wogiflow 2.29.7 → 2.29.9

package/.claude/docs/claude-code-compatibility.md

@@ -78,6 +78,23 @@ flow parallel check  # See available parallel tasks
 | 2.27.0+ | 2.1.116+ | Sandbox dangerous-path safety on auto-allow, agent frontmatter hooks for `--agent`, `/resume` large-session speedup, MCP stdio concurrent startup |
 | 2.27.0+ | 2.1.117+ | Native bfs/ugrep via Bash (hook audit documented), Opus 4.7 /context fix (estimator already percentage-based), Pro/Max effort default shift (advisory delta documented), agent frontmatter `mcpServers` for `--agent`, subagent model-mismatch malware-warning fix, managed-settings plugin marketplace enforcement |
 | 2.29.6+ | 2.1.132+ | Statusline `context_window` token-count accuracy fix (release notes: was reporting cumulative session totals — may have affected `wogi-statusline-setup` percentage presets if percentage was derived from cumulative tokens), Bedrock/Vertex `ENABLE_PROMPT_CACHING_1H` 400-error fix (recommendation now safe on those providers), `CLAUDE_CODE_SESSION_ID` available in Bash subprocess env |
+| 2.29.7+ | 2.1.133+ | **Subagent skill discovery fix** (CRITICAL for IGR — Architect/Adversary/Skeptical-Evaluator are subagents; if they were missing skills, IGR was silently impaired across versions 2.1.128–2.1.132); **`worktree.baseRef` setting (fresh\|head) reverted to `origin/<default>` default** (was local HEAD since 2.1.128) — wogi-flow's `scripts/flow-worktree.js` users with unpushed local commits should set `worktree.baseRef: "head"` in `.claude/settings.json` to preserve prior behavior; **hooks now receive `effort.level` JSON field + `$CLAUDE_EFFORT` env var** (opportunity for wogi-flow gates to adjust thresholds based on effort — not yet wired); `/effort` no longer leaks across concurrent sessions (workspace-mode benefit); Edit/Write allow rules at drive-root fixed; `sandbox.bwrapPath`/`sandbox.socatPath` managed settings (Linux/WSL); `parentSettingsBehavior` admin-tier key |
+| 2.29.7+ | 2.1.136+ | **`AskUserQuestion` multi-select array discard fixed** (wogi-flow uses AskUserQuestion extensively across skills — automatic fix); **`settings.autoMode.hard_deny`** new unconditional-block mechanism (potential future wogi-flow use for non-bypassable gates like routing/deferral); extended-thinking redacted-block API 400 fixed (wogi-flow's IGR Architect on Opus benefits); MCP servers no longer silently disappear after `/clear`; OAuth refresh-token races fixed (better stability for multi-MCP users); `--resume`/`--continue` no longer fails on underscored project paths; plan mode now correctly blocks file writes when matching Edit allow rule exists; subagent file pickers find files in dirs with >100 entries; many TUI cosmetic fixes (CJK rendering, autocomplete, color artifacts) |
+
+### Worktree-baseRef recommendation (2.1.133+)
+
+If you use wogi-flow's worktree feature for parallel task execution AND have unpushed local commits you want available in new worktrees:
+
+```json
+// .claude/settings.json
+{
+  "worktree": {
+    "baseRef": "head"
+  }
+}
+```
+
+Without this, new worktrees branch from `origin/<default>` (the 2.1.133 default) and your unpushed commits won't be available in them. wogi-flow's `scripts/flow-worktree.js` doesn't currently configure this — it inherits whatever Claude Code's default is.
 
 ### Environment Variables (2.1.19+)
 

package/.claude/settings.json

@@ -170,6 +170,6 @@
   },
   "_comment_dynamicHooks": "TaskCreated (2.1.84+) and PermissionDenied (2.1.88+) are added by postinstall.js when the CC version supports them. They must NOT be committed statically — CC rejects the entire settings file if it encounters an unknown hook event name.",
   "_wogiFlowManaged": true,
-  "_wogiFlowVersion": "2.27.0",
+  "_wogiFlowVersion": "2.29.7",
   "_comment": "Shared WogiFlow hook configuration. Committed to repo for team use. User-specific overrides go in settings.local.json."
 }

package/lib/workspace-channel-server.js

@@ -79,7 +79,7 @@ const PEERS = parsePeers(PEERS_RAW);
 // Minimal MCP Protocol (JSON-RPC 2.0 over stdio)
 // ============================================================
 
-let initialized = false;
+let _initialized = false;
 
 /**
  * Send a JSON-RPC message to Claude Code via stdout.
@@ -198,7 +198,7 @@ function handleRequest(msg) {
   }
 
   if (msg.method === 'notifications/initialized') {
-    initialized = true;
+    _initialized = true;
     return;
   }
 

package/lib/workspace-task-injector.js

@@ -20,6 +20,11 @@ const fs = require('node:fs');
 const path = require('node:path');
 const crypto = require('node:crypto');
 
+// wf-3c968989: use safeJsonParse for prototype-pollution protection on
+// the workspace manifest read. Throw-on-failure contract preserved below
+// via explicit null check (manifest is mandatory for workspace mode).
+const { safeJsonParse } = require('../scripts/flow-io');
+
 const VALID_REPO_NAME = /^[a-zA-Z0-9_-]{1,64}$/;
 const VALID_TASK_ID = /^wf-[0-9a-f]{8}$/i;
 const REQUIRED_FIELDS = ['id', 'title', 'type'];
@@ -42,11 +47,12 @@ function getWorkerReadyPath(workspaceRoot, repoName) {
   }
 
   const configPath = path.join(workspaceRoot, 'wogi-workspace.json');
-  let manifest;
-  try {
-    manifest = JSON.parse(fs.readFileSync(configPath, 'utf-8'));
-  } catch (err) {
-    throw new Error(`Cannot read workspace manifest at ${configPath}: ${err.message}`);
+  // wf-3c968989: safeJsonParse adds DANGEROUS_KEYS protection. It returns
+  // null on missing/corrupt/array-typed input — manifest is mandatory, so
+  // we preserve the original throw-on-failure contract via null check.
+  const manifest = safeJsonParse(configPath, null);
+  if (!manifest) {
+    throw new Error(`Cannot read workspace manifest at ${configPath}`);
   }
 
   const member = manifest.members?.[repoName];

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "wogiflow",
-  "version": "2.29.7",
+  "version": "2.29.9",
   "description": "AI-powered development workflow management system with multi-model support",
   "main": "lib/index.js",
   "bin": {
@@ -10,7 +10,7 @@
   },
   "scripts": {
     "flow": "./scripts/flow",
-    "test": "NODE_ENV=test node --test tests/auto-compact-prompt.test.js tests/flow-paths.test.js tests/flow-io.test.js tests/flow-config-loader.test.js tests/flow-damage-control.test.js tests/flow-output.test.js tests/flow-constants.test.js tests/flow-session-state.test.js tests/flow-hooks-integration.test.js tests/flow-utils.test.js tests/flow-security.test.js tests/flow-memory-db.test.js tests/flow-durable-session.test.js tests/flow-skill-matcher.test.js tests/flow-bridge.test.js tests/flow-proactive-compact.test.js tests/flow-cascade-completion.test.js tests/flow-capture-gate.test.js tests/flow-correction-detector-hybrid.test.js tests/flow-promote.test.js tests/flow-archive-runs.test.js tests/flow-memory.test.js tests/flow-hooks-pre-tool-helpers.test.js tests/flow-hooks-bugfix-scope-gate.test.js tests/flow-hooks-routing-gate.test.js tests/flow-hooks-phase-read-gate.test.js tests/flow-hooks-commit-log-gate.test.js tests/flow-hooks-deploy-gate.test.js tests/flow-hooks-todowrite-gate.test.js tests/flow-hooks-git-safety-gate.test.js tests/flow-hooks-scope-mutation-gate.test.js tests/flow-hooks-strike-gate.test.js tests/flow-hooks-component-check.test.js tests/flow-hooks-scope-gate.test.js tests/flow-hooks-implementation-gate.test.js tests/flow-hooks-research-gate.test.js tests/flow-hooks-loop-check.test.js tests/flow-hooks-manager-boundary-gate.test.js tests/flow-hooks-phase-gate.test.js tests/flow-hooks-pre-tool-orchestrator.test.js tests/flow-hooks-observation-capture.test.js tests/flow-hooks-task-gate.test.js tests/flow-durable-session-suspension.test.js tests/flow-health-mcp-scopes.test.js tests/flow-lean-config.test.js tests/flow-workspace-autopickup.test.js tests/flow-worker-boundary-gate.test.js tests/flow-worker-question-classifier.test.js tests/flow-completion-truth-gate-contradictions.test.js tests/flow-structure-sensor.test.js tests/flow-workspace-dispatch-tracking.test.js tests/workspace-ipc-sqlite.test.js tests/workspace-ipc-multi-worker.test.js tests/flow-story-gates.test.js tests/flow-workspace-restart-handoff.test.js tests/flow-wogi-claude-wrapper.test.js tests/flow-wave1-integrations.test.js tests/flow-wave2-integrations.test.js tests/flow-wave3-integrations.test.js tests/flow-commit-claims-gate.test.js tests/auto-review.test.js tests/gate-telemetry-surface.test.js tests/agents-md-alias.test.js tests/flow-skill-manage.test.js tests/fuzzy-patch.test.js tests/mode-schema.test.js tests/flow-feature-dossier.test.js tests/flow-autonomous-mode.test.js tests/flow-epic-cascade.test.js tests/flow-workspace-summary.test.js tests/flow-hooks-research-evidence-gate.test.js tests/flow-worker-mcp-strip.test.js tests/flow-orchestrate-corrections.test.js tests/flow-source-fidelity.test.js tests/flow-hooks-long-input-enforcement.test.js tests/workspace-channel-tracking.test.js tests/flow-hooks-deletion-log.test.js tests/flow-task-boundary-reset.test.js tests/flow-deferral-gate.test.js tests/flow-research-required-gate.test.js && NODE_ENV=test node tests/run-quality-gates.test.js",
+    "test": "NODE_ENV=test node --test tests/auto-compact-prompt.test.js tests/flow-paths.test.js tests/flow-io.test.js tests/flow-audit-gates.test.js tests/flow-standards-hook-three-layer.test.js tests/flow-correction-detector-reconcile.test.js tests/flow-correction-backfill.test.js tests/flow-audit-gates-feature-output-health.test.js tests/flow-config-loader.test.js tests/flow-damage-control.test.js tests/flow-output.test.js tests/flow-constants.test.js tests/flow-session-state.test.js tests/flow-hooks-integration.test.js tests/flow-utils.test.js tests/flow-security.test.js tests/flow-memory-db.test.js tests/flow-durable-session.test.js tests/flow-skill-matcher.test.js tests/flow-bridge.test.js tests/flow-proactive-compact.test.js tests/flow-cascade-completion.test.js tests/flow-capture-gate.test.js tests/flow-correction-detector-hybrid.test.js tests/flow-promote.test.js tests/flow-archive-runs.test.js tests/flow-memory.test.js tests/flow-hooks-pre-tool-helpers.test.js tests/flow-hooks-bugfix-scope-gate.test.js tests/flow-hooks-routing-gate.test.js tests/flow-hooks-phase-read-gate.test.js tests/flow-hooks-commit-log-gate.test.js tests/flow-hooks-deploy-gate.test.js tests/flow-hooks-todowrite-gate.test.js tests/flow-hooks-git-safety-gate.test.js tests/flow-hooks-scope-mutation-gate.test.js tests/flow-hooks-strike-gate.test.js tests/flow-hooks-component-check.test.js tests/flow-hooks-scope-gate.test.js tests/flow-hooks-implementation-gate.test.js tests/flow-hooks-research-gate.test.js tests/flow-hooks-loop-check.test.js tests/flow-hooks-manager-boundary-gate.test.js tests/flow-hooks-phase-gate.test.js tests/flow-hooks-pre-tool-orchestrator.test.js tests/flow-hooks-observation-capture.test.js tests/flow-hooks-task-gate.test.js tests/flow-durable-session-suspension.test.js tests/flow-health-mcp-scopes.test.js tests/flow-lean-config.test.js tests/flow-workspace-autopickup.test.js tests/flow-worker-boundary-gate.test.js tests/flow-worker-question-classifier.test.js tests/flow-completion-truth-gate-contradictions.test.js tests/flow-structure-sensor.test.js tests/flow-workspace-dispatch-tracking.test.js tests/workspace-ipc-sqlite.test.js tests/workspace-ipc-multi-worker.test.js tests/flow-story-gates.test.js tests/flow-workspace-restart-handoff.test.js tests/flow-wogi-claude-wrapper.test.js tests/flow-wave1-integrations.test.js tests/flow-wave2-integrations.test.js tests/flow-wave3-integrations.test.js tests/flow-commit-claims-gate.test.js tests/auto-review.test.js tests/gate-telemetry-surface.test.js tests/agents-md-alias.test.js tests/flow-skill-manage.test.js tests/fuzzy-patch.test.js tests/mode-schema.test.js tests/flow-feature-dossier.test.js tests/flow-autonomous-mode.test.js tests/flow-epic-cascade.test.js tests/flow-workspace-summary.test.js tests/flow-hooks-research-evidence-gate.test.js tests/flow-worker-mcp-strip.test.js tests/flow-orchestrate-corrections.test.js tests/flow-source-fidelity.test.js tests/flow-hooks-long-input-enforcement.test.js tests/workspace-channel-tracking.test.js tests/flow-hooks-deletion-log.test.js tests/flow-task-boundary-reset.test.js tests/flow-deferral-gate.test.js tests/flow-research-required-gate.test.js && NODE_ENV=test node tests/run-quality-gates.test.js",
     "test:syntax": "find scripts/ lib/ -name '*.js' -not -path '*/node_modules/*' -exec node --check {} +",
     "lint": "eslint scripts/ lib/ tests/",
     "lint:ci": "eslint scripts/ lib/ tests/ --max-warnings 0",
@@ -74,6 +74,9 @@
   "engines": {
     "node": ">=18.0.0"
   },
+  "overrides": {
+    "protobufjs": ">=7.5.5"
+  },
   "publishConfig": {
     "access": "public"
   }

package/scripts/flow-audit-gates.js

@@ -34,6 +34,7 @@ const fs = require('node:fs');
 const path = require('node:path');
 
 const { PATHS, safeJsonParse } = require('./flow-utils');
+const { safeJsonParseString } = require('./flow-io');
 
 // ============================================================
 // Score Cap Thresholds
@@ -282,19 +283,77 @@ function checkLintConfigIntegrity() {
   return result;
 }
 
+/**
+ * Parse test failure count from Node test runner stdout.
+ *
+ * Bug fixed 2026-05-08 (wf-e111d850): previously inherited the generic
+ * runProjectScript regex `/error TS\d+|Error:|ERROR/gi` which matched the
+ * substring "error" in passing test descriptions (e.g., 'trimRetryErrors',
+ * 'classifier error path', 'returns null on git unavailable / error'),
+ * inflating errorCount even when 0 tests actually failed. Compounded by
+ * Node test runner v22 sometimes exiting non-zero on all-pass.
+ *
+ * Strategy:
+ *   1. Primary — parse Node test runner "Results: N passed, M failed" summary
+ *      lines (one per suite when running multiple files). Sum the M values.
+ *   2. Fallback — count TAP "not ok N" lines if no summary present.
+ *   3. Default — 0 (graceful) if neither parser finds anything.
+ *
+ * @param {string} output — combined stdout+stderr from `npm run test`
+ * @returns {{ errorCount: number, source: 'summary' | 'tap' | 'default' }}
+ */
+function parseTestErrorCount(output) {
+  if (typeof output !== 'string' || output.length === 0) {
+    return { errorCount: 0, source: 'default' };
+  }
+
+  // Primary: Node test runner summary line(s).
+  // Format: "Results: N passed, M failed" (color codes already stripped via
+  // FORCE_COLOR=0 / NO_COLOR=1 in runProjectScript).
+  const summaryRe = /Results:\s*\d+\s*passed,\s*(\d+)\s*failed/gi;
+  let summaryFound = false;
+  let total = 0;
+  for (const m of output.matchAll(summaryRe)) {
+    summaryFound = true;
+    total += parseInt(m[1], 10) || 0;
+  }
+  if (summaryFound) return { errorCount: total, source: 'summary' };
+
+  // Fallback: TAP "not ok N - ..." line count
+  const tap = (output.match(/^not ok \d+/gm) || []).length;
+  if (tap > 0) return { errorCount: tap, source: 'tap' };
+
+  return { errorCount: 0, source: 'default' };
+}
+
 /**
  * Gate: Tests — do tests pass?
+ *
+ * Uses parseTestErrorCount() to override the generic regex from
+ * runProjectScript. See parseTestErrorCount() comment for bug history.
  */
 function checkTests() {
   const result = runProjectScript('test', 120000);
+  const parseSource = result.rawOutput || result.output || '';
+  const { errorCount, source: parserSource } = parseTestErrorCount(parseSource);
+
+  // Trust the parser over npm exit code: Node test runner v22 can exit
+  // non-zero in some configurations even when all tests pass. If the parser
+  // finds 0 failures via the summary line, that's authoritative.
+  const passed = errorCount === 0;
+
   return {
     gate: 'tests',
     ...result,
+    errorCount,
+    passed,
+    parserSource,
     scoreCap: 100, // Test failure doesn't cap, but is a HIGH finding
     severity: !result.exists ? 'info' :
-      result.passed ? 'pass' : 'high',
+      passed ? 'pass' : 'high',
     message: !result.exists ? 'No test script defined' :
-      result.passed ? 'Tests pass' : 'Tests FAIL'
+      passed ? 'Tests pass' :
+        `Tests FAIL: ${errorCount} failure(s)`
   };
 }
 
@@ -583,6 +642,114 @@ function compareTrend(currentResults, previousAudit) {
 // Main: Run All Gates
 // ============================================================
 
+/**
+ * Gate: Feature Output Health (wf-6c58953a)
+ *
+ * Inspects DATA produced by features, not just CODE that produces it.
+ * Catches "silent feature no-op" — feature runs without errors, persists
+ * data, but the persisted data has all-null structured fields. This class
+ * is invisible to traditional code review/lint/typecheck/tests.
+ *
+ * Discovered 2026-05-09 when wogiflow-cli investigation found the
+ * correction-extractor was capturing user frustration but writing null
+ * structured fields. The /wogi-audit ran B+ and missed it because every
+ * agent inspects code, not output.
+ *
+ * Rule registry — explicit per-file checks, NOT a generic walker (per
+ * challenge round: blanket "all-null is bug" is false-positive city).
+ *
+ * @param {string} [projectRoot=PATHS.root] — project to inspect (default: current)
+ * @returns {Object} gate result with severity + findings
+ */
+function checkFeatureOutputHealth(projectRoot = PATHS.root) {
+  const findings = [];
+  const stateDir = path.join(projectRoot, '.workflow', 'state');
+  const corrDir = path.join(projectRoot, '.workflow', 'corrections');
+
+  // ---- Rule 1: pending-corrections.json null-fields ratio ----
+  // Note: pending-corrections.json is a top-level ARRAY, so safeJsonParse
+  // (which rejects arrays) won't work. Use file-read + safeJsonParseString.
+  const pcPath = path.join(stateDir, 'pending-corrections.json');
+  if (fs.existsSync(pcPath)) {
+    let records = [];
+    try {
+      const content = fs.readFileSync(pcPath, 'utf-8');
+      records = safeJsonParseString(content, []);
+    } catch (_err) { /* fail-open */ }
+    const arr = Array.isArray(records) ? records : [];
+    if (arr.length > 0) {
+      const nullCount = arr.filter(r =>
+        r && typeof r === 'object' &&
+        (r.whatWasWrong == null) &&
+        (r.whatUserWants == null)
+      ).length;
+      const ratio = nullCount / arr.length;
+      if (ratio >= 0.5) {
+        findings.push({
+          rule: 'pending-corrections-null-fields',
+          severity: ratio === 1 ? 'high' : 'medium',
+          message: `${nullCount}/${arr.length} (${Math.round(ratio * 100)}%) pending-corrections records have null structured fields. Likely correction-detector extraction failure. Run \`flow-correction-backfill\` or restore via Layer 2 enrichment.`,
+          evidence: `${path.relative(projectRoot, pcPath)}: ${arr.length} records analyzed; ${nullCount} fully null`
+        });
+      }
+    }
+  }
+
+  // ---- Rule 2: prompt-history × corrections cross-reference ----
+  // prompt-history.json is also typically a top-level array.
+  const phPath = path.join(stateDir, 'prompt-history.json');
+  if (fs.existsSync(phPath)) {
+    let ph = [];
+    try {
+      const content = fs.readFileSync(phPath, 'utf-8');
+      ph = safeJsonParseString(content, []);
+    } catch (_err) { /* fail-open */ }
+    const phArr = Array.isArray(ph) ? ph : (ph && Array.isArray(ph.prompts) ? ph.prompts : []);
+
+    // Frustration markers (regex per known-pattern set)
+    const frustrationRe = /\b(don'?t|stop|wait|actually|why did|why is|you keep|you always|fucking|seriously)\b/i;
+    let frustrationCount = 0;
+    for (const entry of phArr) {
+      if (!entry || typeof entry !== 'object') continue;
+      const text = entry.prompt || entry.text || entry.userMessage || '';
+      if (typeof text === 'string' && frustrationRe.test(text)) frustrationCount++;
+    }
+
+    let corrCount = 0;
+    if (fs.existsSync(corrDir)) {
+      try {
+        corrCount = fs.readdirSync(corrDir).filter(f => f.endsWith('.md')).length;
+      } catch (_err) { /* fail-open */ }
+    }
+
+    if (frustrationCount >= 3 && corrCount === 0) {
+      findings.push({
+        rule: 'prompt-history-vs-corrections-mismatch',
+        severity: 'high',
+        message: `prompt-history.json has ${frustrationCount} frustration markers but corrections/ is empty. Correction-extractor pipeline appears non-functional (captures input, fails to materialize records).`,
+        evidence: `prompt-history: ${frustrationCount} matches across ${phArr.length} entries; corrections/: ${corrCount} files`
+      });
+    }
+  }
+
+  // Determine overall gate severity
+  const hasHigh = findings.some(f => f.severity === 'high');
+  const hasMed = findings.some(f => f.severity === 'medium');
+  const severity = hasHigh ? 'high' : hasMed ? 'medium' : 'pass';
+
+  return {
+    gate: 'feature-output-health',
+    exists: true,
+    passed: findings.length === 0,
+    findings,
+    severity,
+    scoreCap: 100, // doesn't cap score directly; surfaces as audit findings
+    message: findings.length === 0
+      ? 'Feature output health: no issues detected'
+      : `Feature output health: ${findings.length} finding(s) — ${findings.map(f => f.rule).join(', ')}`
+  };
+}
+
 /**
  * Run all Gate 0 checks and return consolidated results.
  * @returns {Object} gate results with score cap
@@ -596,6 +763,7 @@ function runAllGates() {
   gates.push(checkLintConfigIntegrity());
   gates.push(checkTests());
   gates.push(checkScriptCompleteness());
+  gates.push(checkFeatureOutputHealth());
 
   const cap = calculateScoreCap(gates);
   const framework = detectFramework();
@@ -658,6 +826,14 @@ function main() {
       console.log(JSON.stringify(checkScriptCompleteness(), null, 2));
       break;
 
+    case 'feature-output-health': {
+      // Optional --project=<path> argument for cross-project audit
+      const projArg = process.argv.find(a => a.startsWith('--project='));
+      const projectRoot = projArg ? projArg.slice('--project='.length) : PATHS.root;
+      console.log(JSON.stringify(checkFeatureOutputHealth(projectRoot), null, 2));
+      break;
+    }
+
     case 'eslint-disable':
       console.log(JSON.stringify(countEslintDisables(), null, 2));
       break;
@@ -767,7 +943,9 @@ module.exports = {
   checkLint,
   checkLintConfigIntegrity,
   checkTests,
+  parseTestErrorCount, // wf-e111d850: exposed for unit testing
   checkScriptCompleteness,
+  checkFeatureOutputHealth, // wf-6c58953a: feature output health gate
 
   // Extended checks
   countEslintDisables,

package/scripts/flow-config-defaults.js

@@ -1038,6 +1038,24 @@ const CONFIG_DEFAULTS = {
     claudeCode: { installPath: '.claude/settings.local.json' }
   },
 
+  // --- Standards Check (wf-00c5067b) ---
+  // Hook three-layer enforcement: entry files ≤120 LOC + ≤2 core/ imports.
+  // Exemption list documents pre-extraction violators; clear each entry as
+  // its corresponding Phase 2 task ships.
+  standardsCheck: {
+    hookThreeLayer: {
+      enabled: true,
+      maxLoc: 120,
+      maxCoreImports: 2,
+      exemptions: {
+        'scripts/hooks/entry/claude-code/stop.js': 'Phase 2 — wf-c1e892fa entry-file extraction (orchestration logic to core); remove exemption when extracted',
+        'scripts/hooks/entry/claude-code/session-start.js': 'Phase 2 — wf-c1e892fa entry-file extraction (orchestration logic to core); remove exemption when extracted',
+        'scripts/hooks/entry/claude-code/user-prompt-submit.js': 'Phase 2 — wf-c1e892fa entry-file extraction (orchestration logic to core); remove exemption when extracted',
+        'scripts/hooks/entry/claude-code/post-tool-use.js': 'Phase 2 — wf-c1e892fa entry-file extraction (orchestration logic to core); remove exemption when extracted'
+      }
+    }
+  },
+
   // --- Metrics ---
   metrics: { enabled: false },
 

package/scripts/flow-correction-backfill.js

@@ -0,0 +1,148 @@
+#!/usr/bin/env node
+
+/**
+ * Wogi Flow — Pending-Corrections Backfill (wf-6c58953a)
+ *
+ * Backfills records in `.workflow/state/pending-corrections.json` that have
+ * null `whatWasWrong` / `whatUserWants` fields. The fix lands at code level
+ * (flow-correction-detector.js Layer 1+2 reconciliation), but historical
+ * records persisted before the fix already have null fields. This tool
+ * applies the same deterministic-fallback extraction retroactively.
+ *
+ * Strategy:
+ *   - Read pending-corrections.json
+ *   - For each record where userMessage is populated AND
+ *     (whatWasWrong is null OR whatUserWants is null)
+ *   - Apply deterministic extraction: whatWasWrong = first 200 chars of
+ *     userMessage; whatUserWants stays null (intent inference is an LLM job
+ *     — honest null > wrong guess; live extractor will populate going forward)
+ *   - Mark `enrichmentSource: "backfill-<date>"` so consumers can distinguish
+ *     backfilled from live extractions
+ *   - Atomic write: write-temp + rename
+ *
+ * Usage:
+ *   node scripts/flow-correction-backfill.js                        # current project
+ *   node scripts/flow-correction-backfill.js --project=<path>      # explicit project
+ *   node scripts/flow-correction-backfill.js --dry-run             # report only
+ */
+
+'use strict';
+
+const fs = require('node:fs');
+const path = require('node:path');
+
+const { PATHS } = require('./flow-utils');
+const { safeJsonParseString } = require('./flow-io');
+const { deterministicWhatWasWrong } = require('./flow-correction-detector');
+
+const BACKFILL_DATE = new Date().toISOString().slice(0, 10); // YYYY-MM-DD
+
+/**
+ * Backfill a single project's pending-corrections.json.
+ *
+ * @param {string} projectRoot — project directory containing .workflow/
+ * @param {Object} [opts]
+ * @param {boolean} [opts.dryRun=false] — if true, return what WOULD change without writing
+ * @returns {{ found: number, backfilled: number, alreadyPopulated: number, written: boolean, path: string|null, dryRun: boolean }}
+ */
+function backfillPendingCorrections(projectRoot, opts = {}) {
+  const { dryRun = false } = opts;
+  const pcPath = path.join(projectRoot, '.workflow', 'state', 'pending-corrections.json');
+
+  const result = {
+    found: 0,
+    backfilled: 0,
+    alreadyPopulated: 0,
+    written: false,
+    path: null,
+    dryRun
+  };
+
+  if (!fs.existsSync(pcPath)) {
+    result.path = pcPath;
+    return result;
+  }
+
+  let content;
+  try {
+    content = fs.readFileSync(pcPath, 'utf-8');
+  } catch (err) {
+    throw new Error(`Cannot read pending-corrections at ${pcPath}: ${err.message}`);
+  }
+
+  const records = safeJsonParseString(content, []);
+  if (!Array.isArray(records)) {
+    throw new Error(`Expected array at ${pcPath}; got ${typeof records}`);
+  }
+
+  result.found = records.length;
+  result.path = pcPath;
+
+  let changed = false;
+  for (const r of records) {
+    if (!r || typeof r !== 'object') continue;
+    const userMsg = r.userMessage;
+    if (typeof userMsg !== 'string' || !userMsg.trim()) continue;
+
+    const needsFill = (r.whatWasWrong == null) && (r.whatUserWants == null);
+    if (!needsFill) {
+      result.alreadyPopulated += 1;
+      continue;
+    }
+
+    // Apply deterministic extraction (whatWasWrong only — whatUserWants
+    // stays null; intent inference is the live extractor's job going forward)
+    r.whatWasWrong = deterministicWhatWasWrong(userMsg);
+    r.enrichmentSource = `backfill-${BACKFILL_DATE}`;
+    result.backfilled += 1;
+    changed = true;
+  }
+
+  if (changed && !dryRun) {
+    // Atomic write: write-temp + rename
+    const tmpPath = `${pcPath}.tmp-${process.pid}`;
+    fs.writeFileSync(tmpPath, JSON.stringify(records, null, 2) + '\n');
+    fs.renameSync(tmpPath, pcPath);
+    result.written = true;
+  }
+
+  return result;
+}
+
+// ============================================================
+// CLI
+// ============================================================
+
+function main() {
+  const argv = process.argv.slice(2);
+  const projArg = argv.find(a => a.startsWith('--project='));
+  const dryRun = argv.includes('--dry-run');
+
+  const projectRoot = projArg ? projArg.slice('--project='.length) : PATHS.root;
+
+  let result;
+  try {
+    result = backfillPendingCorrections(projectRoot, { dryRun });
+  } catch (err) {
+    console.error(`Error: ${err.message}`);
+    process.exit(1);
+  }
+
+  console.log(JSON.stringify({
+    project: projectRoot,
+    pendingCorrectionsPath: result.path,
+    found: result.found,
+    backfilled: result.backfilled,
+    alreadyPopulated: result.alreadyPopulated,
+    written: result.written,
+    dryRun: result.dryRun
+  }, null, 2));
+}
+
+module.exports = {
+  backfillPendingCorrections
+};
+
+if (require.main === module) {
+  main();
+}

package/scripts/flow-correction-detector.js

@@ -329,14 +329,106 @@ function recordHybridTelemetry(verdict, runCtx = {}) {
   }
 }
 
+// ============================================================================
+// Layer 1 + Layer 2 Reconciliation (wf-6c58953a)
+// ============================================================================
+
+/**
+ * Deterministic fallback for `whatWasWrong` — preserves the user's literal
+ * frustration text when LLM extraction is unavailable or fails. Better than
+ * null: a 200-char excerpt is honest signal; null is data loss.
+ *
+ * @param {string} message — user message
+ * @returns {string|null}
+ */
+function deterministicWhatWasWrong(message) {
+  if (typeof message !== 'string') return null;
+  const trimmed = message.trim();
+  if (!trimmed) return null;
+  return trimmed.slice(0, 200);
+}
+
+/**
+ * Reconcile Layer 1 (keyword classifier) + Layer 2 (Haiku LLM) results.
+ *
+ * Pre-fix bug: Layer 1 returned `{whatWasWrong: null, whatUserWants: null}`
+ * when keyword matched, never calling Layer 2. The user's actual frustration
+ * was captured but structured fields stayed null — silent feature no-op.
+ *
+ * Post-fix design:
+ *   - Layer 1 hit + Layer 2 success: trust Layer 1's classification (high-
+ *     precision keyword match), use Layer 2's strings if non-null else
+ *     deterministic fallback. Record `llmDisagreed` if Layer 2 said
+ *     `isCorrection: false` (e.g., user said "I'm just asking a question").
+ *   - Layer 1 hit + Layer 2 fail/skip: deterministic fallback for `whatWasWrong`
+ *     (first 200 chars). `whatUserWants` stays null (intent inference is an
+ *     LLM job; honest null > wrong guess).
+ *   - Layer 1 miss + Layer 2 success: Layer 2 is primary classifier (existing path).
+ *   - Both miss: not a correction.
+ *
+ * Pure function — testable in isolation, no LLM mock needed.
+ *
+ * @param {Object|null} layer1 — Layer 1 result {isCorrection, confidence, correctionType, method, matchedPattern}
+ * @param {Object|null} layer2 — Layer 2 (LLM) result {isCorrection, confidence, correctionType, whatWasWrong, whatUserWants}
+ * @param {string} trimmed — trimmed user message (for deterministic fallback)
+ * @returns {Object|null} reconciled record OR null if not a correction
+ */
+function reconcileExtraction(layer1, layer2, trimmed) {
+  // Both layers ran
+  if (layer1 && layer2) {
+    const what = layer2.whatWasWrong || deterministicWhatWasWrong(trimmed);
+    const wants = layer2.whatUserWants || null;
+    return {
+      isCorrection: true, // Layer 1 high-precision keyword match wins binary
+      confidence: layer1.confidence,
+      correctionType: layer1.correctionType || layer2.correctionType || 'behavior',
+      whatWasWrong: what,
+      whatUserWants: wants,
+      method: 'keyword+ai',
+      matchedPattern: layer1.matchedPattern,
+      enrichmentSource: layer2.whatWasWrong ? 'haiku' : 'deterministic-fallback',
+      llmDisagreed: layer2.isCorrection === false,
+    };
+  }
+  // Layer 1 only (Layer 2 unavailable: no API key, network error, etc.)
+  if (layer1) {
+    return {
+      isCorrection: true,
+      confidence: layer1.confidence,
+      correctionType: layer1.correctionType || 'behavior',
+      whatWasWrong: deterministicWhatWasWrong(trimmed),
+      whatUserWants: null,
+      method: layer1.method,
+      matchedPattern: layer1.matchedPattern,
+      enrichmentSource: 'deterministic-fallback',
+    };
+  }
+  // Layer 2 only (Layer 1 missed)
+  if (layer2 && layer2.isCorrection) {
+    return {
+      isCorrection: true,
+      confidence: layer2.confidence,
+      correctionType: layer2.correctionType || null,
+      whatWasWrong: layer2.whatWasWrong || null,
+      whatUserWants: layer2.whatUserWants || null,
+      method: 'ai',
+      enrichmentSource: 'haiku',
+    };
+  }
+  // Both missed → not a correction
+  return null;
+}
+
 // ============================================================================
 // AI-Based Detection (Haiku — language-agnostic)
 // ============================================================================
 
 /**
  * Detect if a message is a correction using Claude Haiku.
- * This is the ONLY detection method — no regex fallback.
- * Works in any language.
+ * Hybrid: Layer 1 keyword classifier (fast) + Layer 2 Haiku enrichment.
+ *
+ * wf-6c58953a (2026-05-09): Layer 1 hit no longer short-circuits structured
+ * extraction. See reconcileExtraction() for the post-fix design rationale.
  *
  * @param {string} userMessage - The user's message
  * @param {string} previousContext - Summary of what the AI was doing
@@ -354,8 +446,12 @@ async function detectCorrection(userMessage, previousContext = '') {
     return { isCorrection: false, confidence: 0, method: 'skipped', reason: 'length-filter' };
   }
 
-  // Layer 1 (wf-e6d65edf) — keyword pre-classifier. Skips Haiku entirely on a hit.
+  // Layer 1 (wf-e6d65edf) — keyword pre-classifier.
+  // wf-6c58953a: NO longer short-circuits structured extraction. Layer 1's
+  // classification is captured; reconcile with Layer 2 (or deterministic
+  // fallback when Layer 2 unavailable) at end.
   const hybridCfg = getHybridConfig();
+  let layer1Result = null;
   if (hybridCfg.hybridEnabled) {
     const matched = findKeywordMatch(trimmed);
     if (matched) {
@@ -368,12 +464,10 @@ async function detectCorrection(userMessage, previousContext = '') {
         confidence: conf,
         durationMs: Date.now() - start,
       });
-      return {
+      layer1Result = {
         isCorrection: true,
         confidence: conf,
         correctionType: 'behavior',
-        whatWasWrong: null,
-        whatUserWants: null,
         method: 'keyword',
         matchedPattern: matched.phrase,
       };
@@ -383,6 +477,10 @@ async function detectCorrection(userMessage, previousContext = '') {
   // Check if API key is available
   const apiKey = process.env.ANTHROPIC_API_KEY;
   if (!apiKey) {
+    // wf-6c58953a: Layer 1 hit + no API key → deterministic fallback (not null)
+    if (layer1Result) {
+      return reconcileExtraction(layer1Result, null, trimmed);
+    }
     return { isCorrection: false, confidence: 0, method: 'skipped', reason: 'no-api-key' };
   }
 
@@ -492,11 +590,19 @@ Respond with JSON only (no markdown, no explanation):
       durationMs: Date.now() - start,
     });
 
+    // wf-6c58953a: reconcile Layer 1 + Layer 2 (or just Layer 2 if Layer 1 missed)
+    const reconciled = reconcileExtraction(layer1Result, aiResult, trimmed);
+    if (reconciled) return reconciled;
+    // Both layers say no-correction
     return aiResult;
   } catch (err) {
     if (process.env.DEBUG) {
       console.error(`[DEBUG] AI correction detection failed: ${err.message}`);
     }
+    // wf-6c58953a: Layer 2 failure with Layer 1 hit → deterministic fallback
+    if (layer1Result) {
+      return reconcileExtraction(layer1Result, null, trimmed);
+    }
     return { isCorrection: false, confidence: 0, method: 'ai', reason: err.message };
   }
 }
@@ -1295,11 +1401,15 @@ function correlateWithPriorGates(correction) {
 // ============================================================================
 
 module.exports = {
-  // Detection (AI-only)
+  // Detection (hybrid Layer 1 + Layer 2)
   detectCorrection,
   batchAnalyzePrompts,
   spawnBackgroundDetection,
 
+  // wf-6c58953a: reconciliation helpers exposed for unit testing + backfill
+  reconcileExtraction,
+  deterministicWhatWasWrong,
+
   // Queue management
   loadPendingCorrections,
   queuePendingCorrection,

package/scripts/flow-defer-auth.js

@@ -14,7 +14,6 @@
  *   flow defer-auth status
  */
 
-const path = require('node:path');
 const gate = require('./hooks/core/deferral-gate');
 
 function parseArgs(argv) {

package/scripts/flow-export-scanner.js

@@ -20,7 +20,7 @@ const { PATHS, getConfig, readJson, success } = require('./flow-utils');
 
 // Default to PATHS.root from flow-utils, can be overridden via setProjectRoot() or CLI arg
 let PROJECT_ROOT = PATHS.root;
-let CONFIG_PATH = path.join(PROJECT_ROOT, '.workflow/config.json');
+let _CONFIG_PATH = path.join(PROJECT_ROOT, '.workflow/config.json');
 let CACHE_PATH = path.join(PROJECT_ROOT, '.workflow/state/export-map.json');
 const CACHE_MAX_AGE_MS = 5 * 60 * 1000; // 5 minutes
 
@@ -31,7 +31,7 @@ const CACHE_MAX_AGE_MS = 5 * 60 * 1000; // 5 minutes
  */
 function setProjectRoot(root) {
   PROJECT_ROOT = path.resolve(root);
-  CONFIG_PATH = path.join(PROJECT_ROOT, '.workflow/config.json');
+  _CONFIG_PATH = path.join(PROJECT_ROOT, '.workflow/config.json');
   CACHE_PATH = path.join(PROJECT_ROOT, '.workflow/state/export-map.json');
 }
 
@@ -700,7 +700,7 @@ function formatExportMapForTemplate(exportMap) {
   // Components
   if (Object.keys(exportMap.components).length > 0) {
     lines.push('#### Components');
-    for (const [name, info] of Object.entries(exportMap.components)) {
+    for (const [_name, info] of Object.entries(exportMap.components)) {
       const exports = info.exports.join(', ') || (info.defaultExport ? `default: ${info.defaultExport}` : '');
       if (exports) {
         lines.push(`- \`import { ${info.exports.join(', ')} } from '${info.importPath}'\``);
@@ -712,7 +712,7 @@ function formatExportMapForTemplate(exportMap) {
   // Hooks
   if (Object.keys(exportMap.hooks).length > 0) {
     lines.push('#### Hooks');
-    for (const [name, info] of Object.entries(exportMap.hooks)) {
+    for (const [_name, info] of Object.entries(exportMap.hooks)) {
       const exports = info.exports.join(', ');
       if (exports) {
         lines.push(`- \`import { ${exports} } from '${info.importPath}'\``);
@@ -724,7 +724,7 @@ function formatExportMapForTemplate(exportMap) {
   // Services
   if (Object.keys(exportMap.services).length > 0) {
     lines.push('#### Services');
-    for (const [name, info] of Object.entries(exportMap.services)) {
+    for (const [_name, info] of Object.entries(exportMap.services)) {
       const exports = info.exports.join(', ');
       if (exports) {
         lines.push(`- \`import { ${exports} } from '${info.importPath}'\``);
@@ -736,7 +736,7 @@ function formatExportMapForTemplate(exportMap) {
   // Types
   if (Object.keys(exportMap.types).length > 0) {
     lines.push('#### Types');
-    for (const [name, info] of Object.entries(exportMap.types)) {
+    for (const [_name, info] of Object.entries(exportMap.types)) {
       const types = info.types.join(', ');
       if (types) {
         lines.push(`- \`import type { ${types} } from '${info.importPath}'\``);
@@ -748,7 +748,7 @@ function formatExportMapForTemplate(exportMap) {
   // Utils
   if (Object.keys(exportMap.utils).length > 0) {
     lines.push('#### Utilities');
-    for (const [name, info] of Object.entries(exportMap.utils)) {
+    for (const [_name, info] of Object.entries(exportMap.utils)) {
       const exports = info.exports.join(', ');
       if (exports) {
         lines.push(`- \`import { ${exports} } from '${info.importPath}'\``);
@@ -784,7 +784,7 @@ function validateComponentUsage(code, exportMap = null) {
 
   // Collect all array exports from components
   const arrayExports = new Set();
-  for (const [name, info] of Object.entries(exportMap.components || {})) {
+  for (const [_name, info] of Object.entries(exportMap.components || {})) {
     if (info.arrayExports) {
       info.arrayExports.forEach(e => arrayExports.add(e));
     }
@@ -841,7 +841,7 @@ function validateComponentUsage(code, exportMap = null) {
       // Check if the actual export exists
       const wrongName = pattern.source.replace(/\\/g, '').replace(/\(\)/g, '');
       let found = false;
-      for (const [name, info] of Object.entries(exportMap.hooks || {})) {
+      for (const [_name, info] of Object.entries(exportMap.hooks || {})) {
         if (info.exports?.includes(wrongName)) {
           found = true;
           break;

package/scripts/flow-figma-match.js

@@ -572,10 +572,12 @@ async function main() {
   const matcher = new SimilarityMatcher(registry);
 
   // Parse threshold argument
-  let threshold = MATCH_CONFIG.thresholds.VARIANT_CANDIDATE;
+  // _threshold: parsed from --threshold CLI arg but not currently passed to
+  // the matcher (real bug; see audit notes; out of scope for lint cleanup).
+  let _threshold = MATCH_CONFIG.thresholds.VARIANT_CANDIDATE;
   const thresholdIndex = args.indexOf('--threshold');
   if (thresholdIndex !== -1 && args[thresholdIndex + 1]) {
-    threshold = parseInt(args[thresholdIndex + 1]);
+    _threshold = parseInt(args[thresholdIndex + 1]);
   }
 
   if (input === '--stdin') {

package/scripts/flow-hypothesis-generator.js

@@ -32,12 +32,13 @@ try {
   adaptiveLearning = null;
 }
 
-// Import error recovery for integration
-let errorRecovery;
+// Import error recovery for integration (currently loaded for side-effect /
+// future-use; not yet referenced — _ prefix per naming convention).
+let _errorRecovery;
 try {
-  errorRecovery = require('./flow-error-recovery');
+  _errorRecovery = require('./flow-error-recovery');
 } catch (_err) {
-  errorRecovery = null;
+  _errorRecovery = null;
 }
 
 // ============================================================

package/scripts/flow-model-router.js

@@ -38,10 +38,10 @@ const { loadRegistry, loadStats } = require('./flow-model-types');
 
 // Smart Context System integration
 let contextGatherer = null;
-let instructionRichness = null;
+let _instructionRichness = null;
 try {
   contextGatherer = require('./flow-context-gatherer');
-  instructionRichness = require('./flow-instruction-richness');
+  _instructionRichness = require('./flow-instruction-richness');
 } catch (_err) {
   // Smart Context modules not available
 }

package/scripts/flow-prompt-template.js

@@ -17,8 +17,7 @@ const fs = require('node:fs');
 const path = require('node:path');
 const {
   getConfig,
-  PATHS,
-  fileExists
+  PATHS
 } = require('./flow-utils');
 
 // ============================================================
@@ -59,7 +58,7 @@ function parseSimpleYaml(content) {
   const lines = content.split('\n');
   let currentKey = null;
   let currentSection = null;
-  let currentList = null;
+  let _currentList = null;
   let indentLevel = 0;
   let multilineValue = '';
   let inMultiline = false;
@@ -100,7 +99,7 @@ function parseSimpleYaml(content) {
       if (BLOCKED_KEYS.has(key)) continue;
 
       currentSection = null;
-      currentList = null;
+      _currentList = null;
 
       if (value === '' || value === '|') {
         // Start of nested section or multi-line
@@ -128,7 +127,7 @@ function parseSimpleYaml(content) {
 
       if (BLOCKED_KEYS.has(key)) continue;
 
-      currentList = null;
+      _currentList = null;
       currentKey = key;
 
       if (value === '|') {

package/scripts/flow-repo-map.js

@@ -23,6 +23,7 @@ const { execFileSync } = require('node:child_process');
 
 const { PATHS } = require('./flow-paths');
 const { getConfig } = require('./flow-config-loader');
+const { safeJsonParse } = require('./flow-io');
 
 const DEFAULT_BUDGET_BYTES = 16 * 1024; // ~4k tokens
 const IGNORED_DIRS = new Set(['node_modules', '.git', 'dist', 'build', 'coverage', '.next', '.workflow', '.worktrees', 'out']);
@@ -46,12 +47,15 @@ function resolveChangedFiles(opts = {}) {
   if (Array.isArray(opts.changedFiles)) return opts.changedFiles;
 
   // Try task-checkpoint.json
+  // wf-3c968989: safeJsonParse adds DANGEROUS_KEYS protection. Returns null
+  // (the explicit default) on missing/corrupt/array — preserves the
+  // original silent-fallthrough contract via the null check below.
   const checkpointPath = path.join(PATHS.state, 'task-checkpoint.json');
   if (fs.existsSync(checkpointPath)) {
-    try {
-      const cp = JSON.parse(fs.readFileSync(checkpointPath, 'utf8'));
-      if (Array.isArray(cp.changedFiles) && cp.changedFiles.length > 0) return cp.changedFiles;
-    } catch { /* fall through */ }
+    const cp = safeJsonParse(checkpointPath, null);
+    if (cp && Array.isArray(cp.changedFiles) && cp.changedFiles.length > 0) {
+      return cp.changedFiles;
+    }
   }
 
   // Git diff

package/scripts/flow-source-fidelity.js

@@ -39,7 +39,6 @@
 'use strict';
 
 const fs = require('node:fs');
-const path = require('node:path');
 
 const VERBATIM_HEADER_REGEX = /^##\s+Original Request \(verbatim\)\s*$/m;
 const MANIFEST_HEADER_REGEX = /^##\s+Item Manifest\s*$/m;

package/scripts/flow-standards-checker.js

@@ -20,7 +20,8 @@ const {
   fileExists,
   readFile,
   safeJsonParse,
-  color
+  color,
+  getConfig
 } = require('./flow-utils');
 const {
   calculateCombinedSimilarity,
@@ -76,19 +77,23 @@ const MATCH_LEVEL_SEVERITY = {
 };
 
 // Task type to check type mapping for smart scoping
+// wf-00c5067b: 'hook-three-layer' added to all task types — entry-file LOC
+// + import-count rule (per .claude/rules/architecture/hook-three-layer.md)
+// is universally applicable; the exemption list in config covers known
+// pre-extraction violators (see ARCH-001, ARCH-002 in .workflow/state/last-audit.json).
 const TASK_CHECK_MAP = {
-  'component': ['naming', 'components', 'security'],
-  'utility': ['naming', 'functions', 'security'],
-  'api': ['naming', 'api', 'security'],
-  'feature': ['naming', 'components', 'functions', 'api', 'schemas', 'services', 'security'],
-  'bugfix': ['naming', 'security'],
-  'refactor': ['naming', 'components', 'functions', 'api', 'schemas', 'services', 'security'],
-  'story': ['naming', 'components', 'functions', 'api', 'schemas', 'services', 'security'],
-  'default': ['naming', 'components', 'functions', 'api', 'schemas', 'services', 'security']
+  'component': ['naming', 'components', 'security', 'hook-three-layer'],
+  'utility': ['naming', 'functions', 'security', 'hook-three-layer'],
+  'api': ['naming', 'api', 'security', 'hook-three-layer'],
+  'feature': ['naming', 'components', 'functions', 'api', 'schemas', 'services', 'security', 'hook-three-layer'],
+  'bugfix': ['naming', 'security', 'hook-three-layer'],
+  'refactor': ['naming', 'components', 'functions', 'api', 'schemas', 'services', 'security', 'hook-three-layer'],
+  'story': ['naming', 'components', 'functions', 'api', 'schemas', 'services', 'security', 'hook-three-layer'],
+  'default': ['naming', 'components', 'functions', 'api', 'schemas', 'services', 'security', 'hook-three-layer']
 };
 
 // All available check types
-const ALL_CHECK_TYPES = ['naming', 'components', 'functions', 'api', 'schemas', 'services', 'security'];
+const ALL_CHECK_TYPES = ['naming', 'components', 'functions', 'api', 'schemas', 'services', 'security', 'hook-three-layer'];
 
 // ============================================================================
 // Parse Standards Files
@@ -552,6 +557,88 @@ function checkSecurityPatterns(file, _securityRules) {
  * @param {Object} matchConfig - Semantic match config — optional, auto-loaded if omitted
  * @returns {Object[]} Array of violations
  */
+/**
+ * wf-00c5067b — Hook Three-Layer enforcement.
+ *
+ * Per `.claude/rules/architecture/hook-three-layer.md`:
+ *   - Entry files (`scripts/hooks/entry/<cli>/*.js`) must be ≤120 LOC and
+ *     import from at most 2 `core/` modules (single-entry-point principle).
+ *   - Core files (`scripts/hooks/core/*.js`) should be CLI-agnostic.
+ *
+ * This check enforces the LOC + import-count rules. Core CLI-identifier
+ * grep is intentionally NOT enforced here (false-positive prone — adversary
+ * critique 2026-05-08 found 1/4 supposed violations was actually config data).
+ *
+ * Exemptions: read from config.standardsCheck.hookThreeLayer.exemptions
+ * map of `{relativePath: reason}`. Each exemption MUST cite a rationale
+ * (typically a Phase 2 task ID for entries awaiting orchestrator extraction).
+ *
+ * @param {Object} file - File with path and content
+ * @param {Object} hookThreeLayerConfig - {enabled, exemptions, maxLoc, maxCoreImports}
+ * @returns {Object[]} Array of violations
+ */
+function checkHookThreeLayer(file, hookThreeLayerConfig = {}) {
+  const violations = [];
+  const {
+    enabled = true,
+    exemptions = {},
+    maxLoc = 120,
+    maxCoreImports = 2
+  } = hookThreeLayerConfig;
+
+  if (!enabled) return violations;
+
+  // Normalize path to repo-root-relative form for exemption lookup
+  const relPath = file.path.startsWith('/')
+    ? path.relative(PATHS.root, file.path)
+    : file.path;
+
+  // Only apply to hook entry files
+  const isEntry = /^scripts\/hooks\/entry\/[^/]+\/[^/]+\.js$/.test(relPath);
+  if (!isEntry) return violations;
+
+  // Skip if exempted (with rationale)
+  if (Object.prototype.hasOwnProperty.call(exemptions, relPath)) return violations;
+
+  const content = file.content || '';
+  const lines = content.split('\n');
+
+  // Rule 1: LOC ceiling
+  if (lines.length > maxLoc) {
+    violations.push({
+      type: 'hook-three-layer',
+      severity: 'must-fix',
+      file: file.path,
+      line: null,
+      message: `Hook entry file exceeds ${maxLoc} LOC (${lines.length} lines). Extract orchestration logic to core/. Add to config.standardsCheck.hookThreeLayer.exemptions with rationale to defer.`,
+      rule: 'hook-three-layer.md'
+    });
+  }
+
+  // Rule 2: Core import count
+  // Match `require('../core/...')` or `require('../../core/...')` etc.
+  // Capture each core path; count distinct core modules imported.
+  const coreImportRegex = /require\(['"][^'"]*\/core\/([^'"/]+)['"]\)/g;
+  const coreModules = new Set();
+  let match;
+  while ((match = coreImportRegex.exec(content)) !== null) {
+    coreModules.add(match[1]);
+  }
+
+  if (coreModules.size > maxCoreImports) {
+    violations.push({
+      type: 'hook-three-layer',
+      severity: 'must-fix',
+      file: file.path,
+      line: null,
+      message: `Hook entry imports from ${coreModules.size} core/ modules (limit: ${maxCoreImports}). Single-entry-point principle violated. Refactor to dispatch through one orchestrator-core. Modules: ${[...coreModules].sort().join(', ')}`,
+      rule: 'hook-three-layer.md'
+    });
+  }
+
+  return violations;
+}
+
 function checkApiDuplication(file, existingEndpoints, matchConfig) {
   const violations = [];
   const content = file.content || '';
@@ -1009,6 +1096,16 @@ function runStandardsCheck(files, options = {}) {
   const services = checksToRun.includes('services') ? parseServiceMap() : [];
 
   const allViolations = [];
+
+  // wf-00c5067b: load hook-three-layer config (with sensible defaults if unset)
+  const config = getConfig();
+  const hookThreeLayerConfig = (config?.standardsCheck?.hookThreeLayer) || {
+    enabled: checksToRun.includes('hook-three-layer'),
+    exemptions: {},
+    maxLoc: 120,
+    maxCoreImports: 2
+  };
+
   const checksSummary = {
     'decisions.md': { checked: true, violations: 0 },
     'app-map.md': { checked: checksToRun.includes('components') && components.length > 0, violations: 0 },
@@ -1017,7 +1114,8 @@ function runStandardsCheck(files, options = {}) {
     'schema-map.md': { checked: checksToRun.includes('schemas') && schemas.length > 0, violations: 0 },
     'service-map.md': { checked: checksToRun.includes('services') && services.length > 0, violations: 0 },
     'naming-conventions': { checked: checksToRun.includes('naming'), violations: 0 },
-    'security-patterns': { checked: checksToRun.includes('security'), violations: 0 }
+    'security-patterns': { checked: checksToRun.includes('security'), violations: 0 },
+    'hook-three-layer': { checked: checksToRun.includes('hook-three-layer'), violations: 0 }
   };
 
   for (const file of files) {
@@ -1076,6 +1174,13 @@ function runStandardsCheck(files, options = {}) {
       allViolations.push(...securityViolations);
       checksSummary['security-patterns'].violations += securityViolations.length;
     }
+
+    // Hook three-layer architecture (wf-00c5067b)
+    if (checksToRun.includes('hook-three-layer')) {
+      const hookViolations = checkHookThreeLayer(file, hookThreeLayerConfig);
+      allViolations.push(...hookViolations);
+      checksSummary['hook-three-layer'].violations += hookViolations.length;
+    }
   }
 
   // Count must-fix violations
@@ -1309,6 +1414,7 @@ module.exports = {
   checkApiDuplication,
   checkRegistryDuplication,
   checkSecurityPatterns,
+  checkHookThreeLayer,
   extractDeclaredNames,
   discoverAllRegistries,
   collectReuseCandidates,

package/scripts/hooks/core/deferral-gate.js

@@ -192,7 +192,7 @@ function isAuthorized(deferralChanges) {
   return { authorized: false, reason: 'auth-malformed-scope' };
 }
 
-function consumeAuth(deferralChanges) {
+function consumeAuth(_deferralChanges) {
   // Auth is single-use: once a deferral write succeeds, the marker is removed
   // to prevent reuse on subsequent unrelated deferrals.
   clearAuth();

package/scripts/hooks/core/long-input-enforcement.js

@@ -46,6 +46,7 @@
 const fs = require('node:fs');
 const path = require('node:path');
 const { PATHS } = require('../../flow-utils');
+const { safeJsonParse } = require('../../flow-io');
 
 const PENDING_PATH = path.join(PATHS.state, 'long-input-pending.json');
 
@@ -210,10 +211,10 @@ function isLongInputPending() {
 }
 
 function readLongInputPending() {
-  try {
-    if (!fs.existsSync(PENDING_PATH)) return null;
-    return JSON.parse(fs.readFileSync(PENDING_PATH, 'utf-8'));
-  } catch (_err) { return null; }
+  // wf-3c968989: safeJsonParse adds DANGEROUS_KEYS protection. Returns null
+  // on missing/corrupt/array input — exact behavior match for the prior
+  // try/catch + return-null contract.
+  return safeJsonParse(PENDING_PATH, null);
 }
 
 /**