@bhargavvc/sdd-cc 1.30.1 → 1.35.0

package/sdd/bin/lib/phase.cjs

@@ -4,9 +4,9 @@
 
 const fs = require('fs');
 const path = require('path');
-const { escapeRegex, loadConfig, normalizePhaseName, comparePhaseNum, findPhaseInternal, getArchivedPhaseDirs, generateSlugInternal, getMilestonePhaseFilter, stripShippedMilestones, extractCurrentMilestone, replaceInCurrentMilestone, toPosixPath, planningDir, output, error, readSubdirectories } = require('./core.cjs');
+const { escapeRegex, loadConfig, normalizePhaseName, comparePhaseNum, findPhaseInternal, getArchivedPhaseDirs, generateSlugInternal, getMilestonePhaseFilter, stripShippedMilestones, extractCurrentMilestone, replaceInCurrentMilestone, toPosixPath, planningDir, withPlanningLock, output, error, readSubdirectories, phaseTokenMatches } = require('./core.cjs');
 const { extractFrontmatter } = require('./frontmatter.cjs');
-const { writeStateMd, stateExtractField, stateReplaceField, stateReplaceFieldWithFallback } = require('./state.cjs');
+const { writeStateMd, readModifyWriteStateMd, stateExtractField, stateReplaceField, stateReplaceFieldWithFallback, updatePerformanceMetricsSection } = require('./state.cjs');
 
 function cmdPhasesList(cwd, options, raw) {
   const phasesDir = path.join(planningDir(cwd), 'phases');
@@ -41,7 +41,7 @@ function cmdPhasesList(cwd, options, raw) {
     // If filtering by phase number
     if (phase) {
       const normalized = normalizePhaseName(phase);
-      const match = dirs.find(d => d.startsWith(normalized));
+      const match = dirs.find(d => phaseTokenMatches(d, normalized));
       if (!match) {
         output({ files: [], count: 0, phase_dir: null, error: 'Phase not found' }, raw, '');
         return;
@@ -88,50 +88,49 @@ function cmdPhaseNextDecimal(cwd, basePhase, raw) {
   const phasesDir = path.join(planningDir(cwd), 'phases');
   const normalized = normalizePhaseName(basePhase);
 
-  // Check if phases directory exists
-  if (!fs.existsSync(phasesDir)) {
-    output(
-      {
-        found: false,
-        base_phase: normalized,
-        next: `${normalized}.1`,
-        existing: [],
-      },
-      raw,
-      `${normalized}.1`
-    );
-    return;
-  }
-
   try {
-    const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
-    const dirs = entries.filter(e => e.isDirectory()).map(e => e.name);
-
-    // Check if base phase exists
-    const baseExists = dirs.some(d => d.startsWith(normalized + '-') || d === normalized);
+    let baseExists = false;
+    const decimalSet = new Set();
 
-    // Find existing decimal phases for this base
-    const decimalPattern = new RegExp(`^${normalized}\\.(\\d+)`);
-    const existingDecimals = [];
+    // Scan directory names for existing decimal phases
+    if (fs.existsSync(phasesDir)) {
+      const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
+      const dirs = entries.filter(e => e.isDirectory()).map(e => e.name);
+      baseExists = dirs.some(d => phaseTokenMatches(d, normalized));
 
-    for (const dir of dirs) {
-      const match = dir.match(decimalPattern);
-      if (match) {
-        existingDecimals.push(`${normalized}.${match[1]}`);
+      const dirPattern = new RegExp(`^(?:[A-Z]{1,6}-)?${escapeRegex(normalized)}\\.(\\d+)`);
+      for (const dir of dirs) {
+        const match = dir.match(dirPattern);
+        if (match) decimalSet.add(parseInt(match[1], 10));
       }
     }
 
-    // Sort numerically
-    existingDecimals.sort((a, b) => comparePhaseNum(a, b));
+    // Also scan ROADMAP.md for phase entries that may not have directories yet
+    const roadmapPath = path.join(planningDir(cwd), 'ROADMAP.md');
+    if (fs.existsSync(roadmapPath)) {
+      try {
+        const roadmapContent = fs.readFileSync(roadmapPath, 'utf-8');
+        const phasePattern = new RegExp(
+          `#{2,4}\\s*Phase\\s+0*${escapeRegex(normalized)}\\.(\\d+)\\s*:`, 'gi'
+        );
+        let pm;
+        while ((pm = phasePattern.exec(roadmapContent)) !== null) {
+          decimalSet.add(parseInt(pm[1], 10));
+        }
+      } catch { /* ROADMAP.md read failure is non-fatal */ }
+    }
+
+    // Build sorted list of existing decimals
+    const existingDecimals = Array.from(decimalSet)
+      .sort((a, b) => a - b)
+      .map(n => `${normalized}.${n}`);
 
     // Calculate next decimal
     let nextDecimal;
-    if (existingDecimals.length === 0) {
+    if (decimalSet.size === 0) {
       nextDecimal = `${normalized}.1`;
     } else {
-      const lastDecimal = existingDecimals[existingDecimals.length - 1];
-      const lastNum = parseInt(lastDecimal.split('.')[1], 10);
-      nextDecimal = `${normalized}.${lastNum + 1}`;
+      nextDecimal = `${normalized}.${Math.max(...decimalSet) + 1}`;
     }
 
     output(
@@ -163,13 +162,15 @@ function cmdFindPhase(cwd, phase, raw) {
     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 => d.startsWith(normalized));
+    const match = dirs.find(d => phaseTokenMatches(d, normalized));
     if (!match) {
       output(notFound, raw, '');
       return;
     }
 
-    const dirMatch = match.match(/^(\d+[A-Z]?(?:\.\d+)*)-?(.*)/i);
+    // 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;
 
@@ -212,7 +213,7 @@ function cmdPhasePlanIndex(cwd, phase, raw) {
   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 => d.startsWith(normalized));
+    const match = dirs.find(d => phaseTokenMatches(d, normalized));
     if (match) {
       phaseDir = path.join(phasesDir, match);
       phaseDirName = match;
@@ -319,53 +320,81 @@ function cmdPhaseAdd(cwd, description, raw, customId) {
     error('ROADMAP.md not found');
   }
 
-  const rawContent = fs.readFileSync(roadmapPath, 'utf-8');
-  const content = extractCurrentMilestone(rawContent, cwd);
   const slug = generateSlugInternal(description);
 
-  let newPhaseId;
-  let dirName;
-
-  if (customId || config.phase_naming === 'custom') {
-    // Custom phase naming: use provided ID or generate from description
-    newPhaseId = customId || slug.toUpperCase().replace(/-/g, '-');
-    if (!newPhaseId) error('--id required when phase_naming is "custom"');
-    dirName = `${newPhaseId}-${slug}`;
-  } else {
-    // Sequential mode: find highest integer phase number (in current milestone only)
-    const phasePattern = /#{2,4}\s*Phase\s+(\d+)[A-Z]?(?:\.\d+)*:/gi;
-    let maxPhase = 0;
-    let m;
-    while ((m = phasePattern.exec(content)) !== null) {
-      const num = parseInt(m[1], 10);
-      if (num > maxPhase) maxPhase = num;
-    }
+  // Wrap entire read-modify-write in lock to prevent concurrent corruption
+  const { newPhaseId, dirName } = withPlanningLock(cwd, () => {
+    const rawContent = fs.readFileSync(roadmapPath, 'utf-8');
+    const content = extractCurrentMilestone(rawContent, cwd);
 
-    newPhaseId = maxPhase + 1;
-    const paddedNum = String(newPhaseId).padStart(2, '0');
-    dirName = `${paddedNum}-${slug}`;
-  }
+    // Optional project code prefix (e.g., 'CK' → 'CK-01-foundation')
+    const projectCode = config.project_code || '';
+    const prefix = projectCode ? `${projectCode}-` : '';
 
-  const dirPath = path.join(planningDir(cwd), 'phases', dirName);
+    let _newPhaseId;
+    let _dirName;
 
-  // Create directory with .gitkeep so git tracks empty folders
-  fs.mkdirSync(dirPath, { recursive: true });
-  fs.writeFileSync(path.join(dirPath, '.gitkeep'), '');
+    if (customId || config.phase_naming === 'custom') {
+      // Custom phase naming: use provided ID or generate from description
+      _newPhaseId = customId || slug.toUpperCase().replace(/-/g, '-');
+      if (!_newPhaseId) error('--id required when phase_naming is "custom"');
+      _dirName = `${prefix}${_newPhaseId}-${slug}`;
+    } else {
+      // Sequential mode: find highest integer phase number from two sources:
+      // 1. ROADMAP.md (current milestone only)
+      // 2. .planning/phases/ on disk (orphan directories not tracked in roadmap)
+      // Skip 999.x backlog phases — they live outside the active sequence
+      const phasePattern = /#{2,4}\s*Phase\s+(\d+)[A-Z]?(?:\.\d+)*:/gi;
+      let maxPhase = 0;
+      let m;
+      while ((m = phasePattern.exec(content)) !== null) {
+        const num = parseInt(m[1], 10);
+        if (num >= 999) continue; // backlog phases use 999.x numbering
+        if (num > maxPhase) maxPhase = num;
+      }
 
-  // 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`;
+      // Also scan .planning/phases/ for orphan directories not tracked in ROADMAP.
+      // Directory names follow: [PREFIX-]NN-slug (e.g. 03-api or CK-05-old-feature).
+      // Strip the optional project_code prefix before extracting the leading integer.
+      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; // skip backlog orphans
+          if (num > maxPhase) maxPhase = num;
+        }
+      }
 
-  // Find insertion point: before last "---" or at end
-  let updatedContent;
-  const lastSeparator = rawContent.lastIndexOf('\n---');
-  if (lastSeparator > 0) {
-    updatedContent = rawContent.slice(0, lastSeparator) + phaseEntry + rawContent.slice(lastSeparator);
-  } else {
-    updatedContent = rawContent + phaseEntry;
-  }
+      _newPhaseId = maxPhase + 1;
+      const paddedNum = String(_newPhaseId).padStart(2, '0');
+      _dirName = `${prefix}${paddedNum}-${slug}`;
+    }
+
+    const dirPath = path.join(planningDir(cwd), 'phases', _dirName);
 
-  fs.writeFileSync(roadmapPath, updatedContent, 'utf-8');
+    // Create directory with .gitkeep so git tracks empty folders
+    fs.mkdirSync(dirPath, { recursive: true });
+    fs.writeFileSync(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`;
+
+    // Find insertion point: before last "---" or at end
+    let updatedContent;
+    const lastSeparator = rawContent.lastIndexOf('\n---');
+    if (lastSeparator > 0) {
+      updatedContent = rawContent.slice(0, lastSeparator) + phaseEntry + rawContent.slice(lastSeparator);
+    } else {
+      updatedContent = rawContent + phaseEntry;
+    }
+
+    fs.writeFileSync(roadmapPath, updatedContent, 'utf-8');
+    return { newPhaseId: _newPhaseId, dirName: _dirName };
+  });
 
   const result = {
     phase_number: typeof newPhaseId === 'number' ? newPhaseId : String(newPhaseId),
@@ -389,66 +418,84 @@ function cmdPhaseInsert(cwd, afterPhase, description, raw) {
     error('ROADMAP.md not found');
   }
 
-  const rawContent = fs.readFileSync(roadmapPath, 'utf-8');
-  const content = extractCurrentMilestone(rawContent, cwd);
   const slug = generateSlugInternal(description);
 
-  // Normalize input then strip leading zeros for flexible matching
-  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');
-  if (!targetPattern.test(content)) {
-    error(`Phase ${afterPhase} not found in ROADMAP.md`);
-  }
-
-  // Calculate next decimal using existing logic
-  const phasesDir = path.join(planningDir(cwd), 'phases');
-  const normalizedBase = normalizePhaseName(afterPhase);
-  let existingDecimals = [];
-
-  try {
-    const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
-    const dirs = entries.filter(e => e.isDirectory()).map(e => e.name);
-    const decimalPattern = new RegExp(`^${normalizedBase}\\.(\\d+)`);
-    for (const dir of dirs) {
-      const dm = dir.match(decimalPattern);
-      if (dm) existingDecimals.push(parseInt(dm[1], 10));
+  // Wrap entire read-modify-write in lock to prevent concurrent corruption
+  const { decimalPhase, dirName } = withPlanningLock(cwd, () => {
+    const rawContent = fs.readFileSync(roadmapPath, 'utf-8');
+    const content = extractCurrentMilestone(rawContent, cwd);
+
+    // Normalize input then strip leading zeros for flexible matching
+    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');
+    if (!targetPattern.test(content)) {
+      error(`Phase ${afterPhase} not found in ROADMAP.md`);
     }
-  } catch { /* intentionally empty */ }
 
-  const nextDecimal = existingDecimals.length === 0 ? 1 : Math.max(...existingDecimals) + 1;
-  const decimalPhase = `${normalizedBase}.${nextDecimal}`;
-  const dirName = `${decimalPhase}-${slug}`;
-  const dirPath = path.join(planningDir(cwd), 'phases', dirName);
+    // Calculate next decimal by scanning both directories AND ROADMAP.md entries
+    const phasesDir = path.join(planningDir(cwd), 'phases');
+    const normalizedBase = normalizePhaseName(afterPhase);
+    const decimalSet = new Set();
 
-  // Create directory with .gitkeep so git tracks empty folders
-  fs.mkdirSync(dirPath, { recursive: true });
-  fs.writeFileSync(path.join(dirPath, '.gitkeep'), '');
+    try {
+      const entries = fs.readdirSync(phasesDir, { withFileTypes: true });
+      const dirs = entries.filter(e => e.isDirectory()).map(e => e.name);
+      const decimalPattern = new RegExp(`^(?:[A-Z]{1,6}-)?${escapeRegex(normalizedBase)}\\.(\\d+)`);
+      for (const dir of dirs) {
+        const dm = dir.match(decimalPattern);
+        if (dm) decimalSet.add(parseInt(dm[1], 10));
+      }
+    } catch { /* intentionally empty */ }
 
-  // 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 ${decimalPhase} to break down)\n`;
+    // Also scan ROADMAP.md content (already loaded) for decimal entries
+    const rmPhasePattern = new RegExp(
+      `#{2,4}\\s*Phase\\s+0*${escapeRegex(normalizedBase)}\\.(\\d+)\\s*:`, 'gi'
+    );
+    let rmMatch;
+    while ((rmMatch = rmPhasePattern.exec(rawContent)) !== null) {
+      decimalSet.add(parseInt(rmMatch[1], 10));
+    }
 
-  // Insert after the target phase section
-  const headerPattern = new RegExp(`(#{2,4}\\s*Phase\\s+0*${afterPhaseEscaped}:[^\\n]*\\n)`, 'i');
-  const headerMatch = rawContent.match(headerPattern);
-  if (!headerMatch) {
-    error(`Could not find Phase ${afterPhase} header`);
-  }
+    const nextDecimal = decimalSet.size === 0 ? 1 : Math.max(...decimalSet) + 1;
+    const _decimalPhase = `${normalizedBase}.${nextDecimal}`;
+    // Optional project code prefix
+    const insertConfig = loadConfig(cwd);
+    const projectCode = insertConfig.project_code || '';
+    const pfx = projectCode ? `${projectCode}-` : '';
+    const _dirName = `${pfx}${_decimalPhase}-${slug}`;
+    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'), '');
+
+    // 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 ${_decimalPhase} to break down)\n`;
+
+    // Insert after the target phase section
+    const headerPattern = new RegExp(`(#{2,4}\\s*Phase\\s+0*${afterPhaseEscaped}:[^\\n]*\\n)`, 'i');
+    const headerMatch = rawContent.match(headerPattern);
+    if (!headerMatch) {
+      error(`Could not find Phase ${afterPhase} header`);
+    }
 
-  const headerIdx = rawContent.indexOf(headerMatch[0]);
-  const afterHeader = rawContent.slice(headerIdx + headerMatch[0].length);
-  const nextPhaseMatch = afterHeader.match(/\n#{2,4}\s+Phase\s+\d/i);
+    const headerIdx = rawContent.indexOf(headerMatch[0]);
+    const afterHeader = rawContent.slice(headerIdx + headerMatch[0].length);
+    const nextPhaseMatch = afterHeader.match(/\n#{2,4}\s+Phase\s+\d/i);
 
-  let insertIdx;
-  if (nextPhaseMatch) {
-    insertIdx = headerIdx + headerMatch[0].length + nextPhaseMatch.index;
-  } else {
-    insertIdx = rawContent.length;
-  }
+    let insertIdx;
+    if (nextPhaseMatch) {
+      insertIdx = headerIdx + headerMatch[0].length + nextPhaseMatch.index;
+    } else {
+      insertIdx = rawContent.length;
+    }
 
-  const updatedContent = rawContent.slice(0, insertIdx) + phaseEntry + rawContent.slice(insertIdx);
-  fs.writeFileSync(roadmapPath, updatedContent, 'utf-8');
+    const updatedContent = rawContent.slice(0, insertIdx) + phaseEntry + rawContent.slice(insertIdx);
+    fs.writeFileSync(roadmapPath, updatedContent, 'utf-8');
+    return { decimalPhase: _decimalPhase, dirName: _dirName };
+  });
 
   const result = {
     phase_number: decimalPhase,
@@ -536,29 +583,32 @@ function renameIntegerPhases(phasesDir, removedInt) {
 /**
  * Remove a phase section from ROADMAP.md and renumber all subsequent integer phases.
  */
-function updateRoadmapAfterPhaseRemoval(roadmapPath, targetPhase, isDecimal, removedInt) {
-  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'), '');
-  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}`);
+function updateRoadmapAfterPhaseRemoval(roadmapPath, targetPhase, isDecimal, removedInt, cwd) {
+  // Wrap entire read-modify-write in lock to prevent concurrent corruption
+  withPlanningLock(cwd, () => {
+    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'), '');
+    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}`);
+      }
     }
-  }
 
-  fs.writeFileSync(roadmapPath, content, 'utf-8');
+    fs.writeFileSync(roadmapPath, content, 'utf-8');
+  });
 }
 
 function cmdPhaseRemove(cwd, targetPhase, options, raw) {
@@ -575,7 +625,7 @@ function cmdPhaseRemove(cwd, targetPhase, options, raw) {
 
   // Find target directory
   const targetDir = readSubdirectories(phasesDir, true)
-    .find(d => d.startsWith(normalized + '-') || d === normalized) || null;
+    .find(d => phaseTokenMatches(d, normalized)) || null;
 
   // Guard against removing executed work
   if (targetDir && !force) {
@@ -599,21 +649,22 @@ function cmdPhaseRemove(cwd, targetPhase, options, raw) {
   } catch { /* intentionally empty */ }
 
   // Update ROADMAP.md
-  updateRoadmapAfterPhaseRemoval(roadmapPath, targetPhase, isDecimal, parseInt(normalized, 10));
+  updateRoadmapAfterPhaseRemoval(roadmapPath, targetPhase, isDecimal, parseInt(normalized, 10), cwd);
 
-  // Update STATE.md phase count
+  // Update STATE.md phase count atomically (#P4.4)
   const statePath = path.join(planningDir(cwd), 'STATE.md');
   if (fs.existsSync(statePath)) {
-    let stateContent = fs.readFileSync(statePath, 'utf-8');
-    const totalRaw = stateExtractField(stateContent, 'Total Phases');
-    if (totalRaw) {
-      stateContent = stateReplaceField(stateContent, 'Total Phases', String(parseInt(totalRaw, 10) - 1)) || stateContent;
-    }
-    const ofMatch = stateContent.match(/(\bof\s+)(\d+)(\s*(?:\(|phases?))/i);
-    if (ofMatch) {
-      stateContent = stateContent.replace(/(\bof\s+)(\d+)(\s*(?:\(|phases?))/i, `$1${parseInt(ofMatch[2], 10) - 1}$3`);
-    }
-    writeStateMd(statePath, stateContent, cwd);
+    readModifyWriteStateMd(statePath, (stateContent) => {
+      const totalRaw = stateExtractField(stateContent, 'Total Phases');
+      if (totalRaw) {
+        stateContent = stateReplaceField(stateContent, 'Total Phases', String(parseInt(totalRaw, 10) - 1)) || stateContent;
+      }
+      const ofMatch = stateContent.match(/(\bof\s+)(\d+)(\s*(?:\(|phases?))/i);
+      if (ofMatch) {
+        stateContent = stateContent.replace(/(\bof\s+)(\d+)(\s*(?:\(|phases?))/i, `$1${parseInt(ofMatch[2], 10) - 1}$3`);
+      }
+      return stateContent;
+    }, cwd);
   }
 
   output({
@@ -668,84 +719,108 @@ function cmdPhaseComplete(cwd, phaseNum, raw) {
     }
   } catch {}
 
-  // Update ROADMAP.md: mark phase complete
+  // Update ROADMAP.md and REQUIREMENTS.md atomically under lock
   if (fs.existsSync(roadmapPath)) {
-    let roadmapContent = fs.readFileSync(roadmapPath, 'utf-8');
-
-    // Checkbox: - [ ] Phase N: → - [x] Phase N: (...completed DATE)
-    const checkboxPattern = new RegExp(
-      `(-\\s*\\[)[ ](\\]\\s*.*Phase\\s+${escapeRegex(phaseNum)}[:\\s][^\\n]*)`,
-      'i'
-    );
-    roadmapContent = replaceInCurrentMilestone(roadmapContent, 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'
-    );
-    roadmapContent = roadmapContent.replace(tableRowPattern, (fullRow) => {
-      const cells = fullRow.split('|').slice(1, -1);
-      if (cells.length === 5) {
-        // 5-col: Phase | Milestone | Plans | Status | Completed
-        cells[3] = ' Complete    ';
-        cells[4] = ` ${today} `;
-      } else if (cells.length === 4) {
-        // 4-col: Phase | Plans | Status | Completed
-        cells[2] = ' Complete    ';
-        cells[3] = ` ${today} `;
-      }
-      return '|' + cells.join('|') + '|';
-    });
-
-    // Update plan count in phase section
-    const planCountPattern = new RegExp(
-      `(#{2,4}\\s*Phase\\s+${phaseEscaped}[\\s\\S]*?\\*\\*Plans:\\*\\*\\s*)[^\\n]+`,
-      'i'
-    );
-    roadmapContent = replaceInCurrentMilestone(
-      roadmapContent, planCountPattern,
-      `$1${summaryCount}/${planCount} plans complete`
-    );
+    withPlanningLock(cwd, () => {
+      let roadmapContent = fs.readFileSync(roadmapPath, 'utf-8');
 
-    fs.writeFileSync(roadmapPath, roadmapContent, 'utf-8');
-
-    // 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);
-      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')
+      // Checkbox: - [ ] Phase N: → - [x] Phase N: (...completed DATE)
+      const checkboxPattern = new RegExp(
+        `(-\\s*\\[)[ ](\\]\\s*.*Phase\\s+${escapeRegex(phaseNum)}[:\\s][^\\n]*)`,
+        'i'
       );
+      roadmapContent = roadmapContent.replace(checkboxPattern, `$1x$2 (completed ${today})`);
 
-      const sectionText = phaseSectionMatch ? phaseSectionMatch[1] : '';
-      const reqMatch = sectionText.match(/\*\*Requirements:\*\*\s*([^\n]+)/i);
-
-      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);
-          // Update checkbox: - [ ] **REQ-ID** → - [x] **REQ-ID**
-          reqContent = reqContent.replace(
-            new RegExp(`(-\\s*\\[)[ ](\\]\\s*\\*\\*${reqEscaped}\\*\\*)`, 'gi'),
-            '$1x$2'
-          );
-          // Update traceability table: | REQ-ID | Phase N | Pending/In Progress | → | REQ-ID | Phase N | Complete |
-          reqContent = reqContent.replace(
-            new RegExp(`(\\|\\s*${reqEscaped}\\s*\\|[^|]+\\|)\\s*(?:Pending|In Progress)\\s*(\\|)`, 'gi'),
-            '$1 Complete $2'
-          );
+      // Progress table: update Status to Complete, add date (handles 4 or 5 column tables)
+      const phaseEscaped = escapeRegex(phaseNum);
+      const tableRowPattern = new RegExp(
+        `^(\\|\\s*${phaseEscaped}\\.?\\s[^|]*(?:\\|[^\\n]*))$`,
+        'im'
+      );
+      roadmapContent = roadmapContent.replace(tableRowPattern, (fullRow) => {
+        const cells = fullRow.split('|').slice(1, -1);
+        if (cells.length === 5) {
+          // 5-col: Phase | Milestone | Plans | Status | Completed
+          cells[2] = ` ${summaryCount}/${planCount} `;
+          cells[3] = ' Complete    ';
+          cells[4] = ` ${today} `;
+        } else if (cells.length === 4) {
+          // 4-col: Phase | Plans | Status | Completed
+          cells[1] = ` ${summaryCount}/${planCount} `;
+          cells[2] = ' Complete    ';
+          cells[3] = ` ${today} `;
         }
+        return '|' + cells.join('|') + '|';
+      });
+
+      // Update plan count in phase section.
+      // Use direct .replace() rather than replaceInCurrentMilestone() so this
+      // works when the current milestone section is itself inside a <details>
+      // block (the standard /sdd-new-project layout). replaceInCurrentMilestone
+      // scopes to content after the last </details>, which misses content inside
+      // the current milestone's own <details> wrapper (#2005).
+      // The phase-scoped heading pattern is specific enough to avoid matching
+      // archived phases (which belong to different milestones).
+      const planCountPattern = new RegExp(
+        `(#{2,4}\\s*Phase\\s+${phaseEscaped}[\\s\\S]*?\\*\\*Plans:\\*\\*\\s*)[^\\n]+`,
+        'i'
+      );
+      roadmapContent = roadmapContent.replace(
+        planCountPattern,
+        `$1${summaryCount}/${planCount} plans complete`
+      );
 
-        fs.writeFileSync(reqPath, reqContent, 'utf-8');
-        requirementsUpdated = true;
+      // Mark completed plan checkboxes (safety net for missed per-plan updates)
+      // Handles both plain IDs ("- [ ] 01-01-PLAN.md") and bold-wrapped IDs ("- [ ] **01-01**")
+      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$2');
       }
-    }
+
+      fs.writeFileSync(roadmapPath, roadmapContent, 'utf-8');
+
+      // Update REQUIREMENTS.md traceability for this phase's requirements
+      const reqPath = path.join(planningDir(cwd), 'REQUIREMENTS.md');
+      if (fs.existsSync(reqPath)) {
+        // Extract the current phase section from roadmap (scoped to avoid cross-phase matching)
+        const phaseEsc = escapeRegex(phaseNum);
+        const currentMilestoneRoadmap = extractCurrentMilestone(roadmapContent, cwd);
+        const phaseSectionMatch = currentMilestoneRoadmap.match(
+          new RegExp(`(#{2,4}\\s*Phase\\s+${phaseEsc}[:\\s][\\s\\S]*?)(?=#{2,4}\\s*Phase\\s+|$)`, 'i')
+        );
+
+        const sectionText = phaseSectionMatch ? phaseSectionMatch[1] : '';
+        const reqMatch = sectionText.match(/\*\*Requirements:\*\*\s*([^\n]+)/i);
+
+        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);
+            // Update checkbox: - [ ] **REQ-ID** → - [x] **REQ-ID**
+            reqContent = reqContent.replace(
+              new RegExp(`(-\\s*\\[)[ ](\\]\\s*\\*\\*${reqEscaped}\\*\\*)`, 'gi'),
+              '$1x$2'
+            );
+            // Update traceability table: | REQ-ID | Phase N | Pending/In Progress | → | REQ-ID | Phase N | Complete |
+            reqContent = reqContent.replace(
+              new RegExp(`(\\|\\s*${reqEscaped}\\s*\\|[^|]+\\|)\\s*(?:Pending|In Progress)\\s*(\\|)`, 'gi'),
+              '$1 Complete $2'
+            );
+          }
+
+          fs.writeFileSync(reqPath, reqContent, 'utf-8');
+          requirementsUpdated = true;
+        }
+      }
+    });
   }
 
   // Find next phase — check both filesystem AND roadmap
@@ -794,68 +869,72 @@ function cmdPhaseComplete(cwd, phaseNum, raw) {
     } catch { /* intentionally empty */ }
   }
 
-  // Update STATE.md — use shared helpers that handle both **bold:** and plain Field: formats
+  // Update STATE.md atomically — hold lock across read-modify-write (#P4.4).
+  // Previously read outside the lock; a crash between the ROADMAP update
+  // (locked above) and this write left ROADMAP/STATE inconsistent.
   if (fs.existsSync(statePath)) {
-    let stateContent = fs.readFileSync(statePath, 'utf-8');
-
-    // Update Current Phase — preserve "X of Y (Name)" compound format
-    const phaseValue = nextPhaseNum || phaseNum;
-    const existingPhaseField = stateExtractField(stateContent, 'Current Phase')
-      || stateExtractField(stateContent, 'Phase');
-    let newPhaseValue = String(phaseValue);
-    if (existingPhaseField) {
-      const totalMatch = existingPhaseField.match(/of\s+(\d+)/);
-      const nameMatch = existingPhaseField.match(/\(([^)]+)\)/);
-      if (totalMatch) {
-        const total = totalMatch[1];
-        const nameStr = nextPhaseName ? ` (${nextPhaseName.replace(/-/g, ' ')})` : (nameMatch ? ` (${nameMatch[1]})` : '');
-        newPhaseValue = `${phaseValue} of ${total}${nameStr}`;
+    readModifyWriteStateMd(statePath, (stateContent) => {
+      // Update Current Phase — preserve "X of Y (Name)" compound format
+      const phaseValue = nextPhaseNum || phaseNum;
+      const existingPhaseField = stateExtractField(stateContent, 'Current Phase')
+        || stateExtractField(stateContent, 'Phase');
+      let newPhaseValue = String(phaseValue);
+      if (existingPhaseField) {
+        const totalMatch = existingPhaseField.match(/of\s+(\d+)/);
+        const nameMatch = existingPhaseField.match(/\(([^)]+)\)/);
+        if (totalMatch) {
+          const total = totalMatch[1];
+          const nameStr = nextPhaseName ? ` (${nextPhaseName.replace(/-/g, ' ')})` : (nameMatch ? ` (${nameMatch[1]})` : '');
+          newPhaseValue = `${phaseValue} of ${total}${nameStr}`;
+        }
       }
-    }
-    stateContent = stateReplaceFieldWithFallback(stateContent, 'Current Phase', 'Phase', newPhaseValue);
+      stateContent = stateReplaceFieldWithFallback(stateContent, 'Current Phase', 'Phase', newPhaseValue);
 
-    // Update Current Phase Name
-    if (nextPhaseName) {
-      stateContent = stateReplaceFieldWithFallback(stateContent, 'Current Phase Name', null, nextPhaseName.replace(/-/g, ' '));
-    }
-
-    // Update Status
-    stateContent = stateReplaceFieldWithFallback(stateContent, 'Status', null,
-      isLastPhase ? 'Milestone complete' : 'Ready to plan');
-
-    // Update Current Plan
-    stateContent = stateReplaceFieldWithFallback(stateContent, 'Current Plan', 'Plan', 'Not started');
-
-    // Update Last Activity
-    stateContent = stateReplaceFieldWithFallback(stateContent, 'Last Activity', 'Last activity', today);
-
-    // Update Last Activity Description
-    stateContent = stateReplaceFieldWithFallback(stateContent, 'Last Activity Description', null,
-      `Phase ${phaseNum} complete${nextPhaseNum ? `, transitioned to Phase ${nextPhaseNum}` : ''}`);
-
-    // Increment Completed Phases counter (#956)
-    const completedRaw = stateExtractField(stateContent, 'Completed Phases');
-    if (completedRaw) {
-      const newCompleted = parseInt(completedRaw, 10) + 1;
-      stateContent = stateReplaceField(stateContent, 'Completed Phases', String(newCompleted)) || stateContent;
+      // Update Current Phase Name
+      if (nextPhaseName) {
+        stateContent = stateReplaceFieldWithFallback(stateContent, 'Current Phase Name', null, nextPhaseName.replace(/-/g, ' '));
+      }
 
-      // Recalculate percent based on completed / total (#956)
-      const totalRaw = stateExtractField(stateContent, 'Total Phases');
-      if (totalRaw) {
-        const totalPhases = parseInt(totalRaw, 10);
-        if (totalPhases > 0) {
-          const newPercent = Math.round((newCompleted / totalPhases) * 100);
-          stateContent = stateReplaceField(stateContent, 'Progress', `${newPercent}%`) || stateContent;
-          // Also update percent field if it exists separately
-          stateContent = stateContent.replace(
-            /(percent:\s*)\d+/,
-            `$1${newPercent}`
-          );
+      // Update Status
+      stateContent = stateReplaceFieldWithFallback(stateContent, 'Status', null,
+        isLastPhase ? 'Milestone complete' : 'Ready to plan');
+
+      // Update Current Plan
+      stateContent = stateReplaceFieldWithFallback(stateContent, 'Current Plan', 'Plan', 'Not started');
+
+      // Update Last Activity
+      stateContent = stateReplaceFieldWithFallback(stateContent, 'Last Activity', 'Last activity', today);
+
+      // Update Last Activity Description
+      stateContent = stateReplaceFieldWithFallback(stateContent, 'Last Activity Description', null,
+        `Phase ${phaseNum} complete${nextPhaseNum ? `, transitioned to Phase ${nextPhaseNum}` : ''}`);
+
+      // Increment Completed Phases counter (#956)
+      const completedRaw = stateExtractField(stateContent, 'Completed Phases');
+      if (completedRaw) {
+        const newCompleted = parseInt(completedRaw, 10) + 1;
+        stateContent = stateReplaceField(stateContent, 'Completed Phases', String(newCompleted)) || stateContent;
+
+        // Recalculate percent based on completed / total (#956)
+        const totalRaw = stateExtractField(stateContent, 'Total Phases');
+        if (totalRaw) {
+          const totalPhases = parseInt(totalRaw, 10);
+          if (totalPhases > 0) {
+            const newPercent = Math.round((newCompleted / totalPhases) * 100);
+            stateContent = stateReplaceField(stateContent, 'Progress', `${newPercent}%`) || stateContent;
+            stateContent = stateContent.replace(
+              /(percent:\s*)\d+/,
+              `$1${newPercent}`
+            );
+          }
         }
       }
-    }
 
-    writeStateMd(statePath, stateContent, cwd);
+      // Gate 4: Update Performance Metrics section (#1627)
+      stateContent = updatePerformanceMetricsSection(stateContent, cwd, phaseNum, planCount, summaryCount);
+
+      return stateContent;
+    }, cwd);
   }
 
   const result = {