@bhargavvc/sdd-cc 1.35.0 → 1.42.3

package/sdd/bin/lib/phase.cjs

@@ -4,10 +4,64 @@
 
 const fs = require('fs');
 const path = require('path');
-const { escapeRegex, loadConfig, normalizePhaseName, comparePhaseNum, findPhaseInternal, getArchivedPhaseDirs, generateSlugInternal, getMilestonePhaseFilter, stripShippedMilestones, extractCurrentMilestone, replaceInCurrentMilestone, toPosixPath, planningDir, withPlanningLock, output, error, readSubdirectories, phaseTokenMatches } = require('./core.cjs');
+const { escapeRegex, loadConfig, normalizePhaseName, phaseMarkdownRegexSource, comparePhaseNum, findPhaseInternal, getArchivedPhaseDirs, generateSlugInternal, getMilestonePhaseFilter, stripShippedMilestones, extractCurrentMilestone, replaceInCurrentMilestone, toPosixPath, output, error, readSubdirectories, phaseTokenMatches, ERROR_REASON } = require('./core.cjs');
+const { platformWriteSync, platformReadSync, platformEnsureDir } = require('./shell-command-projection.cjs');
+const { planningDir, withPlanningLock } = require('./planning-workspace.cjs');
 const { extractFrontmatter } = require('./frontmatter.cjs');
 const { writeStateMd, readModifyWriteStateMd, stateExtractField, stateReplaceField, stateReplaceFieldWithFallback, updatePerformanceMetricsSection } = require('./state.cjs');
 
+// #2893 — strict canonical filter: `{padded_phase}-{NN}-PLAN.md` or `PLAN.md`.
+// Documented in agents/sdd-planner.md (write_phase_prompt step). The wider
+// "looks like a plan but isn't canonical" probe below is used to surface a
+// loud warning instead of silently returning zero plans.
+const isCanonicalPlanFile = (f) => f.endsWith('-PLAN.md') || f === 'PLAN.md';
+
+// Any .md file with PLAN anywhere in the basename — the diagnostic net for
+// catching agent deviations like `01-PLAN-01-foundation.md` (#2893).
+// Excludes derivative files (`-PLAN-OUTLINE.md`, `*.pre-bounce.md`, etc.) that
+// the planner legitimately produces alongside canonical plans.
+const PLAN_OUTLINE_RE = /-PLAN-OUTLINE\.md$/i;
+const PLAN_PRE_BOUNCE_RE = /-PLAN.*\.pre-bounce\.md$/i;
+const looksLikePlanFile = (f) =>
+  /\.md$/i.test(f)
+  && /PLAN/i.test(f)
+  && !PLAN_OUTLINE_RE.test(f)
+  && !PLAN_PRE_BOUNCE_RE.test(f);
+
+/**
+ * Detect plan-shaped files that the canonical filter would reject. Returns
+ * a warning string when offenders exist, else null. Centralised so every
+ * read site (phase-plan-index, phases list --type plans, find-phase) emits
+ * the same message.
+ *
+ * @param {string[]} dirFiles — readdirSync output for one phase directory
+ * @param {string[]} matchedFiles — what the canonical filter accepted
+ * @returns {string|null}
+ */
+function describeNonCanonicalPlans(dirFiles, matchedFiles) {
+  const matched = new Set(matchedFiles);
+  const offenders = dirFiles.filter((f) => looksLikePlanFile(f) && !matched.has(f));
+  if (offenders.length === 0) return null;
+  return (
+    `Found ${offenders.length} plan-shaped file(s) in this phase that don't match the canonical ` +
+    `naming convention "{padded_phase}-{NN}-PLAN.md" (or bare "PLAN.md") and were skipped: ` +
+    offenders.map((f) => `"${f}"`).join(', ') +
+    `. Rename to the canonical form (e.g. "01-01-PLAN.md") so the executor can detect them. ` +
+    `See agents/sdd-planner.md write_phase_prompt step for the full contract.`
+  );
+}
+
+function extractCanonicalPlanId(filename) {
+  const base = filename.replace(/-PLAN\.md$/i, '').replace(/-SUMMARY\.md$/i, '').replace(/\.md$/i, '');
+  const parts = base.split('-').filter(Boolean);
+  const tokenRe = /^\d+[A-Z]?(?:\.\d+)*$/i;
+  const phaseIdx = parts.findIndex(p => tokenRe.test(p));
+  if (phaseIdx >= 0 && phaseIdx + 1 < parts.length && tokenRe.test(parts[phaseIdx + 1])) {
+    return `${parts[phaseIdx]}-${parts[phaseIdx + 1]}`;
+  }
+  return base;
+}
+
 function cmdPhasesList(cwd, options, raw) {
   const phasesDir = path.join(planningDir(cwd), 'phases');
   const { type, phase, includeArchived } = options;
@@ -52,13 +106,18 @@ function cmdPhasesList(cwd, options, raw) {
     // If listing files of a specific type
     if (type) {
       const files = [];
+      const warnings = [];
       for (const dir of dirs) {
         const dirPath = path.join(phasesDir, dir);
         const dirFiles = fs.readdirSync(dirPath);
 
         let filtered;
         if (type === 'plans') {
-          filtered = dirFiles.filter(f => f.endsWith('-PLAN.md') || f === 'PLAN.md');
+          filtered = dirFiles.filter(isCanonicalPlanFile);
+          // #2893 — surface plan-shaped files the canonical filter rejected
+          // so callers (executor init, etc.) don't silently see zero plans.
+          const w = describeNonCanonicalPlans(dirFiles, filtered);
+          if (w) warnings.push(`${dir}: ${w}`);
         } else if (type === 'summaries') {
           filtered = dirFiles.filter(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md');
         } else {
@@ -73,6 +132,7 @@ function cmdPhasesList(cwd, options, raw) {
         count: files.length,
         phase_dir: phase ? dirs[0].replace(/^\d+(?:\.\d+)*-?/, '') : null,
       };
+      if (warnings.length) result.warning = warnings.join(' | ');
       output(result, raw, files.join('\n'));
       return;
     }
@@ -110,8 +170,10 @@ function cmdPhaseNextDecimal(cwd, basePhase, raw) {
     if (fs.existsSync(roadmapPath)) {
       try {
         const roadmapContent = fs.readFileSync(roadmapPath, 'utf-8');
+        // #3537: padding-tolerant on both sides — `0*${escapeRegex(...)}`
+        // tolerated extra padding but not missing.
         const phasePattern = new RegExp(
-          `#{2,4}\\s*Phase\\s+0*${escapeRegex(normalized)}\\.(\\d+)\\s*:`, 'gi'
+          `#{2,4}\\s*Phase\\s+${phaseMarkdownRegexSource(normalized)}\\.(\\d+)\\s*:`, 'gi'
         );
         let pm;
         while ((pm = phasePattern.exec(roadmapContent)) !== null) {
@@ -148,50 +210,128 @@ function cmdPhaseNextDecimal(cwd, basePhase, raw) {
   }
 }
 
+function getRoadmapModeForPhase(cwd, phaseNum) {
+  const roadmapPath = path.join(planningDir(cwd), 'ROADMAP.md');
+  if (!fs.existsSync(roadmapPath)) return null;
+
+  const rawContent = fs.readFileSync(roadmapPath, 'utf-8');
+  const milestoneContent = extractCurrentMilestone(rawContent, cwd);
+  const fullContent = stripShippedMilestones(rawContent);
+  const escapedPhase = phaseMarkdownRegexSource(phaseNum);
+  const phaseHeader = new RegExp(`#{2,4}\\s*Phase\\s+${escapedPhase}\\s*:`, 'i');
+
+  for (const content of [milestoneContent, fullContent]) {
+    const headerMatch = content.match(phaseHeader);
+    if (!headerMatch || headerMatch.index === undefined) continue;
+
+    const sectionStart = headerMatch.index;
+    const rest = content.slice(sectionStart);
+    const nextHeader = rest.slice(headerMatch[0].length).match(/\n#{2,4}\s+Phase\s+\S/i);
+    const sectionEnd = nextHeader ? sectionStart + headerMatch[0].length + nextHeader.index : content.length;
+    const section = content.slice(sectionStart, sectionEnd);
+    const modeMatch = section.match(/\*\*Mode(?::\*\*|\*\*:)\s*([^\n]+)/i);
+    if (modeMatch) return modeMatch[1].trim().toLowerCase();
+  }
+
+  return null;
+}
+
+function cmdPhaseMvpMode(cwd, args, raw) {
+  const phaseNum = args[0];
+  if (!phaseNum) {
+    error('Usage: phase.mvp-mode <phase-number> [--cli-flag]', ERROR_REASON.USAGE);
+  }
+
+  const cliFlagPresent = args.includes('--cli-flag');
+  const roadmapMode = getRoadmapModeForPhase(cwd, phaseNum);
+  const config = loadConfig(cwd);
+  const configMvpMode = Boolean(config.mvp_mode);
+
+  let active = false;
+  let source = 'none';
+  if (cliFlagPresent) {
+    active = true;
+    source = 'cli_flag';
+  } else if (roadmapMode === 'mvp') {
+    active = true;
+    source = 'roadmap';
+  } else if (configMvpMode) {
+    active = true;
+    source = 'config';
+  }
+
+  output({
+    active,
+    source,
+    roadmap_mode: roadmapMode,
+    config_mvp_mode: configMvpMode,
+    cli_flag_present: cliFlagPresent,
+  }, raw);
+}
+
 function cmdFindPhase(cwd, phase, raw) {
   if (!phase) {
     error('phase identifier required');
   }
 
-  const phasesDir = path.join(planningDir(cwd), 'phases');
+  const planBase = planningDir(cwd);
   const normalized = normalizePhaseName(phase);
+  const notFound = { found: false, directory: null, phase_number: null, phase_name: null, plans: [], summaries: [], searched_directories: [] };
 
-  const notFound = { found: false, directory: null, phase_number: null, phase_name: null, plans: [], summaries: [] };
-
+  // Build candidate search dirs: flat layout first, then milestone-archive layout.
+  const searchDirs = [];
+  const flatPhasesDir = path.join(planBase, 'phases');
+  if (fs.existsSync(flatPhasesDir)) searchDirs.push(flatPhasesDir);
   try {
-    const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
-    const dirs = entries.filter(e => e.isDirectory()).map(e => e.name).sort((a, b) => comparePhaseNum(a, b));
-
-    const match = dirs.find(d => phaseTokenMatches(d, normalized));
-    if (!match) {
-      output(notFound, raw, '');
-      return;
+    const milestonesDir = path.join(planBase, 'milestones');
+    const entries = fs.readdirSync(milestonesDir, { withFileTypes: true })
+      .filter(e => e.isDirectory() && /^v\d+.*-phases$/.test(e.name))
+      .sort((a, b) => a.name.localeCompare(b.name, undefined, { numeric: true }));
+    for (const e of entries) {
+      searchDirs.push(path.join(milestonesDir, e.name));
     }
+  } catch { /* no milestones dir */ }
 
-    // Extract phase number — supports project-code-prefixed (CK-01-name), numeric (01-name), and custom IDs
-    const dirMatch = match.match(/^(?:[A-Z]{1,6}-)(\d+[A-Z]?(?:\.\d+)*)-?(.*)/i)
-      || match.match(/^(\d+[A-Z]?(?:\.\d+)*)-?(.*)/i);
-    const phaseNumber = dirMatch ? dirMatch[1] : normalized;
-    const phaseName = dirMatch && dirMatch[2] ? dirMatch[2] : null;
-
-    const phaseDir = path.join(phasesDir, match);
-    const phaseFiles = fs.readdirSync(phaseDir);
-    const plans = phaseFiles.filter(f => f.endsWith('-PLAN.md') || f === 'PLAN.md').sort();
-    const summaries = phaseFiles.filter(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md').sort();
-
-    const result = {
-      found: true,
-      directory: toPosixPath(path.join(path.relative(cwd, planningDir(cwd)), 'phases', match)),
-      phase_number: phaseNumber,
-      phase_name: phaseName,
-      plans,
-      summaries,
-    };
+  notFound.searched_directories = searchDirs.map((searchDir) =>
+    toPosixPath(path.join(path.relative(cwd, planBase), path.relative(planBase, searchDir))));
 
-    output(result, raw, result.directory);
-  } catch {
-    output(notFound, raw, '');
+  for (const searchDir of searchDirs) {
+    try {
+      const entries = fs.readdirSync(searchDir, { withFileTypes: true });
+      const dirs = entries.filter(e => e.isDirectory()).map(e => e.name).sort((a, b) => comparePhaseNum(a, b));
+
+      const match = dirs.find(d => phaseTokenMatches(d, normalized));
+      if (!match) continue;
+
+      // Extract phase number — supports project-code-prefixed (CK-01-name), numeric (01-name), and custom IDs
+      const dirMatch = match.match(/^(?:[A-Z]{1,6}-)(\d+[A-Z]?(?:\.\d+)*)-?(.*)/i)
+        || match.match(/^(\d+[A-Z]?(?:\.\d+)*)-?(.*)/i);
+      const phaseNumber = dirMatch ? dirMatch[1] : normalized;
+      const phaseName = dirMatch && dirMatch[2] ? dirMatch[2] : null;
+
+      const phaseDir = path.join(searchDir, match);
+      const phaseFiles = fs.readdirSync(phaseDir);
+      const plans = phaseFiles.filter(isCanonicalPlanFile).sort();
+      const summaries = phaseFiles.filter(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md').sort();
+      // #2893 — same diagnostic as phase-plan-index for consistency.
+      const planNamingWarning = describeNonCanonicalPlans(phaseFiles, plans);
+
+      const result = {
+        found: true,
+        directory: toPosixPath(path.join(path.relative(cwd, planBase), path.relative(planBase, searchDir), match)),
+        phase_number: phaseNumber,
+        phase_name: phaseName,
+        plans,
+        summaries,
+      };
+      if (planNamingWarning) result.warning = planNamingWarning;
+
+      output(result, raw, result.directory);
+      return;
+    } catch { continue; }
   }
+
+  output(notFound, raw, '');
 }
 
 function extractObjective(content) {
@@ -229,18 +369,24 @@ function cmdPhasePlanIndex(cwd, phase, raw) {
 
   // Get all files in phase directory
   const phaseFiles = fs.readdirSync(phaseDir);
-  const planFiles = phaseFiles.filter(f => f.endsWith('-PLAN.md') || f === 'PLAN.md').sort();
+  const planFiles = phaseFiles.filter(isCanonicalPlanFile).sort();
   const summaryFiles = phaseFiles.filter(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md');
+  // #2893 — surface plan-shaped files the canonical filter rejected so a
+  // misnamed plan never silently produces plan_count: 0 at executor init.
+  const planNamingWarning = describeNonCanonicalPlans(phaseFiles, planFiles);
 
   // Build set of plan IDs with summaries
   const completedPlanIds = new Set(
-    summaryFiles.map(s => s.replace('-SUMMARY.md', '').replace('SUMMARY.md', ''))
+    summaryFiles.flatMap(s => {
+      const exact = s.replace('-SUMMARY.md', '').replace('SUMMARY.md', '');
+      const canonical = extractCanonicalPlanId(s);
+      return canonical === exact ? [exact] : [exact, canonical];
+    })
   );
 
-  const plans = [];
-  const waves = {};
-  const incomplete = [];
-  let hasCheckpoints = false;
+  // ── Pass 1: parse each plan file ─────────────────────────────────────────
+
+  const rawPlans = [];
 
   for (const planFile of planFiles) {
     const planId = planFile.replace('-PLAN.md', '').replace('PLAN.md', '');
@@ -253,8 +399,20 @@ function cmdPhasePlanIndex(cwd, phase, raw) {
     const mdTasks = content.match(/##\s*Task\s*\d+/gi) || [];
     const taskCount = xmlTasks.length || mdTasks.length;
 
-    // Parse wave as integer
-    const wave = parseInt(fm.wave, 10) || 1;
+    // Parse wave as integer — use nullish handling so wave: 0 is preserved.
+    // parseInt returns NaN for missing/non-numeric values; fall back to null
+    // (meaning "no declared wave") so downstream can apply the topo default.
+    const parsedWave = parseInt(fm.wave, 10);
+    const declaredWave = Number.isNaN(parsedWave) ? null : parsedWave;
+
+    // Parse depends_on — normalise to string[]
+    let dependsOn = [];
+    const fmDeps = fm['depends_on'];
+    if (Array.isArray(fmDeps)) {
+      dependsOn = fmDeps.map(String);
+    } else if (typeof fmDeps === 'string' && fmDeps.trim() !== '') {
+      dependsOn = [fmDeps];
+    }
 
     // Parse autonomous (default true if not specified)
     let autonomous = true;
@@ -262,10 +420,6 @@ function cmdPhasePlanIndex(cwd, phase, raw) {
       autonomous = fm.autonomous === 'true' || fm.autonomous === true;
     }
 
-    if (!autonomous) {
-      hasCheckpoints = true;
-    }
-
     // Parse files_modified (underscore is canonical; also accept hyphenated for compat)
     let filesModified = [];
     const fmFiles = fm['files_modified'] || fm['files-modified'];
@@ -273,29 +427,130 @@ function cmdPhasePlanIndex(cwd, phase, raw) {
       filesModified = Array.isArray(fmFiles) ? fmFiles : [fmFiles];
     }
 
-    const hasSummary = completedPlanIds.has(planId);
-    if (!hasSummary) {
-      incomplete.push(planId);
-    }
+    const hasSummary = completedPlanIds.has(planId) || completedPlanIds.has(extractCanonicalPlanId(planFile));
 
-    const plan = {
+    rawPlans.push({
       id: planId,
-      wave,
+      declaredWave,
+      dependsOn,
       autonomous,
       objective: extractObjective(content) || fm.objective || null,
-      files_modified: filesModified,
-      task_count: taskCount,
-      has_summary: hasSummary,
+      filesModified,
+      taskCount,
+      hasSummary,
+    });
+  }
+
+  // ── Pass 2: topological level assignment via depends_on DAG ──────────────
+
+  // Build a map from plan ID → raw plan for fast lookup.
+  // Deps that reference plans outside this phase are treated as external and ignored.
+  const planMap = new Map(rawPlans.map(p => [p.id, p]));
+  // Secondary index: canonical prefix → full plan ID, so depends_on: ['03-01'] resolves
+  // to '03-01-auth-hardening-PLAN.md'-derived ID '03-01-auth-hardening' (k015).
+  const canonicalToId = new Map(rawPlans.map(p => [extractCanonicalPlanId(p.id), p.id]));
+
+  // Kahn's algorithm — compute in-degree and adjacency for in-phase deps only.
+  const level = new Map();
+  const inDeg = new Map();
+  const adj = new Map();
+
+  for (const p of rawPlans) {
+    if (!inDeg.has(p.id)) inDeg.set(p.id, 0);
+    if (!adj.has(p.id)) adj.set(p.id, []);
+    for (const dep of p.dependsOn) {
+      // Accept both full-stem ('03-01-auth-hardening') and canonical-prefix ('03-01') forms.
+      const resolvedDep = planMap.has(dep) ? dep : canonicalToId.get(dep);
+      if (!resolvedDep) continue; // external dep — ignore
+      if (!adj.has(resolvedDep)) adj.set(resolvedDep, []);
+      adj.get(resolvedDep).push(p.id);
+      inDeg.set(p.id, (inDeg.get(p.id) ?? 0) + 1);
+    }
+  }
+
+  // Start with nodes that have no in-phase dependencies.
+  const queue = [];
+  for (const p of rawPlans) {
+    if ((inDeg.get(p.id) ?? 0) === 0) {
+      queue.push(p.id);
+      level.set(p.id, 0);
+    }
+  }
+
+  let visited = 0;
+  while (queue.length > 0) {
+    const cur = queue.shift();
+    visited++;
+    const curLevel = level.get(cur);
+    for (const dep of (adj.get(cur) ?? [])) {
+      const newLevel = curLevel + 1;
+      if (newLevel > (level.get(dep) ?? -1)) {
+        level.set(dep, newLevel);
+      }
+      inDeg.set(dep, inDeg.get(dep) - 1);
+      if (inDeg.get(dep) === 0) {
+        queue.push(dep);
+      }
+    }
+  }
+
+  // Cycle detection — any node not visited has a cycle.
+  if (visited < rawPlans.length) {
+    const cycleNodes = rawPlans.filter(p => !level.has(p.id)).map(p => p.id);
+    error(`depends_on cycle detected in phase ${normalized} — cycle involves: ${cycleNodes.join(', ')}`);
+    return;
+  }
+
+  // ── Pass 3: determine lowest bucket key and build output ─────────────────
+
+  // If any plan has declared wave: 0, the lowest level maps to "0"; otherwise "1".
+  const anyWaveZero = rawPlans.some(p => p.declaredWave === 0);
+  const levelOffset = anyWaveZero ? 0 : 1;
+
+  const plans = [];
+  const waves = {};
+  const incomplete = [];
+  let hasCheckpoints = false;
+  const warnings = [];
+
+  for (const raw of rawPlans) {
+    if (!raw.autonomous) {
+      hasCheckpoints = true;
+    }
+    if (!raw.hasSummary) {
+      incomplete.push(raw.id);
+    }
+
+    // Computed wave = topological level + offset (so lowest level → 0 or 1).
+    const computedWave = (level.get(raw.id) ?? 0) + levelOffset;
+
+    // The effective wave used for bucketing is always the computed topo level.
+    // If the plan declared a wave that disagrees, emit a non-fatal warning.
+    const effectiveWave = computedWave;
+    if (raw.declaredWave !== null && raw.declaredWave !== computedWave) {
+      warnings.push(
+        `Plan ${raw.id}: declared wave: ${raw.declaredWave} but depends_on DAG places it in wave ${computedWave}`,
+      );
+    }
+
+    const plan = {
+      id: raw.id,
+      wave: effectiveWave,
+      depends_on: raw.dependsOn,
+      autonomous: raw.autonomous,
+      objective: raw.objective,
+      files_modified: raw.filesModified,
+      task_count: raw.taskCount,
+      has_summary: raw.hasSummary,
     };
 
     plans.push(plan);
 
-    // Group by wave
-    const waveKey = String(wave);
+    const waveKey = String(effectiveWave);
     if (!waves[waveKey]) {
       waves[waveKey] = [];
     }
-    waves[waveKey].push(planId);
+    waves[waveKey].push(raw.id);
   }
 
   const result = {
@@ -305,6 +560,8 @@ function cmdPhasePlanIndex(cwd, phase, raw) {
     incomplete,
     has_checkpoints: hasCheckpoints,
   };
+  if (planNamingWarning) result.warning = planNamingWarning;
+  if (warnings.length > 0) result.warnings = warnings;
 
   output(result, raw);
 }
@@ -376,12 +633,12 @@ function cmdPhaseAdd(cwd, description, raw, customId) {
     const dirPath = path.join(planningDir(cwd), 'phases', _dirName);
 
     // Create directory with .gitkeep so git tracks empty folders
-    fs.mkdirSync(dirPath, { recursive: true });
-    fs.writeFileSync(path.join(dirPath, '.gitkeep'), '');
+    platformEnsureDir(dirPath);
+    platformWriteSync(path.join(dirPath, '.gitkeep'), '');
 
     // Build phase entry
     const dependsOn = config.phase_naming === 'custom' ? '' : `\n**Depends on:** Phase ${typeof _newPhaseId === 'number' ? _newPhaseId - 1 : 'TBD'}`;
-    const phaseEntry = `\n### Phase ${_newPhaseId}: ${description}\n\n**Goal:** [To be planned]\n**Requirements**: TBD${dependsOn}\n**Plans:** 0 plans\n\nPlans:\n- [ ] TBD (run /sdd-plan-phase ${_newPhaseId} to break down)\n`;
+    const phaseEntry = `\n### Phase ${_newPhaseId}: ${description}\n\n**Goal:** [To be planned]\n**Requirements**: TBD${dependsOn}\n**Plans:** 0 plans\n\nPlans:\n- [ ] TBD (run /sdd:plan-phase ${_newPhaseId} to break down)\n`;
 
     // Find insertion point: before last "---" or at end
     let updatedContent;
@@ -392,7 +649,7 @@ function cmdPhaseAdd(cwd, description, raw, customId) {
       updatedContent = rawContent + phaseEntry;
     }
 
-    fs.writeFileSync(roadmapPath, updatedContent, 'utf-8');
+    platformWriteSync(roadmapPath, updatedContent);
     return { newPhaseId: _newPhaseId, dirName: _dirName };
   });
 
@@ -408,6 +665,76 @@ function cmdPhaseAdd(cwd, description, raw, customId) {
   output(result, raw, result.padded);
 }
 
+function cmdPhaseAddBatch(cwd, descriptions, raw) {
+  if (!Array.isArray(descriptions) || descriptions.length === 0) {
+    error('descriptions array required for phase add-batch');
+  }
+  const config = loadConfig(cwd);
+  const roadmapPath = path.join(planningDir(cwd), 'ROADMAP.md');
+  if (!fs.existsSync(roadmapPath)) { error('ROADMAP.md not found'); }
+  const projectCode = config.project_code || '';
+  const prefix = projectCode ? `${projectCode}-` : '';
+
+  const results = withPlanningLock(cwd, () => {
+    let rawContent = fs.readFileSync(roadmapPath, 'utf-8');
+    const content = extractCurrentMilestone(rawContent, cwd);
+    let maxPhase = 0;
+    if (config.phase_naming !== 'custom') {
+      const phasePattern = /#{2,4}\s*Phase\s+(\d+)[A-Z]?(?:\.\d+)*:/gi;
+      let m;
+      while ((m = phasePattern.exec(content)) !== null) {
+        const num = parseInt(m[1], 10);
+        if (num >= 999) continue;
+        if (num > maxPhase) maxPhase = num;
+      }
+      const phasesOnDisk = path.join(planningDir(cwd), 'phases');
+      if (fs.existsSync(phasesOnDisk)) {
+        const dirNumPattern = /^(?:[A-Z][A-Z0-9]*-)?(\d+)-/;
+        for (const entry of fs.readdirSync(phasesOnDisk)) {
+          const match = entry.match(dirNumPattern);
+          if (!match) continue;
+          const num = parseInt(match[1], 10);
+          if (num >= 999) continue;
+          if (num > maxPhase) maxPhase = num;
+        }
+      }
+    }
+    const added = [];
+    for (const description of descriptions) {
+      const slug = generateSlugInternal(description);
+      let newPhaseId, dirName;
+      if (config.phase_naming === 'custom') {
+        newPhaseId = slug.toUpperCase().replace(/-/g, '-');
+        dirName = `${prefix}${newPhaseId}-${slug}`;
+      } else {
+        maxPhase += 1;
+        newPhaseId = maxPhase;
+        dirName = `${prefix}${String(newPhaseId).padStart(2, '0')}-${slug}`;
+      }
+      const dirPath = path.join(planningDir(cwd), 'phases', dirName);
+      platformEnsureDir(dirPath);
+      platformWriteSync(path.join(dirPath, '.gitkeep'), '');
+      const dependsOn = config.phase_naming === 'custom' ? '' : `\n**Depends on:** Phase ${typeof newPhaseId === 'number' ? newPhaseId - 1 : 'TBD'}`;
+      const phaseEntry = `\n### Phase ${newPhaseId}: ${description}\n\n**Goal:** [To be planned]\n**Requirements**: TBD${dependsOn}\n**Plans:** 0 plans\n\nPlans:\n- [ ] TBD (run /sdd:plan-phase ${newPhaseId} to break down)\n`;
+      const lastSeparator = rawContent.lastIndexOf('\n---');
+      rawContent = lastSeparator > 0
+        ? rawContent.slice(0, lastSeparator) + phaseEntry + rawContent.slice(lastSeparator)
+        : rawContent + phaseEntry;
+      added.push({
+        phase_number: typeof newPhaseId === 'number' ? newPhaseId : String(newPhaseId),
+        padded: typeof newPhaseId === 'number' ? String(newPhaseId).padStart(2, '0') : String(newPhaseId),
+        name: description,
+        slug,
+        directory: toPosixPath(path.join(path.relative(cwd, planningDir(cwd)), 'phases', dirName)),
+        naming_mode: config.phase_naming,
+      });
+    }
+    platformWriteSync(roadmapPath, rawContent);
+    return added;
+  });
+  output({ phases: results, count: results.length }, raw);
+}
+
 function cmdPhaseInsert(cwd, afterPhase, description, raw) {
   if (!afterPhase || !description) {
     error('after-phase and description required for phase insert');
@@ -425,12 +752,17 @@ function cmdPhaseInsert(cwd, afterPhase, description, raw) {
     const rawContent = fs.readFileSync(roadmapPath, 'utf-8');
     const content = extractCurrentMilestone(rawContent, cwd);
 
-    // Normalize input then strip leading zeros for flexible matching
+    // Normalize input then route through canonical padding-tolerant fragment
+    // (#3537). The prior hand-rolled `0*${unpadded}` worked for the integer
+    // base but duplicated logic — funnel it through the shared helper.
     const normalizedAfter = normalizePhaseName(afterPhase);
-    const unpadded = normalizedAfter.replace(/^0+/, '');
-    const afterPhaseEscaped = unpadded.replace(/\./g, '\\.');
-    const targetPattern = new RegExp(`#{2,4}\\s*Phase\\s+0*${afterPhaseEscaped}:`, 'i');
+    const afterPhaseEscaped = phaseMarkdownRegexSource(normalizedAfter);
+    const targetPattern = new RegExp(`#{2,4}\\s*Phase\\s+${afterPhaseEscaped}:`, 'i');
     if (!targetPattern.test(content)) {
+      const checklistPattern = new RegExp(`-\\s*\\[[ x]\\]\\s*\\*\\*Phase\\s+${afterPhaseEscaped}:`, 'i');
+      if (checklistPattern.test(content)) {
+        error(`Phase ${afterPhase} exists in roadmap summary but is missing a detail section (### Phase ${afterPhase}: ...).`);
+      }
       error(`Phase ${afterPhase} not found in ROADMAP.md`);
     }
 
@@ -449,9 +781,11 @@ function cmdPhaseInsert(cwd, afterPhase, description, raw) {
       }
     } catch { /* intentionally empty */ }
 
-    // Also scan ROADMAP.md content (already loaded) for decimal entries
+    // Also scan ROADMAP.md content (already loaded) for decimal entries.
+    // #3537: padding-tolerant fragment so un-padded `Phase 2.7:` is found
+    // when caller passes the padded base `02`.
     const rmPhasePattern = new RegExp(
-      `#{2,4}\\s*Phase\\s+0*${escapeRegex(normalizedBase)}\\.(\\d+)\\s*:`, 'gi'
+      `#{2,4}\\s*Phase\\s+${phaseMarkdownRegexSource(normalizedBase)}\\.(\\d+)\\s*:`, 'gi'
     );
     let rmMatch;
     while ((rmMatch = rmPhasePattern.exec(rawContent)) !== null) {
@@ -468,14 +802,14 @@ function cmdPhaseInsert(cwd, afterPhase, description, raw) {
     const dirPath = path.join(planningDir(cwd), 'phases', _dirName);
 
     // Create directory with .gitkeep so git tracks empty folders
-    fs.mkdirSync(dirPath, { recursive: true });
-    fs.writeFileSync(path.join(dirPath, '.gitkeep'), '');
+    platformEnsureDir(dirPath);
+    platformWriteSync(path.join(dirPath, '.gitkeep'), '');
 
     // Build phase entry
-    const phaseEntry = `\n### Phase ${_decimalPhase}: ${description} (INSERTED)\n\n**Goal:** [Urgent work - to be planned]\n**Requirements**: TBD\n**Depends on:** Phase ${afterPhase}\n**Plans:** 0 plans\n\nPlans:\n- [ ] TBD (run /sdd-plan-phase ${_decimalPhase} to break down)\n`;
+    const phaseEntry = `\n### Phase ${_decimalPhase}: ${description} (INSERTED)\n\n**Goal:** [Urgent work - to be planned]\n**Requirements**: TBD\n**Depends on:** Phase ${afterPhase}\n**Plans:** 0 plans\n\nPlans:\n- [ ] TBD (run /sdd:plan-phase ${_decimalPhase} to break down)\n`;
 
     // Insert after the target phase section
-    const headerPattern = new RegExp(`(#{2,4}\\s*Phase\\s+0*${afterPhaseEscaped}:[^\\n]*\\n)`, 'i');
+    const headerPattern = new RegExp(`(#{2,4}\\s*Phase\\s+${afterPhaseEscaped}:[^\\n]*\\n)`, 'i');
     const headerMatch = rawContent.match(headerPattern);
     if (!headerMatch) {
       error(`Could not find Phase ${afterPhase} header`);
@@ -493,7 +827,7 @@ function cmdPhaseInsert(cwd, afterPhase, description, raw) {
     }
 
     const updatedContent = rawContent.slice(0, insertIdx) + phaseEntry + rawContent.slice(insertIdx);
-    fs.writeFileSync(roadmapPath, updatedContent, 'utf-8');
+    platformWriteSync(roadmapPath, updatedContent);
     return { decimalPhase: _decimalPhase, dirName: _dirName };
   });
 
@@ -515,10 +849,12 @@ function cmdPhaseInsert(cwd, afterPhase, description, raw) {
  */
 function renameDecimalPhases(phasesDir, baseInt, removedDecimal) {
   const renamedDirs = [], renamedFiles = [];
-  const decPattern = new RegExp(`^${baseInt}\\.(\\d+)-(.+)$`);
+  // Capture the zero-padded prefix (e.g. "06" from "06.3-slug") so the renamed
+  // directory preserves the original padding format.
+  const decPattern = new RegExp(`^(0*${baseInt})\\.(\\d+)-(.+)$`);
   const dirs = readSubdirectories(phasesDir, true);
   const toRename = dirs
-    .map(dir => { const m = dir.match(decPattern); return m ? { dir, oldDecimal: parseInt(m[1], 10), slug: m[2] } : null; })
+    .map(dir => { const m = dir.match(decPattern); return m ? { dir, prefix: m[1], oldDecimal: parseInt(m[2], 10), slug: m[3] } : null; })
     .filter(item => item && item.oldDecimal > removedDecimal)
     .sort((a, b) => b.oldDecimal - a.oldDecimal); // descending to avoid conflicts
 
@@ -526,7 +862,7 @@ function renameDecimalPhases(phasesDir, baseInt, removedDecimal) {
     const newDecimal = item.oldDecimal - 1;
     const oldPhaseId = `${baseInt}.${item.oldDecimal}`;
     const newPhaseId = `${baseInt}.${newDecimal}`;
-    const newDirName = `${baseInt}.${newDecimal}-${item.slug}`;
+    const newDirName = `${item.prefix}.${newDecimal}-${item.slug}`;
     fs.renameSync(path.join(phasesDir, item.dir), path.join(phasesDir, newDirName));
     renamedDirs.push({ from: item.dir, to: newDirName });
     for (const f of fs.readdirSync(path.join(phasesDir, newDirName))) {
@@ -553,7 +889,7 @@ function renameIntegerPhases(phasesDir, removedInt) {
       const m = dir.match(/^(\d+)([A-Z])?(?:\.(\d+))?-(.+)$/i);
       if (!m) return null;
       const dirInt = parseInt(m[1], 10);
-      return dirInt > removedInt ? { dir, oldInt: dirInt, letter: m[2] ? m[2].toUpperCase() : '', decimal: m[3] ? parseInt(m[3], 10) : null, slug: m[4] } : null;
+      return (dirInt > removedInt && dirInt < 999) ? { dir, oldInt: dirInt, letter: m[2] ? m[2].toUpperCase() : '', decimal: m[3] ? parseInt(m[3], 10) : null, slug: m[4] } : null;
     })
     .filter(Boolean)
     .sort((a, b) => a.oldInt !== b.oldInt ? b.oldInt - a.oldInt : (b.decimal || 0) - (a.decimal || 0));
@@ -580,6 +916,26 @@ function renameIntegerPhases(phasesDir, removedInt) {
   return { renamedDirs, renamedFiles };
 }
 
+function decrementRoadmapPhaseNumber(raw, removedInt) {
+  const num = parseInt(raw, 10);
+  if (!Number.isInteger(num) || num <= removedInt || num >= 999) return raw;
+  return String(num - 1);
+}
+
+function decrementRoadmapPhaseToken(raw, removedInt) {
+  const match = String(raw).match(/^(\d+)(\.\d+)?$/);
+  if (!match) return raw;
+  const num = parseInt(match[1], 10);
+  if (!Number.isInteger(num) || num <= removedInt || num >= 999) return raw;
+  return `${num - 1}${match[2] || ''}`;
+}
+
+function decrementRoadmapPaddedPhaseNumber(raw, removedInt) {
+  const num = parseInt(raw, 10);
+  if (!Number.isInteger(num) || num <= removedInt || num >= 999) return raw;
+  return String(num - 1).padStart(raw.length, '0');
+}
+
 /**
  * Remove a phase section from ROADMAP.md and renumber all subsequent integer phases.
  */
@@ -589,25 +945,64 @@ function updateRoadmapAfterPhaseRemoval(roadmapPath, targetPhase, isDecimal, rem
     let content = fs.readFileSync(roadmapPath, 'utf-8');
     const escaped = escapeRegex(targetPhase);
 
-    content = content.replace(new RegExp(`\\n?#{2,4}\\s*Phase\\s+${escaped}\\s*:[\\s\\S]*?(?=\\n#{2,4}\\s+Phase\\s+\\d|$)`, 'i'), '');
+    // #3601: the end-of-section lookahead is depth-aware. It captures the
+    // hash count of the header being removed and stops only at a subsequent
+    // header of the SAME depth, whether integer or decimal. This preserves
+    // two existing contracts:
+    //
+    //   (#3601 case) Remove `### Phase 2:` and stop at `### Phase 2.1:` —
+    //   `Phase 2.1` is a peer-level decimal phase (depth 3) and must be
+    //   preserved.
+    //
+    //   (#3355 case) Remove `### Phase 27:` and continue past
+    //   `#### Phase 27.1:` (depth 4 — a child of Phase 27) until the next
+    //   depth-3 header. The child decimal is part of the integer phase
+    //   being removed.
+    //
+    // The `(?!#)` negative lookahead after the backreference prevents the
+    // depth-3 match from being satisfied by a depth-4+ header that starts
+    // with the same three hashes.
+    content = content.replace(new RegExp(`\\n?(?<h>#{2,4})\\s*Phase\\s+${escaped}\\s*:[\\s\\S]*?(?=\\n\\k<h>(?!#)\\s+Phase\\s+[^\\n:]+\\s*:|$)`, 'i'), '');
     content = content.replace(new RegExp(`\\n?-\\s*\\[[ x]\\]\\s*.*Phase\\s+${escaped}[:\\s][^\\n]*`, 'gi'), '');
     content = content.replace(new RegExp(`\\n?\\|\\s*${escaped}\\.?\\s[^|]*\\|[^\\n]*`, 'gi'), '');
 
     if (!isDecimal) {
-      const MAX_PHASE = 99;
-      for (let oldNum = MAX_PHASE; oldNum > removedInt; oldNum--) {
-        const newNum = oldNum - 1;
-        const oldStr = String(oldNum), newStr = String(newNum);
-        const oldPad = oldStr.padStart(2, '0'), newPad = newStr.padStart(2, '0');
-        content = content.replace(new RegExp(`(#{2,4}\\s*Phase\\s+)${oldStr}(\\s*:)`, 'gi'), `$1${newStr}$2`);
-        content = content.replace(new RegExp(`(Phase\\s+)${oldStr}([:\\s])`, 'g'), `$1${newStr}$2`);
-        content = content.replace(new RegExp(`${oldPad}-(\\d{2})`, 'g'), `${newPad}-$1`);
-        content = content.replace(new RegExp(`(\\|\\s*)${oldStr}\\.\\s`, 'g'), `$1${newStr}. `);
-        content = content.replace(new RegExp(`(Depends on:\\*\\*\\s*Phase\\s+)${oldStr}\\b`, 'gi'), `$1${newStr}`);
-      }
+      content = content.replace(
+        /(#{2,4}\s*Phase\s+)(\d+(?:\.\d+)?)(\s*:)/gi,
+        (_match, prefix, num, suffix) => `${prefix}${decrementRoadmapPhaseToken(num, removedInt)}${suffix}`
+      );
+      content = content.replace(
+        /(-\s*\[[ x]\]\s*.*?Phase\s+)(\d+)(\s*:|\s+)/gi,
+        (_match, prefix, num, suffix) => `${prefix}${decrementRoadmapPhaseNumber(num, removedInt)}${suffix}`
+      );
+      content = content.replace(
+        /(\|\s*)(\d+)(\.\s)/g,
+        (_match, prefix, num, suffix) => `${prefix}${decrementRoadmapPhaseNumber(num, removedInt)}${suffix}`
+      );
+      // #3602: extend the suffix lookahead so slugged plan filenames like
+      // `07-01-cherry-pick-foundation-PLAN.md` match too. The previous
+      // pattern only allowed a compact `-(PLAN|SUMMARY).md` immediately
+      // after the plan number (or no suffix at all); a slug between the
+      // number and the `-PLAN.md` / `-SUMMARY.md` suffix made the
+      // lookahead fail and left the stale `07-01-` prefix in ROADMAP
+      // text while the on-disk file was already renamed to `06-01-…`.
+      // The slug segment `(?:-[A-Za-z][A-Za-z0-9-]*)*` allows any number
+      // of kebab-case tokens before the canonical PLAN/SUMMARY suffix.
+      content = content.replace(
+        /(?<![0-9-])(\d{2})-(\d{2})(?=(?:(?:-[A-Za-z][A-Za-z0-9-]*)*-(?:PLAN|SUMMARY)\.md)|(?![0-9-]))/g,
+        (_match, phaseNum, planNum) => `${decrementRoadmapPaddedPhaseNumber(phaseNum, removedInt)}-${planNum}`
+      );
+      content = content.replace(
+        /(\*\*Depends on\*\*\s*:\s*Phase\s+)(\d+(?:\.\d+)?)\b/gi,
+        (_match, prefix, num) => `${prefix}${decrementRoadmapPhaseToken(num, removedInt)}`
+      );
+      content = content.replace(
+        /(Depends on:\*\*\s*Phase\s+)(\d+(?:\.\d+)?)\b/gi,
+        (_match, prefix, num) => `${prefix}${decrementRoadmapPhaseToken(num, removedInt)}`
+      );
     }
 
-    fs.writeFileSync(roadmapPath, content, 'utf-8');
+    platformWriteSync(roadmapPath, content);
   });
 }
 
@@ -642,7 +1037,7 @@ function cmdPhaseRemove(cwd, targetPhase, options, raw) {
   let renamedDirs = [], renamedFiles = [];
   try {
     const renamed = isDecimal
-      ? renameDecimalPhases(phasesDir, normalized.split('.')[0], parseInt(normalized.split('.')[1], 10))
+      ? renameDecimalPhases(phasesDir, parseInt(normalized.split('.')[0], 10), parseInt(normalized.split('.')[1], 10))
       : renameIntegerPhases(phasesDir, parseInt(normalized, 10));
     renamedDirs = renamed.renamedDirs;
     renamedFiles = renamed.renamedFiles;
@@ -725,14 +1120,16 @@ function cmdPhaseComplete(cwd, phaseNum, raw) {
       let roadmapContent = fs.readFileSync(roadmapPath, 'utf-8');
 
       // Checkbox: - [ ] Phase N: → - [x] Phase N: (...completed DATE)
+      // #3537: padding-tolerant fragment so the caller-resolved padded id
+      // matches un-padded ROADMAP prose.
+      const phaseEscaped = phaseMarkdownRegexSource(phaseNum);
       const checkboxPattern = new RegExp(
-        `(-\\s*\\[)[ ](\\]\\s*.*Phase\\s+${escapeRegex(phaseNum)}[:\\s][^\\n]*)`,
+        `(-\\s*\\[)[ ](\\]\\s*.*Phase\\s+${phaseEscaped}[:\\s][^\\n]*)`,
         'i'
       );
       roadmapContent = roadmapContent.replace(checkboxPattern, `$1x$2 (completed ${today})`);
 
       // Progress table: update Status to Complete, add date (handles 4 or 5 column tables)
-      const phaseEscaped = escapeRegex(phaseNum);
       const tableRowPattern = new RegExp(
         `^(\\|\\s*${phaseEscaped}\\.?\\s[^|]*(?:\\|[^\\n]*))$`,
         'im'
@@ -756,7 +1153,7 @@ function cmdPhaseComplete(cwd, phaseNum, raw) {
       // Update plan count in phase section.
       // Use direct .replace() rather than replaceInCurrentMilestone() so this
       // works when the current milestone section is itself inside a <details>
-      // block (the standard /sdd-new-project layout). replaceInCurrentMilestone
+      // block (the standard /sdd:new-project layout). replaceInCurrentMilestone
       // scopes to content after the last </details>, which misses content inside
       // the current milestone's own <details> wrapper (#2005).
       // The phase-scoped heading pattern is specific enough to avoid matching
@@ -783,24 +1180,31 @@ function cmdPhaseComplete(cwd, phaseNum, raw) {
         roadmapContent = roadmapContent.replace(planCheckboxPattern, '$1x$2');
       }
 
-      fs.writeFileSync(roadmapPath, roadmapContent, 'utf-8');
+      platformWriteSync(roadmapPath, roadmapContent);
 
       // Update REQUIREMENTS.md traceability for this phase's requirements
       const reqPath = path.join(planningDir(cwd), 'REQUIREMENTS.md');
       if (fs.existsSync(reqPath)) {
-        // Extract the current phase section from roadmap (scoped to avoid cross-phase matching)
-        const phaseEsc = escapeRegex(phaseNum);
+        // Extract the current phase section from roadmap (scoped to avoid cross-phase matching).
+        // #3537: padding-tolerant fragment so an un-padded `Phase 2.7:` heading
+        // is found when caller resolved to padded `02.7`.
+        const phaseEsc = phaseMarkdownRegexSource(phaseNum);
         const currentMilestoneRoadmap = extractCurrentMilestone(roadmapContent, cwd);
         const phaseSectionMatch = currentMilestoneRoadmap.match(
           new RegExp(`(#{2,4}\\s*Phase\\s+${phaseEsc}[:\\s][\\s\\S]*?)(?=#{2,4}\\s*Phase\\s+|$)`, 'i')
         );
 
         const sectionText = phaseSectionMatch ? phaseSectionMatch[1] : '';
-        const reqMatch = sectionText.match(/\*\*Requirements:\*\*\s*([^\n]+)/i);
+        // Accept all bold/colon variants (#2769) — the previous pattern only
+        // matched **Requirements:** (colon inside bold) and silently skipped
+        // **Requirements**: (colon outside), preventing the matching REQ-IDs
+        // from being ticked off in REQUIREMENTS.md on phase completion.
+        const reqMatch = sectionText.match(/\*\*Requirements:?\*\*[^\S\n]*:?[^\S\n]*([^\n]+)/i);
+
+        let reqContent = fs.readFileSync(reqPath, 'utf-8');
 
         if (reqMatch) {
           const reqIds = reqMatch[1].replace(/[\[\]]/g, '').split(/[,\s]+/).map(r => r.trim()).filter(Boolean);
-          let reqContent = fs.readFileSync(reqPath, 'utf-8');
 
           for (const reqId of reqIds) {
             const reqEscaped = escapeRegex(reqId);
@@ -815,10 +1219,40 @@ function cmdPhaseComplete(cwd, phaseNum, raw) {
               '$1 Complete $2'
             );
           }
+        }
 
-          fs.writeFileSync(reqPath, reqContent, 'utf-8');
-          requirementsUpdated = true;
+        // Scan body for all **REQ-ID** patterns, warn about any missing from the Traceability table.
+        // Always runs regardless of whether the roadmap has a Requirements: line.
+        const bodyReqIds = [];
+        const bodyReqPattern = /\*\*([A-Z][A-Z0-9]*-\d+)\*\*/g;
+        let bodyMatch;
+        while ((bodyMatch = bodyReqPattern.exec(reqContent)) !== null) {
+          const id = bodyMatch[1];
+          if (!bodyReqIds.includes(id)) bodyReqIds.push(id);
         }
+
+        // Collect REQ-IDs present in the Traceability section only, to avoid
+        // picking up IDs from other tables in the document.
+        const traceabilityHeadingMatch = reqContent.match(/^#{1,6}\s+Traceability\b/im);
+        const traceabilitySection = traceabilityHeadingMatch
+          ? reqContent.slice(traceabilityHeadingMatch.index)
+          : '';
+        const tableReqIds = new Set();
+        const tableRowPattern = /^\|\s*([A-Z][A-Z0-9]*-\d+)\s*\|/gm;
+        let tableMatch;
+        while ((tableMatch = tableRowPattern.exec(traceabilitySection)) !== null) {
+          tableReqIds.add(tableMatch[1]);
+        }
+
+        const unregistered = bodyReqIds.filter(id => !tableReqIds.has(id));
+        if (unregistered.length > 0) {
+          warnings.push(
+            `REQUIREMENTS.md: ${unregistered.length} REQ-ID(s) found in body but missing from Traceability table: ${unregistered.join(', ')} — add them manually to keep traceability in sync`
+          );
+        }
+
+        platformWriteSync(reqPath, reqContent);
+        requirementsUpdated = true;
       }
     });
   }
@@ -838,9 +1272,11 @@ function cmdPhaseComplete(cwd, phaseNum, raw) {
       .sort((a, b) => comparePhaseNum(a, b));
 
     // Find the next phase directory after current
+    // Skip backlog phases (999.x) — they are parked ideas, not sequential work (#2129)
     for (const dir of dirs) {
       const dm = dir.match(/^(\d+[A-Z]?(?:\.\d+)*)-?(.*)/i);
       if (dm) {
+        if (/^999(?:\.|$)/.test(dm[1])) continue;
         if (comparePhaseNum(dm[1], phaseNum) > 0) {
           nextPhaseNum = dm[1];
           nextPhaseName = dm[2] || null;
@@ -937,6 +1373,21 @@ function cmdPhaseComplete(cwd, phaseNum, raw) {
     }, cwd);
   }
 
+  // Auto-prune STATE.md on phase boundary when configured (#2087)
+  let autoPruned = false;
+  try {
+    const configPath = path.join(planningDir(cwd), 'config.json');
+    if (fs.existsSync(configPath)) {
+      const rawConfig = JSON.parse(fs.readFileSync(configPath, 'utf-8'));
+      const autoPruneEnabled = rawConfig.workflow && rawConfig.workflow.auto_prune_state === true;
+      if (autoPruneEnabled && fs.existsSync(statePath)) {
+        const { cmdStatePrune } = require('./state.cjs');
+        cmdStatePrune(cwd, { keepRecent: '3', dryRun: false, silent: true }, true);
+        autoPruned = true;
+      }
+    }
+  } catch { /* intentionally empty — auto-prune is best-effort */ }
+
   const result = {
     completed_phase: phaseNum,
     phase_name: phaseInfo.phase_name,
@@ -948,6 +1399,7 @@ function cmdPhaseComplete(cwd, phaseNum, raw) {
     roadmap_updated: fs.existsSync(roadmapPath),
     state_updated: fs.existsSync(statePath),
     requirements_updated: requirementsUpdated,
+    auto_pruned: autoPruned,
     warnings,
     has_warnings: warnings.length > 0,
   };
@@ -961,6 +1413,8 @@ module.exports = {
   cmdFindPhase,
   cmdPhasePlanIndex,
   cmdPhaseAdd,
+  cmdPhaseAddBatch,
+  cmdPhaseMvpMode,
   cmdPhaseInsert,
   cmdPhaseRemove,
   cmdPhaseComplete,