch[1].trim() : null;

    const modeMatch = section.match(/\*\*Mode(?::\*\*|\*\*:)\s*([^\n]+)/i);
    const mode = modeMatch ? modeMatch[1].trim().toLowerCase() : null;

    const dependsMatch = section.match(/\*\*Depends on(?::\*\*|\*\*:)\s*([^\n]+)/i);
    const depends_on = dependsMatch ? dependsMatch[1].trim() : null;

    // Check completion on disk
    const normalized = normalizePhaseName(phaseNum);
    let diskStatus = 'no_directory';
    let planCount = 0;
    let summaryCount = 0;
    let hasContext = false;
    let hasResearch = false;

    try {
      const dirMatch = _phaseDirNames.find(d => phaseTokenMatches(d, normalized));

      if (dirMatch) {
        const counts = countPhasePlansAndSummaries(path.join(phasesDir, dirMatch));
        planCount = counts.planCount;
        summaryCount = counts.summaryCount;
        hasContext = counts.hasContext;
        hasResearch = counts.hasResearch;

        if (summaryCount >= planCount && planCount > 0) diskStatus = 'complete';
        else if (summaryCount > 0) diskStatus = 'partial';
        else if (planCount > 0) diskStatus = 'planned';
        else if (hasResearch) diskStatus = 'researched';
        else if (hasContext) diskStatus = 'discussed';
        else diskStatus = 'empty';
      }
    } catch { /* intentionally empty */ }

    // Check ROADMAP checkbox status.
    // #3537: padding-tolerant fragment — the heading discovered above may use
    // a different padding than the summary-bullet checkbox below it (mixed
    // padding inside one ROADMAP is legal and seen in real projects).
    const checkboxPattern = new RegExp(`-\\s*\\[(x| )\\]\\s*.*Phase\\s+${phaseMarkdownRegexSource(phaseNum)}[:\\s]`, 'i');
    const checkboxMatch = content.match(checkboxPattern);
    const roadmapComplete = checkboxMatch ? checkboxMatch[1] === 'x' : false;

    // If roadmap marks phase complete, trust that over disk file structure.
    // Phases completed before GSD tracking (or via external tools) may lack
    // the standard PLAN/SUMMARY pairs but are still done.
    if (roadmapComplete && diskStatus !== 'complete') {
      diskStatus = 'complete';
    }

    phases.push({
      number: phaseNum,
      name: phaseName,
      goal,
      mode,
      depends_on,
      plan_count: planCount,
      summary_count: summaryCount,
      has_context: hasContext,
      has_research: hasResearch,
      disk_status: diskStatus,
      roadmap_complete: roadmapComplete,
    });
  }

  // Extract milestone info
  const milestones: Array<{ heading: string; version: string }> = [];
  const milestonePattern = /##\s*(.*v(\d+(?:\.\d+)+)[^(\n]*)/gi;
  let mMatch: RegExpExecArray | null;
  while ((mMatch = milestonePattern.exec(content)) !== null) {
    milestones.push({
      heading: mMatch[1].trim(),
      version: 'v' + mMatch[2],
    });
  }

  // Find current and next phase
  const currentPhase = phases.find(p => p.disk_status === 'planned' || p.disk_status === 'partial') || null;
  const nextPhase = phases.find(p => p.disk_status === 'empty' || p.disk_status === 'no_directory' || p.disk_status === 'discussed' || p.disk_status === 'researched') || null;

  // Aggregated stats
  const totalPlans = phases.reduce((sum, p) => sum + p.plan_count, 0);
  const totalSummaries = phases.reduce((sum, p) => sum + p.summary_count, 0);
  const completedPhases = phases.filter(p => p.disk_status === 'complete').length;

  // Detect phases in summary list without detail sections (malformed ROADMAP)
  const checklistPattern = /-\s*\[[ x]\]\s*\*\*Phase\s+(\d+[A-Z]?(?:\.\d+)*)/gi;
  const checklistPhases = new Set<string>();
  let checklistMatch: RegExpExecArray | null;
  while ((checklistMatch = checklistPattern.exec(content)) !== null) {
    checklistPhases.add(checklistMatch[1]);
  }
  const detailPhases = new Set(phases.map(p => p.number));
  const missingDetails = [...checklistPhases].filter(p => !detailPhases.has(p));

  const result = {
    milestones,
    phases,
    phase_count: phases.length,
    completed_phases: completedPhases,
    total_plans: totalPlans,
    total_summaries: totalSummaries,
    progress_percent: totalPlans > 0 ? Math.min(100, Math.round((totalSummaries / totalPlans) * 100)) : 0,
    current_phase: currentPhase ? currentPhase.number : null,
    next_phase: nextPhase ? nextPhase.number : null,
    missing_phase_details: missingDetails.length > 0 ? missingDetails : null,
  };

  output(result, raw, undefined);
}

// ─── cmdRoadmapUpdatePlanProgress ─────────────────────────────────────────────

function cmdRoadmapUpdatePlanProgress(cwd: string, phaseNum: string | null | undefined, raw: boolean): void {
  if (!phaseNum) {
    error('phase number required for roadmap update-plan-progress');
  }

  const roadmapPath = planningPaths(cwd).roadmap;

  const phaseInfo = findPhaseInternal(cwd, phaseNum);
  if (!phaseInfo) {
    error(`Phase ${phaseNum} not found`);
  }

  const planCount = phaseInfo!.plans.length;
  const summaryCount = phaseInfo!.summaries.length;

  if (planCount === 0) {
    output({ updated: false, reason: 'No plans found', plan_count: 0, summary_count: 0 }, raw, 'no plans');
    return;
  }

  const isComplete = summaryCount >= planCount;
  const status = isComplete ? 'Complete' : summaryCount > 0 ? 'In Progress' : 'Planned';
  const today = new Date().toISOString().split('T')[0];

  if (!fs.existsSync(roadmapPath)) {
    output({ updated: false, reason: 'ROADMAP.md not found', plan_count: planCount, summary_count: summaryCount }, raw, 'no roadmap');
    return;
  }

  // Wrap entire read-modify-write in lock to prevent concurrent corruption
  withPlanningLock(cwd, () => {
    let roadmapContent = fs.readFileSync(roadmapPath, 'utf-8');
    const phasePattern = phaseMarkdownRegexSource(phaseNum);

    // Progress table row: update Plans/Status/Date columns (handles 4 or 5 column tables)
    const tableRowPattern = new RegExp(
      `^(\\|\\s*${phasePattern}\\.?\\s[^|]*(?:\\|[^\\n]*))$`,
      'im'
    );
    const dateField = isComplete ? ` ${today} ` : '  ';
    roadmapContent = roadmapContent.replace(tableRowPattern, (fullRow) => {
      const cells = fullRow.split('|').slice(1, -1); // drop leading/trailing empty from split
      if (cells.length === 5) {
        // 5-col: Phase | Milestone | Plans | Status | Completed
        cells[2] = ` ${summaryCount}/${planCount} `;
        cells[3] = ` ${status.padEnd(11)}`;
        cells[4] = dateField;
      } else if (cells.length === 4) {
        // 4-col: Phase | Plans | Status | Completed
        cells[1] = ` ${summaryCount}/${planCount} `;
        cells[2] = ` ${status.padEnd(11)}`;
        cells[3] = dateField;
      }
      return '|' + cells.join('|') + '|';
    });

    // Update plan count in phase detail section
    const planCountPattern = new RegExp(
      `(#{2,4}\\s*Phase\\s+${phasePattern}(?=[:\\s])[\\s\\S]*?\\*\\*Plans:\\*\\*\\s*)[^\\n]+`,
      'i'
    );
    const planCountText = isComplete
      ? `${summaryCount}/${planCount} plans complete`
      : `${summaryCount}/${planCount} plans executed`;
    roadmapContent = replaceInCurrentMilestone(roadmapContent, planCountPattern, `$1${planCountText}`);

    // If complete: check checkbox
    if (isComplete) {
      const checkboxPattern = new RegExp(
        `(-\\s*\\[)[ ](\\]\\s*.*Phase\\s+${phasePattern}[:\\s][^\\n]*)`,
        'i'
      );
      roadmapContent = replaceInCurrentMilestone(roadmapContent, checkboxPattern, `$1x$2 (completed ${today})`);
    }

    // Mark completed plan checkboxes (e.g. "- [ ] 50-01-PLAN.md", "- [ ] 50-01:", or "- [ ] **50-01**")
    for (const summaryFile of phaseInfo!.summaries) {
      const planId = summaryFile.replace('-SUMMARY.md', '').replace('SUMMARY.md', '');
      if (!planId) continue;
      const planEscaped = escapeRegex(planId);
      const planCheckboxPattern = new RegExp(
        `(-\\s*\\[) (\\]\\s*(?:\\*\\*)?${planEscaped}(?:\\*\\*)?)`,
        'i'
      );
      roadmapContent = roadmapContent.replace(planCheckboxPattern, '$1x$2');
    }

    platformWriteSync(roadmapPath, roadmapContent);
  });
  output({
    updated: true,
    phase: phaseNum,
    plan_count: planCount,
    summary_count: summaryCount,
    status,
    complete: isComplete,
  }, raw, `${summaryCount}/${planCount} ${status}`);
}

// ─── cmdRoadmapAnnotateDependencies ───────────────────────────────────────────

/**
 * Annotate the ROADMAP.md plan list for a phase with wave dependency notes
 * and a cross-cutting constraints subsection derived from PLAN frontmatter.
 *
 * Wave dependency notes: "Wave 2 — blocked on Wave 1 completion" inserted as
 * bold headers before each wave group in the plan checklist.
 *
 * Cross-cutting constraints: must_haves.truths strings that appear in 2+ plans
 * are surfaced in a "Cross-cutting constraints" subsection below the plan list.
 *
 * The operation is idempotent: if wave headers already exist in the section
 * the function returns without modifying the file.
 */
function cmdRoadmapAnnotateDependencies(cwd: string, phaseNum: string | null | undefined, raw: boolean): void {
  if (!phaseNum) {
    error('phase number required for roadmap annotate-dependencies');
  }

  const roadmapPath = planningPaths(cwd).roadmap;
  if (!fs.existsSync(roadmapPath)) {
    output({ updated: false, reason: 'ROADMAP.md not found' }, raw, 'no roadmap');
    return;
  }

  const phaseInfo = findPhaseInternal(cwd, phaseNum);
  if (!phaseInfo || phaseInfo.plans.length === 0) {
    output({ updated: false, reason: 'no plans found for phase', phase: phaseNum }, raw, 'no plans');
    return;
  }

  // Read each PLAN.md and extract wave + must_haves.truths
  const planData: Array<{ planFile: string; planId: string; wave: number; truths: unknown[] }> = [];
  for (const planFile of phaseInfo.plans) {
    const planPath = path.join(path.resolve(cwd, phaseInfo.directory), planFile);
    try {
      const content = fs.readFileSync(planPath, 'utf-8');
      const fm = extractFrontmatter(content);
      const wave = parseInt(fm.wave as string, 10) || 1;
      const planId = planFile.replace(/-PLAN\.md$/i, '').replace(/PLAN\.md$/i, '');
      const truths = parseMustHavesBlock(content, 'truths') || [];
      planData.push({ planFile, planId, wave, truths });
    } catch { /* skip unreadable plans */ }
  }

  if (planData.length === 0) {
    output({ updated: false, reason: 'could not read plan frontmatter' }, raw, 'no frontmatter');
    return;
  }

  // Group plans by wave (sorted)
  const waveGroups = new Map<number, typeof planData>();
  for (const p of planData) {
    if (!waveGroups.has(p.wave)) waveGroups.set(p.wave, []);
    waveGroups.get(p.wave)!.push(p);
  }
  const waves = [...waveGroups.keys()].sort((a, b) => a - b);

  // Find cross-cutting truths: appear in 2+ plans (de-duplicated, case-insensitive).
  //
  // Issue #2770: must **coerce, not skip**. A previous guard
  // `if (typeof t !== 'string') continue` silently dropped numeric scalars
  // (YAML ints like `- 3`) and kv-shaped truths (`- title: X`), so the
  // cross-cutting analysis lost real constraints rather than crashing on
  // `t.trim()`. We coerce primitives via `String(t)` and extract a sensible
  // string field from object-shaped items produced by parseMustHavesBlock's
  // continuation-kv path (issue #2757 produces those shapes for nested keys).
  const truthCounts = new Map<string, TruthValue>();
  for (const { truths } of planData) {
    const seen = new Set<string>();
    for (const t of truths) {
      const text = coerceTruthToString(t);
      if (!text) continue;
      const trimmed = text.trim();
      const key = trimmed.toLowerCase();
      if (!key || seen.has(key)) continue;
      seen.add(key);
      if (!truthCounts.has(key)) truthCounts.set(key, { count: 0, text: trimmed });
      truthCounts.get(key)!.count++;
    }
  }
  const crossCuttingTruths = [...truthCounts.values()]
    .filter(v => v.count >= 2)
    .map(v => v.text);

  // Patch ROADMAP.md
  let updated = false;
  withPlanningLock(cwd, () => {
    const content = fs.readFileSync(roadmapPath, 'utf-8');

    // Find the phase section.
    // #3537: padding-tolerant fragment so the caller's resolved padded id
    // matches un-padded ROADMAP headings.
    const phaseEscaped = phaseMarkdownRegexSource(phaseNum);
    const phaseHeaderPattern = new RegExp(`(#{2,4}\\s*Phase\\s+${phaseEscaped}:[^\\n]*)`, 'i');
    const phaseMatch = content.match(phaseHeaderPattern);
    if (!phaseMatch) return;

    const phaseStart = phaseMatch.index!;
    const restAfterHeader = content.slice(phaseStart);
    const nextPhaseOffset = restAfterHeader.slice(1).search(/\n#{2,4}\s+Phase\s+\d/i);
    const phaseEnd = nextPhaseOffset >= 0 ? phaseStart + 1 + nextPhaseOffset : content.length;
    const phaseSection = content.slice(phaseStart, phaseEnd);

    // Idempotency: skip if annotation markers already present
    if (
      /\*\*Wave\s+\d+/i.test(phaseSection) ||
      /\*\*Cross-cutting constraints:\*\*/i.test(phaseSection)
    ) return;

    // Find the Plans: section within the phase section.
    // #3691 Bug 1: `Plans:\s*\n` required no text after the colon, missing variants like
    // `Plans: 3 plans across 2 waves\n` or `**Plans:** 3 plans\n` (bold-wrapped).
    // `\*{0,2}Plans\*{0,2}:[^\n]*\n` accepts any text (or none) after the colon
    // and tolerates optional `**` markdown bold wrappers on either side.
    // The checklist group uses `+` (not `*`) so that a bold `**Plans:**` description
    // line with no immediately-following checklist items (e.g. a summary line above a
    // separate bare `Plans:` block) does not consume the match and prevent the actual
    // list from being found.
    // Review fix (F2): `(?:^|\n)` anchors the match to start-of-line so mid-line
    // occurrences like `***Plans:***` embedded in a sentence or `OpenPlans: foo`
    // do not trigger a false match. Groups 1 and 2 retain the same semantics.
    const plansBlockMatch = phaseSection.match(/(?:^|\n)(\*{0,2}Plans\*{0,2}:[^\n]*\n)((?:\s*-\s*\[[ x]\][^\n]*\n?)+)/i);
    if (!plansBlockMatch) return;

    const plansHeader = plansBlockMatch[1];
    const existingList = plansBlockMatch[2];
    const listLines = existingList.split('\n').filter(l => /^\s*-\s*\[/.test(l));

    if (listLines.length === 0) return;

    // #314 perf: build a first-wins Map so per-line lookup is O(1) instead of O(plans).
    // First-wins mirrors .find() semantics: if the same planId appears more than once
    // in planData, the earlier entry wins — identical to what .find() returned before.
    const planById = new Map<string, typeof planData[number]>();
    for (const p of planData) {
      if (!planById.has(p.planId)) planById.set(p.planId, p);
    }

    // Build wave-annotated plan list
    const linesByWave = new Map<number, string[]>();
    for (const line of listLines) {
      // Match plan ID from line: "- [ ] 01-01-PLAN.md — ..." or "- [ ] 01-01: ..."
      // #3691 Bug 3: `[\w-]+?` excluded `.`, so decimal IDs like `02.3-01` were captured
      // as `02` only and never matched planData entries. `[\w.-]+?` preserves the
      // terminating alternation (`-PLAN.md|.md|:|\s—`) as the boundary anchor.
      const idMatch = line.match(/\[\s*[x ]\s*\]\s*([\w.-]+?)(?:-PLAN\.md|\.md|:|\s—)/i);
      const planId = idMatch ? idMatch[1] : null;
      // Review fix (F3): reject malformed IDs that start with `.`, contain consecutive
      // dots, or otherwise violate the `^\w[\w.-]*$` contract. A leading-dot ID
      // (e.g. `.invalid-PLAN.md`) would silently default to wave 1 — defensively
      // skip the line instead so corrupted ROADMAP entries don't corrupt wave layout.
      if (planId && !/^\w[\w.-]*$/.test(planId)) continue;
      const planEntry = planId ? (planById.get(planId) || null) : null;
      const wave = planEntry ? planEntry.wave : 1;
      if (!linesByWave.has(wave)) linesByWave.set(wave, []);
      linesByWave.get(wave)!.push(line);
    }

    const annotatedLines: string[] = [];
    const sortedWaves = [...linesByWave.keys()].sort((a, b) => a - b);
    for (let i = 0; i < sortedWaves.length; i++) {
      const w = sortedWaves[i];
      const waveLines = linesByWave.get(w)!;
      if (sortedWaves.length > 1) {
        const dep = i > 0 ? ` *(blocked on Wave ${sortedWaves[i - 1]} completion)*` : '';
        annotatedLines.push(`**Wave ${w}**${dep}`);
      }
      annotatedLines.push(...waveLines);
      if (i < sortedWaves.length - 1) annotatedLines.push('');
    }

    // Append cross-cutting constraints subsection if any found
    if (crossCuttingTruths.length > 0) {
      annotatedLines.push('');
      annotatedLines.push('**Cross-cutting constraints:**');
      for (const t of crossCuttingTruths) {
        annotatedLines.push(`- ${t}`);
      }
    }

    const newListBlock = annotatedLines.join('\n') + '\n';
    const newPhaseSection = phaseSection.replace(
      plansBlockMatch[0],
      plansHeader + newListBlock
    );

    const nextContent = content.slice(0, phaseStart) + newPhaseSection + content.slice(phaseEnd);
    if (nextContent === content) return;
    platformWriteSync(roadmapPath, nextContent);
    updated = true;
  });

  output({
    updated,
    phase: phaseNum,
    waves: waves.length,
    cross_cutting_constraints: crossCuttingTruths.length,
  }, raw, updated ? `annotated ${waves.length} wave(s), ${crossCuttingTruths.length} constraint(s)` : 'skipped (already annotated or no plan list)');
}

export = {
  cmdRoadmapGetPhase,
  cmdRoadmapAnalyze,
  cmdRoadmapUpdatePlanProgress,
  cmdRoadmapAnnotateDependencies,
};