@opengsd/get-shit-done-redux 1.0.0

package/sdk/src/query/phase-lifecycle.ts

@@ -0,0 +1,2210 @@
+/**
+ * Phase lifecycle handlers — add, insert, scaffold operations.
+ *
+ * Ported from get-shit-done/bin/lib/phase.cjs and commands.cjs.
+ * Provides phaseAdd (append phase), phaseAddBatch (append multiple phases),
+ * phaseInsert (decimal phase insertion), and phaseScaffold (template file/directory creation).
+ *
+ * Shared helpers replaceInCurrentMilestone and readModifyWriteRoadmapMd
+ * are exported for use by downstream handlers (phaseComplete in Plan 03).
+ *
+ * @example
+ * ```typescript
+ * import { phaseAdd, phaseInsert, phaseScaffold } from './phase-lifecycle.js';
+ *
+ * await phaseAdd(['New Feature'], '/project');
+ * await phaseInsert(['10', 'Urgent Fix'], '/project');
+ * await phaseScaffold(['context', '9'], '/project');
+ * ```
+ */
+
+import { readFile, writeFile, mkdir, readdir, rename, rm } from 'node:fs/promises';
+import { existsSync } from 'node:fs';
+import { join, relative } from 'node:path';
+import { GSDError, ErrorClassification } from '../errors.js';
+import {
+  escapeRegex,
+  normalizeMd,
+  normalizePhaseName,
+  comparePhaseNum,
+  phaseTokenMatches,
+  toPosixPath,
+  planningPaths,
+} from './helpers.js';
+import { extractFrontmatter } from './frontmatter.js';
+import { extractCurrentMilestone, phaseMarkdownRegexSource } from './roadmap.js';
+import { getMilestonePhaseFilter } from './state.js';
+import { isCanonicalPlanFile, describeNonCanonicalPlans } from './phase.js';
+import {
+  acquireStateLock,
+  readModifyWriteStateMdFull,
+  releaseStateLock,
+  stateReplaceField,
+} from './state-mutation.js';
+import { stateExtractField, stateReplaceFieldWithFallback } from './state-document.js';
+import type { QueryHandler } from './utils.js';
+import {
+  assertNoNullBytes,
+  assertSafePhaseDirName,
+  assertSafeProjectCode,
+  buildPhaseRoadmapEntry,
+  collectDecimalSuffixesFromDirNames,
+  collectDecimalSuffixesFromRoadmap,
+  computeNextDecimalPhase,
+  computeNextSequentialPhaseId,
+  computePhaseDirectory,
+  extractOneLinerFromBody,
+  generatePhaseSlug,
+  parseMultiwordArg,
+} from './phase-lifecycle-policy.js';
+import {
+  archiveDirectories,
+  ensureDirectoryWithGitkeep,
+  listDirectories,
+} from './phase-filesystem-adapter.js';
+import {
+  readModifyWriteRoadmapMd,
+  replaceInCurrentMilestone,
+} from './phase-roadmap-mutation.js';
+
+export { readModifyWriteRoadmapMd, replaceInCurrentMilestone };
+
+// ─── Milestone-scoped directory helpers (#3816) ───────────────────────────
+
+/**
+ * Read the current milestone identifier from STATE.md.
+ * Returns null on any error (absent, unreadable, or no `milestone:` field).
+ */
+async function readCurrentMilestoneFromState(
+  projectDir: string,
+  workstream?: string,
+): Promise<string | null> {
+  try {
+    const statePath = planningPaths(projectDir, workstream).state;
+    const content = await readFile(statePath, 'utf-8');
+    const m = content.match(/^milestone:\s*(.+)$/m);
+    if (!m) return null;
+    return m[1].trim().replace(/^["']|["']$/g, '');
+  } catch {
+    return null;
+  }
+}
+
+/**
+ * Resolve the phases directory for a `phase.add` / `phase.add-batch` write.
+ *
+ * When the project uses a milestone-scoped layout (`.planning/milestones/
+ * <milestone>-phases/` already exists on disk), return that path so newly
+ * created phase directories land in the correct location alongside existing
+ * phases (#3816 fix for Symptom 3a).
+ *
+ * Falls back to the flat `.planning/phases/` path for all other projects.
+ */
+async function resolveWritePhasesDir(
+  projectDir: string,
+  workstream?: string,
+): Promise<string> {
+  const flatPhasesDir = planningPaths(projectDir, workstream).phases;
+  try {
+    const milestone = await readCurrentMilestoneFromState(projectDir, workstream);
+    if (!milestone) return flatPhasesDir;
+    const milestoneScopedDir = join(projectDir, '.planning', 'milestones', `${milestone}-phases`);
+    if (existsSync(milestoneScopedDir)) {
+      return milestoneScopedDir;
+    }
+  } catch { /* fall through to flat layout */ }
+  return flatPhasesDir;
+}
+
+/**
+ * Find the insertion point for a new phase entry in the ROADMAP.md content.
+ *
+ * #3816 fix for Symptom 3b: the previous implementation used
+ * `lastIndexOf('\n---')` which would place a new phase AFTER the Backlog
+ * section when Backlog precedes the trailing `---`. The new implementation
+ * inserts at the end of the active milestone section (just before the next
+ * `## Backlog` / `## Planned` / etc. heading, or before the trailing `---`).
+ *
+ * Returns the index at which the new phase entry should be inserted.
+ */
+function findPhaseInsertionPoint(rawContent: string): number {
+  // Look for the next top-level (## or ###) section that marks the end of the
+  // active phases list: Backlog, Planned milestones, or similar.
+  // Matches lines starting with ## or ### that are NOT the trailing `---`.
+  // We insert BEFORE this heading.
+  const backlogBoundaryRe = /\n(#{2,3}\s+(?:Backlog|Planned|Shipped|Archived)\b[^\n]*)/i;
+  const boundaryMatch = rawContent.match(backlogBoundaryRe);
+  if (boundaryMatch && boundaryMatch.index !== undefined) {
+    return boundaryMatch.index;
+  }
+
+  // Fallback: insert before the last `\n---` separator (original behaviour for
+  // ROADMAPs without a Backlog section).
+  const lastSeparator = rawContent.lastIndexOf('\n---');
+  if (lastSeparator > 0) return lastSeparator;
+
+  return rawContent.length;
+}
+
+// ─── phaseAdd handler ───────────────────────────────────────────────────
+
+/**
+ * Query handler for phase.add.
+ *
+ * Port of cmdPhaseAdd from phase.cjs lines 312-392.
+ * Creates a new phase directory with .gitkeep, appends a phase section
+ * to ROADMAP.md before the last "---" separator.
+ *
+ * @param args - description (required), optional customId, optional --dry-run flag.
+ *   Recognized flags: --dry-run (compute result without writing to disk).
+ *   Any other --flag argument is rejected with a validation error.
+ * @param projectDir - Project root directory
+ * @returns QueryResult with { phase_number, padded, name, slug, directory, naming_mode }
+ *   In --dry-run mode also includes { dry_run: true, roadmap_entry: string }
+ */
+export const phaseAdd: QueryHandler = async (args, projectDir, workstream) => {
+  // ── Flag parsing ────────────────────────────────────────────────────────
+  // Mirrors the CJS phase add router (phase-command-router.cjs): recognise
+  // --dry-run and --id <value>; reject every other --flag; ignore --raw so it
+  // never leaks into the description; join the remaining positional tokens
+  // with a single space so multi-word descriptions like `phase add User
+  // Dashboard` produce description "User Dashboard". customId comes from the
+  // --id flag, never from positional[1].
+  let dryRun = false;
+  let customIdArg: string | null = null;
+  const positional: string[] = [];
+
+  for (let i = 0; i < args.length; i++) {
+    const arg = args[i]!;
+    if (arg === '--raw') {
+      // CJS router strips --raw before invoking the handler; preserve parity
+      // so a stray --raw never poisons the description.
+      continue;
+    }
+    if (arg === '--dry-run') {
+      dryRun = true;
+      continue;
+    }
+    if (arg === '--id') {
+      const id = args[i + 1];
+      if (!id || id.startsWith('--')) {
+        throw new GSDError('--id requires a value', ErrorClassification.Validation);
+      }
+      customIdArg = id;
+      i++;
+      continue;
+    }
+    if (arg.startsWith('--')) {
+      throw new GSDError(`phase add does not support ${arg}`, ErrorClassification.Validation);
+    }
+    positional.push(arg);
+  }
+
+  const description = positional.join(' ').trim();
+  if (!description) {
+    throw new GSDError('description required for phase add', ErrorClassification.Validation);
+  }
+  assertNoNullBytes(description, 'description');
+
+  const configPath = planningPaths(projectDir, workstream).config;
+  let config: Record<string, unknown> = {};
+  try {
+    config = JSON.parse(await readFile(configPath, 'utf-8'));
+  } catch { /* use defaults */ }
+
+  const slug = generatePhaseSlug(description);
+  // customId always comes from the --id flag; positional tokens are reserved
+  // for the description (which is joined above).
+  const customId = customIdArg;
+
+  // Optional project code prefix (e.g., 'CK' -> 'CK-01-foundation')
+  const projectCode = (config.project_code as string) || '';
+  assertSafeProjectCode(projectCode);
+  const prefix = projectCode ? `${projectCode}-` : '';
+
+  // ── Helper: compute newPhaseId / dirName / computedPhaseEntry from raw ROADMAP content ──
+  // Extracted as a local async function so it can be called both inside the
+  // roadmap lock (non-dry-run) and outside (dry-run, where no write occurs and
+  // there is no race condition to guard against).
+  const computePhaseFields = async (rawRoadmapContent: string) => {
+    const milestoneContent = await extractCurrentMilestone(rawRoadmapContent, projectDir);
+    // #3816: use milestone-scoped directory if it exists, otherwise flat layout
+    const phasesDir = await resolveWritePhasesDir(projectDir, workstream);
+    const dirNames = await listDirectories(phasesDir);
+
+    const nextSequentialPhaseId = computeNextSequentialPhaseId(milestoneContent, dirNames);
+    const { phaseId: resolvedPhaseId, dirName: resolvedDirName } = computePhaseDirectory(
+      config.phase_naming,
+      slug,
+      prefix,
+      nextSequentialPhaseId,
+      customId || undefined,
+    );
+
+    if (!resolvedDirName) {
+      throw new GSDError('Phase directory name was not computed', ErrorClassification.Execution);
+    }
+    if (resolvedPhaseId === '') {
+      throw new GSDError('Phase ID was not computed', ErrorClassification.Execution);
+    }
+
+    const resolvedEntry = buildPhaseRoadmapEntry(resolvedPhaseId, description, config.phase_naming);
+
+    return { resolvedPhaseId, resolvedDirName, resolvedEntry };
+  };
+
+  let newPhaseId: number | string = '';
+  let dirName = '';
+  let computedPhaseEntry = '';
+
+  if (dryRun) {
+    // Dry-run: no write, no race condition — compute outside the lock.
+    const roadmapPath = planningPaths(projectDir, workstream).roadmap;
+    let rawRoadmapContent = '';
+    try {
+      rawRoadmapContent = await readFile(roadmapPath, 'utf-8');
+    } catch { /* ROADMAP.md may not exist yet */ }
+
+    const { resolvedPhaseId, resolvedDirName, resolvedEntry } = await computePhaseFields(rawRoadmapContent);
+    newPhaseId = resolvedPhaseId;
+    dirName = resolvedDirName;
+    computedPhaseEntry = resolvedEntry;
+  } else {
+    // Real write path: hold the roadmap lock across the entire read → compute → write
+    // cycle so that two concurrent phase.add calls cannot both observe the same
+    // maxPhase and produce duplicate phase IDs.
+    await readModifyWriteRoadmapMd(projectDir, async (roadmapRaw) => {
+      const { resolvedPhaseId, resolvedDirName, resolvedEntry } = await computePhaseFields(roadmapRaw);
+      newPhaseId = resolvedPhaseId;
+      dirName = resolvedDirName;
+      computedPhaseEntry = resolvedEntry;
+
+      // #3816: resolve to milestone-scoped dir if it exists
+      const phasesWriteDir = await resolveWritePhasesDir(projectDir, workstream);
+      const dirPath = join(phasesWriteDir, dirName);
+
+      // Create directory with .gitkeep so git tracks empty folders
+      await ensureDirectoryWithGitkeep(dirPath);
+
+      // #3816: insert before Backlog/Planned boundary, not after last `---`
+      const insertIdx = findPhaseInsertionPoint(roadmapRaw);
+      return roadmapRaw.slice(0, insertIdx) + computedPhaseEntry + roadmapRaw.slice(insertIdx);
+    }, workstream);
+  }
+
+  const result: Record<string, unknown> = {
+    phase_number: typeof newPhaseId === 'number' ? newPhaseId : String(newPhaseId),
+    padded: typeof newPhaseId === 'number' ? String(newPhaseId).padStart(2, '0') : String(newPhaseId),
+    name: description,
+    slug,
+    // #3816: result.directory must reflect the actual write location
+    directory: toPosixPath(relative(projectDir, join(await resolveWritePhasesDir(projectDir, workstream), dirName))),
+    naming_mode: config.phase_naming || 'sequential',
+  };
+
+  if (dryRun) {
+    result.dry_run = true;
+    result.roadmap_entry = computedPhaseEntry;
+  }
+
+  return { data: result };
+};
+
+// ─── phaseAddBatch handler ────────────────────────────────────────────────
+
+/**
+ * Query handler for phase.add-batch.
+ *
+ * Port of cmdPhaseAddBatch from phase.cjs lines 411-478.
+ * Appends multiple phases in one locked ROADMAP pass (sequential or custom naming).
+ *
+ * @param args - Either `--descriptions` followed by a JSON array string, or one description per arg (`--raw` ignored)
+ */
+export const phaseAddBatch: QueryHandler = async (args, projectDir, workstream) => {
+  let descriptions: string[];
+  const descIdx = args.indexOf('--descriptions');
+  if (descIdx !== -1) {
+    // CJS router parity (phase-command-router.cjs): a dangling --descriptions
+    // or one whose value is another flag must surface the same JSON-array error
+    // string, not silently fall through to positional parsing or throw a
+    // different "valid JSON" variant.
+    const rawValue = args[descIdx + 1];
+    if (rawValue === undefined || rawValue.startsWith('--')) {
+      throw new GSDError('--descriptions must be a JSON array', ErrorClassification.Validation);
+    }
+    let parsed: unknown;
+    try {
+      parsed = JSON.parse(rawValue);
+    } catch {
+      throw new GSDError('--descriptions must be a JSON array', ErrorClassification.Validation);
+    }
+    if (!Array.isArray(parsed)) {
+      throw new GSDError('--descriptions must be a JSON array', ErrorClassification.Validation);
+    }
+    descriptions = parsed.map((x) => String(x));
+  } else {
+    descriptions = args.filter((a) => a !== '--raw');
+  }
+
+  if (descriptions.length === 0) {
+    throw new GSDError('descriptions array required for phase add-batch', ErrorClassification.Validation);
+  }
+
+  for (const d of descriptions) {
+    assertNoNullBytes(d, 'description');
+    if (!d.trim()) {
+      throw new GSDError('description must be non-empty', ErrorClassification.Validation);
+    }
+  }
+
+  const roadmapPath = planningPaths(projectDir, workstream).roadmap;
+  if (!existsSync(roadmapPath)) {
+    throw new GSDError('ROADMAP.md not found', ErrorClassification.Validation);
+  }
+
+  let config: Record<string, unknown> = {};
+  try {
+    config = JSON.parse(await readFile(planningPaths(projectDir, workstream).config, 'utf-8'));
+  } catch { /* use defaults */ }
+
+  const projectCode = (config.project_code as string) || '';
+  assertSafeProjectCode(projectCode);
+  const prefix = projectCode ? `${projectCode}-` : '';
+
+  const added: Array<{
+    phase_number: string | number;
+    padded: string;
+    name: string;
+    slug: string;
+    directory: string;
+    naming_mode: unknown;
+  }> = [];
+
+  await readModifyWriteRoadmapMd(projectDir, async (initialContent) => {
+    let rawContent = initialContent;
+    const content = await extractCurrentMilestone(rawContent, projectDir);
+    let maxPhase = 0;
+
+    // #3816: resolve to milestone-scoped dir if it exists for the whole batch
+    const phasesWriteDir = await resolveWritePhasesDir(projectDir, workstream);
+
+    if (config.phase_naming !== 'custom') {
+      const dirNames = await listDirectories(phasesWriteDir);
+      maxPhase = computeNextSequentialPhaseId(content, dirNames) - 1;
+    }
+
+    for (const description of descriptions) {
+      const slug = generatePhaseSlug(description);
+      let newPhaseId: number | string;
+      let dirName: string;
+
+      if (config.phase_naming === 'custom') {
+        // Match CJS cmdPhaseAddBatch: slug.toUpperCase().replace(/-/g, '-') (identity on hyphens)
+        newPhaseId = slug.toUpperCase();
+        dirName = `${prefix}${newPhaseId}-${slug}`;
+      } else {
+        maxPhase += 1;
+        newPhaseId = maxPhase;
+        dirName = `${prefix}${String(newPhaseId).padStart(2, '0')}-${slug}`;
+      }
+
+      assertSafePhaseDirName(dirName);
+      // #3816: use resolved milestone-scoped dir for directory creation
+      const dirPath = join(phasesWriteDir, dirName);
+      await ensureDirectoryWithGitkeep(dirPath);
+
+      const phaseEntry =
+        buildPhaseRoadmapEntry(newPhaseId, description, config.phase_naming);
+
+      // #3816: insert before Backlog/Planned boundary, not after last `---`
+      const insertIdx = findPhaseInsertionPoint(rawContent);
+      rawContent = rawContent.slice(0, insertIdx) + phaseEntry + rawContent.slice(insertIdx);
+
+      added.push({
+        phase_number: typeof newPhaseId === 'number' ? newPhaseId : String(newPhaseId),
+        padded: typeof newPhaseId === 'number' ? String(newPhaseId).padStart(2, '0') : String(newPhaseId),
+        name: description,
+        slug,
+        // #3816: result.directory reflects the actual write location
+        directory: toPosixPath(relative(projectDir, join(phasesWriteDir, dirName))),
+        naming_mode: config.phase_naming || 'sequential',
+      });
+    }
+
+    return rawContent;
+  }, workstream);
+
+  return { data: { phases: added, count: added.length } };
+};
+
+// ─── phaseInsert handler ────────────────────────────────────────────────
+
+/**
+ * Query handler for phase.insert.
+ *
+ * Port of cmdPhaseInsert from phase.cjs lines 394-492.
+ * Creates a decimal phase directory after a target phase, inserting
+ * the phase section in ROADMAP.md after the target.
+ *
+ * @param args - args[0]: afterPhase (required), args[1]: description (required)
+ * @param projectDir - Project root directory
+ * @returns QueryResult with { phase_number, after_phase, name, slug, directory }
+ */
+export const phaseInsert: QueryHandler = async (args, projectDir, workstream) => {
+  // CJS router parity (phase-command-router.cjs): explicitly reject
+  // --dry-run (insert is destructive on disk + roadmap and has no preview
+  // path), strip --raw, and join all positional args after `afterPhase` into
+  // a single space-delimited description so `phase insert 1 Fix Critical Bug`
+  // produces description "Fix Critical Bug" instead of just "Fix".
+  const positional: string[] = [];
+  for (const arg of args) {
+    if (arg === '--dry-run') {
+      throw new GSDError('phase insert does not support --dry-run', ErrorClassification.Validation);
+    }
+    if (arg === '--raw') continue;
+    if (arg.startsWith('--')) {
+      throw new GSDError(`phase insert does not support ${arg}`, ErrorClassification.Validation);
+    }
+    positional.push(arg);
+  }
+
+  const afterPhase = positional[0];
+  const description = positional.slice(1).join(' ').trim();
+
+  if (!afterPhase || !description) {
+    throw new GSDError('after-phase and description required for phase insert', ErrorClassification.Validation);
+  }
+  assertNoNullBytes(afterPhase, 'afterPhase');
+  assertNoNullBytes(description, 'description');
+
+  const slug = generatePhaseSlug(description);
+  let decimalPhase = '';
+  let dirName = '';
+
+  await readModifyWriteRoadmapMd(projectDir, async (rawContent) => {
+    const content = await extractCurrentMilestone(rawContent, projectDir);
+
+    // Normalize input then strip leading zeros for flexible matching
+    const normalizedAfter = normalizePhaseName(afterPhase);
+    const unpadded = normalizedAfter.replace(/^0+/, '');
+    const afterPhaseEscaped = unpadded.replace(/\./g, '\\.');
+    const targetPattern = new RegExp(`#{2,4}\\s*Phase\\s+0*${afterPhaseEscaped}:`, 'i');
+    const headingMatch = targetPattern.test(content);
+
+    // #3815: also recognise the checked-bullet phase format used by projects
+    // that list phases as `- [ ] **Phase N: name**` or `- [ ] Phase N: name`
+    // (both bold and plain variants).  This mirrors the patterns already used
+    // by phaseRemove / phaseComplete so insert is consistent with its siblings.
+    //
+    // Bullet-style is only used when there are NO heading-style phases at all in
+    // the milestone content.  If the ROADMAP mixes headings + bullets (hybrid
+    // format), a bullet-only match means the detail section is missing — that
+    // is the #3098 case and must continue to produce the "missing a detail
+    // section" error.  Only a purely bullet-style ROADMAP (zero heading-style
+    // phase entries in the milestone) goes through the bullet insert path.
+    const bulletPattern = new RegExp(
+      `-\\s*\\[[ x]\\]\\s*(?:\\*\\*)?Phase\\s+0*${afterPhaseEscaped}[:\\s]`,
+      'i',
+    );
+    const anyHeadingPattern = /#{2,4}\s*Phase\s+\d/i;
+    const roadmapHasHeadingPhases = anyHeadingPattern.test(content);
+    const isBulletStyle = !headingMatch && bulletPattern.test(content) && !roadmapHasHeadingPhases;
+
+    if (!headingMatch && !isBulletStyle) {
+      // Bug #3098 parity: when the ROADMAP uses heading-style phases and only
+      // the summary checklist exists for this phase (no `### Phase N:` detail
+      // section), point the user at the missing detail section rather than
+      // implying the phase is absent.
+      const checklistPattern = new RegExp(
+        `-\\s*\\[[ x]\\]\\s*(?:\\*\\*)?Phase\\s+0*${afterPhaseEscaped}[:\\s]`,
+        'i',
+      );
+      if (checklistPattern.test(content)) {
+        throw new GSDError(
+          `Phase ${afterPhase} exists in roadmap summary but is missing a detail section (### Phase ${afterPhase}: ...).`,
+          ErrorClassification.Validation,
+        );
+      }
+      throw new GSDError(`Phase ${afterPhase} not found in ROADMAP.md`, ErrorClassification.Validation);
+    }
+
+    // Calculate next decimal by scanning both directories AND ROADMAP.md entries
+    const phasesDir = planningPaths(projectDir, workstream).phases;
+    const normalizedBase = normalizePhaseName(afterPhase);
+    const decimalSet = new Set<number>();
+
+    try {
+      const dirs = await listDirectories(phasesDir);
+      for (const suffix of collectDecimalSuffixesFromDirNames(normalizedBase, dirs)) {
+        decimalSet.add(suffix);
+      }
+    } catch { /* intentionally empty */ }
+
+    // Also scan ROADMAP.md content for decimal entries
+    for (const suffix of collectDecimalSuffixesFromRoadmap(normalizedBase, rawContent)) {
+      decimalSet.add(suffix);
+    }
+    decimalPhase = computeNextDecimalPhase(normalizedBase, decimalSet).next;
+
+    // Optional project code prefix
+    let insertConfig: Record<string, unknown> = {};
+    try {
+      insertConfig = JSON.parse(await readFile(planningPaths(projectDir, workstream).config, 'utf-8'));
+    } catch { /* use defaults */ }
+    const projectCode = (insertConfig.project_code as string) || '';
+    assertSafeProjectCode(projectCode);
+    const pfx = projectCode ? `${projectCode}-` : '';
+    dirName = `${pfx}${decimalPhase}-${slug}`;
+    assertSafePhaseDirName(dirName);
+    const dirPath = join(phasesDir, dirName);
+
+    // Create directory with .gitkeep
+    await ensureDirectoryWithGitkeep(dirPath);
+
+    if (isBulletStyle) {
+      // #3815: Insert in checked-bullet format, mirroring the style of the
+      // surrounding entries.  Detect whether the matched bullet uses bold
+      // (`**Phase N: …**`) to preserve file-internal format consistency.
+      const boldBulletPattern = new RegExp(
+        `-\\s*\\[[ x]\\]\\s*\\*\\*Phase\\s+0*${afterPhaseEscaped}:`,
+        'i',
+      );
+      const useBold = boldBulletPattern.test(content);
+      const phaseLabel = useBold
+        ? `**Phase ${decimalPhase}: ${description}**`
+        : `Phase ${decimalPhase}: ${description}`;
+      const bulletEntry = `\n- [ ] ${phaseLabel}`;
+
+      // Locate the target bullet line in the raw content
+      const targetBulletPattern = new RegExp(
+        `(-\\s*\\[[ x]\\]\\s*(?:\\*\\*)?Phase\\s+0*${afterPhaseEscaped}[:\\s][^\\n]*)`,
+        'i',
+      );
+      const bulletMatchResult = rawContent.match(targetBulletPattern);
+      if (!bulletMatchResult) {
+        throw new GSDError(`Could not find Phase ${afterPhase} bullet line`, ErrorClassification.Execution);
+      }
+
+      const bulletLineEnd = rawContent.indexOf(bulletMatchResult[0]) + bulletMatchResult[0].length;
+      // Find where the next phase bullet starts (or use end of content)
+      const afterBullet = rawContent.slice(bulletLineEnd);
+      const nextBulletMatch = afterBullet.match(/\n-\s*\[[ x]\]\s*(?:\*\*)?Phase\s+\d/i);
+
+      let insertIdx: number;
+      if (nextBulletMatch && nextBulletMatch.index !== undefined) {
+        insertIdx = bulletLineEnd + nextBulletMatch.index;
+      } else {
+        insertIdx = bulletLineEnd;
+      }
+
+      return rawContent.slice(0, insertIdx) + bulletEntry + rawContent.slice(insertIdx);
+    }
+
+    // Heading-style insert (original path)
+    // 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 /gsd-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) {
+      throw new GSDError(`Could not find Phase ${afterPhase} header`, ErrorClassification.Execution);
+    }
+
+    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: number;
+    if (nextPhaseMatch && nextPhaseMatch.index !== undefined) {
+      insertIdx = headerIdx + headerMatch[0].length + nextPhaseMatch.index;
+    } else {
+      insertIdx = rawContent.length;
+    }
+
+    return rawContent.slice(0, insertIdx) + phaseEntry + rawContent.slice(insertIdx);
+  }, workstream);
+
+  if (!decimalPhase) {
+    throw new GSDError('Decimal phase was not computed', ErrorClassification.Execution);
+  }
+  if (!dirName) {
+    throw new GSDError('Phase directory name was not computed', ErrorClassification.Execution);
+  }
+
+  const result = {
+    phase_number: decimalPhase,
+    after_phase: afterPhase,
+    name: description,
+    slug,
+    directory: toPosixPath(relative(projectDir, join(planningPaths(projectDir, workstream).phases, dirName))),
+  };
+
+  return { data: result };
+};
+
+// ─── phaseScaffold handler ──────────────────────────────────────────────
+
+/**
+ * Internal helper: find phase directory matching a phase identifier.
+ *
+ * Reuses the same logic as findPhase handler but returns just the directory info.
+ */
+async function findPhaseDir(
+  projectDir: string,
+  phase: string,
+  workstream?: string,
+): Promise<{ dirPath: string; dirName: string; phaseName: string | null } | null> {
+  const phasesDir = planningPaths(projectDir, workstream).phases;
+  const normalized = normalizePhaseName(phase);
+  const dirs = await listDirectories(phasesDir);
+  const match = dirs.find((d) => phaseTokenMatches(d, normalized));
+  if (!match) return null;
+
+  // Extract phase name from directory
+  const dirMatch = match.match(/^(?:[A-Z]{1,6}-)?\d+[A-Z]?(?:\.\d+)*-(.+)/i);
+  const phaseName = dirMatch ? dirMatch[1] : null;
+
+  return {
+    dirPath: join(phasesDir, match),
+    dirName: match,
+    phaseName,
+  };
+}
+
+/**
+ * Query handler for phase.scaffold.
+ *
+ * Port of cmdScaffold from commands.cjs lines 750-806.
+ * Creates template files (context, uat, verification) or phase directories.
+ *
+ * @param args - Positional `[type, phase, name?]` **or** gsd-tools style
+ *   `[type, '--phase', N, '--name', title]` (name may be multiple words).
+ * @param projectDir - Project root directory
+ * @returns QueryResult with { created, path } or { created: false, reason: 'already_exists' }
+ */
+function normalizeScaffoldArgs(args: string[]): string[] {
+  const type = args[0];
+  if (!type || !args.includes('--phase')) {
+    return args;
+  }
+  const phaseIdx = args.indexOf('--phase');
+  const phase = phaseIdx !== -1 && args[phaseIdx + 1] && !args[phaseIdx + 1].startsWith('--')
+    ? args[phaseIdx + 1]
+    : '';
+  const nameIdx = args.indexOf('--name');
+  let name: string | undefined;
+  if (nameIdx !== -1) {
+    const tail = args.slice(nameIdx + 1);
+    const stop = tail.findIndex(a => a.startsWith('--'));
+    const parts = stop === -1 ? tail : tail.slice(0, stop);
+    name = parts.join(' ').trim() || undefined;
+  }
+  return [type, phase, ...(name !== undefined && name !== '' ? [name] : [])];
+}
+
+export const phaseScaffold: QueryHandler = async (args, projectDir, workstream) => {
+  const normalized = normalizeScaffoldArgs(args);
+  const type = normalized[0];
+  const phase = normalized[1];
+  const name = normalized[2] || undefined;
+
+  if (!type) {
+    throw new GSDError('type required for scaffold', ErrorClassification.Validation);
+  }
+
+  const validTypes = new Set(['context', 'uat', 'verification', 'phase-dir']);
+  if (!validTypes.has(type)) {
+    throw new GSDError(
+      `Unknown scaffold type: ${type}. Available: context, uat, verification, phase-dir`,
+      ErrorClassification.Validation,
+    );
+  }
+
+  if (phase) {
+    assertNoNullBytes(phase, 'phase');
+  }
+  if (name) {
+    assertNoNullBytes(name, 'name');
+  }
+
+  const padded = phase ? normalizePhaseName(phase) : '00';
+  const today = new Date().toISOString().split('T')[0];
+
+  // Handle phase-dir type separately
+  if (type === 'phase-dir') {
+    if (!phase || !name) {
+      throw new GSDError('phase and name required for phase-dir scaffold', ErrorClassification.Validation);
+    }
+    const slug = generatePhaseSlug(name);
+    // #3287: apply project_code prefix to stay consistent with phase.add/phase.insert
+    let scaffoldConfig: Record<string, unknown> = {};
+    try {
+      scaffoldConfig = JSON.parse(await readFile(planningPaths(projectDir, workstream).config, 'utf-8'));
+    } catch { /* use defaults */ }
+    const scaffoldProjectCode = (scaffoldConfig.project_code as string) || '';
+    assertSafeProjectCode(scaffoldProjectCode);
+    const scaffoldPrefix = scaffoldProjectCode ? `${scaffoldProjectCode}-` : '';
+    const dirNameNew = `${scaffoldPrefix}${padded}-${slug}`;
+    assertSafePhaseDirName(dirNameNew, 'scaffold phase directory');
+    const phasesParent = planningPaths(projectDir, workstream).phases;
+    await mkdir(phasesParent, { recursive: true });
+    const dirPath = join(phasesParent, dirNameNew);
+    await ensureDirectoryWithGitkeep(dirPath);
+    return {
+      data: {
+        created: true,
+        directory: toPosixPath(relative(projectDir, dirPath)),
+        path: dirPath,
+      },
+    };
+  }
+
+  // For context/uat/verification types, find the phase directory
+  const phaseInfo = phase ? await findPhaseDir(projectDir, phase, workstream) : null;
+  if (phase && !phaseInfo) {
+    throw new GSDError(`Phase ${phase} directory not found`, ErrorClassification.Blocked);
+  }
+
+  const phaseDir = phaseInfo!.dirPath;
+  const phaseName = name || phaseInfo?.phaseName || 'Unnamed';
+
+  let filePath: string;
+  let content: string;
+
+  switch (type) {
+    case 'context': {
+      filePath = join(phaseDir, `${padded}-CONTEXT.md`);
+      content = `---\nphase: "${padded}"\nname: "${phaseName}"\ncreated: ${today}\n---\n\n# Phase ${phase}: ${phaseName} — Context\n\n## Decisions\n\n_Decisions will be captured during /gsd-discuss-phase ${phase}_\n\n## Discretion Areas\n\n_Areas where the executor can use judgment_\n\n## Deferred Ideas\n\n_Ideas to consider later_\n`;
+      break;
+    }
+    case 'uat': {
+      filePath = join(phaseDir, `${padded}-UAT.md`);
+      content = `---\nphase: "${padded}"\nname: "${phaseName}"\ncreated: ${today}\nstatus: pending\n---\n\n# Phase ${phase}: ${phaseName} — User Acceptance Testing\n\n## Test Results\n\n| # | Test | Status | Notes |\n|---|------|--------|-------|\n\n## Summary\n\n_Pending UAT_\n`;
+      break;
+    }
+    case 'verification': {
+      filePath = join(phaseDir, `${padded}-VERIFICATION.md`);
+      content = `---\nphase: "${padded}"\nname: "${phaseName}"\ncreated: ${today}\nstatus: pending\n---\n\n# Phase ${phase}: ${phaseName} — Verification\n\n## Goal-Backward Verification\n\n**Phase Goal:** [From ROADMAP.md]\n\n## Checks\n\n| # | Requirement | Status | Evidence |\n|---|------------|--------|----------|\n\n## Result\n\n_Pending verification_\n`;
+      break;
+    }
+    default:
+      throw new GSDError(`Unknown scaffold type: ${type}`, ErrorClassification.Validation);
+  }
+
+  // Check if file already exists
+  if (existsSync(filePath)) {
+    return {
+      data: {
+        created: false,
+        reason: 'already_exists',
+        path: filePath,
+      },
+    };
+  }
+
+  await writeFile(filePath, content, 'utf-8');
+  const relPath = toPosixPath(relative(projectDir, filePath));
+  return { data: { created: true, path: relPath } };
+};
+
+// ─── renameDecimalPhases ───────────────────────────────────────────────
+
+/**
+ * Renumber sibling decimal phases after a decimal phase is removed.
+ *
+ * Port of renameDecimalPhases from phase.cjs lines 499-524.
+ * e.g. removing 06.2 -> 06.3 becomes 06.2, 06.4 becomes 06.3, etc.
+ * Renames directories AND files inside them that contain the old phase ID.
+ *
+ * CRITICAL: Sorted in DESCENDING order to avoid rename conflicts.
+ *
+ * @param phasesDir - Path to the phases directory
+ * @param baseInt - The integer part of the decimal phase (e.g. "06")
+ * @param removedDecimal - The decimal part that was removed (e.g. 2 for 06.2)
+ * @returns { renamedDirs, renamedFiles }
+ */
+async function renameDecimalPhases(
+  phasesDir: string,
+  baseInt: string,
+  removedDecimal: number,
+): Promise<{ renamedDirs: Array<{ from: string; to: string }>; renamedFiles: Array<{ from: string; to: string }> }> {
+  const renamedDirs: Array<{ from: string; to: string }> = [];
+  const renamedFiles: Array<{ from: string; to: string }> = [];
+
+  const decPattern = new RegExp(`^${escapeRegex(baseInt)}\\.(\\d+)-(.+)$`);
+  const entries = await readdir(phasesDir, { withFileTypes: true });
+  const dirs = entries.filter(e => e.isDirectory()).map(e => e.name);
+
+  const toRename = dirs
+    .map(dir => {
+      const m = dir.match(decPattern);
+      return m ? { dir, oldDecimal: parseInt(m[1], 10), slug: m[2] } : null;
+    })
+    .filter((item): item is NonNullable<typeof item> => item !== null && item.oldDecimal > removedDecimal)
+    .sort((a, b) => b.oldDecimal - a.oldDecimal); // DESCENDING to avoid conflicts
+
+  for (const item of toRename) {
+    const newDecimal = item.oldDecimal - 1;
+    const oldPhaseId = `${baseInt}.${item.oldDecimal}`;
+    const newPhaseId = `${baseInt}.${newDecimal}`;
+    const newDirName = `${baseInt}.${newDecimal}-${item.slug}`;
+
+    await rename(join(phasesDir, item.dir), join(phasesDir, newDirName));
+    renamedDirs.push({ from: item.dir, to: newDirName });
+
+    // Rename files inside that contain the old phase ID
+    const files = await readdir(join(phasesDir, newDirName));
+    for (const f of files) {
+      if (f.includes(oldPhaseId)) {
+        const newFileName = f.replace(oldPhaseId, newPhaseId);
+        await rename(join(phasesDir, newDirName, f), join(phasesDir, newDirName, newFileName));
+        renamedFiles.push({ from: f, to: newFileName });
+      }
+    }
+  }
+
+  return { renamedDirs, renamedFiles };
+}
+
+// ─── renameIntegerPhases ───────────────────────────────────────────────
+
+/**
+ * Renumber all integer phases after a removed integer phase.
+ *
+ * Port of renameIntegerPhases from phase.cjs lines 531-564.
+ * e.g. removing phase 5 -> phase 6 becomes 5, phase 7 becomes 6, etc.
+ * Handles letter suffixes (12A) and decimals (6.1).
+ *
+ * CRITICAL: Sorted in DESCENDING order to avoid rename conflicts.
+ *
+ * @param phasesDir - Path to the phases directory
+ * @param removedInt - The integer phase number that was removed
+ * @returns { renamedDirs, renamedFiles }
+ */
+async function renameIntegerPhases(
+  phasesDir: string,
+  removedInt: number,
+): Promise<{ renamedDirs: Array<{ from: string; to: string }>; renamedFiles: Array<{ from: string; to: string }> }> {
+  const renamedDirs: Array<{ from: string; to: string }> = [];
+  const renamedFiles: Array<{ from: string; to: string }> = [];
+
+  const entries = await readdir(phasesDir, { withFileTypes: true });
+  const dirs = entries.filter(e => e.isDirectory()).map(e => e.name);
+
+  const toRename = dirs
+    .map(dir => {
+      const m = dir.match(/^(\d+)([A-Z])?(?:\.(\d+))?-(.+)$/i);
+      if (!m) return null;
+      const dirInt = parseInt(m[1], 10);
+      // CJS parity: skip backlog phases (999.x). These are parked ideas with a
+      // numbering convention that lives outside the active sequence; renumbering
+      // them would clobber the convention and corrupt downstream lookups.
+      // (bug-2434)
+      if (dirInt <= removedInt || dirInt >= 999) return null;
+      return {
+        dir,
+        oldInt: dirInt,
+        letter: m[2] ? m[2].toUpperCase() : '',
+        decimal: m[3] !== undefined ? parseInt(m[3], 10) : null,
+        slug: m[4],
+      };
+    })
+    .filter((item): item is NonNullable<typeof item> => item !== null)
+    .sort((a, b) => a.oldInt !== b.oldInt
+      ? b.oldInt - a.oldInt
+      : (b.decimal ?? 0) - (a.decimal ?? 0)); // DESCENDING
+
+  for (const item of toRename) {
+    const newInt = item.oldInt - 1;
+    const newPadded = String(newInt).padStart(2, '0');
+    const oldPadded = String(item.oldInt).padStart(2, '0');
+    const letterSuffix = item.letter || '';
+    const decimalSuffix = item.decimal !== null ? `.${item.decimal}` : '';
+    const oldPrefix = `${oldPadded}${letterSuffix}${decimalSuffix}`;
+    const newPrefix = `${newPadded}${letterSuffix}${decimalSuffix}`;
+    const newDirName = `${newPrefix}-${item.slug}`;
+
+    await rename(join(phasesDir, item.dir), join(phasesDir, newDirName));
+    renamedDirs.push({ from: item.dir, to: newDirName });
+
+    // Rename files that start with the old prefix
+    const files = await readdir(join(phasesDir, newDirName));
+    for (const f of files) {
+      if (f.startsWith(oldPrefix)) {
+        const newFileName = newPrefix + f.slice(oldPrefix.length);
+        await rename(join(phasesDir, newDirName, f), join(phasesDir, newDirName, newFileName));
+        renamedFiles.push({ from: f, to: newFileName });
+      }
+    }
+  }
+
+  return { renamedDirs, renamedFiles };
+}
+
+// ─── updateRoadmapAfterPhaseRemoval ────────────────────────────────────
+
+/**
+ * Decrement integer phase number while skipping non-renumbered ranges. Mirrors
+ * `decrementRoadmapPhaseNumber` in phase.cjs lines 860-864.
+ *
+ * Skips when:
+ *   • not an integer
+ *   • num <= removedInt (already-renumbered phases stay put)
+ *   • num >= 999 (backlog/parked-idea numbering range)
+ *
+ * Returns the original raw string when the guards trip so the regex pass
+ * leaves dates and unrelated numerics intact.
+ */
+function decrementRoadmapPhaseNumber(raw: string, removedInt: number): string {
+  const num = parseInt(raw, 10);
+  if (!Number.isInteger(num) || num <= removedInt || num >= 999) return raw;
+  return String(num - 1);
+}
+
+/**
+ * Decrement integer or decimal phase token (e.g. "5" or "5.2"). Mirrors
+ * `decrementRoadmapPhaseToken` in phase.cjs lines 866-872 — preserves the
+ * decimal suffix when present and applies the same guards.
+ */
+function decrementRoadmapPhaseToken(raw: string, removedInt: number): string {
+  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] || ''}`;
+}
+
+/**
+ * Decrement zero-padded phase number while preserving the original pad width.
+ * Mirrors `decrementRoadmapPaddedPhaseNumber` in phase.cjs lines 874-878.
+ */
+function decrementRoadmapPaddedPhaseNumber(raw: string, removedInt: number): string {
+  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 subsequent integer phases.
+ *
+ * Port of updateRoadmapAfterPhaseRemoval from phase.cjs lines 880-922.
+ * Uses readModifyWriteRoadmapMd for atomic writes.
+ *
+ * The renumbering pass uses **5 targeted regex replacements** (not a loop)
+ * because the loop approach is dangerous:
+ *   • It can match YYYY-MM-DD substrings and corrupt dates (bug-2435).
+ *   • It can rename backlog phases (999.x) that should stay frozen (bug-2434).
+ *   • It can renumber the same phase multiple times if the regex matches
+ *     overlap (bug-3355 — phase 7 → 6 → 5 → ...).
+ *
+ * The CJS pattern uses negative lookbehind/ahead on the padded-prefix regex
+ * to skip dates and decrement helpers that guard against `num >= 999`. Keep
+ * this implementation byte-for-byte in lockstep with phase.cjs:880-922 —
+ * deviations are how the three bugs above slipped in.
+ *
+ * @param projectDir - Project root directory
+ * @param targetPhase - Phase identifier that was removed
+ * @param isDecimal - Whether the removed phase was a decimal phase
+ * @param removedInt - The integer part of the removed phase
+ */
+async function updateRoadmapAfterPhaseRemoval(
+  projectDir: string,
+  targetPhase: string,
+  isDecimal: boolean,
+  removedInt: number,
+  workstream?: string,
+): Promise<void> {
+  await readModifyWriteRoadmapMd(projectDir, (content) => {
+    const escaped = escapeRegex(targetPhase);
+
+    // Remove the phase section (header + body until next phase header or end).
+    //
+    // #3601: the end-of-section lookahead is DEPTH-AWARE. The named capture
+    // (?<h>#{2,4}) records the hash count of the header being removed and the
+    // lookahead requires the same depth via \k<h>(?!#). Two contracts are
+    // preserved:
+    //
+    //   (#3601 case) Remove `### Phase 2:` and stop at `### Phase 2.1:` —
+    //   Phase 2.1 is a peer-level decimal phase (depth 3) and must survive.
+    //
+    //   (#3355 case) Remove `### Phase 27:` and CONTINUE past
+    //   `#### Phase 27.1:` (depth 4 — 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. `[^\n:]+` accepts numeric, decimal, AND
+    // custom phase IDs (PROJ-42) as terminators.
+    content = content.replace(
+      new RegExp(
+        `\\n?(?<h>#{2,4})\\s*Phase\\s+${escaped}\\s*:[\\s\\S]*?(?=\\n\\k<h>(?!#)\\s+Phase\\s+[^\\n:]+\\s*:|$)`,
+        'i',
+      ),
+      '',
+    );
+
+    // Remove checkbox lines referencing the phase
+    content = content.replace(
+      new RegExp(`\\n?-\\s*\\[[ x]\\]\\s*.*Phase\\s+${escaped}[:\\s][^\\n]*`, 'gi'),
+      '',
+    );
+
+    // Remove table rows referencing the phase
+    content = content.replace(
+      new RegExp(`\\n?\\|\\s*${escaped}\\.?\\s[^|]*\\|[^\\n]*`, 'gi'),
+      '',
+    );
+
+    if (!isDecimal) {
+      // Phase headers: ### Phase N:  /  ### Phase N.M:
+      content = content.replace(
+        /(#{2,4}\s*Phase\s+)(\d+(?:\.\d+)?)(\s*:)/gi,
+        (_match, prefix: string, num: string, suffix: string) =>
+          `${prefix}${decrementRoadmapPhaseToken(num, removedInt)}${suffix}`,
+      );
+
+      // Checkbox-list summary references: `- [ ] Phase N:`
+      content = content.replace(
+        /(-\s*\[[ x]\]\s*.*?Phase\s+)(\d+)(\s*:|\s+)/gi,
+        (_match, prefix: string, num: string, suffix: string) =>
+          `${prefix}${decrementRoadmapPhaseNumber(num, removedInt)}${suffix}`,
+      );
+
+      // Table-row phase numbers: `| N. ` — bare integer in a cell.
+      content = content.replace(
+        /(\|\s*)(\d+)(\.\s)/g,
+        (_match, prefix: string, num: string, suffix: string) =>
+          `${prefix}${decrementRoadmapPhaseNumber(num, removedInt)}${suffix}`,
+      );
+
+      // Padded plan references: NN-NN (optionally followed by an arbitrary
+      // kebab-case slug, then -PLAN.md / -SUMMARY.md).
+      //
+      // #2435: negative lookbehind `(?<![0-9-])` and negative lookahead
+      // `(?![0-9-])` exclude YYYY-MM-DD substrings.
+      //
+      // #3602: the original pattern only allowed a compact `-(PLAN|SUMMARY).md`
+      // immediately after the plan number; a slug between the number and the
+      // `-PLAN.md` / `-SUMMARY.md` suffix (e.g.
+      // `07-01-cherry-pick-foundation-PLAN.md`) made the lookahead fail and
+      // left the stale `07-01-` prefix in ROADMAP text while the on-disk file
+      // was already renumbered 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: string, planNum: string) =>
+          `${decrementRoadmapPaddedPhaseNumber(phaseNum, removedInt)}-${planNum}`,
+      );
+
+      // Depends-on references — two bold-colon variants in the wild.
+      content = content.replace(
+        /(\*\*Depends on\*\*\s*:\s*Phase\s+)(\d+(?:\.\d+)?)\b/gi,
+        (_match, prefix: string, num: string) =>
+          `${prefix}${decrementRoadmapPhaseToken(num, removedInt)}`,
+      );
+      content = content.replace(
+        /(Depends on:\*\*\s*Phase\s+)(\d+(?:\.\d+)?)\b/gi,
+        (_match, prefix: string, num: string) =>
+          `${prefix}${decrementRoadmapPhaseToken(num, removedInt)}`,
+      );
+    }
+
+    return content;
+  }, workstream);
+}
+
+// ─── phaseRemove handler ───────────────────────────────────────────────
+
+/**
+ * Query handler for phase.remove.
+ *
+ * Port of cmdPhaseRemove from phase.cjs lines 597-661.
+ * Deletes phase directory, renumbers subsequent phases on disk,
+ * updates ROADMAP.md (removes section + renumbers), and decrements
+ * STATE.md total_phases count.
+ *
+ * @param args - args[0]: targetPhase (required), args[1]: '--force' (optional)
+ * @param projectDir - Project root directory
+ * @returns QueryResult with { removed, directory_deleted, renamed_directories, renamed_files, roadmap_updated, state_updated }
+ */
+export const phaseRemove: QueryHandler = async (args, projectDir, workstream) => {
+  let force = false;
+  const positional: string[] = [];
+  for (const token of args) {
+    if (token === '--force') {
+      force = true;
+      continue;
+    }
+    if (token.startsWith('--')) {
+      throw new GSDError(`phase remove does not support ${token}`, ErrorClassification.Validation);
+    }
+    positional.push(token);
+  }
+
+  if (positional.length > 1) {
+    throw new GSDError('phase remove accepts exactly one phase number', ErrorClassification.Validation);
+  }
+
+  const targetPhase = positional[0];
+  if (!targetPhase) {
+    throw new GSDError('phase number required for phase remove', ErrorClassification.Validation);
+  }
+  assertNoNullBytes(targetPhase, 'targetPhase');
+
+  const paths = planningPaths(projectDir, workstream);
+  const phasesDir = paths.phases;
+
+  if (!existsSync(paths.roadmap)) {
+    throw new GSDError('ROADMAP.md not found', ErrorClassification.Validation);
+  }
+
+  const normalized = normalizePhaseName(targetPhase);
+  const isDecimal = targetPhase.includes('.');
+
+  // Find target directory
+  const entries = await readdir(phasesDir, { withFileTypes: true });
+  const dirs = entries.filter(e => e.isDirectory()).map(e => e.name);
+  const targetDir = dirs.find(d => phaseTokenMatches(d, normalized)) ?? null;
+  if (!targetDir) {
+    throw new GSDError(`Phase ${targetPhase} not found`, ErrorClassification.Validation);
+  }
+
+  // Guard against removing executed work
+  if (!force) {
+    const files = await readdir(join(phasesDir, targetDir));
+    const summaries = files.filter(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md');
+    if (summaries.length > 0) {
+      throw new GSDError(
+        `Phase ${targetPhase} has ${summaries.length} executed plan(s). Use --force to remove anyway.`,
+        ErrorClassification.Validation,
+      );
+    }
+  }
+
+  // Delete directory
+  await rm(join(phasesDir, targetDir), { recursive: true, force: true });
+
+  // Renumber subsequent phases on disk
+  let renamedDirs: Array<{ from: string; to: string }> = [];
+  let renamedFiles: Array<{ from: string; to: string }> = [];
+  try {
+    let renamed: { renamedDirs: Array<{ from: string; to: string }>; renamedFiles: Array<{ from: string; to: string }> };
+    if (isDecimal) {
+      const parts = normalized.split('.');
+      if (parts.length < 2 || !parts[1]) {
+        throw new GSDError(`Invalid decimal phase identifier: ${targetPhase}`, ErrorClassification.Validation);
+      }
+      const decimalPart = parseInt(parts[1], 10);
+      if (isNaN(decimalPart)) {
+        throw new GSDError(`Invalid decimal part in phase: ${targetPhase}`, ErrorClassification.Validation);
+      }
+      renamed = await renameDecimalPhases(phasesDir, parts[0], decimalPart);
+    } else {
+      renamed = await renameIntegerPhases(phasesDir, parseInt(normalized, 10));
+    }
+    renamedDirs = renamed.renamedDirs;
+    renamedFiles = renamed.renamedFiles;
+  } catch { /* intentionally empty — renaming is best-effort */ }
+
+  // Update ROADMAP.md
+  await updateRoadmapAfterPhaseRemoval(projectDir, targetPhase, isDecimal, parseInt(normalized, 10), workstream);
+
+  // Update STATE.md: decrement total_phases
+  let stateUpdated = false;
+  const statePath = paths.state;
+  if (existsSync(statePath)) {
+    const lockPath = await acquireStateLock(statePath);
+    try {
+      let stateContent = await readFile(statePath, 'utf-8');
+
+      // Decrement total_phases in frontmatter
+      const totalPhasesMatch = stateContent.match(/total_phases:\s*(\d+)/);
+      if (totalPhasesMatch) {
+        const oldTotal = parseInt(totalPhasesMatch[1], 10);
+        stateContent = stateContent.replace(
+          /total_phases:\s*\d+/,
+          `total_phases: ${oldTotal - 1}`,
+        );
+      }
+
+      // Decrement "of N" pattern in body (e.g., "Plan: 2 of 3")
+      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`,
+        );
+      }
+
+      // Also try stateReplaceField for "Total Phases" field
+      const totalRaw = stateExtractField(stateContent, 'Total Phases');
+      if (totalRaw) {
+        const replaced = stateReplaceField(stateContent, 'Total Phases', String(parseInt(totalRaw, 10) - 1));
+        if (replaced) stateContent = replaced;
+      }
+
+      await writeFile(statePath, stateContent, 'utf-8');
+      stateUpdated = true;
+    } finally {
+      await releaseStateLock(lockPath);
+    }
+  }
+
+  return {
+    data: {
+      removed: targetPhase,
+      directory_deleted: targetDir,
+      renamed_directories: renamedDirs,
+      renamed_files: renamedFiles,
+      roadmap_updated: true,
+      state_updated: stateUpdated,
+    },
+  };
+};
+
+// ─── updatePerformanceMetricsSection ───────────────────────────────────────
+
+/**
+ * Update the Performance Metrics section in STATE.md content.
+ *
+ * Port of updatePerformanceMetricsSection from state.cjs lines 1125-1156.
+ * Updates "Total plans completed" counter and upserts a row in the By Phase table.
+ *
+ * @param content - STATE.md content
+ * @param phaseNum - Phase number being completed
+ * @param planCount - Total number of plans in the phase
+ * @param summaryCount - Number of completed summaries
+ * @returns Modified content
+ */
+function updatePerformanceMetricsSection(
+  content: string,
+  phaseNum: string,
+  planCount: number,
+  summaryCount: number,
+): string {
+  // Update Velocity: Total plans completed
+  const totalMatch = content.match(/Total plans completed:\s*(\d+|\[N\])/);
+  const prevTotal = totalMatch && totalMatch[1] !== '[N]' ? parseInt(totalMatch[1], 10) : 0;
+  const newTotal = prevTotal + summaryCount;
+  content = content.replace(
+    /Total plans completed:\s*(\d+|\[N\])/,
+    `Total plans completed: ${newTotal}`,
+  );
+
+  // Update By Phase table — upsert row for this phase
+  const byPhaseTablePattern = /(\|\s*Phase\s*\|\s*Plans\s*\|\s*Total\s*\|\s*Avg\/Plan\s*\|[ \t]*\n\|(?:[- :\t]+\|)+[ \t]*\n)((?:[ \t]*\|[^\n]*\n)*)(?=\n|$)/i;
+  const byPhaseMatch = content.match(byPhaseTablePattern);
+  if (byPhaseMatch) {
+    let tableBody = byPhaseMatch[2].trim();
+    const phaseRowPattern = new RegExp(`^\\|\\s*${escapeRegex(String(phaseNum))}\\s*\\|.*$`, 'm');
+    const newRow = `| ${phaseNum} | ${summaryCount} | - | - |`;
+
+    if (phaseRowPattern.test(tableBody)) {
+      // Update existing row
+      tableBody = tableBody.replace(new RegExp(`^\\|\\s*${escapeRegex(String(phaseNum))}\\s*\\|.*$`, 'm'), newRow);
+    } else {
+      // Remove placeholder row and add new row
+      tableBody = tableBody.replace(/^\|\s*-\s*\|\s*-\s*\|\s*-\s*\|\s*-\s*\|$/m, '').trim();
+      tableBody = tableBody ? tableBody + '\n' + newRow : newRow;
+    }
+
+    content = content.replace(byPhaseTablePattern, `$1${tableBody}\n`);
+  }
+
+  return content;
+}
+
+// ─── phaseComplete handler ────────────────────────────────────────────────
+
+/**
+ * Query handler for phase.complete.
+ *
+ * Port of cmdPhaseComplete from phase.cjs lines 663-932.
+ * Marks a phase as done — updates ROADMAP.md (checkbox, progress table,
+ * plan count, plan checkboxes), REQUIREMENTS.md (requirement checkboxes,
+ * traceability table), and STATE.md (current phase, status, progress,
+ * performance metrics) atomically with per-file locks.
+ *
+ * @param args - args[0]: phaseNum (required)
+ * @param projectDir - Project root directory
+ * @returns QueryResult with completion details and warnings
+ */
+export const phaseComplete: QueryHandler = async (args, projectDir, workstream) => {
+  const phaseNum = args[0];
+  if (!phaseNum) {
+    throw new GSDError('phase number required for phase complete', ErrorClassification.Validation);
+  }
+  assertNoNullBytes(phaseNum, 'phaseNum');
+
+  const paths = planningPaths(projectDir, workstream);
+  const today = new Date().toISOString().split('T')[0];
+
+  // Step A: Validate phase exists and get info
+  const phaseInfo = await findPhaseDir(projectDir, phaseNum, workstream);
+  if (!phaseInfo) {
+    throw new GSDError(`Phase ${phaseNum} not found`, ErrorClassification.Validation);
+  }
+
+  const phaseDir = phaseInfo.dirPath;
+  let phaseFiles: string[];
+  try {
+    phaseFiles = await readdir(phaseDir);
+  } catch {
+    phaseFiles = [];
+  }
+
+  const plans = phaseFiles.filter(f => f.endsWith('-PLAN.md') || f === 'PLAN.md');
+  const summaries = phaseFiles.filter(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md');
+  const planCount = plans.length;
+  const summaryCount = summaries.length;
+  let requirementsUpdated = false;
+
+  // Step B: Check for verification warnings (non-blocking)
+  const warnings: string[] = [];
+  for (const file of phaseFiles.filter(f => f.includes('-UAT') && f.endsWith('.md'))) {
+    try {
+      const content = await readFile(join(phaseDir, file), 'utf-8');
+      if (/result: pending/.test(content)) warnings.push(`${file}: has pending tests`);
+      if (/result: blocked/.test(content)) warnings.push(`${file}: has blocked tests`);
+      if (/status: partial/.test(content)) warnings.push(`${file}: testing incomplete (partial)`);
+      if (/status: diagnosed/.test(content)) warnings.push(`${file}: has diagnosed gaps`);
+    } catch { /* intentionally empty */ }
+  }
+  for (const file of phaseFiles.filter(f => f.includes('-VERIFICATION') && f.endsWith('.md'))) {
+    try {
+      const content = await readFile(join(phaseDir, file), 'utf-8');
+      if (/status: human_needed/.test(content)) warnings.push(`${file}: needs human verification`);
+      if (/status: gaps_found/.test(content)) warnings.push(`${file}: has unresolved gaps`);
+    } catch { /* intentionally empty */ }
+  }
+
+  // Step C: Update ROADMAP.md atomically
+  if (existsSync(paths.roadmap)) {
+    await readModifyWriteRoadmapMd(projectDir, async (roadmapContent) => {
+      // Padding-tolerant fragment so a padded input like "02.7" still matches
+      // un-padded ROADMAP prose ("### Phase 2.7:").  CJS routes every phase-
+      // number ROADMAP regex through phaseMarkdownRegexSource (#3537) —
+      // mirror that contract here so phase.complete with the padded form
+      // produces the same ROADMAP as the un-padded form.
+      const phaseEscaped = phaseMarkdownRegexSource(phaseNum);
+
+      // Checkbox: - [ ] Phase N: -> - [x] Phase N: (...completed DATE)
+      // CJS parity (phase.cjs): direct replace, NOT scoped through
+      // replaceInCurrentMilestone. Same reasoning as the plan-count
+      // update below — milestone wrapped in <details> would otherwise be
+      // skipped (bug-2005).
+      const checkboxPattern = new RegExp(
+        `(-\\s*\\[)[ ](\\]\\s*.*Phase\\s+${phaseEscaped}[:\\s][^\\n]*)`,
+        'i',
+      );
+      roadmapContent = roadmapContent.replace(checkboxPattern, `$1x$2 (completed ${today})`);
+
+      // Progress table: update Status to Complete, add date
+      const tableRowPattern = new RegExp(
+        `^(\\|\\s*${phaseEscaped}\\.?\\s[^|]*(?:\\|[^\\n]*))$`,
+        'im',
+      );
+      roadmapContent = roadmapContent.replace(tableRowPattern, (fullRow) => {
+        const cells = fullRow.split('|').slice(1, -1);
+        if (cells.length === 5) {
+          cells[2] = ` ${summaryCount}/${planCount} `;
+          cells[3] = ' Complete    ';
+          cells[4] = ` ${today} `;
+        } else if (cells.length === 4) {
+          cells[1] = ` ${summaryCount}/${planCount} `;
+          cells[2] = ' Complete    ';
+          cells[3] = ` ${today} `;
+        }
+        return '|' + cells.join('|') + '|';
+      });
+
+      // Update plan count in phase section.
+      // CJS parity (phase.cjs:1076-1083): direct replace, NOT scoped through
+      // replaceInCurrentMilestone. Scoping to "after last </details>" fails
+      // when the current milestone itself is wrapped in <details open>...
+      // </details> — there's no content after the close tag, so the regex
+      // never matches and **Plans:** stays at 0/N (bug-2005).
+      const planCountPattern = new RegExp(
+        `(#{2,4}\\s*Phase\\s+${phaseEscaped}(?:(?!\\n#{2,4})[\\s\\S])*?\\*\\*Plans:\\*\\*[ \\t]*)[^\\n]+`,
+        'i',
+      );
+      roadmapContent = roadmapContent.replace(
+        planCountPattern,
+        `$1${summaryCount}/${planCount} plans complete`,
+      );
+
+      // Mark completed plan checkboxes
+      for (const summaryFile of summaries) {
+        const planId = summaryFile.replace('-SUMMARY.md', '').replace('SUMMARY.md', '');
+        if (!planId) continue;
+        const planEscaped = escapeRegex(planId);
+        const planCheckboxPattern = new RegExp(
+          `(-\\s*\\[) (\\]\\s*(?:\\*\\*)?${planEscaped}(?:\\*\\*)?)`,
+          'i',
+        );
+        roadmapContent = roadmapContent.replace(planCheckboxPattern, '$1x$2');
+      }
+
+      // Step D: Update REQUIREMENTS.md
+      const reqPath = paths.requirements;
+      if (existsSync(reqPath)) {
+        const currentMilestoneRoadmap = await extractCurrentMilestone(roadmapContent, projectDir);
+        const phaseSectionMatch = currentMilestoneRoadmap.match(
+          new RegExp(`(#{2,4}\\s*Phase\\s+${phaseEscaped}[:\\s][\\s\\S]*?)(?=#{2,4}\\s*Phase\\s+|$)`, 'i'),
+        );
+
+        const sectionText = phaseSectionMatch ? phaseSectionMatch[1] : '';
+        const reqMatch = sectionText.match(/\*\*Requirements\*?\*?:?\s*([^\n]+)/i);
+
+        let reqContent = await readFile(reqPath, 'utf-8');
+        let reqContentChanged = false;
+
+        if (reqMatch) {
+          const reqIds = reqMatch[1].replace(/[[\]]/g, '').split(/[,\s]+/).map(r => r.trim()).filter(Boolean);
+
+          for (const reqId of reqIds) {
+            const reqEscaped = escapeRegex(reqId);
+            const before = reqContent;
+            // Update checkbox: - [ ] **REQ-ID** -> - [x] **REQ-ID**
+            reqContent = reqContent.replace(
+              new RegExp(`(-\\s*\\[)[ ](\\]\\s*\\*\\*${reqEscaped}\\*\\*)`, 'gi'),
+              '$1x$2',
+            );
+            // Update traceability table: Pending/In Progress -> Complete
+            reqContent = reqContent.replace(
+              new RegExp(`(\\|\\s*${reqEscaped}\\s*\\|[^|]+\\|)\\s*(?:Pending|In Progress)\\s*(\\|)`, 'gi'),
+              '$1 Complete $2',
+            );
+            if (reqContent !== before) reqContentChanged = true;
+          }
+        }
+
+        // Bug #2526 parity (phase.cjs:1140-1167): independent of whether the
+        // roadmap declared a Requirements: line, scan the REQUIREMENTS.md
+        // body for `**REQ-ID**` references and compare against the IDs that
+        // actually appear in the Traceability table.  Surface every body
+        // ID that has no traceability row so the operator can keep the
+        // table in sync.
+        const bodyReqIds: string[] = [];
+        const bodyReqPattern = /\*\*([A-Z][A-Z0-9]*-\d+)\*\*/g;
+        let bodyMatch: RegExpExecArray | null;
+        while ((bodyMatch = bodyReqPattern.exec(reqContent)) !== null) {
+          if (!bodyReqIds.includes(bodyMatch[1]!)) bodyReqIds.push(bodyMatch[1]!);
+        }
+
+        const traceabilityHeadingMatch = reqContent.match(/^#{1,6}\s+Traceability\b/im);
+        const traceabilitySection = traceabilityHeadingMatch
+          ? reqContent.slice(traceabilityHeadingMatch.index!)
+          : '';
+        const tableReqIds = new Set<string>();
+        const tableRowPattern = /^\|\s*([A-Z][A-Z0-9]*-\d+)\s*\|/gm;
+        let tableMatch: RegExpExecArray | null;
+        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`,
+          );
+        }
+
+        if (reqContentChanged) {
+          await writeFile(reqPath, reqContent, 'utf-8');
+          requirementsUpdated = true;
+        }
+      }
+
+      return roadmapContent;
+    }, workstream);
+  }
+
+  // Step E: Find next phase — filesystem first, then ROADMAP.md fallback
+  let nextPhaseNum: string | null = null;
+  let nextPhaseName: string | null = null;
+  let isLastPhase = true;
+  // Tracks whether the completed phase belongs to the primary milestone in STATE.md.
+  // When false (parallel-milestone case, Bug #2676), the milestone filter is bypassed
+  // for next-phase detection so phases from the same secondary milestone are visible.
+  let completedPhaseInPrimaryMilestone = true;
+
+  try {
+    const isDirInMilestone = await getMilestonePhaseFilter(projectDir, workstream);
+    const entries = await readdir(paths.phases, { withFileTypes: true });
+    const allDirs = entries.filter(e => e.isDirectory()).map(e => e.name);
+
+    // Guard: if the completed phase's directory is not in the current-milestone filter
+    // set, the filter was built from a different (primary) milestone in STATE.md.
+    // In that case skip the filter so we can find the true next phase on disk.
+    // This handles parallel-milestone workflows where STATE.md's `milestone:` field
+    // points at the primary milestone but the phase being completed belongs to a
+    // secondary in-flight milestone. (Bug #2676)
+    const completedDirInFilter = allDirs.some((d) => {
+      const dm = d.match(/^(\d+[A-Z]?(?:\.\d+)*)-?/i);
+      return dm && comparePhaseNum(dm[1], phaseNum) === 0 && isDirInMilestone(d);
+    });
+    completedPhaseInPrimaryMilestone = completedDirInFilter;
+    const effectiveFilter = completedDirInFilter ? isDirInMilestone : (_d: string) => true;
+
+    const dirs = allDirs
+      .filter(effectiveFilter)
+      .sort((a, b) => comparePhaseNum(a, b));
+
+    for (const dir of dirs) {
+      const dm = dir.match(/^(\d+[A-Z]?(?:\.\d+)*)-?(.*)/i);
+      if (dm) {
+        // Bug #2129 parity: skip backlog phases (999.x). They are parked
+        // ideas with reserved numbering, not part of the active sequence.
+        // Without this, completing phase 2 in a project that has a 999.1
+        // backlog directory would jump next_phase to 999.1 instead of the
+        // intended Phase 3 from ROADMAP.
+        if (/^999(?:\.|$)/.test(dm[1]!)) continue;
+        if (comparePhaseNum(dm[1], phaseNum) > 0) {
+          nextPhaseNum = dm[1];
+          nextPhaseName = dm[2] || null;
+          isLastPhase = false;
+          break;
+        }
+      }
+    }
+  } catch { /* intentionally empty */ }
+
+  // Fallback: check ROADMAP.md for phases not yet scaffolded.
+  // When the completed phase is from a parallel (non-primary) milestone, scan the
+  // full ROADMAP rather than the primary-milestone slice so 41.3 is visible when
+  // completing 41.2 for a secondary milestone. (Bug #2676)
+  if (isLastPhase && existsSync(paths.roadmap)) {
+    try {
+      const roadmapContent = await readFile(paths.roadmap, 'utf-8');
+      const roadmapForPhases = completedPhaseInPrimaryMilestone
+        ? await extractCurrentMilestone(roadmapContent, projectDir)
+        : roadmapContent;
+      const phasePattern = /#{2,4}\s*Phase\s+(\d+[A-Z]?(?:\.\d+)*)\s*:\s*([^\n]+)/gi;
+      let pm: RegExpExecArray | null;
+      while ((pm = phasePattern.exec(roadmapForPhases)) !== null) {
+        if (comparePhaseNum(pm[1], phaseNum) > 0) {
+          nextPhaseNum = pm[1];
+          nextPhaseName = pm[2].replace(/\(INSERTED\)/i, '').trim().toLowerCase().replace(/\s+/g, '-');
+          isLastPhase = false;
+          break;
+        }
+      }
+    } catch { /* intentionally empty */ }
+  }
+
+  // Step F: Update STATE.md atomically
+  let stateUpdated = false;
+  if (existsSync(paths.state)) {
+    const lockPath = await acquireStateLock(paths.state);
+    try {
+      const rawState = await readFile(paths.state, 'utf-8');
+
+      // Split into frontmatter and body to prevent field replacement from
+      // matching YAML keys (e.g., `status:` in frontmatter vs `Status:` in body).
+      // Pattern 11: Strip frontmatter before modifier (from Phase 11 decisions).
+      const fmMatch = rawState.match(/^(---\r?\n[\s\S]*?\r?\n---)\s*/);
+      let frontmatter = fmMatch ? fmMatch[1] : '';
+      let body = fmMatch ? rawState.slice(fmMatch[0].length) : rawState;
+
+      // Update Current Phase — preserve "X of Y (Name)" compound format
+      const phaseValue = nextPhaseNum || phaseNum;
+      const existingPhaseField = stateExtractField(body, 'Current Phase')
+        || stateExtractField(body, '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}`;
+        }
+      }
+      body = stateReplaceFieldWithFallback(body, 'Current Phase', 'Phase', newPhaseValue);
+
+      // Update Status
+      body = stateReplaceFieldWithFallback(body, 'Status', null,
+        isLastPhase ? 'Milestone complete' : 'Ready to plan');
+
+      // Update Current Plan
+      body = stateReplaceFieldWithFallback(body, 'Current Plan', 'Plan', 'Not started');
+
+      // Update Last Activity
+      body = stateReplaceFieldWithFallback(body, 'Last Activity', 'Last activity', today);
+
+      // Update Performance Metrics section (operates on body only)
+      body = updatePerformanceMetricsSection(body, phaseNum, planCount, summaryCount);
+
+      // ── Root cause 1 fix: derive completed_phases from ROADMAP, not blind increment ──
+      // Read the freshly-updated ROADMAP (after Step C) to count Complete rows.
+      // This makes phase.complete idempotent: running it twice on the same phase
+      // produces the same completed_phases value.
+      let derivedCompletedPhases: number | null = null;
+      let derivedTotalPhases: number | null = null;
+      let derivedTotalPlans: number | null = null;
+      if (existsSync(paths.roadmap)) {
+        try {
+          const freshRoadmap = await readFile(paths.roadmap, 'utf-8');
+          // Count Complete rows in the progress table (Status column = "Complete")
+          const tableCompletePattern = /\|\s*\d+[A-Z]?\S*\s*\|[^|]*\|\s*Complete\s*\|/gi;
+          const completeMatches = freshRoadmap.match(tableCompletePattern);
+          derivedCompletedPhases = completeMatches ? completeMatches.length : null;
+
+          // Count total phase rows in progress table (header + separator + data rows)
+          // Identify the progress table by looking for Phase|Plans|Status|Completed header
+          const progressTableMatch = freshRoadmap.match(
+            /\|\s*Phase\s*\|\s*Plans\s*\|\s*Status\s*\|\s*Completed\s*\|(.*\n)*?(?:\n|$)/i,
+          );
+          if (progressTableMatch) {
+            const tableText = progressTableMatch[0];
+            const dataRowPattern = /^\|\s*\d+[A-Z]?\S*\s*\|/gm;
+            const dataRows = tableText.match(dataRowPattern);
+            derivedTotalPhases = dataRows ? dataRows.length : null;
+          }
+
+          // Sum plan counts from M/N or 0/N columns in the progress table
+          let totalPlansSum = 0;
+          const planCellPattern = /\|\s*\d+[A-Z]?\S*\s*\|\s*(\d+)\/(\d+)\s*\|/gi;
+          let pm: RegExpExecArray | null;
+          while ((pm = planCellPattern.exec(freshRoadmap)) !== null) {
+            totalPlansSum += parseInt(pm[2], 10);
+          }
+          if (totalPlansSum > 0) derivedTotalPlans = totalPlansSum;
+        } catch { /* intentionally empty — fall through to existing values */ }
+      }
+
+      // Count completed plans from all SUMMARY files across phase dirs
+      let derivedCompletedPlans: number | null = null;
+      try {
+        const phaseEntries = await readdir(paths.phases, { withFileTypes: true });
+        let summaryTotal = 0;
+        for (const entry of phaseEntries) {
+          if (!entry.isDirectory()) continue;
+          try {
+            const files = await readdir(join(paths.phases, entry.name));
+            summaryTotal += files.filter(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md').length;
+          } catch { /* intentionally empty */ }
+        }
+        derivedCompletedPlans = summaryTotal;
+      } catch { /* intentionally empty */ }
+
+      // ── Root cause 2 fix: update all stale frontmatter fields ──
+
+      // completed_phases — derived from ROADMAP (idempotent)
+      if (derivedCompletedPhases !== null && frontmatter.includes('completed_phases:')) {
+        frontmatter = frontmatter.replace(
+          /completed_phases:\s*\d+/,
+          `completed_phases: ${derivedCompletedPhases}`,
+        );
+      }
+
+      // total_phases — keep in sync with ROADMAP
+      if (derivedTotalPhases !== null && frontmatter.includes('total_phases:')) {
+        frontmatter = frontmatter.replace(
+          /total_phases:\s*\d+/,
+          `total_phases: ${derivedTotalPhases}`,
+        );
+      }
+
+      // total_plans — derived from ROADMAP plan column sums
+      if (derivedTotalPlans !== null && frontmatter.includes('total_plans:')) {
+        frontmatter = frontmatter.replace(
+          /total_plans:\s*\d+/,
+          `total_plans: ${derivedTotalPlans}`,
+        );
+      }
+
+      // completed_plans — count of SUMMARY files on disk
+      if (derivedCompletedPlans !== null && frontmatter.includes('completed_plans:')) {
+        frontmatter = frontmatter.replace(
+          /completed_plans:\s*\d+/,
+          `completed_plans: ${derivedCompletedPlans}`,
+        );
+      }
+
+      // percent — recompute from fresh derived values
+      const effectiveCompleted = derivedCompletedPhases ?? parseInt(frontmatter.match(/completed_phases:\s*(\d+)/)?.[1] ?? '0', 10);
+      const effectiveTotal = derivedTotalPhases ?? parseInt(frontmatter.match(/total_phases:\s*(\d+)/)?.[1] ?? '0', 10);
+      if (effectiveTotal > 0 && frontmatter.includes('percent:')) {
+        const newPercent = Math.round((effectiveCompleted / effectiveTotal) * 100);
+        frontmatter = frontmatter.replace(/(percent:\s*)\d+/, `$1${newPercent}`);
+      }
+
+      // last_updated — refresh to current timestamp
+      const nowIso = new Date().toISOString();
+      if (frontmatter.includes('last_updated:')) {
+        frontmatter = frontmatter.replace(/last_updated:\s*\S+/, `last_updated: ${nowIso}`);
+      }
+
+      // stopped_at — set to phase completion message
+      const stoppedAtValue = isLastPhase
+        ? `Milestone complete (Phase ${phaseNum} was final phase)`
+        : `Phase ${phaseNum} complete (${summaryCount}/${planCount}) — ready to discuss Phase ${nextPhaseNum}`;
+      if (frontmatter.includes('stopped_at:')) {
+        frontmatter = frontmatter.replace(/stopped_at:\s*.+/, `stopped_at: ${stoppedAtValue}`);
+      } else {
+        // Insert stopped_at before closing ---
+        frontmatter = frontmatter.replace(/(---\s*)$/, `stopped_at: ${stoppedAtValue}\n$1`);
+      }
+
+      // ── Root cause 2 fix: update body Current focus ──
+      const focusValue = isLastPhase
+        ? 'Milestone complete'
+        : (nextPhaseName
+          ? `Phase ${nextPhaseNum} — ${nextPhaseName.replace(/-/g, ' ')}`
+          : `Phase ${nextPhaseNum}`);
+      const focusPattern = /(\*\*Current focus:\*\*\s*).*/i;
+      if (focusPattern.test(body)) {
+        body = body.replace(focusPattern, (_m: string, prefix: string) => `${prefix}${focusValue}`);
+      }
+
+      // Update frontmatter status field
+      frontmatter = frontmatter.replace(
+        /status:\s*.+/,
+        `status: ${isLastPhase ? 'milestone_complete' : 'ready_to_plan'}`,
+      );
+
+      // Reassemble and write
+      const stateContent = frontmatter + '\n\n' + body;
+      await writeFile(paths.state, stateContent, 'utf-8');
+      stateUpdated = true;
+    } finally {
+      await releaseStateLock(lockPath);
+    }
+  }
+
+  // Step F2: Auto-prune STATE.md decisions when `workflow.auto_prune_state`
+  // is true. Mirrors CJS cmdPhaseComplete (bin/lib/phase.cjs:1378-1390) which
+  // calls cmdStatePrune({keepRecent:'3', dryRun:false, silent:true}). Without
+  // this, completing phase N with auto_prune_state=true leaves stale [Phase
+  // 1..N-3] decisions in STATE.md forever. (#2087)
+  let autoPruned = false;
+  try {
+    if (existsSync(paths.config)) {
+      const rawConfig = JSON.parse(await readFile(paths.config, 'utf-8')) as Record<string, unknown>;
+      const wf = rawConfig.workflow as Record<string, unknown> | undefined;
+      if (wf && wf.auto_prune_state === true && existsSync(paths.state)) {
+        const { statePrune } = await import('./state-mutation.js');
+        await statePrune(['--keep-recent', '3', '--silent'], projectDir, workstream);
+        autoPruned = true;
+      }
+    }
+  } catch { /* best-effort, matches CJS */ }
+
+  // Step G: Return result
+  return {
+    data: {
+      completed_phase: phaseNum,
+      phase_name: phaseInfo.phaseName,
+      plans_executed: `${summaryCount}/${planCount}`,
+      next_phase: nextPhaseNum,
+      next_phase_name: nextPhaseName,
+      is_last_phase: isLastPhase,
+      date: today,
+      roadmap_updated: existsSync(paths.roadmap),
+      state_updated: stateUpdated,
+      requirements_updated: requirementsUpdated,
+      auto_pruned: autoPruned,
+      warnings,
+      has_warnings: warnings.length > 0,
+    },
+  };
+};
+
+// ─── phasesClear handler ──────────────────────────────────────────────────
+
+/**
+ * Query handler for phases.clear.
+ *
+ * Port of cmdPhasesClear from milestone.cjs lines 250-277.
+ * Deletes all phase directories except 999.x backlog phases.
+ * Requires --confirm flag to proceed.
+ *
+ * @param args - args[0]: '--confirm' to proceed (optional)
+ * @param projectDir - Project root directory
+ * @returns QueryResult with { cleared: count }
+ */
+export const phasesClear: QueryHandler = async (args, projectDir, workstream) => {
+  const phasesDir = planningPaths(projectDir, workstream).phases;
+  const confirm = Array.isArray(args) && args.includes('--confirm');
+  let cleared = 0;
+
+  if (existsSync(phasesDir)) {
+    const entries = await readdir(phasesDir, { withFileTypes: true });
+    const dirs = entries.filter(e => e.isDirectory() && !/^999(?:\.|$)/.test(e.name));
+
+    if (dirs.length > 0 && !confirm) {
+      throw new GSDError(
+        `phases clear would delete ${dirs.length} phase director${dirs.length === 1 ? 'y' : 'ies'}. ` +
+        `Pass --confirm to proceed.`,
+        ErrorClassification.Validation,
+      );
+    }
+
+    for (const entry of dirs) {
+      await rm(join(phasesDir, entry.name), { recursive: true, force: true });
+      cleared++;
+    }
+  }
+
+  return { data: { cleared } };
+};
+
+// ─── phasesArchive handler ────────────────────────────────────────────────
+
+/**
+ * Query handler for phases.archive.
+ *
+ * Extracted from cmdMilestoneComplete, milestone.cjs lines 210-227.
+ * Moves milestone phase directories to milestones/{version}-phases/.
+ *
+ * @param args - args[0]: version string (e.g., "v3.0")
+ * @param projectDir - Project root directory
+ * @returns QueryResult with { archived: count, version, archive_directory }
+ */
+export const phasesList: QueryHandler = async (args, projectDir, workstream) => {
+  const paths = planningPaths(projectDir, workstream);
+  const phasesDir = paths.phases;
+
+  const typeIdx = args.indexOf('--type');
+  const phaseIdx = args.indexOf('--phase');
+  const type = typeIdx !== -1 ? args[typeIdx + 1] : null;
+  const phase = phaseIdx !== -1 ? args[phaseIdx + 1] : null;
+  const includeArchived = args.includes('--include-archived');
+
+  if (!existsSync(phasesDir)) {
+    return { data: type ? { files: [], count: 0 } : { directories: [], count: 0 } };
+  }
+
+  const entries = await readdir(phasesDir, { withFileTypes: true });
+  let dirs = entries.filter(e => e.isDirectory()).map(e => e.name);
+
+  if (includeArchived) {
+    const milestonesDir = join(paths.planning, 'milestones');
+    if (existsSync(milestonesDir)) {
+      const milestoneEntries = await readdir(milestonesDir, { withFileTypes: true });
+      for (const mDir of milestoneEntries.filter(e => e.isDirectory() && e.name.endsWith('-phases'))) {
+        const milestone = mDir.name.replace(/-phases$/, '');
+        const archivedEntries = await readdir(join(milestonesDir, mDir.name), { withFileTypes: true });
+        for (const a of archivedEntries.filter(e => e.isDirectory())) {
+          dirs.push(`${a.name} [${milestone}]`);
+        }
+      }
+    }
+  }
+
+  dirs.sort((a, b) => comparePhaseNum(a, b));
+
+  if (phase) {
+    const normalized = normalizePhaseName(phase);
+    const match = dirs.find(d => phaseTokenMatches(d, normalized));
+    if (!match) {
+      return { data: { files: [], count: 0, phase_dir: null, error: 'Phase not found' } };
+    }
+    dirs = [match];
+  }
+
+  if (type) {
+    const files: string[] = [];
+    const warnings: string[] = [];
+    for (const dir of dirs) {
+      const dirPath = join(phasesDir, dir);
+      if (!existsSync(dirPath)) continue;
+      const dirFiles = await readdir(dirPath);
+      let filtered: string[];
+      if (type === 'plans') {
+        filtered = dirFiles.filter(isCanonicalPlanFile);
+        // #2893 parity — surface plan-shaped files the canonical filter
+        // rejected so callers (executor init, etc.) don't silently see zero
+        // plans. Per-dir prefix mirrors phase.cjs:120.
+        const w = describeNonCanonicalPlans(dirFiles, filtered);
+        if (w) warnings.push(`${dir}: ${w}`);
+      } else if (type === 'summaries') {
+        filtered = dirFiles.filter(f => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md');
+      } else {
+        filtered = dirFiles;
+      }
+      files.push(...filtered.sort());
+    }
+    const result: Record<string, unknown> = {
+      files,
+      count: files.length,
+      phase_dir: phase ? dirs[0]?.replace(/^\d+(?:\.\d+)*-?/, '') : null,
+    };
+    if (warnings.length) result['warning'] = warnings.join(' | ');
+    return { data: result };
+  }
+
+  return { data: { directories: dirs, count: dirs.length } };
+};
+
+export const phaseNextDecimal: QueryHandler = async (args, projectDir, workstream) => {
+  const basePhase = args[0];
+  if (!basePhase) {
+    throw new GSDError('base phase number required', ErrorClassification.Validation);
+  }
+  assertNoNullBytes(basePhase, 'basePhase');
+
+  const paths = planningPaths(projectDir, workstream);
+  const phasesDir = paths.phases;
+  const normalized = normalizePhaseName(basePhase);
+  const decimalSet = new Set<number>();
+  let baseExists = false;
+
+  const dirNames = await listDirectories(phasesDir);
+  baseExists = dirNames.some((d) => phaseTokenMatches(d, normalized));
+  for (const suffix of collectDecimalSuffixesFromDirNames(normalized, dirNames)) {
+    decimalSet.add(suffix);
+  }
+
+  const roadmapPath = paths.roadmap;
+  if (existsSync(roadmapPath)) {
+    try {
+      const roadmapContent = await readFile(roadmapPath, 'utf-8');
+      for (const suffix of collectDecimalSuffixesFromRoadmap(normalized, roadmapContent)) {
+        decimalSet.add(suffix);
+      }
+    } catch { /* ROADMAP.md read failure is non-fatal */ }
+  }
+
+  const { next: nextDecimal, existing: existingDecimals } = computeNextDecimalPhase(normalized, decimalSet);
+
+  return {
+    data: {
+      found: baseExists,
+      base_phase: normalized,
+      next: nextDecimal,
+      existing: existingDecimals,
+    },
+  };
+};
+
+export const phasesArchive: QueryHandler = async (args, projectDir, workstream) => {
+  const version = args[0];
+  if (!version) {
+    throw new GSDError('version required for phases archive', ErrorClassification.Validation);
+  }
+  assertNoNullBytes(version, 'version');
+
+  const paths = planningPaths(projectDir, workstream);
+  const phasesDir = paths.phases;
+  const isDirInMilestone = await getMilestonePhaseFilter(projectDir, workstream);
+
+  const archiveDir = join(paths.planning, 'milestones', `${version}-phases`);
+  const archivedCount = await archiveDirectories(phasesDir, archiveDir, (dirName) => isDirInMilestone(dirName));
+
+  return {
+    data: {
+      archived: archivedCount,
+      version,
+      archive_directory: toPosixPath(relative(projectDir, archiveDir)),
+    },
+  };
+};
+
+// ─── milestoneComplete ────────────────────────────────────────────────────
+
+/**
+ * Query handler for `milestone.complete` — port of `cmdMilestoneComplete` from `milestone.cjs`.
+ */
+export const milestoneComplete: QueryHandler = async (args, projectDir, workstream) => {
+  const version = args[0];
+  if (!version) {
+    throw new GSDError('version required for milestone complete (e.g., v1.0)', ErrorClassification.Validation);
+  }
+  // #3259: defense-in-depth — reject --help / -h as a version value before
+  // any disk write, regardless of whether the dispatcher guard intercepted first.
+  if (version === '--help' || version === '-h') {
+    throw new GSDError(
+      `"${version}" is not a valid milestone version; see \`gsd-sdk query --help\` for command list`,
+      ErrorClassification.Validation,
+    );
+  }
+  assertNoNullBytes(version, 'version');
+
+  const nameOpt = parseMultiwordArg(args, 'name');
+  const archivePhases = args.includes('--archive-phases');
+
+  const paths = planningPaths(projectDir, workstream);
+  const roadmapPath = paths.roadmap;
+  const reqPath = paths.requirements;
+  const statePath = paths.state;
+  const milestonesPath = join(paths.planning, 'MILESTONES.md');
+  const archiveDir = join(paths.planning, 'milestones');
+  const phasesDir = paths.phases;
+  const today = new Date().toISOString().split('T')[0]!;
+  const milestoneName = nameOpt || version;
+
+  await mkdir(archiveDir, { recursive: true });
+
+  const isDirInMilestone = await getMilestonePhaseFilter(projectDir, workstream);
+
+  let phaseCount = 0;
+  let totalPlans = 0;
+  let totalTasks = 0;
+  const accomplishments: string[] = [];
+
+  try {
+    const dirs = (await listDirectories(phasesDir)).sort();
+
+    for (const dir of dirs) {
+      if (!isDirInMilestone(dir)) continue;
+
+      phaseCount++;
+      const phaseFiles = await readdir(join(phasesDir, dir));
+      const plans = phaseFiles.filter((f) => f.endsWith('-PLAN.md') || f === 'PLAN.md');
+      const summaries = phaseFiles.filter((f) => f.endsWith('-SUMMARY.md') || f === 'SUMMARY.md');
+      totalPlans += plans.length;
+
+      for (const s of summaries) {
+        try {
+          const content = await readFile(join(phasesDir, dir, s), 'utf-8');
+          const fm = extractFrontmatter(content);
+          const oneLiner =
+            (fm['one-liner'] as string | undefined) || extractOneLinerFromBody(content);
+          if (oneLiner) {
+            accomplishments.push(oneLiner);
+          }
+          const tasksFieldMatch = content.match(/\*\*Tasks:\*\*\s*(\d+)/);
+          if (tasksFieldMatch) {
+            totalTasks += parseInt(tasksFieldMatch[1]!, 10);
+          } else {
+            const xmlTaskMatches = content.match(/<task[\s>]/gi) || [];
+            const mdTaskMatches = content.match(/##\s*Task\s*\d+/gi) || [];
+            totalTasks += xmlTaskMatches.length || mdTaskMatches.length;
+          }
+        } catch {
+          /* intentionally empty */
+        }
+      }
+    }
+  } catch {
+    /* intentionally empty */
+  }
+
+  if (existsSync(roadmapPath)) {
+    const roadmapContent = await readFile(roadmapPath, 'utf-8');
+    await writeFile(join(archiveDir, `${version}-ROADMAP.md`), roadmapContent, 'utf-8');
+  }
+
+  if (existsSync(reqPath)) {
+    const reqContent = await readFile(reqPath, 'utf-8');
+    const archiveHeader =
+      `# Requirements Archive: ${version} ${milestoneName}\n\n` +
+      `**Archived:** ${today}\n**Status:** SHIPPED\n\n` +
+      `For current requirements, see \`.planning/REQUIREMENTS.md\`.\n\n---\n\n`;
+    await writeFile(join(archiveDir, `${version}-REQUIREMENTS.md`), archiveHeader + reqContent, 'utf-8');
+  }
+
+  const auditFile = join(projectDir, '.planning', `${version}-MILESTONE-AUDIT.md`);
+  if (existsSync(auditFile)) {
+    await rename(auditFile, join(archiveDir, `${version}-MILESTONE-AUDIT.md`));
+  }
+
+  const accomplishmentsList = accomplishments.map((a) => `- ${a}`).join('\n');
+  const milestoneEntry =
+    `## ${version} ${milestoneName} (Shipped: ${today})\n\n` +
+    `**Phases completed:** ${phaseCount} phases, ${totalPlans} plans, ${totalTasks} tasks\n\n` +
+    `**Key accomplishments:**\n${accomplishmentsList || '- (none recorded)'}\n\n---\n\n`;
+
+  if (existsSync(milestonesPath)) {
+    const existing = await readFile(milestonesPath, 'utf-8');
+    if (!existing.trim()) {
+      await writeFile(milestonesPath, normalizeMd(`# Milestones\n\n${milestoneEntry}`), 'utf-8');
+    } else {
+      const headerMatch = existing.match(/^(#{1,3}\s+[^\n]*\n\n?)/);
+      if (headerMatch) {
+        const header = headerMatch[1]!;
+        const rest = existing.slice(header.length);
+        await writeFile(milestonesPath, normalizeMd(header + milestoneEntry + rest), 'utf-8');
+      } else {
+        await writeFile(milestonesPath, normalizeMd(milestoneEntry + existing), 'utf-8');
+      }
+    }
+  } else {
+    await writeFile(milestonesPath, normalizeMd(`# Milestones\n\n${milestoneEntry}`), 'utf-8');
+  }
+
+  if (existsSync(statePath)) {
+    await readModifyWriteStateMdFull(projectDir, (stateContent) => {
+      let next = stateReplaceFieldWithFallback(
+        stateContent,
+        'Status',
+        null,
+        `${version} milestone complete`,
+      );
+      next = stateReplaceFieldWithFallback(next, 'Last Activity', 'Last activity', today);
+      next = stateReplaceFieldWithFallback(
+        next,
+        'Last Activity Description',
+        null,
+        `${version} milestone completed and archived`,
+      );
+
+      const positionPattern = /(##\s*Current Position\s*\n)([\s\S]*?)(?=\n##|$)/i;
+      const closedPositionBody =
+        `\nPhase: Milestone ${version} complete\n` +
+        `Plan: —\n` +
+        `Status: Awaiting next milestone\n` +
+        `Last activity: ${today} — Milestone ${version} completed and archived\n\n`;
+      if (positionPattern.test(next)) {
+        next = next.replace(positionPattern, (_m, header) => `${header}${closedPositionBody}`);
+      } else {
+        next = `${next.trimEnd()}\n\n## Current Position\n${closedPositionBody}`;
+      }
+
+      const operatorPattern = /(##\s*Operator Next Steps\s*\n)([\s\S]*?)(?=\n##|$)/i;
+      if (operatorPattern.test(next)) {
+        next = next.replace(
+          operatorPattern,
+          `$1\n- Start the next milestone with /gsd-new-milestone\n\n`,
+        );
+      } else {
+        next = `${next.trimEnd()}\n\n## Operator Next Steps\n\n- Start the next milestone with /gsd-new-milestone\n`;
+      }
+
+      return next;
+    }, workstream);
+  }
+
+  let phasesArchived = false;
+  if (archivePhases) {
+    try {
+      const phaseArchiveDir = join(archiveDir, `${version}-phases`);
+      const archivedCount = await archiveDirectories(
+        phasesDir,
+        phaseArchiveDir,
+        (dirName) => isDirInMilestone(dirName),
+      );
+      phasesArchived = archivedCount > 0;
+    } catch {
+      /* intentionally empty */
+    }
+  }
+
+  return {
+    data: {
+      version,
+      name: milestoneName,
+      date: today,
+      phases: phaseCount,
+      plans: totalPlans,
+      tasks: totalTasks,
+      accomplishments,
+      archived: {
+        roadmap: existsSync(join(archiveDir, `${version}-ROADMAP.md`)),
+        requirements: existsSync(join(archiveDir, `${version}-REQUIREMENTS.md`)),
+        audit: existsSync(join(archiveDir, `${version}-MILESTONE-AUDIT.md`)),
+        phases: phasesArchived,
+      },
+      milestones_updated: true,
+      state_updated: existsSync(statePath),
+    },
+  };
+};