claudeos-core 2.1.1 → 2.3.0

package/bin/commands/init.js

@@ -1,1518 +1,1673 @@
-/**
- * ClaudeOS-Core — Init Command
- *
- * Runs the full 4-Pass pipeline: analyze → merge → generate → memory scaffold.
- * This is the main entry point for project bootstrapping.
- */
-
-const fs = require("fs");
-const path = require("path");
-const {
-  TOOLS_DIR, PROJECT_ROOT, GENERATED_DIR,
-  SUPPORTED_LANGS, LANG_CODES, isValidLang,
-  log, header, run, runClaudePrompt, runClaudePromptAsync,
-  ensureDir, fileExists, readFile, injectProjectRoot,
-  pad, countFiles, countPass1Files,
-} = require("../lib/cli-utils");
-const { selectLangInteractive } = require("../lib/lang-selector");
-const { selectResumeMode } = require("../lib/resume-selector");
-
-const { EXPECTED_GUIDE_FILES } = require("../../lib/expected-guides");
-const { findMissingOutputs } = require("../../lib/expected-outputs");
-
-class InitError extends Error {
-  constructor(msg) { super(msg); this.name = "InitError"; }
-}
-
-function formatElapsed(ms) {
-  const sec = Math.floor(ms / 1000);
-  if (sec < 60) return `${sec}s`;
-  const min = Math.floor(sec / 60);
-  const rem = sec % 60;
-  return rem > 0 ? `${min}m ${rem}s` : `${min}m`;
-}
-
-// Creates an onTick/clearLine pair for long-running claude -p passes. We can
-// only observe progress externally (elapsed time, sometimes filesystem delta).
-// TTYs get a single \r-rewritten line; CI/piped stdout gets periodic new lines.
-// Modes via opts:
-//   - elapsed-only (no baselineCount): ⏳ label running... 45s
-//   - file delta (baselineCount set):  📝 label generating... 24 new files | 45s
-//   - fixed target (+ totalExpected):  📝 label generating... 8/12 files (67%) | 45s
-function makePassTicker(label, startTime, opts = {}) {
-  const isTTY = Boolean(process.stdout.isTTY);
-  const { baselineCount, totalExpected } = opts;
-  const trackFiles = typeof baselineCount === "number";
-  let lastLineLen = 0;
-  function onTick() {
-    const elapsed = formatElapsed(Date.now() - startTime);
-    let line;
-    if (!trackFiles) {
-      line = `    ⏳ ${label} running... ${elapsed} elapsed`;
-    } else {
-      const current = countFiles();
-      const delta = typeof current === "number" ? Math.max(0, current - baselineCount) : null;
-      let progress;
-      if (delta === null) progress = "? new files";
-      else if (typeof totalExpected === "number" && totalExpected > 0) {
-        const capped = Math.min(delta, totalExpected);
-        const pct = Math.round((capped / totalExpected) * 100);
-        progress = `${capped}/${totalExpected} files (${pct}%)`;
-      } else {
-        progress = `${delta} new files`;
-      }
-      line = `    📝 ${label} generating... ${progress} | ${elapsed} elapsed`;
-    }
-    if (isTTY) {
-      const pad = " ".repeat(Math.max(0, lastLineLen - line.length));
-      process.stdout.write("\r" + line + pad);
-      lastLineLen = line.length;
-    } else {
-      log(line);
-    }
-  }
-  function clearLine() {
-    if (isTTY && lastLineLen > 0) {
-      process.stdout.write("\r" + " ".repeat(lastLineLen) + "\r");
-      lastLineLen = 0;
-    }
-  }
-  return { onTick, clearLine, tickMs: isTTY ? 1000 : 15000 };
-}
-
-// ═══════════════════════════════════════════════════════════════════
-// v2.1: Pass 3 Split Runner
-// ═══════════════════════════════════════════════════════════════════
-//
-// Splits the monolithic Pass 3 into 4 sequential claude -p calls:
-//
-//   3a: Extract facts from pass2-merged.json into pass3a-facts.md
-//       (small document, becomes the shared context for 3b/3c/3d).
-//   3b: Generate CLAUDE.md + standard/ + .claude/rules/ (core files).
-//   3c: Generate skills/ + guide/.
-//   3d: Generate plan/ + database/ + mcp-guide/ (master plans + aux).
-//
-// Each call has fresh context, so the total output volume can far exceed
-// the model's context window without `Prompt is too long` failures.
-// pass3a-facts.md replaces pass2-merged.json as the cross-stage reference,
-// so cross-file consistency (which was the main advantage of the single-call
-// approach) is preserved.
-//
-// Marker schema (pass3-complete.json):
-//   {
-//     "completedAt": "<ISO timestamp of final stage>",
-//     "mode": "split",
-//     "groupsCompleted": ["3a", "3b", "3c", "3d"]
-//   }
-// Partial marker after interruption:
-//   { "mode": "split", "groupsCompleted": ["3a", "3b"] }
-// On re-run, stages in groupsCompleted are skipped.
-//
-// All helper references (injectProjectRoot, fileExists, runClaudePromptAsync,
-// etc.) are passed in via the ctx param rather than being captured by closure,
-// because this function lives outside cmdInit for readability.
-async function runPass3Split(ctx) {
-  const {
-    GENERATED_DIR, PROJECT_ROOT, TOOLS_DIR,
-    pass3Marker, claudeMdPath,
-    injectProjectRoot, readFile, fileExists,
-    runClaudePromptAsync, makePassTicker, formatElapsed,
-    log, countFiles,
-    EXPECTED_GUIDE_FILES, findMissingOutputs,
-    lang, stepTimes,
-  } = ctx;
-
-  const { writeFileSafe, readFileSafe, existsSafe } = require("../../lib/safe-fs");
-  const { moveStagedRules, countFilesRecursive } = require("../../lib/staged-rules");
-
-  const COMMON_DIR = path.join(TOOLS_DIR, "pass-prompts/templates/common");
-  const stagingDir = path.join(GENERATED_DIR, ".staged-rules");
-
-  // ─── Batch sub-division for 3b/3c on large projects ───────────
-  // Even with split mode, a single 3b call that generates standard/ + rules/
-  // for 50+ domains can still hit context overflow within that stage's
-  // session (output accumulation). We sub-divide 3b and 3c into batches of
-  // ~DOMAINS_PER_BATCH domains each when totalDomains > DOMAINS_PER_BATCH.
-  //
-  // 3a is never batched (single fact sheet).
-  // 3d is never batched (master plan aggregation).
-  //
-  // Threshold rationale: 15 domains ≈ 45-60 output files for 3b alone,
-  // which stays within the empirically safe single-session output range.
-  // Beyond 15 we split. ceil(N/15) batches, preserving order from
-  // domain-groups.json (already balanced by plan-installer).
-  const DOMAINS_PER_BATCH = 15;
-
-  function loadDomainOrder() {
-    // Returns an ordered list of domain names for batching 3b/3c.
-    // Primary source: domain-groups.json (already balanced).
-    // Fallback: project-analysis.json backendDomains + frontendDomains.
-    // Final fallback: empty array → single batch (no sub-division).
-    try {
-      const dgPath = path.join(GENERATED_DIR, "domain-groups.json");
-      if (fileExists(dgPath)) {
-        const dg = JSON.parse(readFile(dgPath));
-        const groups = Array.isArray(dg) ? dg : (dg && dg.groups);
-        if (Array.isArray(groups)) {
-          const flat = [];
-          for (const g of groups) {
-            const items = Array.isArray(g.domains) ? g.domains : (Array.isArray(g) ? g : []);
-            for (const d of items) {
-              const name = typeof d === "string" ? d : (d && d.name);
-              if (name) flat.push(name);
-            }
-          }
-          if (flat.length > 0) return flat;
-        }
-      }
-    } catch (_e) { /* fall through to analysis */ }
-
-    try {
-      const paPath = path.join(GENERATED_DIR, "project-analysis.json");
-      if (fileExists(paPath)) {
-        const pa = JSON.parse(readFile(paPath));
-        const backend = Array.isArray(pa.backendDomains) ? pa.backendDomains.map(d => d.name || d) : [];
-        const frontend = Array.isArray(pa.frontendDomains) ? pa.frontendDomains.map(d => d.name || d) : [];
-        return [...backend, ...frontend].filter(Boolean);
-      }
-    } catch (_e) { /* fall through */ }
-
-    return [];
-  }
-
-  function computeBatches(domainOrder) {
-    // Returns an array of batches, where each batch is an array of domain names.
-    // If total <= DOMAINS_PER_BATCH, returns a single-batch array so the caller
-    // can use the backward-compatible "3b"/"3c" marker names.
-    if (!domainOrder || domainOrder.length <= DOMAINS_PER_BATCH) {
-      return [domainOrder || []];
-    }
-    const batches = [];
-    for (let i = 0; i < domainOrder.length; i += DOMAINS_PER_BATCH) {
-      batches.push(domainOrder.slice(i, i + DOMAINS_PER_BATCH));
-    }
-    return batches;
-  }
-
-  const domainOrder = loadDomainOrder();
-  const batches = computeBatches(domainOrder);
-  const isBatched = batches.length > 1;
-
-  if (isBatched) {
-    log(`    📦 Batch sub-division enabled: ${domainOrder.length} domains → ${batches.length} batches per stage (3b, 3c)`);
-    for (let i = 0; i < batches.length; i++) {
-      log(`       • batch ${i + 1}: ${batches[i].slice(0, 3).join(", ")}${batches[i].length > 3 ? ", +" + (batches[i].length - 3) + " more" : ""}`);
-    }
-  }
-
-
-  // ─── Load existing marker to support resume mid-split ─────────
-  // If a prior split run completed 3a and 3b but crashed at 3c, we skip
-  // 3a and 3b automatically. This is the split-mode analog of Guard 3
-  // stale-marker detection in cmdInit.
-  let completedGroups = [];
-  if (fileExists(pass3Marker)) {
-    try {
-      const existing = JSON.parse(readFile(pass3Marker));
-      if (existing && existing.mode === "split" && Array.isArray(existing.groupsCompleted)) {
-        completedGroups = existing.groupsCompleted.slice();
-        if (completedGroups.length > 0) {
-          log(`    ↪️  Resuming Pass 3 split: ${completedGroups.length} stage(s) already done (${completedGroups.join(", ")})`);
-        }
-      } else if (existing && existing.mode !== "split") {
-        // Previous run was NOT split mode but marker exists and is valid.
-        // Caller (cmdInit) should have skipped us already — defensive no-op here.
-        log(`    ℹ️  Pass 3 marker found (non-split mode), skipping split runner`);
-        return;
-      }
-    } catch (_e) {
-      log("    ⚠️  pass3-complete.json malformed, starting Pass 3 split from scratch");
-      completedGroups = [];
-    }
-  }
-
-  // Helper: write marker after each stage so partial progress survives crashes.
-  function persistMarker(complete) {
-    const body = {
-      mode: "split",
-      groupsCompleted: completedGroups.slice(),
-      lastUpdatedAt: new Date().toISOString(),
-    };
-    if (complete) body.completedAt = body.lastUpdatedAt;
-    return writeFileSafe(pass3Marker, JSON.stringify(body, null, 2));
-  }
-
-  // Helper: build a stage prompt by concatenating the common header with
-  // the stack-specific body extracted from the original pass3-prompt.md.
-  // For v2.1 we reuse the full stack template body for 3b/3c/3d, letting
-  // the stage header restrict scope via its "Scope of this step" section.
-  // A future v2.2 could split the stack templates themselves into per-stage
-  // sections; for now this preserves template fidelity while bounding scope.
-  const pass3PromptFile = path.join(GENERATED_DIR, "pass3-prompt.md");
-  if (!fileExists(pass3PromptFile)) {
-    throw new InitError("pass3-prompt.md not found. Re-run plan-installer.");
-  }
-  const fullPass3Body = readFile(pass3PromptFile);
-
-  function buildStagePrompt(stageHeaderFile, includeStackBody) {
-    const headerPath = path.join(COMMON_DIR, stageHeaderFile);
-    if (!existsSafe(headerPath)) {
-      throw new InitError(
-        `Pass 3 split stage header missing: ${stageHeaderFile}\n` +
-        `    Expected at: ${headerPath}\n` +
-        `    Re-install claudeos-core or run plan-installer to regenerate templates.`
-      );
-    }
-    const header = readFileSafe(headerPath);
-    const stackBody = includeStackBody ? ("\n\n" + fullPass3Body) : "";
-    return injectProjectRoot(header + stackBody);
-  }
-
-  // Helper: build a batch scope note injected before "## Scope of this step"
-  // in 3b/3c stage prompts when the project has been sub-divided into batches.
-  // Tells Claude explicitly which domains to process in this particular call,
-  // and which common files to include vs skip.
-  function buildBatchScopeNote(stageKind, batchIndex, totalBatches, batchDomains) {
-    const isLastBatch = batchIndex === totalBatches - 1;
-    const domainList = batchDomains.map(d => `\`${d}\``).join(", ");
-
-    let note = `## Batch scope (${stageKind}-batch ${batchIndex + 1}/${totalBatches})\n\n`;
-    note += `This Pass 3 stage has been sub-divided into ${totalBatches} batches to avoid context overflow.\n`;
-    note += `**You are processing batch ${batchIndex + 1} of ${totalBatches}.**\n\n`;
-
-    if (stageKind === "3b") {
-      note += `**Domains in THIS batch**: ${domainList}\n\n`;
-      note += `**Rules for this batch**:\n`;
-      note += `1. CLAUDE.md and all common standard/ files (00.core/, 30.security-db/, 40.infra/, etc.) are ALREADY GENERATED by the 3b-core stage. DO NOT regenerate them.\n`;
-      note += `2. Generate standard/ entries ONLY for the domains listed above — one section per domain.\n`;
-      note += `3. Generate .claude/rules/ (via staging-override path) — ONLY domain-specific rule files for the domains listed above. Common rules are already generated by 3b-core.\n`;
-      note += `4. DO NOT generate standard/ or rules/ files for domains NOT in the above list — those are/will be processed in other batches.\n`;
-      note += `5. If a file you are about to write already exists with substantive content (Rule B), skip it silently — print \`[SKIP] <path>\` and move on.\n`;
-    } else if (stageKind === "3c") {
-      note += `**Domains in THIS batch**: ${domainList}\n\n`;
-      note += `**Rules for this batch**:\n`;
-      note += `1. ALL guide/ files (01.onboarding, 02.usage, 03.troubleshooting, 04.architecture) are ALREADY GENERATED by the 3c-core stage. DO NOT regenerate.\n`;
-      note += `2. Common skills (00.shared/, orchestrator SKILL.md) are ALREADY GENERATED by 3c-core. DO NOT regenerate.\n`;
-      note += `3. Generate skills/ entries ONLY for the domains listed above — typically under 10.backend-crud/ or 20.frontend-page/ with a per-domain subdirectory.\n`;
-      note += `4. DO NOT generate skills for domains NOT in the above list.\n`;
-      note += `5. Rule B idempotent skip applies: if a skill file already exists, print \`[SKIP] <path>\` and move on.\n`;
-    }
-
-    if (!isLastBatch) {
-      note += `\n**CRITICAL**: Other domains exist in the project but will be processed by LATER batches. Do not attempt to process them now — doing so will consume context that later batches need.\n`;
-    }
-
-    return note + "\n";
-  }
-
-  // Helper: build a "core common files only" prompt for 3b-core / 3c-core
-  // stages. Injected between the stage header and the stack body to restrict
-  // scope to project-wide files (CLAUDE.md, common standards, guides, shared
-  // skills) — explicitly excluding any domain-specific output that belongs
-  // to subsequent batch stages.
-  function buildStageCorePrompt(stageKind, batchesList) {
-    const totalBatches = batchesList.length;
-    const totalDomains = batchesList.reduce((sum, b) => sum + b.length, 0);
-
-    let coreNote = `## Core common files stage (${stageKind}-core)\n\n`;
-    coreNote += `This Pass 3 run has ${totalDomains} domains divided into ${totalBatches} batches.\n`;
-    coreNote += `To keep each stage's output within safe context limits, project-wide common\n`;
-    coreNote += `files are generated in THIS dedicated core stage, BEFORE the per-domain batches.\n\n`;
-
-    if (stageKind === "3b") {
-      coreNote += `**Scope of ${stageKind}-core**:\n`;
-      coreNote += `1. CLAUDE.md at the project root.\n`;
-      coreNote += `2. ALL standard/ files that are NOT tied to a specific domain:\n`;
-      coreNote += `   - claudeos-core/standard/00.core/*.md (project overview, architecture, conventions)\n`;
-      coreNote += `   - claudeos-core/standard/30.security-db/*.md\n`;
-      coreNote += `   - claudeos-core/standard/40.infra/*.md\n`;
-      coreNote += `   - claudeos-core/standard/50.verification/*.md\n`;
-      coreNote += `   - claudeos-core/standard/90.optional/*.md\n`;
-      coreNote += `   - (stack-specific common sections as defined in the pass3 template)\n`;
-      coreNote += `3. ALL rules files (via staging-override path .claude/rules → generated/.staged-rules):\n`;
-      coreNote += `   - common rules that apply regardless of domain.\n\n`;
-      coreNote += `**What NOT to generate in ${stageKind}-core**:\n`;
-      coreNote += `- Per-domain standard/ files (e.g. \`claudeos-core/standard/10.backend/order-api.md\` for a specific domain "order")\n`;
-      coreNote += `- Per-domain rules.\n`;
-      coreNote += `- Anything under claudeos-core/skills/, claudeos-core/guide/, claudeos-core/plan/ — those belong to later stages (3c-core, 3c-N, 3d).\n\n`;
-      coreNote += `**Per-domain files will be generated in subsequent 3b-1, 3b-2, ... batch stages.**\n`;
-    } else if (stageKind === "3c") {
-      coreNote += `**Scope of ${stageKind}-core**:\n`;
-      coreNote += `1. ALL guide/ files (project-wide, domain-independent):\n`;
-      coreNote += `   - claudeos-core/guide/01.onboarding/*.md\n`;
-      coreNote += `   - claudeos-core/guide/02.usage/*.md\n`;
-      coreNote += `   - claudeos-core/guide/03.troubleshooting/*.md\n`;
-      coreNote += `   - claudeos-core/guide/04.architecture/*.md\n`;
-      coreNote += `2. COMMON skills only:\n`;
-      coreNote += `   - claudeos-core/skills/00.shared/*\n`;
-      coreNote += `   - top-level orchestrator SKILL.md files (e.g. \`10.backend-crud/SKILL.md\` without any subfolder)\n\n`;
-      coreNote += `**What NOT to generate in ${stageKind}-core**:\n`;
-      coreNote += `- Per-domain skill sub-directories (e.g. \`10.backend-crud/scaffold-order-feature/\`) — those belong to 3c-1, 3c-2, ... batch stages.\n`;
-      coreNote += `- Anything under plan/, database/, mcp-guide/ — those belong to 3d.\n\n`;
-      coreNote += `**Per-domain skills will be generated in subsequent 3c-1, 3c-2, ... batch stages.**\n`;
-    }
-
-    coreNote += `\nIf you find yourself about to generate a domain-specific file in this stage: STOP. Emit \`[DEFER] <path> — will be generated in 3b-N / 3c-N batch\` and move on.\n\n`;
-
-    const headerFile = stageKind === "3b" ? "pass3b-core-header.md" : "pass3c-skills-guide-header.md";
-    const baseprompt = buildStagePrompt(headerFile, true);
-    return baseprompt.replace(/\n## Scope of this step/, `\n${coreNote}\n## Scope of this step`);
-  }
-
-  // Helper: build the prompt for 3d-aux (the only Pass 3d sub-stage that
-  // actually runs now). Master plan aggregation (standard/rules/skills/guide)
-  // was removed because master plans are an internal tool backup not consumed
-  // by Claude Code at runtime, and aggregating 30+ files in a single session
-  // was the primary source of "Prompt is too long" failures on mid-sized
-  // projects (observed on an 18-domain production run).
-  //
-  // The subStage parameter is kept for forward-compat: if a future version
-  // reintroduces master plans via Node-side aggregation, this helper can
-  // route the extra sub-stages back in.
-  function build3dSubPrompt(subStage) {
-    const baseprompt = buildStagePrompt("pass3d-plan-aux-header.md", true);
-
-    if (subStage !== "aux") {
-      throw new InitError(
-        `build3dSubPrompt called with unsupported subStage "${subStage}". ` +
-        `Master plan sub-stages (standard/rules/skills/guide) were removed in this version. ` +
-        `Only "aux" is supported.`
-      );
-    }
-
-    let scopeNote = `## 3d sub-stage: aux\n\n`;
-    scopeNote += `Pass 3d now produces only auxiliary documentation (database + mcp-guide). Master plan aggregation (standard/rules/skills/guide → plan/*-master.md) was removed because master plans are an internal tool backup not consumed by Claude Code at runtime, and aggregating many files in a single session was the primary cause of "Prompt is too long" failures.\n`;
-    scopeNote += `**You are processing sub-stage \`3d-aux\`.**\n\n`;
-
-    scopeNote += `### Scope of 3d-aux (exclusively)\n\n`;
-    scopeNote += `Generate ONLY auxiliary documentation:\n`;
-    scopeNote += `- \`claudeos-core/database/\` — schema docs and SQL reference. If pass3a-facts.md shows no database was detected, write a single \`README.md\` stub explaining this and stop.\n`;
-    scopeNote += `- \`claudeos-core/mcp-guide/\` — MCP integration guide. If no relevant MCP servers apply, write \`README.md\` stub and stop.\n\n`;
-    scopeNote += `**DO NOT touch \`claudeos-core/plan/\`** — master plans are no longer generated in this version. If the \`plan/\` directory exists from a previous run, leave it untouched (Rule B).\n\n`;
-    scopeNote += `Rule B applies. Absence of database/ or mcp-guide/ is warning-level, so README stubs are acceptable.\n`;
-
-    return baseprompt.replace(/\n## Scope of this step/, `\n${scopeNote}\n## Scope of this step`);
-  }
-
-
-  // Helper: run a single stage with progress ticker, staged-rules move,
-  // and (optionally) per-stage output validation.
-  async function runStage(stageId, label, promptStr, opts = {}) {
-    if (completedGroups.includes(stageId)) {
-      log(`    ⏭️  ${stageId} (${label}) already complete, skipping`);
-      return { skipped: true };
-    }
-
-    // Clear stale staging before each stage. 3a doesn't write rules so
-    // it's a no-op there; 3b/3c/3d may write staged rules.
-    if (fileExists(stagingDir)) {
-      fs.rmSync(stagingDir, { recursive: true, force: true });
-    }
-
-    log("");
-    log(`    🚀 ${stageId} — ${label}`);
-    const t0 = Date.now();
-    const ticker = makePassTicker(`Pass ${stageId}`, t0, { baselineCount: countFiles() });
-    const ok = await runClaudePromptAsync(promptStr, {
-      onTick: ticker.onTick,
-      tickMs: ticker.tickMs,
-    });
-    ticker.clearLine();
-    const elapsed = Date.now() - t0;
-    stepTimes.push(elapsed);
-
-    if (!ok) {
-      throw new InitError(
-        `Pass ${stageId} (${label}) failed. Check the claude error output above.\n` +
-        `    Already-completed stages are preserved; re-running will resume from ${stageId}.\n` +
-        `    If this persists, try: npx claudeos-core init --force`
-      );
-    }
-
-    // Move staged rules after stages that generate rule files (3b, 3c, 3d).
-    // Pass 3a only writes pass3a-facts.md, so no staging to move.
-    if (opts.expectsStagedRules) {
-      const move = moveStagedRules(PROJECT_ROOT);
-      if (move.failed > 0) {
-        log(`    ⚠️  ${stageId} staged-rules: ${move.moved} moved, ${move.failed} failed`);
-        for (const err of move.errors) log(`       • ${err}`);
-        throw new InitError(
-          `Pass ${stageId} finished but ${move.failed} rule file(s) could not be moved from staging.\n` +
-          `    This is usually a transient file-lock issue. Re-run \`npx claudeos-core init\`.`
-        );
-      } else if (move.moved > 0) {
-        log(`    📦 ${stageId} staged-rules: ${move.moved} rule files moved to .claude/rules/`);
-      }
-    }
-
-    // Per-stage output validation (delegates to opts.validate callback).
-    if (typeof opts.validate === "function") {
-      const problems = opts.validate();
-      if (problems && problems.length > 0) {
-        const preview = problems.slice(0, 5).map(p => `       • ${p}`).join("\n");
-        const more = problems.length > 5 ? `\n       • ... and ${problems.length - 5} more` : "";
-        throw new InitError(
-          `Pass ${stageId} (${label}) produced incomplete output:\n` +
-          preview + more + "\n" +
-          `    Already-completed stages are preserved. Re-run to retry from ${stageId}.`
-        );
-      }
-    }
-
-    // Mark stage complete and persist marker so a crash in a later stage
-    // doesn't lose this stage's progress.
-    completedGroups.push(stageId);
-    const persisted = persistMarker(false);
-    if (!persisted) {
-      throw new InitError(
-        `Pass ${stageId} succeeded but failed to persist progress to pass3-complete.json.\n` +
-        `    Check disk space / permissions on ${GENERATED_DIR}/.`
-      );
-    }
-
-    log(`    ✅ ${stageId} complete (${formatElapsed(elapsed)})`);
-    return { skipped: false, elapsed };
-  }
-
-  // ═══ Stage 3a: Extract facts ═══════════════════════════════════
-  const factsFile = path.join(GENERATED_DIR, "pass3a-facts.md");
-  await runStage("3a", "fact extraction", buildStagePrompt("pass3a-facts.md", false), {
-    expectsStagedRules: false,
-    validate: () => {
-      const problems = [];
-      if (!fileExists(factsFile)) {
-        problems.push("pass3a-facts.md was not created");
-      } else {
-        const content = readFileSafe(factsFile, "");
-        const stripped = content.replace(/^\uFEFF/, "").trim();
-        if (stripped.length < 500) {
-          problems.push(`pass3a-facts.md too short (${stripped.length} chars, expected >= 500)`);
-        }
-      }
-      return problems;
-    },
-  });
-
-  // ═══ Stage 3b: CLAUDE.md + standard/ + .claude/rules/ ═══════════
-  //
-  // 단일 배치 (도메인 ≤ 15): 기존 "3b" marker 유지 (backward-compatible).
-  // 다중 배치 (도메인 > 15): "3b-core" 먼저 실행 후 "3b-1", "3b-2", ...
-  //
-  // 3b-core 분리 이유: 다중 배치의 첫 배치가 "CLAUDE.md + 공통 standard
-  // + 15 도메인"을 한 세션에 모두 처리하면 단일 스테이지 부하가 ~70-80
-  // 파일까지 치솟음. 관측된 overflow 임계(약 40 파일)보다 2배 가까이 큼.
-  // 공통 파일을 별도 스테이지로 빼서 각 스테이지가 ~50 파일 이하로
-  // 유지되도록 보장.
-  if (isBatched) {
-    await runStage("3b-core", "core common files (CLAUDE.md + common standard + common rules)",
-      buildStageCorePrompt("3b", batches),
-      {
-        expectsStagedRules: true,
-        validate: () => {
-          const problems = [];
-          if (!fileExists(claudeMdPath)) {
-            problems.push("CLAUDE.md was not created");
-          }
-          const stdSentinel = path.join(PROJECT_ROOT, "claudeos-core/standard/00.core/01.project-overview.md");
-          if (!fileExists(stdSentinel)) {
-            problems.push("claudeos-core/standard/00.core/01.project-overview.md missing");
-          } else {
-            const c = readFileSafe(stdSentinel, "");
-            if (c.replace(/^\uFEFF/, "").trim().length === 0) {
-              problems.push("claudeos-core/standard/00.core/01.project-overview.md is empty");
-            }
-          }
-          // 3b-core는 공통 rules만 생성 — rules 카운트 검증은 3b-N에서.
-          return problems;
-        },
-      }
-    );
-  }
-
-  // 도메인별 배치 루프.
-  // 단일 배치: stageId "3b", 공통 파일 포함 (기존 동작).
-  // 다중 배치: stageId "3b-1", "3b-2", ..., 공통 파일은 3b-core에서 이미 처리됨.
-  for (let bi = 0; bi < batches.length; bi++) {
-    const batchDomains = batches[bi];
-    const stageId = isBatched ? `3b-${bi + 1}` : "3b";
-    const label = isBatched
-      ? `domain batch ${bi + 1}/${batches.length} (${batchDomains.length} domains)`
-      : "core files (CLAUDE.md + standard + rules)";
-
-    // 배치별 프롬프트: 원래 3b 헤더에 이번 배치에서만 처리할 도메인 목록 주입.
-    // 다중 배치에서는 모든 배치가 "도메인 특화 파일만" 생성 (공통 파일은 3b-core에서 처리됨).
-    const batchScopeNote = isBatched
-      ? buildBatchScopeNote("3b", bi, batches.length, batchDomains)
-      : "";
-    const baseprompt = buildStagePrompt("pass3b-core-header.md", true);
-    const promptWithScope = batchScopeNote
-      ? baseprompt.replace(/\n## Scope of this step/, `\n${batchScopeNote}\n## Scope of this step`)
-      : baseprompt;
-
-    await runStage(stageId, label, promptWithScope, {
-      expectsStagedRules: true,
-      validate: () => {
-        const problems = [];
-        // 단일 배치: 공통 파일 검증 (3b-core가 없으므로 여기서 체크).
-        if (!isBatched) {
-          if (!fileExists(claudeMdPath)) {
-            problems.push("CLAUDE.md was not created");
-          }
-          const stdSentinel = path.join(PROJECT_ROOT, "claudeos-core/standard/00.core/01.project-overview.md");
-          if (!fileExists(stdSentinel)) {
-            problems.push("claudeos-core/standard/00.core/01.project-overview.md missing");
-          } else {
-            const c = readFileSafe(stdSentinel, "");
-            if (c.replace(/^\uFEFF/, "").trim().length === 0) {
-              problems.push("claudeos-core/standard/00.core/01.project-overview.md is empty");
-            }
-          }
-        }
-        // 모든 배치에서 rules/ 생성 확인 (최소 1개는 staged-rules가 통과해야 함)
-        const rulesDir = path.join(PROJECT_ROOT, ".claude/rules");
-        const rulesCount = countFilesRecursive(rulesDir);
-        if (rulesCount === 0) {
-          problems.push(".claude/rules/ has 0 files (staging-override may have been ignored)");
-        }
-        return problems;
-      },
-    });
-  }
-
-  // ═══ Stage 3c: skills/ + guide/ ═══════════════════════════════
-  //
-  // 단일 배치 (도메인 ≤ 15): 기존 "3c" marker 유지 (guide + skills 함께).
-  // 다중 배치 (도메인 > 15): "3c-core" 먼저 실행 후 "3c-1", "3c-2", ...
-  //
-  // 3c-core 분리 이유: guide 9개 + 공통 skills는 도메인 수 무관하게 고정.
-  // 도메인 배치와 섞이면 첫 배치 부하가 다른 배치보다 커짐.
-  if (isBatched) {
-    await runStage("3c-core", "common guides and shared skills",
-      buildStageCorePrompt("3c", batches),
-      {
-        expectsStagedRules: true, // shared skills occasionally include rule files
-        validate: () => {
-          const problems = [];
-          const guideDir = path.join(PROJECT_ROOT, "claudeos-core/guide");
-          const missingGuides = EXPECTED_GUIDE_FILES.filter(g => {
-            const fp = path.join(guideDir, g);
-            if (!fileExists(fp)) return true;
-            try {
-              return fs.readFileSync(fp, "utf-8").replace(/^\uFEFF/, "").trim().length === 0;
-            } catch (_e) { return true; }
-          });
-          for (const g of missingGuides) {
-            problems.push(`claudeos-core/guide/${g} missing or empty`);
-          }
-          // skills/ 최종 검증은 마지막 도메인 배치에서 수행.
-          return problems;
-        },
-      }
-    );
-  }
-
-  // 도메인별 skills 배치 루프.
-  // 단일 배치: guide + skills 함께 (기존 동작).
-  // 다중 배치: skills만, guide는 이미 3c-core에서 처리됨.
-  for (let bi = 0; bi < batches.length; bi++) {
-    const batchDomains = batches[bi];
-    const stageId = isBatched ? `3c-${bi + 1}` : "3c";
-    const label = isBatched
-      ? `domain skills batch ${bi + 1}/${batches.length} (${batchDomains.length} domains)`
-      : "skills and guides";
-
-    const batchScopeNote = isBatched
-      ? buildBatchScopeNote("3c", bi, batches.length, batchDomains)
-      : "";
-    const baseprompt = buildStagePrompt("pass3c-skills-guide-header.md", true);
-    const promptWithScope = batchScopeNote
-      ? baseprompt.replace(/\n## Scope of this step/, `\n${batchScopeNote}\n## Scope of this step`)
-      : baseprompt;
-
-    await runStage(stageId, label, promptWithScope, {
-      expectsStagedRules: true, // skills occasionally include rule files
-      validate: () => {
-        const problems = [];
-        // 단일 배치: guide 검증도 여기서 수행 (3c-core가 없으니까).
-        if (!isBatched) {
-          const guideDir = path.join(PROJECT_ROOT, "claudeos-core/guide");
-          const missingGuides = EXPECTED_GUIDE_FILES.filter(g => {
-            const fp = path.join(guideDir, g);
-            if (!fileExists(fp)) return true;
-            try {
-              return fs.readFileSync(fp, "utf-8").replace(/^\uFEFF/, "").trim().length === 0;
-            } catch (_e) { return true; }
-          });
-          for (const g of missingGuides) {
-            problems.push(`claudeos-core/guide/${g} missing or empty`);
-          }
-        }
-        // Skills 최종 검증: 단일 배치 / 마지막 배치에서만 전체 검증.
-        if (!isBatched || bi === batches.length - 1) {
-          const { hasNonEmptyMdRecursive } = require("../../lib/expected-outputs");
-          const skillsDir = path.join(PROJECT_ROOT, "claudeos-core/skills");
-          if (!fileExists(skillsDir) || !hasNonEmptyMdRecursive(skillsDir)) {
-            problems.push("claudeos-core/skills/ has no non-empty .md files");
-          }
-        }
-        return problems;
-      },
-    });
-  }
-
-  // ═══ Stage 3d: plan/ + database/ + mcp-guide/ ═════════════════
-  //
-  // 3d는 원래 standard/rules/skills/guide 를 master plan 으로 집계하고
-  // database/mcp-guide stub 을 만들던 스테이지였다. 하지만 master plan 자체는
-  // Claude Code 런타임에서 읽히지 않는 도구 내부 백업/관리용 파일이었고,
-  // 도메인 수가 많아지면 단일 세션 집계에서 Prompt is too long 발생 원인이
-  // 됐다 (18 도메인 실측에서 3d-standard가 32 파일 집계 시점에 실패).
-  // master plan 생성을 중단하는 것이 안정성 측면에서 올바른
-  // 결정이며, 필요시 사용자가 직접 스크립트로 집계 가능하다.
-  //
-  // 결과적으로 3d는 aux 만 남음:
-  //   3d-aux → database/ + mcp-guide/ (프로젝트 특성 설명 stub)
-
-  // 3d-aux: database/ + mcp-guide/ (absence is warning-level)
-  await runStage("3d-aux", "aux docs (database + mcp-guide)",
-    build3dSubPrompt("aux"),
-    {
-      expectsStagedRules: false,
-      validate: () => [],
-    }
-  );
-
-  // ─── Final marker: all 4 stages done ─────────────────────────
-  const finalPersist = persistMarker(true);
-  if (!finalPersist) {
-    throw new InitError(
-      "Pass 3 split all stages complete but failed to write final marker.\n" +
-      `    Check disk space / permissions on ${GENERATED_DIR}/.`
-    );
-  }
-  // 총 스테이지 수 계산
-  // 3a (1) + 3b 계(단일 1 or core+N) + 3c 계(단일 1 or core+N) + 3d-aux (1)
-  // 단일 배치: 1 + 1 + 1 + 1 = 4
-  // 다중 배치: 1 + (1 + N) + (1 + N) + 1 = 2N + 4
-  const three3dStages = 1; // aux only (master plan aggregation removed)
-  const totalStages = isBatched
-    ? (1 + 1 + batches.length + 1 + batches.length + three3dStages)
-    : (1 + 1 + 1 + three3dStages);
-  log(`    🎉 Pass 3 split complete: ${completedGroups.length}/${totalStages} stages successful`);
-}
-
-async function cmdInit(parsedArgs) {
-  const totalStart = Date.now();
-  // Tracks whether we just wiped generated state via --force or "fresh" resume
-  // mode. Used by the Pass 3 backfill guard below: fresh/force explicitly
-  // means "regenerate from scratch", so a leftover CLAUDE.md from a prior run
-  // must NOT cause Pass 3 to be skipped via the v1.7.x migration backfill.
-  let wasFreshClean = false;
-
-  // ─── Prerequisites check ───────────────────────────────────
-  const hasProjectMarker = [".git", "package.json", "build.gradle", "build.gradle.kts", "pom.xml", "pyproject.toml", "requirements.txt"].some(
-    m => fs.existsSync(path.join(PROJECT_ROOT, m))
-  );
-  if (!hasProjectMarker) {
-    log(`\n  ⚠️  Warning: ${PROJECT_ROOT} does not look like a project root.`);
-    log("  No .git, package.json, build.gradle, or pom.xml found.");
-    log("  Run this command from your project directory.\n");
-  }
-
-  const nodeVersion = parseInt(process.versions.node.split(".")[0]);
-  if (nodeVersion < 18) {
-    throw new InitError(`Node.js v18+ required (current: v${process.versions.node})\n  Install: https://nodejs.org/`);
-  }
-
-  const claudeExists = run("claude --version", { silent: true, ignoreError: true });
-  if (!claudeExists) {
-    throw new InitError("Claude Code CLI not found.\n  Install: https://code.claude.com/docs/en/overview\n  Then run: claude (and complete authentication)");
-  }
-
-  // Verify Claude is authenticated (quick prompt test)
-  const claudeAuth = run('claude -p "echo ok"', { silent: true, ignoreError: true });
-  if (!claudeAuth) {
-    throw new InitError("Claude Code may not be authenticated.\n  Run: claude (and complete authentication)\n  Then retry: npx claudeos-core init");
-  }
-
-  // ─── Language selection (required) ────────────────────────────
-  let lang = parsedArgs.lang;
-  if (!lang) {
-    lang = await selectLangInteractive();
-  }
-  if (!lang) {
-    throw new InitError("Cancelled.");
-  }
-  if (!isValidLang(lang)) {
-    throw new InitError(`Unsupported language: "${lang}"\n  Supported: ${LANG_CODES.join(", ")}`);
-  }
-
-  // Early incompatibility check: CLAUDEOS_SKIP_TRANSLATION is a test-only
-  // env var that short-circuits lib/memory-scaffold.js translation path.
-  // If set AND the user chose a non-English language, Pass 4's static fallback
-  // and gap-fill would throw mid-run with a confusing "translation skipped"
-  // error. Fail fast here with a clear message so the user can unset the var
-  // or pick --lang en before the pipeline starts.
-  if (process.env.CLAUDEOS_SKIP_TRANSLATION === "1" && lang !== "en") {
-    throw new InitError(
-      `CLAUDEOS_SKIP_TRANSLATION=1 is set but --lang='${lang}' requires translation.\n` +
-      `  This env var is a test-only escape hatch that blocks calls to \`claude -p\`\n` +
-      `  from lib/memory-scaffold.js. Pass 4 would crash later with a hard-to-\n` +
-      `  diagnose error.\n\n` +
-      `  Either unset the env var:    unset CLAUDEOS_SKIP_TRANSLATION\n` +
-      `  Or run with English output:  npx claudeos-core init --lang en`
-    );
-  }
-
-  process.env.CLAUDEOS_LANG = lang;
-
-  // ─── Resume / Fresh selection ────────────────────────────
-  if (fs.existsSync(GENERATED_DIR)) {
-    const existingPass1 = fs.readdirSync(GENERATED_DIR).filter(f => f.startsWith("pass1-") && f.endsWith(".json"));
-    const pass2Exists = fileExists(path.join(GENERATED_DIR, "pass2-merged.json"));
-
-    if (existingPass1.length > 0 || pass2Exists) {
-      if (parsedArgs.force) {
-        // --force: clean all generated files for truly fresh start
-        const genFiles = fs.readdirSync(GENERATED_DIR).filter(f => f.endsWith(".json") || f.endsWith(".md"));
-        for (const f of genFiles) fs.unlinkSync(path.join(GENERATED_DIR, f));
-        // Also clean any leftover .staged-rules/ from a prior crashed run
-        // (only .json/.md are unlinked above; directories aren't touched).
-        const stagedDir = path.join(GENERATED_DIR, ".staged-rules");
-        if (fileExists(stagedDir)) fs.rmSync(stagedDir, { recursive: true, force: true });
-        // Also wipe .claude/rules/ so Guard 2 (zero-rules detection) can't
-        // false-negative on stale rules from a previous run when the fresh
-        // Pass 3 run fails silently (e.g. Claude ignores staging-override).
-        // Step [2] recreates the subdirs from scratch. Any manual edits the
-        // user made to rule files are lost — acceptable under --force
-        // ("truly fresh start").
-        const rulesDir = path.join(PROJECT_ROOT, ".claude/rules");
-        if (fileExists(rulesDir)) fs.rmSync(rulesDir, { recursive: true, force: true });
-        wasFreshClean = true;
-        log("  🔄 Previous results deleted (--force)\n");
-      } else {
-        const status = { pass1Done: existingPass1.length, pass2Done: pass2Exists };
-        const mode = await selectResumeMode(lang, status);
-        if (!mode) throw new InitError("Cancelled.");
-        if (mode === "fresh") {
-          for (const f of existingPass1) fs.unlinkSync(path.join(GENERATED_DIR, f));
-          if (pass2Exists) fs.unlinkSync(path.join(GENERATED_DIR, "pass2-merged.json"));
-          // Also reset pass 3 & pass 4 markers so they re-run
-          const pass3M = path.join(GENERATED_DIR, "pass3-complete.json");
-          const pass4M = path.join(GENERATED_DIR, "pass4-memory.json");
-          if (fileExists(pass3M)) fs.unlinkSync(pass3M);
-          if (fileExists(pass4M)) fs.unlinkSync(pass4M);
-          // Clean .staged-rules/ leftover from a prior crashed run (same reason as --force branch).
-          const stagedDir = path.join(GENERATED_DIR, ".staged-rules");
-          if (fileExists(stagedDir)) fs.rmSync(stagedDir, { recursive: true, force: true });
-          // Wipe .claude/rules/ for the same Guard 2 false-negative reason as
-          // the --force branch. Step [2] recreates the subdirs; any manual
-          // edits are lost — acceptable under an explicit "fresh" choice.
-          const rulesDir = path.join(PROJECT_ROOT, ".claude/rules");
-          if (fileExists(rulesDir)) fs.rmSync(rulesDir, { recursive: true, force: true });
-          wasFreshClean = true;
-        } else if (mode === "continue" && existingPass1.length === 0 && pass2Exists) {
-          // pass2 exists but no pass1 → pass2 is stale, force re-run
-          fs.unlinkSync(path.join(GENERATED_DIR, "pass2-merged.json"));
-          log("    ⚠️  pass2-merged.json deleted (no pass1 files to continue from)");
-        }
-      }
-    }
-  }
-
-  log("");
-  log("╔════════════════════════════════════════════════════╗");
-  log("║       ClaudeOS-Core — Bootstrap (4-Pass)          ║");
-  log("╚════════════════════════════════════════════════════╝");
-  log(`    Project root: ${PROJECT_ROOT}`);
-  log(`    Language:     ${SUPPORTED_LANGS[lang]} (${lang})`);
-  log("");
-
-  // ─── [1] Install dependencies ────────────────────────────────
-  header("[1] Installing dependencies...");
-  if (!fileExists(path.join(TOOLS_DIR, "node_modules"))) {
-    run("npm install --silent", { cwd: TOOLS_DIR });
-  }
-  log("    ✅ Done\n");
-
-  // ─── [2] Create directory structure ─────────────────────────
-  header("[2] Creating directory structure...");
-  const dirs = [
-    ".claude/rules/00.core",
-    ".claude/rules/10.backend",
-    ".claude/rules/20.frontend",
-    ".claude/rules/30.security-db",
-    ".claude/rules/40.infra",
-    ".claude/rules/50.sync",
-    "claudeos-core/generated",
-    "claudeos-core/standard/00.core",
-    "claudeos-core/standard/10.backend-api",
-    "claudeos-core/standard/20.frontend-ui",
-    "claudeos-core/standard/30.security-db",
-    "claudeos-core/standard/40.infra",
-    "claudeos-core/standard/50.verification",
-    "claudeos-core/standard/90.optional",
-    "claudeos-core/skills/00.shared",
-    "claudeos-core/skills/10.backend-crud/scaffold-crud-feature",
-    "claudeos-core/skills/20.frontend-page/scaffold-page-feature",
-    "claudeos-core/skills/50.testing",
-    "claudeos-core/skills/90.experimental",
-    "claudeos-core/guide/01.onboarding",
-    "claudeos-core/guide/02.usage",
-    "claudeos-core/guide/03.troubleshooting",
-    "claudeos-core/guide/04.architecture",
-    "claudeos-core/database",
-    "claudeos-core/mcp-guide",
-    "claudeos-core/memory",
-    ".claude/rules/60.memory",
-  ];
-  for (const d of dirs) {
-    ensureDir(path.join(PROJECT_ROOT, d));
-  }
-  log("    ✅ Done\n");
-
-  // ─── [3] Run plan-installer ─────────────────────────
-  header("[3] Analyzing project (plan-installer)...");
-  run(`node "${path.join(TOOLS_DIR, "plan-installer/index.js")}"`);
-  log("");
-
-  // ─── [4] Pass 1: Deep analysis per domain group ──────────────────
-  header("[4] Pass 1 — Deep analysis per domain group...");
-
-  let domainGroups;
-  try {
-    domainGroups = JSON.parse(
-      readFile(path.join(GENERATED_DIR, "domain-groups.json"))
-    );
-  } catch (e) {
-    throw new InitError(`domain-groups.json is missing or malformed: ${e.message}\n    Re-run plan-installer or check claudeos-core/generated/`);
-  }
-  const totalGroups = domainGroups.totalGroups;
-  if (!totalGroups || typeof totalGroups !== "number" || totalGroups < 1) {
-    throw new InitError(`domain-groups.json has invalid totalGroups: ${totalGroups}\n    Re-run plan-installer or check claudeos-core/generated/`);
-  }
-
-  // Load pass1 prompts by type
-  const pass1Prompts = {};
-  for (const type of ["backend", "frontend"]) {
-    const promptFile = path.join(GENERATED_DIR, `pass1-${type}-prompt.md`);
-    if (fileExists(promptFile)) {
-      pass1Prompts[type] = readFile(promptFile);
-    }
-  }
-  // Single-stack backward compatibility
-  if (Object.keys(pass1Prompts).length === 0) {
-    const fallback = path.join(GENERATED_DIR, "pass1-prompt.md");
-    if (fileExists(fallback)) pass1Prompts["backend"] = readFile(fallback);
-  }
-
-  if (!domainGroups.groups || totalGroups !== domainGroups.groups.length) {
-    throw new InitError(`domain-groups.json is malformed: expected ${totalGroups} groups, found ${domainGroups.groups ? domainGroups.groups.length : 0}`);
-  }
-
-  // Progress tracking: Pass 1 (N groups) + Pass 2 + Pass 3 + Pass 4 = totalSteps
-  const totalSteps = totalGroups + 3;
-  let completedSteps = 0;
-  const stepTimes = [];
-  const passStart = Date.now();
-
-  function progressBar(step, label) {
-    const pct = Math.round((step / totalSteps) * 100);
-    const elapsed = Date.now() - passStart;
-    let eta = "";
-    if (stepTimes.length > 0) {
-      const avgMs = stepTimes.reduce((a, b) => a + b, 0) / stepTimes.length;
-      const remaining = (totalSteps - step) * avgMs;
-      eta = ` | ETA ${formatElapsed(remaining)}`;
-    }
-    const filled = Math.round(pct / 5);
-    const bar = "█".repeat(filled) + "░".repeat(20 - filled);
-    log(`    [${bar}] ${pct}% (${step}/${totalSteps}) ${formatElapsed(elapsed)}${eta} — ${label}`);
-  }
-
-  for (let i = 1; i <= totalGroups; i++) {
-    const group = domainGroups.groups[i - 1];
-    const domainList = (group.domains || []).join(", ") || "(unknown)";
-    const estFiles = group.estimatedFiles || 0;
-    const groupType = group.type || "backend";
-    const icon = groupType === "frontend" ? "🎨" : "⚙️";
-
-    log("");
-    log(
-      `    ${icon} [Pass 1-${i}/${totalGroups}] ${groupType}: ${domainList} (~${estFiles} files)`
-    );
-
-    const pass1Json = path.join(GENERATED_DIR, `pass1-${i}.json`);
-    if (fileExists(pass1Json)) {
-      try {
-        const existing = JSON.parse(readFile(pass1Json));
-        if (existing && existing.analysisPerDomain) {
-          log(`    ⏭️  pass1-${i}.json already exists, skipping`);
-          completedSteps++;
-          continue;
-        }
-      } catch (_e) { /* malformed — re-run */ }
-      log(`    ⚠️  pass1-${i}.json exists but is malformed, re-running`);
-    }
-
-    // Select prompt for this type
-    const template = pass1Prompts[groupType] || pass1Prompts["backend"];
-    if (!template) {
-      throw new InitError(`No pass1 prompt found for type: ${groupType}`);
-    }
-
-    // Placeholder substitution — use replacement functions (not string form)
-    // so that `$`, `$1`, `$&`, `$$` etc. in domainList are preserved as
-    // literal characters rather than interpreted as regex back-references.
-    // (Same bug class as bug #18 in lib/plan-parser.js replaceFileBlock.)
-    let prompt = template
-      .replace(/\{\{DOMAIN_GROUP\}\}/g, () => domainList)
-      .replace(/\{\{PASS_NUM\}\}/g, () => String(i));
-    prompt = injectProjectRoot(prompt);
-
-    const t1 = Date.now();
-    const ticker1 = makePassTicker(`Pass 1-${i}/${totalGroups}`, t1);
-    const ok = await runClaudePromptAsync(prompt, {
-      onTick: ticker1.onTick,
-      tickMs: ticker1.tickMs,
-    });
-    ticker1.clearLine();
-    const elapsed1 = Date.now() - t1;
-    stepTimes.push(elapsed1);
-
-    if (!ok) {
-      throw new InitError(`Pass 1-${i} failed. Check the claude error output above.\n    If this persists, try: npx claudeos-core init --force`);
-    }
-
-    if (!fileExists(pass1Json)) {
-      throw new InitError(`pass1-${i}.json was not created. Claude may have run but not produced expected output.\n    Ensure the prompt instructs Claude to write to claudeos-core/generated/pass1-${i}.json`);
-    }
-
-    completedSteps++;
-    progressBar(completedSteps, `pass1-${i}.json created (${formatElapsed(elapsed1)})`);
-  }
-  log("");
-
-  // ─── [5] Pass 2: Merge analysis results ──────────────────────
-  header("[5] Pass 2 — Merging analysis results...");
-
-  const pass2Json = path.join(GENERATED_DIR, "pass2-merged.json");
-
-  // H3: resume-path structural validation. existsSync alone isn't enough —
-  // a prior crashed run may have left a skeleton (`{}`) or malformed JSON
-  // that passes existsSync but silently poisons Pass 3 (which parses this
-  // file as its analysis input). Mirrors pass1's malformed-detection at
-  // the pass1 loop above, and the "<5 top-level keys = INSUFFICIENT_KEYS"
-  // threshold from pass-json-validator/index.js (ERROR level).
-  let pass2IsValid = false;
-  if (fileExists(pass2Json)) {
-    try {
-      const existing = JSON.parse(readFile(pass2Json));
-      if (existing && typeof existing === "object" && !Array.isArray(existing)
-          && Object.keys(existing).length >= 5) {
-        pass2IsValid = true;
-      }
-    } catch (_e) { /* malformed — fall through to re-run */ }
-    if (!pass2IsValid) {
-      log("    ⚠️  pass2-merged.json exists but is malformed or incomplete (<5 top-level keys), re-running");
-      try { fs.unlinkSync(pass2Json); } catch (_e) { /* best-effort cleanup */ }
-    }
-  }
-
-  if (pass2IsValid) {
-    log("    ⏭️  pass2-merged.json already exists, skipping");
-    completedSteps++;
-  } else {
-    const pass2PromptFile = path.join(GENERATED_DIR, "pass2-prompt.md");
-    if (!fileExists(pass2PromptFile)) {
-      throw new InitError("pass2-prompt.md not found. Re-run plan-installer.");
-    }
-    let prompt = injectProjectRoot(readFile(pass2PromptFile));
-
-    const t2 = Date.now();
-    const ticker2 = makePassTicker("Pass 2", t2);
-    const ok = await runClaudePromptAsync(prompt, {
-      onTick: ticker2.onTick,
-      tickMs: ticker2.tickMs,
-    });
-    ticker2.clearLine();
-    const elapsed2 = Date.now() - t2;
-    stepTimes.push(elapsed2);
-
-    if (!ok) {
-      throw new InitError("Pass 2 failed. Check the claude error output above.\n    If this persists, try: npx claudeos-core init --force");
-    }
-
-    if (!fileExists(pass2Json)) {
-      throw new InitError("pass2-merged.json was not created. Claude may have run but not produced expected output.");
-    }
-
-    completedSteps++;
-    progressBar(completedSteps, `pass2-merged.json created (${formatElapsed(elapsed2)})`);
-  }
-  log("");
-
-  // ─── [5.5] v2.1: Build pass3-context.json (slim summary for Pass 3) ──
-  // Writes a small (<5 KB) structured summary derived from project-analysis.json
-  // plus pass2-merged.json signals (size, top-level keys). Pass 3 prompts
-  // reference this INSTEAD OF re-reading pass2-merged.json repeatedly, which
-  // was the primary cause of `Prompt is too long` failures on large projects.
-  //
-  // Silent-on-failure: if pass3-context-builder returns null (e.g.
-  // project-analysis.json missing), we skip writing and let Pass 3 fall back
-  // to the pre-v2.1 behavior of reading pass2-merged.json directly.
-  try {
-    const { buildPass3Context } = require("../../plan-installer/pass3-context-builder");
-    const pass3Ctx = buildPass3Context(GENERATED_DIR);
-    if (pass3Ctx) {
-      const { writeFileSafe: wfsCtx } = require("../../lib/safe-fs");
-      const ctxPath = path.join(GENERATED_DIR, "pass3-context.json");
-      const wrote = wfsCtx(ctxPath, JSON.stringify(pass3Ctx, null, 2));
-      if (wrote) {
-        const sizeKB = Math.round(JSON.stringify(pass3Ctx).length / 1024);
-        const p2KB = pass3Ctx.pass2Merged.sizeKB;
-        log(`    📄 pass3-context.json built (${sizeKB} KB summary of ${p2KB} KB pass2-merged.json)`);
-        if (pass3Ctx.pass2Merged.large) {
-          log(`    ⚠️  pass2-merged.json is large (${p2KB} KB). Pass 3 will rely heavily on pass3-context.json to avoid context overflow.`);
-        }
-      }
-    }
-  } catch (e) {
-    log(`    ⚠️  pass3-context.json build skipped: ${e.message} (Pass 3 will fall back to pass2-merged.json)`);
-  }
-  log("");
-
-  // ─── [6] Pass 3: Generate + verify ─────────────────────────
-  header("[6] Pass 3 — Generating all files...");
-
-  const pass3Marker = path.join(GENERATED_DIR, "pass3-complete.json");
-  const claudeMdPath = path.join(PROJECT_ROOT, "CLAUDE.md");
-
-  // v1.7.1 → v1.7.2 migration: if CLAUDE.md exists from prior version but marker
-  // is missing, backfill marker to preserve user's existing output.
-  //
-  // Gated by !wasFreshClean: --force and "fresh" resume mode wipe the marker
-  // on purpose to force Pass 3 to re-run. They do NOT delete CLAUDE.md (user
-  // may have manual edits worth preserving in the continue flow), so without
-  // this gate the backfill would fire on a fresh run, re-write the marker,
-  // and Pass 3 would skip — leaving stale CLAUDE.md + regenerated pass1/2 +
-  // wiped rules/, which fails sync-checker and content-validator.
-  if (!wasFreshClean && fileExists(claudeMdPath) && !fileExists(pass3Marker) && fileExists(path.join(GENERATED_DIR, "pass2-merged.json"))) {
-    const { writeFileSafe: wfsMig } = require("../../lib/safe-fs");
-    const backfillOk = wfsMig(pass3Marker, JSON.stringify({
-      completedAt: new Date().toISOString(),
-      backfilled: true,
-      reason: "CLAUDE.md exists from prior version; marker backfilled to prevent regeneration. To force re-run, use --force or pick 'fresh' in the resume prompt.",
-    }, null, 2));
-    if (backfillOk) {
-      log("    ℹ️  Detected existing CLAUDE.md — Pass 3 marker backfilled (use --force to regenerate)");
-    } else {
-      log("    ⚠️  CLAUDE.md exists but marker backfill failed — Pass 3 will re-run");
-    }
-  }
-
-  // Stale marker detection (Pass 3). Drops the marker and re-runs Pass 3 if
-  // any of the following is true:
-  //   (a) CLAUDE.md was deleted externally (original check),
-  //   (b) any of EXPECTED_GUIDE_FILES is missing or BOM-aware empty,
-  //   (c) any entry in expected-outputs (standard sentinel / skills / plan) is
-  //       missing or empty.
-  //
-  // (b) and (c) were previously only enforced as Pass 3 post-generation Guards
-  // 3 (H2/H1), which gate marker *creation* on fresh runs. Projects that were
-  // initialized on a pre-v2.0.0 release (before those guards existed) can end
-  // up with a marker on disk even though guide/ or standard/skills/plan are
-  // empty. Without this stale check, such projects hit a permanent
-  // content-validator fail loop because init sees the marker and skips Pass 3
-  // forever. This mirrors the Pass 4 dropStalePass4Marker pattern below.
-  //
-  // Unlink is surfaced as InitError on failure (symmetric with Pass 4).
-  // Silently ignoring the error would leave the stale marker in place, and
-  // the `if (fileExists(pass3Marker))` check below would accept it — skipping
-  // Pass 3 while outputs are still incomplete. That silent-skip is the exact
-  // bug class this audit round closes.
-  function dropStalePass3Marker(reasonLog) {
-    log(reasonLog);
-    try { fs.unlinkSync(pass3Marker); } catch (e) {
-      log(`    ❌ Failed to delete stale pass3-complete.json: ${e.code || e.message}`);
-      throw new InitError(
-        `Could not delete stale pass3-complete.json at:\n    ${pass3Marker}\n` +
-        `    The file is likely locked by another process (Windows antivirus or a file-watcher).\n` +
-        `    Close any editor/AV scanner holding the file and re-run \`npx claudeos-core init\`.`
-      );
-    }
-  }
-  if (fileExists(pass3Marker)) {
-    // v2.1.1: split-mode partial marker 보호.
-    // { mode: "split", groupsCompleted: [...], completedAt: undefined } 형태의
-    // 중간 진행 마커는 stale로 판정하면 안 됨. 3b까지만 완료된 정상 상태에서도
-    // guide/skills/plan이 비어있어서 기존 로직이 잘못 stale 판정하고 marker를
-    // 삭제하면, runPass3Split의 resume 로직이 완료된 스테이지를 못 읽고
-    // 3a부터 전체 재실행하게 됨 (correctness는 OK이지만 토큰 2배 낭비).
-    let markerIsSplitPartial = false;
-    try {
-      const parsed = JSON.parse(readFile(pass3Marker));
-      markerIsSplitPartial =
-        parsed &&
-        parsed.mode === "split" &&
-        Array.isArray(parsed.groupsCompleted) &&
-        !parsed.completedAt;
-    } catch (_e) {
-      // malformed marker → stale check로 넘어감 (이전 동작 유지)
-    }
-
-    if (markerIsSplitPartial) {
-      log(`    ↪️  split-mode partial marker detected — runPass3Split will resume`);
-    } else if (!fileExists(claudeMdPath)) {
-      dropStalePass3Marker("    ⚠️  pass3-complete.json exists but CLAUDE.md is missing — treating marker as stale, re-running Pass 3");
-    } else {
-      const guideDirForStale = path.join(PROJECT_ROOT, "claudeos-core/guide");
-      const staleMissingGuides = EXPECTED_GUIDE_FILES.filter(g => {
-        const fp = path.join(guideDirForStale, g);
-        if (!fileExists(fp)) return true;
-        try {
-          return fs.readFileSync(fp, "utf-8").replace(/^\uFEFF/, "").trim().length === 0;
-        } catch (_e) { return true; }
-      });
-      if (staleMissingGuides.length > 0) {
-        dropStalePass3Marker(
-          `    ⚠️  pass3-complete.json exists but ${staleMissingGuides.length}/${EXPECTED_GUIDE_FILES.length} guide files are missing or empty — treating marker as stale, re-running Pass 3`
-        );
-      } else {
-        const staleMissingOutputs = findMissingOutputs(PROJECT_ROOT);
-        if (staleMissingOutputs.length > 0) {
-          dropStalePass3Marker(
-            `    ⚠️  pass3-complete.json exists but ${staleMissingOutputs.length} required output(s) are missing or empty — treating marker as stale, re-running Pass 3`
-          );
-        }
-      }
-    }
-  }
-
-  // Pass 3 split mode resolution.
-  //
-  // Pass 3 runs as 4 sequential `claude -p` calls (3a facts, 3b core, 3c
-  // skills+guide, 3d-aux database/mcp-guide), each with fresh context.
-  // This eliminates `Prompt is too long` failures by making output
-  // accumulation overflow structurally impossible — each stage starts
-  // with a clean context window. For projects with 16+ domains, 3b and 3c
-  // are further split into core + batched sub-stages.
-  //
-  // Single-call mode (previously toggled by CLAUDEOS_PASS3_SPLIT=0) was
-  // removed because empirical data showed it failed reliably on projects
-  // with more than ~5 domains (output accumulation overflow was not
-  // predictable from input size alone), and split mode is structurally
-  // immune to this failure mode with bounded token overhead.
-  log(`    🚀 Pass 3 split mode (3a → 3b → 3c → 3d-aux)`);
-  try {
-    const ctxPath = path.join(GENERATED_DIR, "pass3-context.json");
-    if (fileExists(ctxPath)) {
-      const ctx = JSON.parse(readFile(ctxPath));
-      const rec = ctx && ctx.splitRecommendation;
-      if (rec) {
-        log(`       • estimated ${rec.estimatedFileCount} files from ${rec.totalDomains} domains`);
-      }
-    }
-  } catch (_e) { /* best-effort log only */ }
-
-  if (!fileExists(pass3Marker)) {
-    await runPass3Split({
-      GENERATED_DIR, PROJECT_ROOT, TOOLS_DIR,
-      pass3Marker, claudeMdPath,
-      injectProjectRoot, readFile, fileExists,
-      runClaudePromptAsync, makePassTicker, formatElapsed,
-      log, countFiles,
-      EXPECTED_GUIDE_FILES, findMissingOutputs,
-      lang, stepTimes,
-    });
-    completedSteps++;
-    progressBar(completedSteps, `Pass 3 complete (split mode)`);
-    log("");
-  } else {
-    log("    ⏭️  pass3-complete.json already exists, skipping");
-    completedSteps++;
-  }
-  log("");
-
-  // ─── [7] Pass 4: L4 memory scaffolding ────────────
-  header("[7] Pass 4 — Memory scaffolding...");
-
-  const pass4Marker = path.join(GENERATED_DIR, "pass4-memory.json");
-  const pass4PromptFile = path.join(GENERATED_DIR, "pass4-prompt.md");
-
-  const { scaffoldMemory, scaffoldRules, appendClaudeMdL4Memory, scaffoldMasterPlans, scaffoldDocWritingGuide, scaffoldSkillsManifest } = require("../../lib/memory-scaffold");
-  const { writeFileSafe } = require("../../lib/safe-fs");
-
-  const memoryPath = path.join(PROJECT_ROOT, "claudeos-core/memory");
-  const planPath = path.join(PROJECT_ROOT, "claudeos-core/plan");
-  const rulesPath = path.join(PROJECT_ROOT, ".claude/rules");
-  const standardCorePath = path.join(PROJECT_ROOT, "claudeos-core/standard/00.core");
-  const skillsSharedPath = path.join(PROJECT_ROOT, "claudeos-core/skills/00.shared");
-
-  function applyStaticFallback() {
-    try {
-      scaffoldMemory(memoryPath, { lang });
-      scaffoldRules(rulesPath, { lang });
-      scaffoldDocWritingGuide(standardCorePath, { lang });
-      scaffoldMasterPlans(planPath, memoryPath, { lang });
-      scaffoldSkillsManifest(skillsSharedPath, { lang });
-      appendClaudeMdL4Memory(claudeMdPath, { lang });
-    } catch (err) {
-      // When lang !== "en", translation is REQUIRED. If it fails, we surface
-      // a clear error rather than silently writing English (which would
-      // contradict the user's --lang choice).
-      throw new InitError(
-        `Static fallback failed while translating to lang='${lang}':\n` +
-        `    ${err.message}\n` +
-        `    Ensure the \`claude\` CLI is available and authenticated, then re-run.\n` +
-        `    Alternatively re-run with --lang en to skip translation.`
-      );
-    }
-    const markerBody = JSON.stringify({
-      analyzedAt: new Date().toISOString(),
-      passNum: 4,
-      fallback: true,
-      lang,
-      memoryFiles: [
-        "claudeos-core/memory/decision-log.md",
-        "claudeos-core/memory/failure-patterns.md",
-        "claudeos-core/memory/compaction.md",
-        "claudeos-core/memory/auto-rule-update.md",
-      ],
-      ruleFiles: [
-        ".claude/rules/00.core/51.doc-writing-rules.md",
-        ".claude/rules/00.core/52.ai-work-rules.md",
-        ".claude/rules/60.memory/01.decision-log.md",
-        ".claude/rules/60.memory/02.failure-patterns.md",
-        ".claude/rules/60.memory/03.compaction.md",
-        ".claude/rules/60.memory/04.auto-rule-update.md",
-      ],
-      // Note: master plan files are no longer generated (previously this
-      // included "claudeos-core/plan/50.memory-master.md"). The marker schema
-      // still accepts an optional planFiles field for backward compatibility.
-      claudeMdAppended: true,
-    }, null, 2);
-    return writeFileSafe(pass4Marker, markerBody);
-  }
-
-  // M1: validate Pass 4 marker CONTENT, not just existence. Claude can emit
-  // a malformed marker on partial failure (e.g. `{"error":"timeout"}`) that
-  // still satisfies fileExists() and would cause the skip path to accept it
-  // forever. Pass 4 prompt (pass-prompts/templates/common/pass4.md:255-283)
-  // specifies the required structure; we check the minimum subset that
-  // distinguishes a real marker from junk: object shape + passNum === 4 +
-  // non-empty memoryFiles array.
-  function isValidPass4Marker(markerPath) {
-    if (!fileExists(markerPath)) return false;
-    try {
-      const data = JSON.parse(readFile(markerPath));
-      if (!data || typeof data !== "object" || Array.isArray(data)) return false;
-      if (data.passNum !== 4) return false;
-      if (!Array.isArray(data.memoryFiles) || data.memoryFiles.length === 0) return false;
-      return true;
-    } catch (_e) { return false; }
-  }
-
-  // Stale / invalid marker detection. Delete and re-run if either:
-  //   (a) memory/ was deleted externally (original stale-detection), OR
-  //   (b) the marker file itself is malformed (M1).
-  //
-  // Unlink can fail on Windows if an AV or file-watcher has the handle open.
-  // We surface that failure to the user — without it, the subsequent
-  // `if (fileExists(pass4Marker))` check below would accept the stale marker
-  // and skip Pass 4 silently, leaving the project with half-scaffolded memory
-  // state (exactly the silent-failure class this audit is eliminating).
-  const memoryAny = fileExists(path.join(PROJECT_ROOT, "claudeos-core/memory/decision-log.md"))
-    || fileExists(path.join(PROJECT_ROOT, "claudeos-core/memory/compaction.md"));
-  function dropStalePass4Marker(reasonLog) {
-    log(reasonLog);
-    try { fs.unlinkSync(pass4Marker); } catch (e) {
-      log(`    ❌ Failed to delete stale pass4-memory.json: ${e.code || e.message}`);
-      throw new InitError(
-        `Could not delete stale pass4-memory.json at:\n    ${pass4Marker}\n` +
-        `    The file is likely locked by another process (Windows antivirus or a file-watcher).\n` +
-        `    Close any editor/AV scanner holding the file and re-run \`npx claudeos-core init\`.`
-      );
-    }
-  }
-  if (fileExists(pass4Marker)) {
-    if (!memoryAny) {
-      dropStalePass4Marker("    ⚠️  pass4-memory.json exists but memory/ is empty — re-running Pass 4");
-    } else if (!isValidPass4Marker(pass4Marker)) {
-      dropStalePass4Marker("    ⚠️  pass4-memory.json exists but is malformed (missing passNum/memoryFiles) — re-running Pass 4");
-    }
-  }
-
-  const pass4Start = Date.now();
-  let pass4Label = "Pass 4 complete";
-
-  if (fileExists(pass4Marker)) {
-    log("    ⏭️  pass4-memory.json already exists, skipping");
-    pass4Label = "Pass 4 already present";
-  } else if (!fileExists(pass4PromptFile)) {
-    log("    ⚠️  pass4-prompt.md not found — falling back to static scaffold");
-    if (applyStaticFallback()) { log("    ✅ Memory/Rules/Plans scaffolded + CLAUDE.md appended (static fallback)"); pass4Label = "Pass 4 (static fallback)"; }
-    else { log("    ❌ Static fallback failed to write marker"); pass4Label = "Pass 4 fallback failed"; }
-  } else {
-    let prompt4 = injectProjectRoot(readFile(pass4PromptFile));
-
-    // Same stale-staging guard as Pass 3 (in case a previous Pass 4 crashed
-    // after writing to the staging dir but before the move could run).
-    const stagedBeforeP4 = path.join(GENERATED_DIR, ".staged-rules");
-    if (fileExists(stagedBeforeP4)) fs.rmSync(stagedBeforeP4, { recursive: true, force: true });
-
-    const t4 = Date.now();
-    // Pass 4's prompt lists 12 required outputs (pass4.md §§1-12). Of these:
-    //   - 11 are file creations (#1-10 + #12)
-    //   - 1 is an append to existing CLAUDE.md (#11, not a new file)
-    // Of the 11 file creations, only 5 are visible to countFiles() during
-    // the run:
-    //   - #1-4 (4 memory files)                                 → observable
-    //   - #5-10 (6 rule files) go to .staged-rules/ under
-    //     claudeos-core/generated/, which countFiles() skips    → invisible
-    //   - #12 (1 standard doc-writing-guide)                    → observable
-    // So totalExpected = 5. (v2.0.x had 6 because plan/50.memory-master.md
-    // was also generated; master plan generation was removed in v2.1.0.)
-    // The final "100%" shows up on the outer progressBar once the staged
-    // move + marker are done.
-    const ticker4 = makePassTicker("Pass 4", t4, {
-      baselineCount: countFiles(),
-      totalExpected: 5,
-    });
-    const ok4 = await runClaudePromptAsync(prompt4, {
-      onTick: ticker4.onTick,
-      tickMs: ticker4.tickMs,
-    });
-    ticker4.clearLine();
-    const elapsed4 = Date.now() - t4;
-
-    // Move any rule files Pass 4 wrote to the staging dir. This runs regardless
-    // of pass4Marker status, because Claude may have written rules before
-    // failing to produce the marker. Static fallback (below) writes directly
-    // to .claude/rules/ and is unaffected by the move (no-op on empty staging).
-    const { moveStagedRules: mvP4 } = require("../../lib/staged-rules");
-    const p4Move = mvP4(PROJECT_ROOT);
-    if (p4Move.failed > 0) {
-      log(`    ⚠️  Pass 4 staged-rules: ${p4Move.moved} moved, ${p4Move.failed} failed`);
-      for (const err of p4Move.errors) log(`       • ${err}`);
-    } else if (p4Move.moved > 0) {
-      log(`    📦 Pass 4 staged-rules: ${p4Move.moved} rule files moved to .claude/rules/`);
-    }
-
-    if (!ok4 || !isValidPass4Marker(pass4Marker)) {
-      log("    ⚠️  Pass 4 did not produce a valid pass4-memory.json — using static fallback");
-      if (applyStaticFallback()) { log("    ✅ Memory/Rules/Plans scaffolded + CLAUDE.md appended (static fallback)"); pass4Label = `Pass 4 (static fallback, ${formatElapsed(elapsed4)})`; }
-      else { log("    ❌ Static fallback failed to write marker"); pass4Label = "Pass 4 fallback failed"; }
-    } else {
-      // Claude-driven Pass 4 succeeded. Ensure memory + rules + plans + standard + CLAUDE.md append exist
-      // (Claude may have created them; fill any gaps with static fallback).
-      // scaffoldMemory is skip-safe: it only writes files that don't already exist,
-      // so it won't overwrite Claude's translated content — it only fills gaps.
-      // When lang !== "en", the gap-fill MUST translate: we do not silently
-      // write English into a non-English project (bug #21).
-      let gapResults;
-      try {
-        const memR   = scaffoldMemory(memoryPath, { lang });
-        const ruleR  = scaffoldRules(rulesPath, { lang });
-        const docR   = scaffoldDocWritingGuide(standardCorePath, { lang });
-        const planR  = scaffoldMasterPlans(planPath, memoryPath, { lang });
-        const manifestR = scaffoldSkillsManifest(skillsSharedPath, { lang });
-        const claudeOk = appendClaudeMdL4Memory(claudeMdPath, { lang });
-        // Collect all statuses into one flat array for summary reporting.
-        gapResults = [
-          ...memR,
-          ...ruleR,
-          ...planR,
-          { file: docR.file, status: docR.status },
-          { file: "skills/00.shared/" + manifestR.file, status: manifestR.status },
-          { file: "CLAUDE.md#(L4)", status: claudeOk ? "present-or-appended" : "error" },
-        ];
-      } catch (err) {
-        throw new InitError(
-          `Pass 4 gap-fill failed while translating to lang='${lang}':\n` +
-          `    ${err.message}\n` +
-          `    Pass 4 Claude succeeded but some files were missing and translation of the ` +
-          `static fallback to ${lang} failed.\n` +
-          `    Re-run when \`claude\` CLI is available, or use --lang en.`
-        );
-      }
-      // Summary: how many were already present (skipped) vs written by gap-fill.
-      // This surfaces the true state regardless of what Claude printed during Pass 4.
-      const skipped = gapResults.filter(r => r.status === "skipped" || r.status === "present-or-appended").length;
-      const written = gapResults.filter(r => r.status === "written").length;
-      const erroredItems = gapResults.filter(r => r.status === "error");
-      const errored = erroredItems.length;
-      log(`    ✅ Pass 4 complete (${formatElapsed(elapsed4)})`);
-      if (written > 0 || errored > 0) {
-        log(`       📋 Gap-fill: ${skipped} already present, ${written} created via fallback, ${errored} errored`);
-      } else {
-        log(`       📋 Gap-fill: all ${skipped} expected files already present`);
-      }
-      // Surface which files errored so the user can investigate (instead of
-      // silently rolling them into a count). Common causes: write permission,
-      // disk full, or appendClaudeMdL4Memory returned false (CLAUDE.md missing
-      // or unwritable). All erroredItems are non-fatal — Pass 4 marker still
-      // gets written, but the user should know what was incomplete.
-      for (const item of erroredItems) {
-        log(`       ❌ ${item.file} — write failed (check disk space, permissions)`);
-      }
-      pass4Label = `Pass 4 complete (${formatElapsed(elapsed4)})`;
-    }
-  }
-  // Record Pass 4 in the overall progress bar, regardless of which branch
-  // (skip / static fallback / Claude-driven) ran above. Only feed stepTimes
-  // when we actually did real work, so ETA for future steps stays meaningful.
-  const pass4Elapsed = Date.now() - pass4Start;
-  if (pass4Elapsed > 500) stepTimes.push(pass4Elapsed);
-  completedSteps++;
-  progressBar(completedSteps, pass4Label);
-  log("");
-
-  // ─── [8] Run verification tools ───────────────────────────────
-  header("[8] Running verification tools...");
-
-  const verifyTools = [
-    { name: "manifest-generator", script: path.join(TOOLS_DIR, "manifest-generator/index.js") },
-    { name: "health-checker",     script: path.join(TOOLS_DIR, "health-checker/index.js") },
-  ];
-
-  for (const t of verifyTools) {
-    if (!fileExists(t.script)) {
-      log(`    ⏭️  ${t.name} — not found, skipping`);
-      continue;
-    }
-    const ok = run(`node "${t.script}"`, { ignoreError: true });
-    if (!ok) {
-      log(`    ⚠️  ${t.name} reported issues (non-fatal)`);
-    }
-  }
-  log("");
-
-  // ─── Complete ─────────────────────────────────────────────
-  const totalFiles = countFiles();
-  const pass1Files = countPass1Files();
-
-  log("");
-  const memoryReady = fileExists(path.join(PROJECT_ROOT, "claudeos-core/memory/decision-log.md"));
-  const rulesReady = fileExists(path.join(PROJECT_ROOT, ".claude/rules/60.memory/01.decision-log.md"));
-  const l4Status = (memoryReady && rulesReady) ? "memory + rules" : "partial";
-  log("╔════════════════════════════════════════════════════╗");
-  log("║  ✅ ClaudeOS-Core — Complete                       ║");
-  log("║                                                    ║");
-  log(`║   Files created:     ${pad(String(totalFiles), 29)}║`);
-  log(`║   Domains analyzed:  ${pad(totalGroups + " groups", 29)}║`);
-  log(`║   Analysis passes:   ${pad(pass1Files + " pass1 files", 29)}║`);
-  log(`║   L4 scaffolded:     ${pad(l4Status, 29)}║`);
-  log(`║   Output language:   ${pad(SUPPORTED_LANGS[lang] || lang, 29)}║`);
-  log(`║   Total time:        ${pad(formatElapsed(Date.now() - totalStart), 29)}║`);
-  log("║                                                    ║");
-  log("║   Verify anytime:                                  ║");
-  log("║   npx claudeos-core health                         ║");
-  log("║                                                    ║");
-  log("║   Start using:                                     ║");
-  log('║   "Create a CRUD for orders"                       ║');
-  log("╚════════════════════════════════════════════════════╝");
-  log("");
-}
-
-module.exports = { cmdInit, InitError };
+/**
+ * ClaudeOS-Core — Init Command
+ *
+ * Runs the full 4-Pass pipeline: analyze → merge → generate → memory scaffold.
+ * This is the main entry point for project bootstrapping.
+ */
+
+const fs = require("fs");
+const path = require("path");
+const {
+  TOOLS_DIR, PROJECT_ROOT, GENERATED_DIR,
+  SUPPORTED_LANGS, LANG_CODES, isValidLang,
+  log, header, run, runClaudePrompt, runClaudePromptAsync,
+  ensureDir, fileExists, readFile, injectProjectRoot,
+  pad, countFiles, countPass1Files,
+} = require("../lib/cli-utils");
+const { selectLangInteractive } = require("../lib/lang-selector");
+const { selectResumeMode } = require("../lib/resume-selector");
+
+const { EXPECTED_GUIDE_FILES } = require("../../lib/expected-guides");
+const { findMissingOutputs } = require("../../lib/expected-outputs");
+
+class InitError extends Error {
+  constructor(msg) { super(msg); this.name = "InitError"; }
+}
+
+function formatElapsed(ms) {
+  const sec = Math.floor(ms / 1000);
+  if (sec < 60) return `${sec}s`;
+  const min = Math.floor(sec / 60);
+  const rem = sec % 60;
+  return rem > 0 ? `${min}m ${rem}s` : `${min}m`;
+}
+
+// Creates an onTick/clearLine pair for long-running claude -p passes. We can
+// only observe progress externally (elapsed time, sometimes filesystem delta).
+// TTYs get a single \r-rewritten line; CI/piped stdout gets periodic new lines.
+// Modes via opts:
+//   - elapsed-only (no baselineCount): ⏳ label running... 45s
+//   - file delta (baselineCount set):  📝 label generating... 24 new files | 45s
+//   - fixed target (+ totalExpected):  📝 label generating... 8/12 files (67%) | 45s
+function makePassTicker(label, startTime, opts = {}) {
+  const isTTY = Boolean(process.stdout.isTTY);
+  const { baselineCount, totalExpected } = opts;
+  const trackFiles = typeof baselineCount === "number";
+  let lastLineLen = 0;
+  function onTick() {
+    const elapsed = formatElapsed(Date.now() - startTime);
+    let line;
+    if (!trackFiles) {
+      line = `    ⏳ ${label} running... ${elapsed} elapsed`;
+    } else {
+      const current = countFiles();
+      const delta = typeof current === "number" ? Math.max(0, current - baselineCount) : null;
+      let progress;
+      if (delta === null) progress = "? new files";
+      else if (typeof totalExpected === "number" && totalExpected > 0) {
+        const capped = Math.min(delta, totalExpected);
+        const pct = Math.round((capped / totalExpected) * 100);
+        progress = `${capped}/${totalExpected} files (${pct}%)`;
+      } else {
+        progress = `${delta} new files`;
+      }
+      line = `    📝 ${label} generating... ${progress} | ${elapsed} elapsed`;
+    }
+    if (isTTY) {
+      const pad = " ".repeat(Math.max(0, lastLineLen - line.length));
+      process.stdout.write("\r" + line + pad);
+      lastLineLen = line.length;
+    } else {
+      log(line);
+    }
+  }
+  function clearLine() {
+    if (isTTY && lastLineLen > 0) {
+      process.stdout.write("\r" + " ".repeat(lastLineLen) + "\r");
+      lastLineLen = 0;
+    }
+  }
+  return { onTick, clearLine, tickMs: isTTY ? 1000 : 15000 };
+}
+
+// ═══════════════════════════════════════════════════════════════════
+// v2.1: Pass 3 Split Runner
+// ═══════════════════════════════════════════════════════════════════
+//
+// Splits the monolithic Pass 3 into 4 sequential claude -p calls:
+//
+//   3a: Extract facts from pass2-merged.json into pass3a-facts.md
+//       (small document, becomes the shared context for 3b/3c/3d).
+//   3b: Generate CLAUDE.md + standard/ + .claude/rules/ (core files).
+//   3c: Generate skills/ + guide/.
+//   3d: Generate plan/ + database/ + mcp-guide/ (master plans + aux).
+//
+// Each call has fresh context, so the total output volume can far exceed
+// the model's context window without `Prompt is too long` failures.
+// pass3a-facts.md replaces pass2-merged.json as the cross-stage reference,
+// so cross-file consistency (which was the main advantage of the single-call
+// approach) is preserved.
+//
+// Marker schema (pass3-complete.json):
+//   {
+//     "completedAt": "<ISO timestamp of final stage>",
+//     "mode": "split",
+//     "groupsCompleted": ["3a", "3b", "3c", "3d"]
+//   }
+// Partial marker after interruption:
+//   { "mode": "split", "groupsCompleted": ["3a", "3b"] }
+// On re-run, stages in groupsCompleted are skipped.
+//
+// All helper references (injectProjectRoot, fileExists, runClaudePromptAsync,
+// etc.) are passed in via the ctx param rather than being captured by closure,
+// because this function lives outside cmdInit for readability.
+async function runPass3Split(ctx) {
+  const {
+    GENERATED_DIR, PROJECT_ROOT, TOOLS_DIR,
+    pass3Marker, claudeMdPath,
+    injectProjectRoot, readFile, fileExists,
+    runClaudePromptAsync, makePassTicker, formatElapsed,
+    log, countFiles,
+    EXPECTED_GUIDE_FILES, findMissingOutputs,
+    lang, stepTimes,
+  } = ctx;
+
+  const { writeFileSafe, readFileSafe, existsSafe } = require("../../lib/safe-fs");
+  const { moveStagedRules, countFilesRecursive } = require("../../lib/staged-rules");
+
+  const COMMON_DIR = path.join(TOOLS_DIR, "pass-prompts/templates/common");
+  const stagingDir = path.join(GENERATED_DIR, ".staged-rules");
+
+  // ─── Batch sub-division for 3b/3c on large projects ───────────
+  // Even with split mode, a single 3b call that generates standard/ + rules/
+  // for 50+ domains can still hit context overflow within that stage's
+  // session (output accumulation). We sub-divide 3b and 3c into batches of
+  // ~DOMAINS_PER_BATCH domains each when totalDomains > DOMAINS_PER_BATCH.
+  //
+  // 3a is never batched (single fact sheet).
+  // 3d is never batched (master plan aggregation).
+  //
+  // Threshold rationale: 15 domains ≈ 45-60 output files for 3b alone,
+  // which stays within the empirically safe single-session output range.
+  // Beyond 15 we split. ceil(N/15) batches, preserving order from
+  // domain-groups.json (already balanced by plan-installer).
+  const DOMAINS_PER_BATCH = 15;
+
+  function loadDomainOrder() {
+    // Returns an ordered list of domain names for batching 3b/3c.
+    // Primary source: domain-groups.json (already balanced).
+    // Fallback: project-analysis.json backendDomains + frontendDomains.
+    // Final fallback: empty array → single batch (no sub-division).
+    try {
+      const dgPath = path.join(GENERATED_DIR, "domain-groups.json");
+      if (fileExists(dgPath)) {
+        const dg = JSON.parse(readFile(dgPath));
+        const groups = Array.isArray(dg) ? dg : (dg && dg.groups);
+        if (Array.isArray(groups)) {
+          const flat = [];
+          for (const g of groups) {
+            const items = Array.isArray(g.domains) ? g.domains : (Array.isArray(g) ? g : []);
+            for (const d of items) {
+              const name = typeof d === "string" ? d : (d && d.name);
+              if (name) flat.push(name);
+            }
+          }
+          if (flat.length > 0) return flat;
+        }
+      }
+    } catch (_e) { /* fall through to analysis */ }
+
+    try {
+      const paPath = path.join(GENERATED_DIR, "project-analysis.json");
+      if (fileExists(paPath)) {
+        const pa = JSON.parse(readFile(paPath));
+        const backend = Array.isArray(pa.backendDomains) ? pa.backendDomains.map(d => d.name || d) : [];
+        const frontend = Array.isArray(pa.frontendDomains) ? pa.frontendDomains.map(d => d.name || d) : [];
+        return [...backend, ...frontend].filter(Boolean);
+      }
+    } catch (_e) { /* fall through */ }
+
+    return [];
+  }
+
+  function computeBatches(domainOrder) {
+    // Returns an array of batches, where each batch is an array of domain names.
+    // If total <= DOMAINS_PER_BATCH, returns a single-batch array so the caller
+    // can use the backward-compatible "3b"/"3c" marker names.
+    if (!domainOrder || domainOrder.length <= DOMAINS_PER_BATCH) {
+      return [domainOrder || []];
+    }
+    const batches = [];
+    for (let i = 0; i < domainOrder.length; i += DOMAINS_PER_BATCH) {
+      batches.push(domainOrder.slice(i, i + DOMAINS_PER_BATCH));
+    }
+    return batches;
+  }
+
+  const domainOrder = loadDomainOrder();
+  const batches = computeBatches(domainOrder);
+  const isBatched = batches.length > 1;
+
+  if (isBatched) {
+    log(`    📦 Batch sub-division enabled: ${domainOrder.length} domains → ${batches.length} batches per stage (3b, 3c)`);
+    for (let i = 0; i < batches.length; i++) {
+      log(`       • batch ${i + 1}: ${batches[i].slice(0, 3).join(", ")}${batches[i].length > 3 ? ", +" + (batches[i].length - 3) + " more" : ""}`);
+    }
+  }
+
+
+  // ─── Load existing marker to support resume mid-split ─────────
+  // If a prior split run completed 3a and 3b but crashed at 3c, we skip
+  // 3a and 3b automatically. This is the split-mode analog of Guard 3
+  // stale-marker detection in cmdInit.
+  let completedGroups = [];
+  if (fileExists(pass3Marker)) {
+    try {
+      const existing = JSON.parse(readFile(pass3Marker));
+      if (existing && existing.mode === "split" && Array.isArray(existing.groupsCompleted)) {
+        completedGroups = existing.groupsCompleted.slice();
+        if (completedGroups.length > 0) {
+          log(`    ↪️  Resuming Pass 3 split: ${completedGroups.length} stage(s) already done (${completedGroups.join(", ")})`);
+        }
+      } else if (existing && existing.mode !== "split") {
+        // Previous run was NOT split mode but marker exists and is valid.
+        // Caller (cmdInit) should have skipped us already — defensive no-op here.
+        log(`    ℹ️  Pass 3 marker found (non-split mode), skipping split runner`);
+        return;
+      }
+    } catch (_e) {
+      log("    ⚠️  pass3-complete.json malformed, starting Pass 3 split from scratch");
+      completedGroups = [];
+    }
+  }
+
+  // Helper: write marker after each stage so partial progress survives crashes.
+  function persistMarker(complete) {
+    const body = {
+      mode: "split",
+      groupsCompleted: completedGroups.slice(),
+      lastUpdatedAt: new Date().toISOString(),
+    };
+    if (complete) body.completedAt = body.lastUpdatedAt;
+    return writeFileSafe(pass3Marker, JSON.stringify(body, null, 2));
+  }
+
+  // Helper: build a stage prompt by concatenating the common header with
+  // the stack-specific body extracted from the original pass3-prompt.md.
+  // For v2.1 we reuse the full stack template body for 3b/3c/3d, letting
+  // the stage header restrict scope via its "Scope of this step" section.
+  // A future v2.2 could split the stack templates themselves into per-stage
+  // sections; for now this preserves template fidelity while bounding scope.
+  const pass3PromptFile = path.join(GENERATED_DIR, "pass3-prompt.md");
+  if (!fileExists(pass3PromptFile)) {
+    throw new InitError("pass3-prompt.md not found. Re-run plan-installer.");
+  }
+  const fullPass3Body = readFile(pass3PromptFile);
+
+  function buildStagePrompt(stageHeaderFile, includeStackBody) {
+    const headerPath = path.join(COMMON_DIR, stageHeaderFile);
+    if (!existsSafe(headerPath)) {
+      throw new InitError(
+        `Pass 3 split stage header missing: ${stageHeaderFile}\n` +
+        `    Expected at: ${headerPath}\n` +
+        `    Re-install claudeos-core or run plan-installer to regenerate templates.`
+      );
+    }
+    const header = readFileSafe(headerPath);
+    const stackBody = includeStackBody ? ("\n\n" + fullPass3Body) : "";
+    return injectProjectRoot(header + stackBody);
+  }
+
+  // Helper: build a batch scope note injected before "## Scope of this step"
+  // in 3b/3c stage prompts when the project has been sub-divided into batches.
+  // Tells Claude explicitly which domains to process in this particular call,
+  // and which common files to include vs skip.
+  function buildBatchScopeNote(stageKind, batchIndex, totalBatches, batchDomains) {
+    const isLastBatch = batchIndex === totalBatches - 1;
+    const domainList = batchDomains.map(d => `\`${d}\``).join(", ");
+
+    let note = `## Batch scope (${stageKind}-batch ${batchIndex + 1}/${totalBatches})\n\n`;
+    note += `This Pass 3 stage has been sub-divided into ${totalBatches} batches to avoid context overflow.\n`;
+    note += `**You are processing batch ${batchIndex + 1} of ${totalBatches}.**\n\n`;
+
+    if (stageKind === "3b") {
+      note += `**Domains in THIS batch**: ${domainList}\n\n`;
+      note += `**Rules for this batch**:\n`;
+      note += `1. CLAUDE.md and all common standard/ files (00.core/, 30.security-db/, 40.infra/, etc.) are ALREADY GENERATED by the 3b-core stage. DO NOT regenerate them.\n`;
+      note += `2. Generate standard/ entries ONLY for the domains listed above — one section per domain.\n`;
+      note += `3. Generate .claude/rules/ (via staging-override path) — ONLY domain-specific rule files for the domains listed above. Common rules are already generated by 3b-core.\n`;
+      note += `4. DO NOT generate standard/ or rules/ files for domains NOT in the above list — those are/will be processed in other batches.\n`;
+      note += `5. If a file you are about to write already exists with substantive content (Rule B), skip it silently — print \`[SKIP] <path>\` and move on.\n`;
+    } else if (stageKind === "3c") {
+      note += `**Domains in THIS batch**: ${domainList}\n\n`;
+      note += `**Rules for this batch**:\n`;
+      note += `1. ALL guide/ files (01.onboarding, 02.usage, 03.troubleshooting, 04.architecture) are ALREADY GENERATED by the 3c-core stage. DO NOT regenerate.\n`;
+      note += `2. Common skills (00.shared/, orchestrator SKILL.md) are ALREADY GENERATED by 3c-core. DO NOT regenerate.\n`;
+      note += `3. Generate skills/ entries ONLY for the domains listed above — typically under 10.backend-crud/ or 20.frontend-page/ with a per-domain subdirectory.\n`;
+      note += `4. DO NOT generate skills for domains NOT in the above list.\n`;
+      note += `5. Rule B idempotent skip applies: if a skill file already exists, print \`[SKIP] <path>\` and move on.\n`;
+    }
+
+    if (!isLastBatch) {
+      note += `\n**CRITICAL**: Other domains exist in the project but will be processed by LATER batches. Do not attempt to process them now — doing so will consume context that later batches need.\n`;
+    }
+
+    return note + "\n";
+  }
+
+  // Helper: build a "core common files only" prompt for 3b-core / 3c-core
+  // stages. Injected between the stage header and the stack body to restrict
+  // scope to project-wide files (CLAUDE.md, common standards, guides, shared
+  // skills) — explicitly excluding any domain-specific output that belongs
+  // to subsequent batch stages.
+  function buildStageCorePrompt(stageKind, batchesList) {
+    const totalBatches = batchesList.length;
+    const totalDomains = batchesList.reduce((sum, b) => sum + b.length, 0);
+
+    let coreNote = `## Core common files stage (${stageKind}-core)\n\n`;
+    coreNote += `This Pass 3 run has ${totalDomains} domains divided into ${totalBatches} batches.\n`;
+    coreNote += `To keep each stage's output within safe context limits, project-wide common\n`;
+    coreNote += `files are generated in THIS dedicated core stage, BEFORE the per-domain batches.\n\n`;
+
+    if (stageKind === "3b") {
+      coreNote += `**Scope of ${stageKind}-core**:\n`;
+      coreNote += `1. CLAUDE.md at the project root.\n`;
+      coreNote += `2. ALL standard/ files that are NOT tied to a specific domain:\n`;
+      coreNote += `   - claudeos-core/standard/00.core/*.md (project overview, architecture, conventions)\n`;
+      coreNote += `   - claudeos-core/standard/30.security-db/*.md\n`;
+      coreNote += `   - claudeos-core/standard/40.infra/*.md\n`;
+      coreNote += `   - claudeos-core/standard/50.verification/*.md\n`;
+      coreNote += `   - claudeos-core/standard/90.optional/*.md\n`;
+      coreNote += `   - (stack-specific common sections as defined in the pass3 template)\n`;
+      coreNote += `3. ALL rules files (via staging-override path .claude/rules → generated/.staged-rules):\n`;
+      coreNote += `   - common rules that apply regardless of domain.\n\n`;
+      coreNote += `**What NOT to generate in ${stageKind}-core**:\n`;
+      coreNote += `- Per-domain standard/ files (e.g. \`claudeos-core/standard/10.backend/order-api.md\` for a specific domain "order")\n`;
+      coreNote += `- Per-domain rules.\n`;
+      coreNote += `- Anything under claudeos-core/skills/, claudeos-core/guide/, claudeos-core/plan/ — those belong to later stages (3c-core, 3c-N, 3d).\n\n`;
+      coreNote += `**Per-domain files will be generated in subsequent 3b-1, 3b-2, ... batch stages.**\n`;
+    } else if (stageKind === "3c") {
+      coreNote += `**Scope of ${stageKind}-core**:\n`;
+      coreNote += `1. ALL guide/ files (project-wide, domain-independent):\n`;
+      coreNote += `   - claudeos-core/guide/01.onboarding/*.md\n`;
+      coreNote += `   - claudeos-core/guide/02.usage/*.md\n`;
+      coreNote += `   - claudeos-core/guide/03.troubleshooting/*.md\n`;
+      coreNote += `   - claudeos-core/guide/04.architecture/*.md\n`;
+      coreNote += `2. COMMON skills only:\n`;
+      coreNote += `   - claudeos-core/skills/00.shared/*\n`;
+      coreNote += `   - top-level orchestrator SKILL.md files (e.g. \`10.backend-crud/SKILL.md\` without any subfolder)\n\n`;
+      coreNote += `**What NOT to generate in ${stageKind}-core**:\n`;
+      coreNote += `- Per-domain skill sub-directories (e.g. \`10.backend-crud/scaffold-order-feature/\`) — those belong to 3c-1, 3c-2, ... batch stages.\n`;
+      coreNote += `- Anything under plan/, database/, mcp-guide/ — those belong to 3d.\n\n`;
+      coreNote += `**Per-domain skills will be generated in subsequent 3c-1, 3c-2, ... batch stages.**\n`;
+    }
+
+    coreNote += `\nIf you find yourself about to generate a domain-specific file in this stage: STOP. Emit \`[DEFER] <path> — will be generated in 3b-N / 3c-N batch\` and move on.\n\n`;
+
+    const headerFile = stageKind === "3b" ? "pass3b-core-header.md" : "pass3c-skills-guide-header.md";
+    const baseprompt = buildStagePrompt(headerFile, true);
+    return baseprompt.replace(/\n## Scope of this step/, `\n${coreNote}\n## Scope of this step`);
+  }
+
+  // Helper: build the prompt for 3d-aux (the only Pass 3d sub-stage that
+  // actually runs now). Master plan aggregation (standard/rules/skills/guide)
+  // was removed because master plans are an internal tool backup not consumed
+  // by Claude Code at runtime, and aggregating 30+ files in a single session
+  // was the primary source of "Prompt is too long" failures on mid-sized
+  // projects (observed on an 18-domain production run).
+  //
+  // The subStage parameter is kept for forward-compat: if a future version
+  // reintroduces master plans via Node-side aggregation, this helper can
+  // route the extra sub-stages back in.
+  function build3dSubPrompt(subStage) {
+    const baseprompt = buildStagePrompt("pass3d-plan-aux-header.md", true);
+
+    if (subStage !== "aux") {
+      throw new InitError(
+        `build3dSubPrompt called with unsupported subStage "${subStage}". ` +
+        `Master plan sub-stages (standard/rules/skills/guide) were removed in this version. ` +
+        `Only "aux" is supported.`
+      );
+    }
+
+    let scopeNote = `## 3d sub-stage: aux\n\n`;
+    scopeNote += `Pass 3d now produces only auxiliary documentation (database + mcp-guide). Master plan aggregation (standard/rules/skills/guide → plan/*-master.md) was removed because master plans are an internal tool backup not consumed by Claude Code at runtime, and aggregating many files in a single session was the primary cause of "Prompt is too long" failures.\n`;
+    scopeNote += `**You are processing sub-stage \`3d-aux\`.**\n\n`;
+
+    scopeNote += `### Scope of 3d-aux (exclusively)\n\n`;
+    scopeNote += `Generate ONLY auxiliary documentation:\n`;
+    scopeNote += `- \`claudeos-core/database/\` — schema docs and SQL reference. If pass3a-facts.md shows no database was detected, write a single \`README.md\` stub explaining this and stop.\n`;
+    scopeNote += `- \`claudeos-core/mcp-guide/\` — MCP integration guide. If no relevant MCP servers apply, write \`README.md\` stub and stop.\n\n`;
+    scopeNote += `**DO NOT touch \`claudeos-core/plan/\`** — master plans are no longer generated in this version. If the \`plan/\` directory exists from a previous run, leave it untouched (Rule B).\n\n`;
+    scopeNote += `Rule B applies. Absence of database/ or mcp-guide/ is warning-level, so README stubs are acceptable.\n`;
+
+    return baseprompt.replace(/\n## Scope of this step/, `\n${scopeNote}\n## Scope of this step`);
+  }
+
+
+  // Helper: run a single stage with progress ticker, staged-rules move,
+  // and (optionally) per-stage output validation.
+  async function runStage(stageId, label, promptStr, opts = {}) {
+    if (completedGroups.includes(stageId)) {
+      log(`    ⏭️  ${stageId} (${label}) already complete, skipping`);
+      return { skipped: true };
+    }
+
+    // Clear stale staging before each stage. 3a doesn't write rules so
+    // it's a no-op there; 3b/3c/3d may write staged rules.
+    if (fileExists(stagingDir)) {
+      fs.rmSync(stagingDir, { recursive: true, force: true });
+    }
+
+    log("");
+    log(`    🚀 ${stageId} — ${label}`);
+    const t0 = Date.now();
+    const ticker = makePassTicker(`Pass ${stageId}`, t0, { baselineCount: countFiles() });
+    const ok = await runClaudePromptAsync(promptStr, {
+      onTick: ticker.onTick,
+      tickMs: ticker.tickMs,
+    });
+    ticker.clearLine();
+    const elapsed = Date.now() - t0;
+    stepTimes.push(elapsed);
+
+    if (!ok) {
+      throw new InitError(
+        `Pass ${stageId} (${label}) failed. Check the claude error output above.\n` +
+        `    Already-completed stages are preserved; re-running will resume from ${stageId}.\n` +
+        `    If this persists, try: npx claudeos-core init --force`
+      );
+    }
+
+    // Move staged rules after stages that generate rule files (3b, 3c, 3d).
+    // Pass 3a only writes pass3a-facts.md, so no staging to move.
+    if (opts.expectsStagedRules) {
+      const move = moveStagedRules(PROJECT_ROOT);
+      if (move.failed > 0) {
+        log(`    ⚠️  ${stageId} staged-rules: ${move.moved} moved, ${move.failed} failed`);
+        for (const err of move.errors) log(`       • ${err}`);
+        throw new InitError(
+          `Pass ${stageId} finished but ${move.failed} rule file(s) could not be moved from staging.\n` +
+          `    This is usually a transient file-lock issue. Re-run \`npx claudeos-core init\`.`
+        );
+      } else if (move.moved > 0) {
+        log(`    📦 ${stageId} staged-rules: ${move.moved} rule files moved to .claude/rules/`);
+      }
+    }
+
+    // Per-stage output validation (delegates to opts.validate callback).
+    if (typeof opts.validate === "function") {
+      const problems = opts.validate();
+      if (problems && problems.length > 0) {
+        const preview = problems.slice(0, 5).map(p => `       • ${p}`).join("\n");
+        const more = problems.length > 5 ? `\n       • ... and ${problems.length - 5} more` : "";
+        throw new InitError(
+          `Pass ${stageId} (${label}) produced incomplete output:\n` +
+          preview + more + "\n" +
+          `    Already-completed stages are preserved. Re-run to retry from ${stageId}.`
+        );
+      }
+    }
+
+    // Mark stage complete and persist marker so a crash in a later stage
+    // doesn't lose this stage's progress.
+    completedGroups.push(stageId);
+    const persisted = persistMarker(false);
+    if (!persisted) {
+      throw new InitError(
+        `Pass ${stageId} succeeded but failed to persist progress to pass3-complete.json.\n` +
+        `    Check disk space / permissions on ${GENERATED_DIR}/.`
+      );
+    }
+
+    log(`    ✅ ${stageId} complete (${formatElapsed(elapsed)})`);
+    return { skipped: false, elapsed };
+  }
+
+  // ═══ Stage 3a: Extract facts ═══════════════════════════════════
+  const factsFile = path.join(GENERATED_DIR, "pass3a-facts.md");
+  await runStage("3a", "fact extraction", buildStagePrompt("pass3a-facts.md", false), {
+    expectsStagedRules: false,
+    validate: () => {
+      const problems = [];
+      if (!fileExists(factsFile)) {
+        problems.push("pass3a-facts.md was not created");
+      } else {
+        const content = readFileSafe(factsFile, "");
+        const stripped = content.replace(/^\uFEFF/, "").trim();
+        if (stripped.length < 500) {
+          problems.push(`pass3a-facts.md too short (${stripped.length} chars, expected >= 500)`);
+        }
+      }
+      return problems;
+    },
+  });
+
+  // ═══ Stage 3b: CLAUDE.md + standard/ + .claude/rules/ ═══════════
+  //
+  // Single batch (domains ≤ 15): keep legacy "3b" marker (backward-compatible).
+  // Multi-batch (domains > 15): run "3b-core" first, then "3b-1", "3b-2", ...
+  //
+  // Rationale for splitting 3b-core: if the first multi-batch stage handled
+  // "CLAUDE.md + common standards + 15 domains" in a single session, that
+  // single stage would hit ~70-80 files — close to 2x the observed overflow
+  // threshold (~40 files). Splitting the common files into their own stage
+  // keeps every stage under ~50 files.
+  if (isBatched) {
+    await runStage("3b-core", "core common files (CLAUDE.md + common standard + common rules)",
+      buildStageCorePrompt("3b", batches),
+      {
+        expectsStagedRules: true,
+        validate: () => {
+          const problems = [];
+          if (!fileExists(claudeMdPath)) {
+            problems.push("CLAUDE.md was not created");
+          }
+          const stdSentinel = path.join(PROJECT_ROOT, "claudeos-core/standard/00.core/01.project-overview.md");
+          if (!fileExists(stdSentinel)) {
+            problems.push("claudeos-core/standard/00.core/01.project-overview.md missing");
+          } else {
+            const c = readFileSafe(stdSentinel, "");
+            if (c.replace(/^\uFEFF/, "").trim().length === 0) {
+              problems.push("claudeos-core/standard/00.core/01.project-overview.md is empty");
+            }
+          }
+          // 3b-core generates only common rules — rules-count validation happens in 3b-N.
+          return problems;
+        },
+      }
+    );
+  }
+
+  // Per-domain batch loop.
+  // Single batch: stageId "3b", common files included (legacy behavior).
+  // Multi-batch: stageId "3b-1", "3b-2", ..., common files already handled in 3b-core.
+  for (let bi = 0; bi < batches.length; bi++) {
+    const batchDomains = batches[bi];
+    const stageId = isBatched ? `3b-${bi + 1}` : "3b";
+    const label = isBatched
+      ? `domain batch ${bi + 1}/${batches.length} (${batchDomains.length} domains)`
+      : "core files (CLAUDE.md + standard + rules)";
+
+    // Per-batch prompt: inject into the original 3b header the list of domains scoped to this batch.
+    // In multi-batch mode every batch generates "domain-specific files only" (common files handled in 3b-core).
+    const batchScopeNote = isBatched
+      ? buildBatchScopeNote("3b", bi, batches.length, batchDomains)
+      : "";
+    const baseprompt = buildStagePrompt("pass3b-core-header.md", true);
+    const promptWithScope = batchScopeNote
+      ? baseprompt.replace(/\n## Scope of this step/, `\n${batchScopeNote}\n## Scope of this step`)
+      : baseprompt;
+
+    await runStage(stageId, label, promptWithScope, {
+      expectsStagedRules: true,
+      validate: () => {
+        const problems = [];
+        // Single batch: validate common files here (no 3b-core exists).
+        if (!isBatched) {
+          if (!fileExists(claudeMdPath)) {
+            problems.push("CLAUDE.md was not created");
+          }
+          const stdSentinel = path.join(PROJECT_ROOT, "claudeos-core/standard/00.core/01.project-overview.md");
+          if (!fileExists(stdSentinel)) {
+            problems.push("claudeos-core/standard/00.core/01.project-overview.md missing");
+          } else {
+            const c = readFileSafe(stdSentinel, "");
+            if (c.replace(/^\uFEFF/, "").trim().length === 0) {
+              problems.push("claudeos-core/standard/00.core/01.project-overview.md is empty");
+            }
+          }
+        }
+        // For every batch, confirm rules/ was generated (at least one staged-rules move must succeed).
+        const rulesDir = path.join(PROJECT_ROOT, ".claude/rules");
+        const rulesCount = countFilesRecursive(rulesDir);
+        if (rulesCount === 0) {
+          problems.push(".claude/rules/ has 0 files (staging-override may have been ignored)");
+        }
+        return problems;
+      },
+    });
+  }
+
+  // ═══ Stage 3c: skills/ + guide/ ═══════════════════════════════
+  //
+  // Single batch (domains ≤ 15): keep legacy "3c" marker (guide + skills together).
+  // Multi-batch (domains > 15): run "3c-core" first, then "3c-1", "3c-2", ...
+  //
+  // Rationale for splitting 3c-core: the 9 guide files + common skills are fixed regardless of domain count.
+  // Mixing them into domain batches makes the first batch heavier than the others.
+  if (isBatched) {
+    await runStage("3c-core", "common guides and shared skills",
+      buildStageCorePrompt("3c", batches),
+      {
+        expectsStagedRules: true, // shared skills occasionally include rule files
+        validate: () => {
+          const problems = [];
+          const guideDir = path.join(PROJECT_ROOT, "claudeos-core/guide");
+          const missingGuides = EXPECTED_GUIDE_FILES.filter(g => {
+            const fp = path.join(guideDir, g);
+            if (!fileExists(fp)) return true;
+            try {
+              return fs.readFileSync(fp, "utf-8").replace(/^\uFEFF/, "").trim().length === 0;
+            } catch (_e) { return true; }
+          });
+          for (const g of missingGuides) {
+            problems.push(`claudeos-core/guide/${g} missing or empty`);
+          }
+          // Final skills/ validation is performed in the last domain batch.
+          return problems;
+        },
+      }
+    );
+  }
+
+  // Per-domain skills batch loop.
+  // Single batch: guide + skills together (legacy behavior).
+  // Multi-batch: skills only; guide was already handled in 3c-core.
+  for (let bi = 0; bi < batches.length; bi++) {
+    const batchDomains = batches[bi];
+    const stageId = isBatched ? `3c-${bi + 1}` : "3c";
+    const label = isBatched
+      ? `domain skills batch ${bi + 1}/${batches.length} (${batchDomains.length} domains)`
+      : "skills and guides";
+
+    const batchScopeNote = isBatched
+      ? buildBatchScopeNote("3c", bi, batches.length, batchDomains)
+      : "";
+    const baseprompt = buildStagePrompt("pass3c-skills-guide-header.md", true);
+    const promptWithScope = batchScopeNote
+      ? baseprompt.replace(/\n## Scope of this step/, `\n${batchScopeNote}\n## Scope of this step`)
+      : baseprompt;
+
+    await runStage(stageId, label, promptWithScope, {
+      expectsStagedRules: true, // skills occasionally include rule files
+      validate: () => {
+        const problems = [];
+        // Single batch: validate guide here as well (no 3c-core).
+        if (!isBatched) {
+          const guideDir = path.join(PROJECT_ROOT, "claudeos-core/guide");
+          const missingGuides = EXPECTED_GUIDE_FILES.filter(g => {
+            const fp = path.join(guideDir, g);
+            if (!fileExists(fp)) return true;
+            try {
+              return fs.readFileSync(fp, "utf-8").replace(/^\uFEFF/, "").trim().length === 0;
+            } catch (_e) { return true; }
+          });
+          for (const g of missingGuides) {
+            problems.push(`claudeos-core/guide/${g} missing or empty`);
+          }
+        }
+        // Final skills validation: full check only in the single-batch case or the last multi-batch.
+        if (!isBatched || bi === batches.length - 1) {
+          const { hasNonEmptyMdRecursive } = require("../../lib/expected-outputs");
+          const skillsDir = path.join(PROJECT_ROOT, "claudeos-core/skills");
+          if (!fileExists(skillsDir) || !hasNonEmptyMdRecursive(skillsDir)) {
+            problems.push("claudeos-core/skills/ has no non-empty .md files");
+          }
+        }
+        return problems;
+      },
+    });
+  }
+
+  // ═══ Stage 3d: plan/ + database/ + mcp-guide/ ═════════════════
+  //
+  // 3d used to aggregate standard/rules/skills/guide into a master plan
+  // and generate database/mcp-guide stubs. But the master plan itself was
+  // an internal backup/management file never loaded by Claude Code at runtime,
+  // and at high domain counts the single-session aggregation caused "Prompt is
+  // too long" failures (at 18 domains, 3d-standard failed at the 32-file mark).
+  // Dropping master plan generation is the correct call for stability, and
+  // users can aggregate manually with their own script when needed.
+  //
+  // As a result, 3d only keeps the aux stage:
+  //   3d-aux → database/ + mcp-guide/ (project-specific stub descriptions)
+
+  // 3d-aux: database/ + mcp-guide/ (absence is warning-level)
+  await runStage("3d-aux", "aux docs (database + mcp-guide)",
+    build3dSubPrompt("aux"),
+    {
+      expectsStagedRules: false,
+      validate: () => [],
+    }
+  );
+
+  // ─── Final marker: all 4 stages done ─────────────────────────
+  const finalPersist = persistMarker(true);
+  if (!finalPersist) {
+    throw new InitError(
+      "Pass 3 split all stages complete but failed to write final marker.\n" +
+      `    Check disk space / permissions on ${GENERATED_DIR}/.`
+    );
+  }
+  // Total stage count
+  // 3a (1) + 3b (1 single or core+N) + 3c (1 single or core+N) + 3d-aux (1)
+  // Single batch: 1 + 1 + 1 + 1 = 4
+  // Multi-batch: 1 + (1 + N) + (1 + N) + 1 = 2N + 4
+  const three3dStages = 1; // aux only (master plan aggregation removed)
+  const totalStages = isBatched
+    ? (1 + 1 + batches.length + 1 + batches.length + three3dStages)
+    : (1 + 1 + 1 + three3dStages);
+  log(`    🎉 Pass 3 split complete: ${completedGroups.length}/${totalStages} stages successful`);
+}
+
+async function cmdInit(parsedArgs) {
+  const totalStart = Date.now();
+  // Tracks whether we just wiped generated state via --force or "fresh" resume
+  // mode. Used by the Pass 3 backfill guard below: fresh/force explicitly
+  // means "regenerate from scratch", so a leftover CLAUDE.md from a prior run
+  // must NOT cause Pass 3 to be skipped via the v1.7.x migration backfill.
+  let wasFreshClean = false;
+
+  // ─── Prerequisites check ───────────────────────────────────
+  const hasProjectMarker = [".git", "package.json", "build.gradle", "build.gradle.kts", "pom.xml", "pyproject.toml", "requirements.txt"].some(
+    m => fs.existsSync(path.join(PROJECT_ROOT, m))
+  );
+  if (!hasProjectMarker) {
+    log(`\n  ⚠️  Warning: ${PROJECT_ROOT} does not look like a project root.`);
+    log("  No .git, package.json, build.gradle, or pom.xml found.");
+    log("  Run this command from your project directory.\n");
+  }
+
+  const nodeVersion = parseInt(process.versions.node.split(".")[0]);
+  if (nodeVersion < 18) {
+    throw new InitError(`Node.js v18+ required (current: v${process.versions.node})\n  Install: https://nodejs.org/`);
+  }
+
+  const claudeExists = run("claude --version", { silent: true, ignoreError: true });
+  if (!claudeExists) {
+    throw new InitError("Claude Code CLI not found.\n  Install: https://code.claude.com/docs/en/overview\n  Then run: claude (and complete authentication)");
+  }
+
+  // Verify Claude is authenticated (quick prompt test)
+  const claudeAuth = run('claude -p "echo ok"', { silent: true, ignoreError: true });
+  if (!claudeAuth) {
+    throw new InitError("Claude Code may not be authenticated.\n  Run: claude (and complete authentication)\n  Then retry: npx claudeos-core init");
+  }
+
+  // ─── Language selection (required) ────────────────────────────
+  let lang = parsedArgs.lang;
+  if (!lang) {
+    lang = await selectLangInteractive();
+  }
+  if (!lang) {
+    throw new InitError("Cancelled.");
+  }
+  if (!isValidLang(lang)) {
+    throw new InitError(`Unsupported language: "${lang}"\n  Supported: ${LANG_CODES.join(", ")}`);
+  }
+
+  // Early incompatibility check: CLAUDEOS_SKIP_TRANSLATION is a test-only
+  // env var that short-circuits lib/memory-scaffold.js translation path.
+  // If set AND the user chose a non-English language, Pass 4's static fallback
+  // and gap-fill would throw mid-run with a confusing "translation skipped"
+  // error. Fail fast here with a clear message so the user can unset the var
+  // or pick --lang en before the pipeline starts.
+  if (process.env.CLAUDEOS_SKIP_TRANSLATION === "1" && lang !== "en") {
+    throw new InitError(
+      `CLAUDEOS_SKIP_TRANSLATION=1 is set but --lang='${lang}' requires translation.\n` +
+      `  This env var is a test-only escape hatch that blocks calls to \`claude -p\`\n` +
+      `  from lib/memory-scaffold.js. Pass 4 would crash later with a hard-to-\n` +
+      `  diagnose error.\n\n` +
+      `  Either unset the env var:    unset CLAUDEOS_SKIP_TRANSLATION\n` +
+      `  Or run with English output:  npx claudeos-core init --lang en`
+    );
+  }
+
+  process.env.CLAUDEOS_LANG = lang;
+
+  // ─── Resume / Fresh selection ────────────────────────────
+  if (fs.existsSync(GENERATED_DIR)) {
+    const existingPass1 = fs.readdirSync(GENERATED_DIR).filter(f => f.startsWith("pass1-") && f.endsWith(".json"));
+    const pass2Exists = fileExists(path.join(GENERATED_DIR, "pass2-merged.json"));
+
+    if (existingPass1.length > 0 || pass2Exists) {
+      if (parsedArgs.force) {
+        // --force: clean all generated files for truly fresh start
+        const genFiles = fs.readdirSync(GENERATED_DIR).filter(f => f.endsWith(".json") || f.endsWith(".md"));
+        for (const f of genFiles) fs.unlinkSync(path.join(GENERATED_DIR, f));
+        // Also clean any leftover .staged-rules/ from a prior crashed run
+        // (only .json/.md are unlinked above; directories aren't touched).
+        const stagedDir = path.join(GENERATED_DIR, ".staged-rules");
+        if (fileExists(stagedDir)) fs.rmSync(stagedDir, { recursive: true, force: true });
+        // Also wipe .claude/rules/ so Guard 2 (zero-rules detection) can't
+        // false-negative on stale rules from a previous run when the fresh
+        // Pass 3 run fails silently (e.g. Claude ignores staging-override).
+        // Step [2] recreates the subdirs from scratch. Any manual edits the
+        // user made to rule files are lost — acceptable under --force
+        // ("truly fresh start").
+        const rulesDir = path.join(PROJECT_ROOT, ".claude/rules");
+        if (fileExists(rulesDir)) fs.rmSync(rulesDir, { recursive: true, force: true });
+        wasFreshClean = true;
+        log("  🔄 Previous results deleted (--force)\n");
+      } else {
+        // v2.2.0 upgrade detection: if project was generated with older claudeos-core
+        // (pre-2.2.0), default "resume" mode will skip regeneration of existing files
+        // per Rule B idempotency, meaning v2.2.0 structural improvements will NOT be
+        // picked up. Detect this case by checking CLAUDE.md for v2.2.0 markers.
+        const claudeMd = path.join(PROJECT_ROOT, "CLAUDE.md");
+        if (fileExists(claudeMd)) {
+          try {
+            const content = fs.readFileSync(claudeMd, "utf-8");
+            // v2.2.0 scaffold enforces EXACTLY 8 top-level `##` sections.
+            // Pre-v2.2.0 CLAUDE.md files typically carry 9+ sections (extra
+            // "Rules Summary" / "Common Rules" / "Required to Observe"
+            // blocks that v2.2.0 forbids). Counting `^## ` headings is a
+            // language-independent heuristic that works across all 10
+            // supported output languages. False positive (an existing
+            // 8-section pre-v2.2.0 CLAUDE.md) is acceptable — the user
+            // simply won't see the upgrade warning and can still run
+            // `--force` manually.
+            const sectionCount = (content.match(/^## /gm) || []).length;
+            const hasV220Section8 = sectionCount === 8;
+            if (!hasV220Section8) {
+              log("\n  ⚠️  v2.2.0 upgrade detected");
+              log("  ─────────────────────────");
+              log("  Your existing CLAUDE.md was generated with an older claudeos-core version.");
+              log("  v2.2.0 introduces structural changes that the default 'resume' mode");
+              log("  CANNOT apply because existing files are preserved under Rule B (idempotency).");
+              log("");
+              log("  To fully adopt v2.2.0, choose one of:");
+              log("    1. Rerun with --force:   npx claudeos-core init --force");
+              log("       (overwrites generated files; your memory/ content is preserved)");
+              log("    2. Choose 'fresh' below  (equivalent to --force)");
+              log("");
+              log("  See CHANGELOG.md Migration section for full details.\n");
+            }
+          } catch (_) { /* Read error is non-fatal; proceed to resume prompt */ }
+        }
+
+        const status = { pass1Done: existingPass1.length, pass2Done: pass2Exists };
+        const mode = await selectResumeMode(lang, status);
+        if (!mode) throw new InitError("Cancelled.");
+        if (mode === "fresh") {
+          for (const f of existingPass1) fs.unlinkSync(path.join(GENERATED_DIR, f));
+          if (pass2Exists) fs.unlinkSync(path.join(GENERATED_DIR, "pass2-merged.json"));
+          // Also reset pass 3 & pass 4 markers so they re-run
+          const pass3M = path.join(GENERATED_DIR, "pass3-complete.json");
+          const pass4M = path.join(GENERATED_DIR, "pass4-memory.json");
+          if (fileExists(pass3M)) fs.unlinkSync(pass3M);
+          if (fileExists(pass4M)) fs.unlinkSync(pass4M);
+          // Clean .staged-rules/ leftover from a prior crashed run (same reason as --force branch).
+          const stagedDir = path.join(GENERATED_DIR, ".staged-rules");
+          if (fileExists(stagedDir)) fs.rmSync(stagedDir, { recursive: true, force: true });
+          // Wipe .claude/rules/ for the same Guard 2 false-negative reason as
+          // the --force branch. Step [2] recreates the subdirs; any manual
+          // edits are lost — acceptable under an explicit "fresh" choice.
+          const rulesDir = path.join(PROJECT_ROOT, ".claude/rules");
+          if (fileExists(rulesDir)) fs.rmSync(rulesDir, { recursive: true, force: true });
+          wasFreshClean = true;
+        } else if (mode === "continue" && existingPass1.length === 0 && pass2Exists) {
+          // pass2 exists but no pass1 → pass2 is stale, force re-run
+          fs.unlinkSync(path.join(GENERATED_DIR, "pass2-merged.json"));
+          log("    ⚠️  pass2-merged.json deleted (no pass1 files to continue from)");
+        }
+      }
+    }
+  }
+
+  log("");
+  log("╔════════════════════════════════════════════════════╗");
+  log("║       ClaudeOS-Core — Bootstrap (4-Pass)          ║");
+  log("╚════════════════════════════════════════════════════╝");
+  log(`    Project root: ${PROJECT_ROOT}`);
+  log(`    Language:     ${SUPPORTED_LANGS[lang]} (${lang})`);
+  log("");
+
+  // ─── [1] Install dependencies ────────────────────────────────
+  header("[1] Installing dependencies...");
+  if (!fileExists(path.join(TOOLS_DIR, "node_modules"))) {
+    run("npm install --silent", { cwd: TOOLS_DIR });
+  }
+  log("    ✅ Done\n");
+
+  // ─── [2] Create directory structure ─────────────────────────
+  header("[2] Creating directory structure...");
+  const dirs = [
+    ".claude/rules/00.core",
+    ".claude/rules/10.backend",
+    ".claude/rules/20.frontend",
+    ".claude/rules/30.security-db",
+    ".claude/rules/40.infra",
+    ".claude/rules/50.sync",
+    "claudeos-core/generated",
+    "claudeos-core/standard/00.core",
+    "claudeos-core/standard/10.backend-api",
+    "claudeos-core/standard/20.frontend-ui",
+    "claudeos-core/standard/30.security-db",
+    "claudeos-core/standard/40.infra",
+    "claudeos-core/standard/50.verification",
+    "claudeos-core/standard/90.optional",
+    "claudeos-core/skills/00.shared",
+    "claudeos-core/skills/10.backend-crud/scaffold-crud-feature",
+    "claudeos-core/skills/20.frontend-page/scaffold-page-feature",
+    "claudeos-core/skills/50.testing",
+    "claudeos-core/skills/90.experimental",
+    "claudeos-core/guide/01.onboarding",
+    "claudeos-core/guide/02.usage",
+    "claudeos-core/guide/03.troubleshooting",
+    "claudeos-core/guide/04.architecture",
+    "claudeos-core/database",
+    "claudeos-core/mcp-guide",
+    "claudeos-core/memory",
+    ".claude/rules/60.memory",
+  ];
+  for (const d of dirs) {
+    ensureDir(path.join(PROJECT_ROOT, d));
+  }
+  log("    ✅ Done\n");
+
+  // ─── [3] Run plan-installer ─────────────────────────
+  header("[3] Analyzing project (plan-installer)...");
+  run(`node "${path.join(TOOLS_DIR, "plan-installer/index.js")}"`);
+  log("");
+
+  // ─── [4] Pass 1: Deep analysis per domain group ──────────────────
+  header("[4] Pass 1 — Deep analysis per domain group...");
+
+  let domainGroups;
+  try {
+    domainGroups = JSON.parse(
+      readFile(path.join(GENERATED_DIR, "domain-groups.json"))
+    );
+  } catch (e) {
+    throw new InitError(`domain-groups.json is missing or malformed: ${e.message}\n    Re-run plan-installer or check claudeos-core/generated/`);
+  }
+  const totalGroups = domainGroups.totalGroups;
+  if (!totalGroups || typeof totalGroups !== "number" || totalGroups < 1) {
+    throw new InitError(`domain-groups.json has invalid totalGroups: ${totalGroups}\n    Re-run plan-installer or check claudeos-core/generated/`);
+  }
+
+  // Load pass1 prompts by type
+  const pass1Prompts = {};
+  for (const type of ["backend", "frontend"]) {
+    const promptFile = path.join(GENERATED_DIR, `pass1-${type}-prompt.md`);
+    if (fileExists(promptFile)) {
+      pass1Prompts[type] = readFile(promptFile);
+    }
+  }
+  // Single-stack backward compatibility
+  if (Object.keys(pass1Prompts).length === 0) {
+    const fallback = path.join(GENERATED_DIR, "pass1-prompt.md");
+    if (fileExists(fallback)) pass1Prompts["backend"] = readFile(fallback);
+  }
+
+  if (!domainGroups.groups || totalGroups !== domainGroups.groups.length) {
+    throw new InitError(`domain-groups.json is malformed: expected ${totalGroups} groups, found ${domainGroups.groups ? domainGroups.groups.length : 0}`);
+  }
+
+  // Progress tracking: Pass 1 (N groups) + Pass 2 + Pass 3 + Pass 4 = totalSteps
+  const totalSteps = totalGroups + 3;
+  let completedSteps = 0;
+  const stepTimes = [];
+  const passStart = Date.now();
+
+  function progressBar(step, label) {
+    const pct = Math.round((step / totalSteps) * 100);
+    const elapsed = Date.now() - passStart;
+    let eta = "";
+    if (stepTimes.length > 0) {
+      const avgMs = stepTimes.reduce((a, b) => a + b, 0) / stepTimes.length;
+      const remaining = (totalSteps - step) * avgMs;
+      eta = ` | ETA ${formatElapsed(remaining)}`;
+    }
+    const filled = Math.round(pct / 5);
+    const bar = "█".repeat(filled) + "░".repeat(20 - filled);
+    log(`    [${bar}] ${pct}% (${step}/${totalSteps}) ${formatElapsed(elapsed)}${eta} — ${label}`);
+  }
+
+  for (let i = 1; i <= totalGroups; i++) {
+    const group = domainGroups.groups[i - 1];
+    const domainList = (group.domains || []).join(", ") || "(unknown)";
+    const estFiles = group.estimatedFiles || 0;
+    const groupType = group.type || "backend";
+    const icon = groupType === "frontend" ? "🎨" : "⚙️";
+
+    log("");
+    log(
+      `    ${icon} [Pass 1-${i}/${totalGroups}] ${groupType}: ${domainList} (~${estFiles} files)`
+    );
+
+    const pass1Json = path.join(GENERATED_DIR, `pass1-${i}.json`);
+    if (fileExists(pass1Json)) {
+      try {
+        const existing = JSON.parse(readFile(pass1Json));
+        if (existing && existing.analysisPerDomain) {
+          log(`    ⏭️  pass1-${i}.json already exists, skipping`);
+          completedSteps++;
+          continue;
+        }
+      } catch (_e) { /* malformed — re-run */ }
+      log(`    ⚠️  pass1-${i}.json exists but is malformed, re-running`);
+    }
+
+    // Select prompt for this type
+    const template = pass1Prompts[groupType] || pass1Prompts["backend"];
+    if (!template) {
+      throw new InitError(`No pass1 prompt found for type: ${groupType}`);
+    }
+
+    // Placeholder substitution — use replacement functions (not string form)
+    // so that `$`, `$1`, `$&`, `$$` etc. in domainList are preserved as
+    // literal characters rather than interpreted as regex back-references.
+    // (Same bug class as bug #18 in lib/plan-parser.js replaceFileBlock.)
+    let prompt = template
+      .replace(/\{\{DOMAIN_GROUP\}\}/g, () => domainList)
+      .replace(/\{\{PASS_NUM\}\}/g, () => String(i));
+    prompt = injectProjectRoot(prompt);
+
+    const t1 = Date.now();
+    const ticker1 = makePassTicker(`Pass 1-${i}/${totalGroups}`, t1);
+    const ok = await runClaudePromptAsync(prompt, {
+      onTick: ticker1.onTick,
+      tickMs: ticker1.tickMs,
+    });
+    ticker1.clearLine();
+    const elapsed1 = Date.now() - t1;
+    stepTimes.push(elapsed1);
+
+    if (!ok) {
+      throw new InitError(`Pass 1-${i} failed. Check the claude error output above.\n    If this persists, try: npx claudeos-core init --force`);
+    }
+
+    if (!fileExists(pass1Json)) {
+      throw new InitError(`pass1-${i}.json was not created. Claude may have run but not produced expected output.\n    Ensure the prompt instructs Claude to write to claudeos-core/generated/pass1-${i}.json`);
+    }
+
+    completedSteps++;
+    progressBar(completedSteps, `pass1-${i}.json created (${formatElapsed(elapsed1)})`);
+  }
+  log("");
+
+  // ─── [5] Pass 2: Merge analysis results ──────────────────────
+  header("[5] Pass 2 — Merging analysis results...");
+
+  const pass2Json = path.join(GENERATED_DIR, "pass2-merged.json");
+
+  // H3: resume-path structural validation. existsSync alone isn't enough —
+  // a prior crashed run may have left a skeleton (`{}`) or malformed JSON
+  // that passes existsSync but silently poisons Pass 3 (which parses this
+  // file as its analysis input). Mirrors pass1's malformed-detection at
+  // the pass1 loop above, and the "<5 top-level keys = INSUFFICIENT_KEYS"
+  // threshold from pass-json-validator/index.js (ERROR level).
+  let pass2IsValid = false;
+  if (fileExists(pass2Json)) {
+    try {
+      const existing = JSON.parse(readFile(pass2Json));
+      if (existing && typeof existing === "object" && !Array.isArray(existing)
+          && Object.keys(existing).length >= 5) {
+        pass2IsValid = true;
+      }
+    } catch (_e) { /* malformed — fall through to re-run */ }
+    if (!pass2IsValid) {
+      log("    ⚠️  pass2-merged.json exists but is malformed or incomplete (<5 top-level keys), re-running");
+      try { fs.unlinkSync(pass2Json); } catch (_e) { /* best-effort cleanup */ }
+    }
+  }
+
+  if (pass2IsValid) {
+    log("    ⏭️  pass2-merged.json already exists, skipping");
+    completedSteps++;
+  } else {
+    const pass2PromptFile = path.join(GENERATED_DIR, "pass2-prompt.md");
+    if (!fileExists(pass2PromptFile)) {
+      throw new InitError("pass2-prompt.md not found. Re-run plan-installer.");
+    }
+    let prompt = injectProjectRoot(readFile(pass2PromptFile));
+
+    const t2 = Date.now();
+    const ticker2 = makePassTicker("Pass 2", t2);
+    const ok = await runClaudePromptAsync(prompt, {
+      onTick: ticker2.onTick,
+      tickMs: ticker2.tickMs,
+    });
+    ticker2.clearLine();
+    const elapsed2 = Date.now() - t2;
+    stepTimes.push(elapsed2);
+
+    if (!ok) {
+      throw new InitError("Pass 2 failed. Check the claude error output above.\n    If this persists, try: npx claudeos-core init --force");
+    }
+
+    if (!fileExists(pass2Json)) {
+      throw new InitError("pass2-merged.json was not created. Claude may have run but not produced expected output.");
+    }
+
+    completedSteps++;
+    progressBar(completedSteps, `pass2-merged.json created (${formatElapsed(elapsed2)})`);
+  }
+  log("");
+
+  // ─── [5.5] v2.1: Build pass3-context.json (slim summary for Pass 3) ──
+  // Writes a small (<5 KB) structured summary derived from project-analysis.json
+  // plus pass2-merged.json signals (size, top-level keys). Pass 3 prompts
+  // reference this INSTEAD OF re-reading pass2-merged.json repeatedly, which
+  // was the primary cause of `Prompt is too long` failures on large projects.
+  //
+  // Silent-on-failure: if pass3-context-builder returns null (e.g.
+  // project-analysis.json missing), we skip writing and let Pass 3 fall back
+  // to the pre-v2.1 behavior of reading pass2-merged.json directly.
+  try {
+    const { buildPass3Context } = require("../../plan-installer/pass3-context-builder");
+    const pass3Ctx = buildPass3Context(GENERATED_DIR);
+    if (pass3Ctx) {
+      const { writeFileSafe: wfsCtx } = require("../../lib/safe-fs");
+      const ctxPath = path.join(GENERATED_DIR, "pass3-context.json");
+      const wrote = wfsCtx(ctxPath, JSON.stringify(pass3Ctx, null, 2));
+      if (wrote) {
+        const sizeKB = Math.round(JSON.stringify(pass3Ctx).length / 1024);
+        const p2KB = pass3Ctx.pass2Merged.sizeKB;
+        log(`    📄 pass3-context.json built (${sizeKB} KB summary of ${p2KB} KB pass2-merged.json)`);
+        if (pass3Ctx.pass2Merged.large) {
+          log(`    ⚠️  pass2-merged.json is large (${p2KB} KB). Pass 3 will rely heavily on pass3-context.json to avoid context overflow.`);
+        }
+      }
+    }
+  } catch (e) {
+    log(`    ⚠️  pass3-context.json build skipped: ${e.message} (Pass 3 will fall back to pass2-merged.json)`);
+  }
+  log("");
+
+  // ─── [6] Pass 3: Generate + verify ─────────────────────────
+  header("[6] Pass 3 — Generating all files...");
+
+  const pass3Marker = path.join(GENERATED_DIR, "pass3-complete.json");
+  const claudeMdPath = path.join(PROJECT_ROOT, "CLAUDE.md");
+
+  // v1.7.1 → v1.7.2 migration: if CLAUDE.md exists from prior version but marker
+  // is missing, backfill marker to preserve user's existing output.
+  //
+  // Gated by !wasFreshClean: --force and "fresh" resume mode wipe the marker
+  // on purpose to force Pass 3 to re-run. They do NOT delete CLAUDE.md (user
+  // may have manual edits worth preserving in the continue flow), so without
+  // this gate the backfill would fire on a fresh run, re-write the marker,
+  // and Pass 3 would skip — leaving stale CLAUDE.md + regenerated pass1/2 +
+  // wiped rules/, which fails sync-checker and content-validator.
+  if (!wasFreshClean && fileExists(claudeMdPath) && !fileExists(pass3Marker) && fileExists(path.join(GENERATED_DIR, "pass2-merged.json"))) {
+    const { writeFileSafe: wfsMig } = require("../../lib/safe-fs");
+    const backfillOk = wfsMig(pass3Marker, JSON.stringify({
+      completedAt: new Date().toISOString(),
+      backfilled: true,
+      reason: "CLAUDE.md exists from prior version; marker backfilled to prevent regeneration. To force re-run, use --force or pick 'fresh' in the resume prompt.",
+    }, null, 2));
+    if (backfillOk) {
+      log("    ℹ️  Detected existing CLAUDE.md — Pass 3 marker backfilled (use --force to regenerate)");
+    } else {
+      log("    ⚠️  CLAUDE.md exists but marker backfill failed — Pass 3 will re-run");
+    }
+  }
+
+  // Stale marker detection (Pass 3). Drops the marker and re-runs Pass 3 if
+  // any of the following is true:
+  //   (a) CLAUDE.md was deleted externally (original check),
+  //   (b) any of EXPECTED_GUIDE_FILES is missing or BOM-aware empty,
+  //   (c) any entry in expected-outputs (standard sentinel / skills / plan) is
+  //       missing or empty.
+  //
+  // (b) and (c) were previously only enforced as Pass 3 post-generation Guards
+  // 3 (H2/H1), which gate marker *creation* on fresh runs. Projects that were
+  // initialized on a pre-v2.0.0 release (before those guards existed) can end
+  // up with a marker on disk even though guide/ or standard/skills/plan are
+  // empty. Without this stale check, such projects hit a permanent
+  // content-validator fail loop because init sees the marker and skips Pass 3
+  // forever. This mirrors the Pass 4 dropStalePass4Marker pattern below.
+  //
+  // Unlink is surfaced as InitError on failure (symmetric with Pass 4).
+  // Silently ignoring the error would leave the stale marker in place, and
+  // the `if (fileExists(pass3Marker))` check below would accept it — skipping
+  // Pass 3 while outputs are still incomplete. That silent-skip is the exact
+  // bug class this audit round closes.
+  function dropStalePass3Marker(reasonLog) {
+    log(reasonLog);
+    try { fs.unlinkSync(pass3Marker); } catch (e) {
+      log(`    ❌ Failed to delete stale pass3-complete.json: ${e.code || e.message}`);
+      throw new InitError(
+        `Could not delete stale pass3-complete.json at:\n    ${pass3Marker}\n` +
+        `    The file is likely locked by another process (Windows antivirus or a file-watcher).\n` +
+        `    Close any editor/AV scanner holding the file and re-run \`npx claudeos-core init\`.`
+      );
+    }
+  }
+  if (fileExists(pass3Marker)) {
+    // v2.1.1: protect split-mode partial markers.
+    // An in-progress marker of the form { mode: "split", groupsCompleted: [...], completedAt: undefined }
+    // must NOT be treated as stale. When the pipeline has normally completed
+    // only through 3b, guide/skills/plan are empty, so the legacy check
+    // falsely flagged the marker as stale. Deleting it made runPass3Split
+    // lose track of completed stages and re-run from 3a (correct but wastes ~2x tokens).
+    let markerIsSplitPartial = false;
+    try {
+      const parsed = JSON.parse(readFile(pass3Marker));
+      markerIsSplitPartial =
+        parsed &&
+        parsed.mode === "split" &&
+        Array.isArray(parsed.groupsCompleted) &&
+        !parsed.completedAt;
+    } catch (_e) {
+      // malformed marker → fall through to the stale check (legacy behavior)
+    }
+
+    if (markerIsSplitPartial) {
+      log(`    ↪️  split-mode partial marker detected — runPass3Split will resume`);
+    } else if (!fileExists(claudeMdPath)) {
+      dropStalePass3Marker("    ⚠️  pass3-complete.json exists but CLAUDE.md is missing — treating marker as stale, re-running Pass 3");
+    } else {
+      const guideDirForStale = path.join(PROJECT_ROOT, "claudeos-core/guide");
+      const staleMissingGuides = EXPECTED_GUIDE_FILES.filter(g => {
+        const fp = path.join(guideDirForStale, g);
+        if (!fileExists(fp)) return true;
+        try {
+          return fs.readFileSync(fp, "utf-8").replace(/^\uFEFF/, "").trim().length === 0;
+        } catch (_e) { return true; }
+      });
+      if (staleMissingGuides.length > 0) {
+        dropStalePass3Marker(
+          `    ⚠️  pass3-complete.json exists but ${staleMissingGuides.length}/${EXPECTED_GUIDE_FILES.length} guide files are missing or empty — treating marker as stale, re-running Pass 3`
+        );
+      } else {
+        const staleMissingOutputs = findMissingOutputs(PROJECT_ROOT);
+        if (staleMissingOutputs.length > 0) {
+          dropStalePass3Marker(
+            `    ⚠️  pass3-complete.json exists but ${staleMissingOutputs.length} required output(s) are missing or empty — treating marker as stale, re-running Pass 3`
+          );
+        }
+      }
+    }
+  }
+
+  // Pass 3 split mode resolution.
+  //
+  // Pass 3 runs as 4 sequential `claude -p` calls (3a facts, 3b core, 3c
+  // skills+guide, 3d-aux database/mcp-guide), each with fresh context.
+  // This eliminates `Prompt is too long` failures by making output
+  // accumulation overflow structurally impossible — each stage starts
+  // with a clean context window. For projects with 16+ domains, 3b and 3c
+  // are further split into core + batched sub-stages.
+  //
+  // Single-call mode (previously toggled by CLAUDEOS_PASS3_SPLIT=0) was
+  // removed because empirical data showed it failed reliably on projects
+  // with more than ~5 domains (output accumulation overflow was not
+  // predictable from input size alone), and split mode is structurally
+  // immune to this failure mode with bounded token overhead.
+  log(`    🚀 Pass 3 split mode (3a → 3b → 3c → 3d-aux)`);
+  try {
+    const ctxPath = path.join(GENERATED_DIR, "pass3-context.json");
+    if (fileExists(ctxPath)) {
+      const ctx = JSON.parse(readFile(ctxPath));
+      const rec = ctx && ctx.splitRecommendation;
+      if (rec) {
+        log(`       • estimated ${rec.estimatedFileCount} files from ${rec.totalDomains} domains`);
+      }
+    }
+  } catch (_e) { /* best-effort log only */ }
+
+  // Decide whether Pass 3 needs to run (from scratch, resumed, or skipped).
+  //
+  // Three states of pass3-complete.json:
+  //   (a) absent — fresh run; call runPass3Split.
+  //   (b) present + mode:"split" + no completedAt — partial marker from a
+  //       prior run that was interrupted mid-pipeline (most commonly a
+  //       Pass 3d-aux stream timeout). runPass3Split inspects
+  //       groupsCompleted and resumes from the next unstarted stage.
+  //       MUST call runPass3Split here.
+  //   (c) present + completedAt set — finished; skip.
+  //
+  // Pre-v2.3.0 bug: the code branched only on fileExists(pass3Marker),
+  // so case (b) fell into the skip branch and the remaining stages
+  // (usually 3d-aux → database/ + mcp-guide/) were silently dropped on
+  // re-run. The detection block earlier in this function correctly
+  // identified the partial marker and logged "runPass3Split will
+  // resume", but resumption never actually happened.
+  let pass3NeedsRun = !fileExists(pass3Marker);
+  let pass3IsResume = false;
+  if (!pass3NeedsRun) {
+    try {
+      const parsed = JSON.parse(readFile(pass3Marker));
+      if (parsed && parsed.mode === "split" && !parsed.completedAt) {
+        pass3NeedsRun = true;
+        pass3IsResume = true;
+      }
+    } catch (_e) {
+      // Malformed marker — the earlier stale check already handles this
+      // path (dropStalePass3Marker). If we still reach here with a bad
+      // marker, fall through to skip; runPass3Split's own resume logic
+      // would throw on malformed input.
+    }
+  }
+
+  if (pass3NeedsRun) {
+    if (pass3IsResume) {
+      log("    ↪️  Resuming Pass 3 split from partial marker");
+    }
+    await runPass3Split({
+      GENERATED_DIR, PROJECT_ROOT, TOOLS_DIR,
+      pass3Marker, claudeMdPath,
+      injectProjectRoot, readFile, fileExists,
+      runClaudePromptAsync, makePassTicker, formatElapsed,
+      log, countFiles,
+      EXPECTED_GUIDE_FILES, findMissingOutputs,
+      lang, stepTimes,
+    });
+    completedSteps++;
+    progressBar(completedSteps, `Pass 3 complete (split mode)`);
+    log("");
+  } else {
+    log("    ⏭️  pass3-complete.json already complete, skipping");
+    completedSteps++;
+  }
+  log("");
+
+  // ─── [7] Pass 4: L4 memory scaffolding ────────────
+  header("[7] Pass 4 — Memory scaffolding...");
+
+  const pass4Marker = path.join(GENERATED_DIR, "pass4-memory.json");
+  const pass4PromptFile = path.join(GENERATED_DIR, "pass4-prompt.md");
+
+  const { scaffoldMemory, scaffoldRules, scaffoldMasterPlans, scaffoldDocWritingGuide, scaffoldSkillsManifest } = require("../../lib/memory-scaffold");
+  const { writeFileSafe } = require("../../lib/safe-fs");
+
+  const memoryPath = path.join(PROJECT_ROOT, "claudeos-core/memory");
+  const planPath = path.join(PROJECT_ROOT, "claudeos-core/plan");
+  const rulesPath = path.join(PROJECT_ROOT, ".claude/rules");
+  const standardCorePath = path.join(PROJECT_ROOT, "claudeos-core/standard/00.core");
+  const skillsSharedPath = path.join(PROJECT_ROOT, "claudeos-core/skills/00.shared");
+
+  function applyStaticFallback() {
+    try {
+      scaffoldMemory(memoryPath, { lang });
+      scaffoldRules(rulesPath, { lang });
+      scaffoldDocWritingGuide(standardCorePath, { lang });
+      scaffoldMasterPlans(planPath, memoryPath, { lang });
+      scaffoldSkillsManifest(skillsSharedPath, { lang });
+      // v2.3.0: do NOT append an L4 memory section to CLAUDE.md. Pass 3
+      // already authored Section 8 "Common Rules & Memory (L4)" covering
+      // all of the content the append function would have added. An
+      // additional `## N. ... (L4)` section would duplicate the memory
+      // file table (one row per file in §8, another row per file in the
+      // appended §9), triggering [S1]/[M-*]/[F2-*] validator errors.
+      // See CHANGELOG v2.3.0 — "Pass 4 CLAUDE.md append retired."
+    } catch (err) {
+      // When lang !== "en", translation is REQUIRED. If it fails, we surface
+      // a clear error rather than silently writing English (which would
+      // contradict the user's --lang choice).
+      throw new InitError(
+        `Static fallback failed while translating to lang='${lang}':\n` +
+        `    ${err.message}\n` +
+        `    Ensure the \`claude\` CLI is available and authenticated, then re-run.\n` +
+        `    Alternatively re-run with --lang en to skip translation.`
+      );
+    }
+    const markerBody = JSON.stringify({
+      analyzedAt: new Date().toISOString(),
+      passNum: 4,
+      fallback: true,
+      lang,
+      memoryFiles: [
+        "claudeos-core/memory/decision-log.md",
+        "claudeos-core/memory/failure-patterns.md",
+        "claudeos-core/memory/compaction.md",
+        "claudeos-core/memory/auto-rule-update.md",
+      ],
+      ruleFiles: [
+        ".claude/rules/00.core/51.doc-writing-rules.md",
+        ".claude/rules/00.core/52.ai-work-rules.md",
+        ".claude/rules/60.memory/01.decision-log.md",
+        ".claude/rules/60.memory/02.failure-patterns.md",
+        ".claude/rules/60.memory/03.compaction.md",
+        ".claude/rules/60.memory/04.auto-rule-update.md",
+      ],
+      // Note: master plan files are no longer generated (previously this
+      // included "claudeos-core/plan/50.memory-master.md"). The marker schema
+      // still accepts an optional planFiles field for backward compatibility.
+      claudeMdAppended: true,
+    }, null, 2);
+    return writeFileSafe(pass4Marker, markerBody);
+  }
+
+  // M1: validate Pass 4 marker CONTENT, not just existence. Claude can emit
+  // a malformed marker on partial failure (e.g. `{"error":"timeout"}`) that
+  // still satisfies fileExists() and would cause the skip path to accept it
+  // forever. Pass 4 prompt (pass-prompts/templates/common/pass4.md:255-283)
+  // specifies the required structure; we check the minimum subset that
+  // distinguishes a real marker from junk: object shape + passNum === 4 +
+  // non-empty memoryFiles array.
+  function isValidPass4Marker(markerPath) {
+    if (!fileExists(markerPath)) return false;
+    try {
+      const data = JSON.parse(readFile(markerPath));
+      if (!data || typeof data !== "object" || Array.isArray(data)) return false;
+      if (data.passNum !== 4) return false;
+      if (!Array.isArray(data.memoryFiles) || data.memoryFiles.length === 0) return false;
+      return true;
+    } catch (_e) { return false; }
+  }
+
+  // Stale / invalid marker detection. Delete and re-run if either:
+  //   (a) memory/ was deleted externally (original stale-detection), OR
+  //   (b) the marker file itself is malformed (M1).
+  //
+  // Unlink can fail on Windows if an AV or file-watcher has the handle open.
+  // We surface that failure to the user — without it, the subsequent
+  // `if (fileExists(pass4Marker))` check below would accept the stale marker
+  // and skip Pass 4 silently, leaving the project with half-scaffolded memory
+  // state (exactly the silent-failure class this audit is eliminating).
+  const memoryAny = fileExists(path.join(PROJECT_ROOT, "claudeos-core/memory/decision-log.md"))
+    || fileExists(path.join(PROJECT_ROOT, "claudeos-core/memory/compaction.md"));
+  function dropStalePass4Marker(reasonLog) {
+    log(reasonLog);
+    try { fs.unlinkSync(pass4Marker); } catch (e) {
+      log(`    ❌ Failed to delete stale pass4-memory.json: ${e.code || e.message}`);
+      throw new InitError(
+        `Could not delete stale pass4-memory.json at:\n    ${pass4Marker}\n` +
+        `    The file is likely locked by another process (Windows antivirus or a file-watcher).\n` +
+        `    Close any editor/AV scanner holding the file and re-run \`npx claudeos-core init\`.`
+      );
+    }
+  }
+  if (fileExists(pass4Marker)) {
+    if (!memoryAny) {
+      dropStalePass4Marker("    ⚠️  pass4-memory.json exists but memory/ is empty — re-running Pass 4");
+    } else if (!isValidPass4Marker(pass4Marker)) {
+      dropStalePass4Marker("    ⚠️  pass4-memory.json exists but is malformed (missing passNum/memoryFiles) — re-running Pass 4");
+    }
+  }
+
+  const pass4Start = Date.now();
+  let pass4Label = "Pass 4 complete";
+
+  if (fileExists(pass4Marker)) {
+    log("    ⏭️  pass4-memory.json already exists, skipping");
+    pass4Label = "Pass 4 already present";
+  } else if (!fileExists(pass4PromptFile)) {
+    log("    ⚠️  pass4-prompt.md not found — falling back to static scaffold");
+    if (applyStaticFallback()) { log("    ✅ Memory/Rules/Plans scaffolded + CLAUDE.md appended (static fallback)"); pass4Label = "Pass 4 (static fallback)"; }
+    else { log("    ❌ Static fallback failed to write marker"); pass4Label = "Pass 4 fallback failed"; }
+  } else {
+    let prompt4 = injectProjectRoot(readFile(pass4PromptFile));
+
+    // Same stale-staging guard as Pass 3 (in case a previous Pass 4 crashed
+    // after writing to the staging dir but before the move could run).
+    const stagedBeforeP4 = path.join(GENERATED_DIR, ".staged-rules");
+    if (fileExists(stagedBeforeP4)) fs.rmSync(stagedBeforeP4, { recursive: true, force: true });
+
+    const t4 = Date.now();
+    // Pass 4's prompt lists 12 required outputs (pass4.md §§1-12). Of these:
+    //   - 11 are file creations (#1-10 + #12)
+    //   - 1 is an append to existing CLAUDE.md (#11, not a new file)
+    // Of the 11 file creations, only 5 are visible to countFiles() during
+    // the run:
+    //   - #1-4 (4 memory files)                                 → observable
+    //   - #5-10 (6 rule files) go to .staged-rules/ under
+    //     claudeos-core/generated/, which countFiles() skips    → invisible
+    //   - #12 (1 standard doc-writing-guide)                    → observable
+    // So totalExpected = 5. (v2.0.x had 6 because plan/50.memory-master.md
+    // was also generated; master plan generation was removed in v2.1.0.)
+    // The final "100%" shows up on the outer progressBar once the staged
+    // move + marker are done.
+    const ticker4 = makePassTicker("Pass 4", t4, {
+      baselineCount: countFiles(),
+      totalExpected: 5,
+    });
+    const ok4 = await runClaudePromptAsync(prompt4, {
+      onTick: ticker4.onTick,
+      tickMs: ticker4.tickMs,
+    });
+    ticker4.clearLine();
+    const elapsed4 = Date.now() - t4;
+
+    // Move any rule files Pass 4 wrote to the staging dir. This runs regardless
+    // of pass4Marker status, because Claude may have written rules before
+    // failing to produce the marker. Static fallback (below) writes directly
+    // to .claude/rules/ and is unaffected by the move (no-op on empty staging).
+    const { moveStagedRules: mvP4 } = require("../../lib/staged-rules");
+    const p4Move = mvP4(PROJECT_ROOT);
+    if (p4Move.failed > 0) {
+      log(`    ⚠️  Pass 4 staged-rules: ${p4Move.moved} moved, ${p4Move.failed} failed`);
+      for (const err of p4Move.errors) log(`       • ${err}`);
+    } else if (p4Move.moved > 0) {
+      log(`    📦 Pass 4 staged-rules: ${p4Move.moved} rule files moved to .claude/rules/`);
+    }
+
+    if (!ok4 || !isValidPass4Marker(pass4Marker)) {
+      log("    ⚠️  Pass 4 did not produce a valid pass4-memory.json — using static fallback");
+      if (applyStaticFallback()) { log("    ✅ Memory/Rules/Plans scaffolded + CLAUDE.md appended (static fallback)"); pass4Label = `Pass 4 (static fallback, ${formatElapsed(elapsed4)})`; }
+      else { log("    ❌ Static fallback failed to write marker"); pass4Label = "Pass 4 fallback failed"; }
+    } else {
+      // Claude-driven Pass 4 succeeded. Ensure memory + rules + plans + standard + CLAUDE.md append exist
+      // (Claude may have created them; fill any gaps with static fallback).
+      // scaffoldMemory is skip-safe: it only writes files that don't already exist,
+      // so it won't overwrite Claude's translated content — it only fills gaps.
+      // When lang !== "en", the gap-fill MUST translate: we do not silently
+      // write English into a non-English project (bug #21).
+      let gapResults;
+      try {
+        const memR   = scaffoldMemory(memoryPath, { lang });
+        const ruleR  = scaffoldRules(rulesPath, { lang });
+        const docR   = scaffoldDocWritingGuide(standardCorePath, { lang });
+        const planR  = scaffoldMasterPlans(planPath, memoryPath, { lang });
+        const manifestR = scaffoldSkillsManifest(skillsSharedPath, { lang });
+        // v2.3.0: CLAUDE.md is never modified by Pass 4 anymore. See the
+        // matching comment in applyStaticFallback above.
+        // Collect all statuses into one flat array for summary reporting.
+        gapResults = [
+          ...memR,
+          ...ruleR,
+          ...planR,
+          { file: docR.file, status: docR.status },
+          { file: "skills/00.shared/" + manifestR.file, status: manifestR.status },
+        ];
+      } catch (err) {
+        throw new InitError(
+          `Pass 4 gap-fill failed while translating to lang='${lang}':\n` +
+          `    ${err.message}\n` +
+          `    Pass 4 Claude succeeded but some files were missing and translation of the ` +
+          `static fallback to ${lang} failed.\n` +
+          `    Re-run when \`claude\` CLI is available, or use --lang en.`
+        );
+      }
+      // Summary: how many were already present (skipped) vs written by gap-fill.
+      // This surfaces the true state regardless of what Claude printed during Pass 4.
+      const skipped = gapResults.filter(r => r.status === "skipped" || r.status === "present-or-appended").length;
+      const written = gapResults.filter(r => r.status === "written").length;
+      const erroredItems = gapResults.filter(r => r.status === "error");
+      const errored = erroredItems.length;
+      log(`    ✅ Pass 4 complete (${formatElapsed(elapsed4)})`);
+      if (written > 0 || errored > 0) {
+        log(`       📋 Gap-fill: ${skipped} already present, ${written} created via fallback, ${errored} errored`);
+      } else {
+        log(`       📋 Gap-fill: all ${skipped} expected files already present`);
+      }
+      // Surface which files errored so the user can investigate (instead of
+      // silently rolling them into a count). Common causes: write permission
+      // or disk full. All erroredItems are non-fatal — Pass 4 marker still
+      // gets written, but the user should know what was incomplete.
+      for (const item of erroredItems) {
+        log(`       ❌ ${item.file} — write failed (check disk space, permissions)`);
+      }
+      pass4Label = `Pass 4 complete (${formatElapsed(elapsed4)})`;
+    }
+  }
+  // Record Pass 4 in the overall progress bar, regardless of which branch
+  // (skip / static fallback / Claude-driven) ran above. Only feed stepTimes
+  // when we actually did real work, so ETA for future steps stays meaningful.
+  const pass4Elapsed = Date.now() - pass4Start;
+  if (pass4Elapsed > 500) stepTimes.push(pass4Elapsed);
+  completedSteps++;
+  progressBar(completedSteps, pass4Label);
+  log("");
+
+  // ─── [8] Run verification tools ───────────────────────────────
+  header("[8] Running verification tools...");
+
+  const verifyTools = [
+    { name: "manifest-generator", script: path.join(TOOLS_DIR, "manifest-generator/index.js") },
+    { name: "health-checker",     script: path.join(TOOLS_DIR, "health-checker/index.js") },
+  ];
+
+  for (const t of verifyTools) {
+    if (!fileExists(t.script)) {
+      log(`    ⏭️  ${t.name} — not found, skipping`);
+      continue;
+    }
+    const ok = run(`node "${t.script}"`, { ignoreError: true });
+    if (!ok) {
+      log(`    ⚠️  ${t.name} reported issues (non-fatal)`);
+    }
+  }
+  log("");
+
+  // ─── Complete ─────────────────────────────────────────────
+  const totalFiles = countFiles();
+  const pass1Files = countPass1Files();
+
+  // ─── Structural lint (v2.3.0+) ────────────────────────────
+  // Run the language-invariant CLAUDE.md validator after all passes
+  // complete. This catches the §9 L4-memory re-declaration anti-pattern
+  // and other structural drift the scaffold + prompt-level instructions
+  // alone cannot reliably prevent across 10 output languages.
+  //
+  // Failures do NOT abort the run — the generated content is still
+  // useful and the user can either re-run with --force or hand-edit the
+  // flagged sections. The report is purely informational here.
+  try {
+    const { validate } = require("../../claude-md-validator");
+    const { formatSummaryLine } = require("../../claude-md-validator/reporter");
+    const claudeMdPath = path.join(PROJECT_ROOT, "CLAUDE.md");
+    if (fileExists(claudeMdPath)) {
+      log("  [Lint] Validating CLAUDE.md structure...");
+      const report = validate(claudeMdPath);
+      log(`    ${formatSummaryLine(report)}`);
+      if (!report.valid) {
+        for (const err of report.errors) {
+          log(`    ❌ [${err.id}] ${err.message}`);
+        }
+        log("");
+        log("    Run `npx claudeos-core lint` for full remediation guidance,");
+        log("    or `npx claudeos-core init --force` to regenerate.");
+      }
+      log("");
+    }
+  } catch (e) {
+    // Lint is best-effort; don't block init completion on a lint bug.
+    log(`    ⚠️  Lint step skipped: ${e.message || e}`);
+    log("");
+  }
+
+  // ─── Content integrity (Guard 4 — v2.3.0+) ─────────────────
+  // Runs content-validator's path-claim + MANIFEST drift checks as a
+  // non-blocking final step after all passes. We deliberately do NOT
+  // throw or unset pass3-complete.json here:
+  //   - Re-running Pass 3 is not guaranteed to fix LLM hallucinations
+  //     (the same fact JSON may trigger the same mis-inference again),
+  //     so a throw could deadlock the user in an `init --force` loop.
+  //   - The report + the non-zero exit of `npx claudeos-core lint`
+  //     already surface the issues. CI pipelines catch them via exit
+  //     code; local users see them inline here.
+  // When real drift is detected, we print a pointer to the standalone
+  // CLI so the user can re-run selectively without repeating init.
+  try {
+    const cvPath = path.join(__dirname, "..", "..", "content-validator", "index.js");
+    if (fileExists(cvPath)) {
+      log("  [Content] Checking path-claims and MANIFEST consistency...");
+      // Run in a child process so its process.exit(1) on errors does
+      // not terminate init. We only surface the exit code as a warning.
+      const { spawnSync } = require("child_process");
+      const result = spawnSync(process.execPath, [cvPath], {
+        cwd: PROJECT_ROOT,
+        env: { ...process.env, CLAUDEOS_ROOT: PROJECT_ROOT },
+        encoding: "utf-8",
+      });
+      // Echo only the final summary line(s) — full output goes to
+      // stale-report.json for later inspection.
+      const out = (result.stdout || "").trim().split(/\r?\n/);
+      const summary = out.slice(-3).join("\n"); // last 3 lines = summary
+      log(summary.split("\n").map((l) => "    " + l).join("\n"));
+      if (result.status !== 0) {
+        log("");
+        log("    ℹ️  Content drift detected. This does NOT invalidate the");
+        log("       generated documents, but indicates stale path references");
+        log("       or MANIFEST ↔ CLAUDE.md mismatch. Details:");
+        log("         - stale-report.json (full error list)");
+        log("         - Re-run: node content-validator/index.js");
+      }
+      log("");
+    }
+  } catch (e) {
+    log(`    ⚠️  Content check skipped: ${e.message || e}`);
+    log("");
+  }
+
+  log("");
+  const memoryReady = fileExists(path.join(PROJECT_ROOT, "claudeos-core/memory/decision-log.md"));
+  const rulesReady = fileExists(path.join(PROJECT_ROOT, ".claude/rules/60.memory/01.decision-log.md"));
+  const l4Status = (memoryReady && rulesReady) ? "memory + rules" : "partial";
+  log("╔════════════════════════════════════════════════════╗");
+  log("║  ✅ ClaudeOS-Core — Complete                       ║");
+  log("║                                                    ║");
+  log(`║   Files created:     ${pad(String(totalFiles), 29)}║`);
+  log(`║   Domains analyzed:  ${pad(totalGroups + " groups", 29)}║`);
+  log(`║   Analysis passes:   ${pad(pass1Files + " pass1 files", 29)}║`);
+  log(`║   L4 scaffolded:     ${pad(l4Status, 29)}║`);
+  log(`║   Output language:   ${pad(SUPPORTED_LANGS[lang] || lang, 29)}║`);
+  log(`║   Total time:        ${pad(formatElapsed(Date.now() - totalStart), 29)}║`);
+  log("║                                                    ║");
+  log("║   Verify anytime:                                  ║");
+  log("║   npx claudeos-core health                         ║");
+  log("║                                                    ║");
+  log("║   Start using:                                     ║");
+  log('║   "Create a CRUD for orders"                       ║');
+  log("╚════════════════════════════════════════════════════╝");
+  log("");
+}
+
+module.exports = { cmdInit, InitError };