sneakoscope 0.7.69 → 0.7.74

package/README.md

@@ -192,7 +192,7 @@ sks qa-loop prepare "http://localhost:3000"
 sks qa-loop run latest --max-cycles 2
 sks goal create "persist this migration workflow"
 sks research prepare "evaluate this approach"
-sks research run latest --max-cycles 3
+sks research run latest --max-cycles 3 --cycle-timeout-minutes 120
 sks research status latest
 sks db scan --json
 sks wiki refresh
@@ -211,7 +211,7 @@ sks skill-dream run --json
 sks code-structure scan --json
 ```
 
-`sks research` prepares a genius-lens scout council, requires every scout to run at `xhigh`, records one literal `Eureka!` idea per scout, runs an evidence-bound debate, maximizes available web/source retrieval before synthesis, and requires `research-report.md`, `research-paper.md`, `source-ledger.json`, `scout-ledger.json`, `debate-ledger.json`, `novelty-ledger.json`, `falsification-ledger.json`, and `research-gate.json` so research runs stay source-backed, adversarially checked, falsifiable, and paper-ready. `research status` reports source entries, counterevidence, xhigh scout count, Eureka moments, debate exchanges, paper presence/sections, scout findings, and falsification cases alongside the gate.
+`sks research` prepares a genius-lens scout council, requires every scout to run at `xhigh`, records one literal `Eureka!` idea per scout, runs an evidence-bound debate, and now creates `research-source-skill.md` as a route-local source collection skill before synthesis. Normal Research is intentionally allowed to take one or two hours when the problem needs it; `--mock` is only for selftests or dry harness checks, and a real run blocks with `research-blocker.json` instead of silently substituting mock output when the Codex execution path is unavailable. The source layer contract separates latest papers, official/government or leading-institution sources, standards/primary docs, current news such as BBC/CNN/GDELT-style sources, public discourse such as X/Reddit, developer/practitioner knowledge such as Stack Overflow/GitHub, and counterevidence/fact-checking; `source-ledger.json` must record layer coverage, source quality, blockers, citations, and cross-layer triangulation. Context7 is optional for `$Research` and only becomes relevant when the research topic specifically depends on package, API, framework, or SDK documentation. Research runs require `research-report.md`, `research-paper.md`, `genius-opinion-summary.md`, `research-source-skill.md`, `source-ledger.json`, `scout-ledger.json`, `debate-ledger.json`, `novelty-ledger.json`, `falsification-ledger.json`, and `research-gate.json` so they stay source-backed, adversarially checked, falsifiable, paper-ready, and clear about every scout lens opinion. `research status` reports source entries, source-layer coverage, triangulation checks, counterevidence, xhigh scout count, Eureka moments, debate exchanges, paper presence/sections, genius-opinion summary coverage, scout findings, and falsification cases alongside the gate.
 
 `sks pipeline plan` shows the active route lane, kept/skipped stages, verification commands, and no-unrequested-fallback invariant. `sks proof-field scan` is the lightweight rubric for small changes; risky or broad signals return to the full Team/Honest path.
 

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "sneakoscope",
   "displayName": "ㅅㅋㅅ",
-  "version": "0.7.69",
+  "version": "0.7.74",
   "description": "Sneakoscope Codex: database-safe Codex CLI/App harness with Team, Goal, AutoResearch, TriWiki, and Honest Mode.",
   "type": "module",
   "homepage": "https://github.com/mandarange/Sneakoscope-Codex#readme",

package/src/cli/install-helpers.mjs

@@ -361,6 +361,7 @@ export function normalizeCodexFastModeUiConfig(text = '') {
   next = removeTomlTableKey(next, 'features', 'codex_hooks');
   next = upsertTopLevelTomlString(next, 'model', 'gpt-5.5');
   next = upsertTopLevelTomlString(next, 'service_tier', 'fast');
+  next = upsertTopLevelTomlBoolean(next, 'suppress_unstable_features_warning', true);
   next = upsertTomlTableKey(next, 'features', 'hooks = true');
   next = upsertTomlTableKey(next, 'features', 'multi_agent = true');
   next = upsertTomlTableKey(next, 'features', 'fast_mode = true');
@@ -457,6 +458,21 @@ function upsertTopLevelTomlString(text, key, value) {
   return lines.join('\n').replace(/^\n+/, '').replace(/\n{3,}/g, '\n\n');
 }
 
+function upsertTopLevelTomlBoolean(text, key, value) {
+  const line = `${key} = ${value ? 'true' : 'false'}`;
+  const lines = String(text || '').split('\n');
+  const firstTable = lines.findIndex((x) => /^\s*\[.+\]\s*$/.test(x));
+  const end = firstTable === -1 ? lines.length : firstTable;
+  for (let i = 0; i < end; i += 1) {
+    if (new RegExp(`^\\s*${escapeRegExp(key)}\\s*=`).test(lines[i])) {
+      lines[i] = line;
+      return lines.join('\n').replace(/\n{3,}/g, '\n\n');
+    }
+  }
+  lines.splice(end, 0, line);
+  return lines.join('\n').replace(/^\n+/, '').replace(/\n{3,}/g, '\n\n');
+}
+
 function upsertTomlTable(text, table, block) {
   let lines = String(text || '').trimEnd().split('\n');
   if (lines.length === 1 && lines[0] === '') lines = [];
@@ -929,15 +945,18 @@ export async function selftestCodexLb(tmp) {
   const codexLbEnv = await safeReadText(path.join(codexLbHome, '.codex', 'sks-codex-lb.env'));
   const codexLbAuth = await safeReadText(path.join(codexLbHome, '.codex', 'auth.json'));
   if (!codexLbSetupJson.ok || codexLbSetupJson.base_url !== 'https://lb.example.test/backend-api/codex' || !codexLbConfig.includes('model_provider = "codex-lb"') || !codexLbConfig.includes('[model_providers.codex-lb]') || !codexLbEnv.includes("CODEX_LB_BASE_URL='https://lb.example.test/backend-api/codex'") || !codexLbEnv.includes("CODEX_LB_API_KEY='sk-test'") || !/(\"auth_mode\"\s*:\s*\"apikey\")/.test(codexLbAuth)) throw new Error('selftest: codex-lb setup');
+  if (!hasCodexUnstableFeatureWarningSuppression(codexLbConfig)) throw new Error('selftest: codex-lb setup did not suppress Codex unstable feature warning');
   await initProject(codexLbHome, { installScope: 'global', force: true, repair: true });
   const codexLbRepairSetupConfig = await safeReadText(path.join(codexLbHome, '.codex', 'config.toml'));
   if (!codexLbRepairSetupConfig.includes('model_provider = "codex-lb"') || !codexLbRepairSetupConfig.includes('[model_providers.codex-lb]') || !codexLbRepairSetupConfig.includes('https://lb.example.test/backend-api/codex') || codexLbRepairSetupConfig.includes('sk-test')) throw new Error('selftest: init codex-lb');
+  if (!hasCodexUnstableFeatureWarningSuppression(codexLbRepairSetupConfig)) throw new Error('selftest: init codex-lb did not suppress Codex unstable feature warning');
   await writeTextAtomic(path.join(codexLbHome, '.codex', 'config.toml'), `${codexLbConfig}\n[mcp_servers.supabase]\nurl = "https://mcp.supabase.com/mcp?project_ref=ref&read_only=true&features=database,docs"\n`);
   const ptmp = path.join(tmp, 'codex-lb-project-config'), prevHome = process.env.HOME;
   try { process.env.HOME = codexLbHome; await initProject(ptmp, { installScope: 'global' }); }
   finally { if (prevHome === undefined) delete process.env.HOME; else process.env.HOME = prevHome; }
   const pcfg = await safeReadText(path.join(ptmp, '.codex', 'config.toml'));
   if (!pcfg.includes('model_provider = "codex-lb"') || !pcfg.includes('[model_providers.codex-lb]') || !pcfg.includes('[mcp_servers.supabase]') || !pcfg.includes('read_only=true')) throw new Error('selftest: project codex-lb');
+  if (!hasCodexUnstableFeatureWarningSuppression(pcfg)) throw new Error('selftest: project codex-lb config did not suppress Codex unstable feature warning');
   await writeTextAtomic(path.join(codexLbHome, '.codex', 'auth.json'), '{"auth_mode":"browser"}\n');
   const codexLbRepair = await runProcess(process.execPath, [path.join(packageRoot(), 'bin', 'sks.mjs'), 'auth', 'repair', '--json'], { cwd: tmp, env: codexLbEnvForSelftest, timeoutMs: 15000, maxOutputBytes: 64 * 1024 });
   if (codexLbRepair.code !== 0) throw new Error(`selftest: codex-lb repair exited ${codexLbRepair.code}: ${codexLbRepair.stderr}`);
@@ -1014,7 +1033,7 @@ export async function selftestCodexLb(tmp) {
   const codexLbDoctorJson = JSON.parse(codexLbDoctorRepair.stdout);
   const codexLbDoctorAuth = await safeReadText(path.join(codexLbHome, '.codex', 'auth.json'));
   const codexLbDoctorConfig = await safeReadText(path.join(codexLbHome, '.codex', 'config.toml'));
-  if (!codexLbDoctorJson.repair?.codex_lb?.ok || !codexLbDoctorJson.repair.codex_lb.config_repaired || !codexLbDoctorJson.codex_lb?.ok || !codexLbDoctorAuth.includes('"auth_mode":"apikey"') || !codexLbDoctorAuth.includes('sk-test') || !codexLbDoctorConfig.includes('model_provider = "codex-lb"') || !codexLbDoctorConfig.includes('https://lb.example.test/backend-api/codex')) throw new Error('selftest: doctor codex-lb');
+  if (!codexLbDoctorJson.repair?.codex_lb?.ok || !codexLbDoctorJson.repair.codex_lb.config_repaired || !codexLbDoctorJson.codex_lb?.ok || !codexLbDoctorAuth.includes('"auth_mode":"apikey"') || !codexLbDoctorAuth.includes('sk-test') || !codexLbDoctorConfig.includes('model_provider = "codex-lb"') || !codexLbDoctorConfig.includes('https://lb.example.test/backend-api/codex') || !hasCodexUnstableFeatureWarningSuppression(codexLbDoctorConfig)) throw new Error('selftest: doctor codex-lb');
   const codexLbContext7Bin = path.join(tmp, 'codex-lb-context7-bin');
   await ensureDir(codexLbContext7Bin);
   await writeTextAtomic(path.join(codexLbContext7Bin, 'codex'), '#!/bin/sh\nif [ "$1" = "--version" ]; then echo "codex-cli 99.0.0"; exit 0; fi\nif [ "$CODEX_LB_API_KEY" ]; then echo "context7 leaked CODEX_LB_API_KEY" >&2; exit 77; fi\nif [ "$1" = "mcp" ] && [ "$2" = "list" ]; then echo ""; exit 0; fi\nif [ "$1" = "mcp" ] && [ "$2" = "add" ]; then echo "context7 added"; exit 0; fi\necho "unexpected codex $*" >&2\nexit 2\n');
@@ -1092,6 +1111,7 @@ export async function selftestCodexLb(tmp) {
   const codexLbStatusText = await runProcess(process.execPath, [path.join(packageRoot(), 'bin', 'sks.mjs'), 'codex-lb', 'status'], { cwd: tmp, env: codexLbEnvForSelftest, timeoutMs: 15000, maxOutputBytes: 64 * 1024 });
   if (!String(codexLbStatusText.stdout || '').includes('Repair auth: sks codex-lb repair')) throw new Error('selftest: codex-lb status did not advertise repair command');
   if (!/^model = "gpt-5\.5"/m.test(codexLbConfig) || !codexLbConfig.includes('service_tier = "fast"') || !codexLbConfig.includes('hooks = true') || hasDeprecatedCodexHooksFeatureFlag(codexLbConfig) || !codexLbConfig.includes('multi_agent = true') || !codexLbConfig.includes('fast_mode = true') || !codexLbConfig.includes('fast_mode_ui = true') || !codexLbConfig.includes('codex_git_commit = true') || !codexLbConfig.includes('computer_use = true') || !codexLbConfig.includes('apps = true') || !codexLbConfig.includes('plugins = true') || !codexLbConfig.includes('[user.fast_mode]') || !codexLbConfig.includes('visible = true') || !codexLbConfig.includes('enabled = true') || !codexLbConfig.includes('default_profile = "sks-fast-high"') || !/\[profiles\.sks-fast-high\][\s\S]*?service_tier = "fast"/.test(codexLbConfig) || codexLbConfig.includes('fast_default_opt_out = true') || hasTopLevelCodexModeLock(codexLbConfig)) throw new Error('selftest: codex-lb setup did not preserve Codex App feature flags, Fast mode defaults, Codex Git commit generation, force GPT-5.5, or migrate the hooks feature flag');
+  if (!hasCodexUnstableFeatureWarningSuppression(codexLbConfig)) throw new Error('selftest: codex-lb setup did not suppress Codex unstable feature warning');
   const codexLbLaunch = codexLaunchCommand(tmp, 'codex', []);
   if (!codexLbLaunch.includes('sks-codex-lb.env')) throw new Error('selftest: tmux launch command does not source codex-lb env file');
   if (!codexLbLaunch.includes("'--model' 'gpt-5.5'")) throw new Error('selftest: tmux launch command without args did not force GPT-5.5');
@@ -1118,3 +1138,7 @@ function hasDeprecatedCodexHooksFeatureFlag(text = '') {
   }
   return lines.slice(start + 1, end).some((line) => /^\s*codex_hooks\s*=/.test(line));
 }
+
+function hasCodexUnstableFeatureWarningSuppression(text = '') {
+  return /(^|\n)\s*suppress_unstable_features_warning\s*=\s*true\s*(?:#.*)?(?=\n|$)/.test(String(text || ''));
+}

package/src/cli/main.mjs

@@ -4,7 +4,7 @@ import fsp from 'node:fs/promises';
 import readline from 'node:readline/promises';
 import { stdin as input, stdout as output } from 'node:process';
 import { projectRoot, readJson, writeJsonAtomic, writeTextAtomic, appendJsonlBounded, nowIso, exists, ensureDir, tmpdir, packageRoot, dirSize, formatBytes, which, runProcess, PACKAGE_VERSION, sksRoot, globalSksRoot, findProjectRoot, readStdin } from '../core/fsx.mjs';
-import { initProject, installSkills, normalizeInstallScope, sksCommandPrefix } from '../core/init.mjs';
+import { assertCodexWarningSuppressed as assertCodexWarn, hasDeprecatedCodexHooksFeatureFlag, hasTopLevelCodexModeLock, initProject, installSkills, missingGeneratedCodexAppFeatureFlags, normalizeInstallScope, sksCommandPrefix } from '../core/init.mjs';
 import { buildCodexExecArgs, getCodexInfo, runCodexExec } from '../core/codex-adapter.mjs';
 import { createMission, loadMission, findLatestMission, missionDir, setCurrent, stateFile } from '../core/mission.mjs';
 import { buildQuestionSchema, writeQuestions } from '../core/questions.mjs';
@@ -22,7 +22,7 @@ import { bumpProjectVersion, installVersionGitHook, runVersionPreCommit, version
 import { rustInfo } from '../core/rust-accelerator.mjs';
 import { renderCartridge, validateCartridge, driftCartridge, snapshotCartridge } from '../core/gx-renderer.mjs';
 import { defaultEvaluationScenario, runEvaluationBenchmark } from '../core/evaluation.mjs';
-import { buildResearchPrompt, evaluateResearchGate, writeMockResearchResult, writeResearchPlan } from '../core/research.mjs';
+import { evaluateResearchGate, writeMockResearchResult, writeResearchPlan } from '../core/research.mjs';
 import {
   PPT_AUDIENCE_STRATEGY_ARTIFACT,
   PPT_CLEANUP_REPORT_ARTIFACT,
@@ -78,7 +78,7 @@ import { OPENCLAW_SKILL_NAME, installOpenClawSkill } from '../core/openclaw.mjs'
 import { buildTmuxLaunchPlan, buildTmuxOpenArgs, codexLaunchCommand, createTmuxSession, defaultCodexLaunchArgs, isTmuxShellSession, runTmuxLaunchPlanSyntaxCheck, shouldAutoAttachTmux, sksAsciiLogo, tmuxReadiness, tmuxStatusKind, defaultTmuxSessionName, formatTmuxBanner, launchMadTmuxUi, launchTmuxTeamView, launchTmuxUi, platformTmuxInstallHint, reconcileTmuxTeamCockpit, runTmuxStatus, sanitizeTmuxSessionName, teamLaneStyle } from '../core/tmux-ui.mjs';
 import { autoReviewProfileName, autoReviewStatus, autoReviewSummary, enableAutoReview, disableAutoReview, enableMadHighProfile, madHighProfileName } from '../core/auto-review.mjs';
 import { context7Command } from './context7-command.mjs';
-import { askPostinstallQuestion, checkContext7, checkRequiredSkills, codexLbStatus, configureCodexLb, ensureCodexCliTool, ensureGlobalCodexSkillsDuringInstall, ensureProjectContext7Config, ensureRelatedCliTools, ensureSksCommandDuringInstall, ensureTmuxCliTool, globalCodexSkillsRoot, maybePromptCodexLbSetupForLaunch, maybePromptCodexUpdateForLaunch, postinstall, postinstallBootstrapDecision, repairCodexLbAuth, selftestCodexLb, shouldAutoApproveInstall } from './install-helpers.mjs';
+import { askPostinstallQuestion, checkContext7, checkRequiredSkills, codexLbStatus, configureCodexLb, ensureCodexCliTool, ensureGlobalCodexFastModeDuringInstall, ensureGlobalCodexSkillsDuringInstall, ensureProjectContext7Config, ensureRelatedCliTools, ensureSksCommandDuringInstall, ensureTmuxCliTool, globalCodexSkillsRoot, maybePromptCodexLbSetupForLaunch, maybePromptCodexUpdateForLaunch, postinstall, postinstallBootstrapDecision, repairCodexLbAuth, selftestCodexLb, shouldAutoApproveInstall } from './install-helpers.mjs';
 import { buildTeamPlan, codeStructureCommand, dbCommand, defaultBeta, defaultVGraph, evalCommand, gcCommand, goalCommand, gxCommand, harnessCommand, hproofCommand, madHighCommand as runMadHighCommand, memoryCommand, migrateWikiContextPack, parseTeamCreateArgs, perfCommand, profileCommand, projectWikiClaims, proofFieldCommand, qaLoopCommand, quickstartCommand, researchCommand, skillDreamCommand, statsCommand, team, teamWorkflowMarkdown, validateArtifactsCommand, wikiCommand, wikiVoxelRowCount, writeWikiContextPack } from './maintenance-commands.mjs';
 import { openClawCommand } from './openclaw-command.mjs';
 
@@ -211,7 +211,7 @@ Usage:
   sks team attach-tmux [mission-id|latest]
   sks team cleanup-tmux [mission-id|latest]
   sks research prepare "topic" [--depth frontier]
-  sks research run <mission-id|latest> [--mock] [--max-cycles N]
+  sks research run <mission-id|latest> [--mock] [--max-cycles N] [--cycle-timeout-minutes N]
   sks research status <mission-id|latest>
   sks db policy
   sks db scan [--migrations] [--json]
@@ -1659,6 +1659,7 @@ async function doctor(args) {
   let conflictScan = await scanHarnessConflicts(root);
   let repairApplied = false;
   let globalSkillsRepair = null;
+  let globalCodexConfigRepair = null;
   let projectRepair = null;
   let codexLbRepair = null;
   const globalCommand = await globalSksCommand();
@@ -1666,6 +1667,7 @@ async function doctor(args) {
     const existingManifest = await readJson(path.join(root, '.sneakoscope', 'manifest.json'), null);
     const fixScope = requestedScope || normalizeInstallScope(existingManifest?.installation?.scope || 'global');
     projectRepair = await initProject(root, { installScope: fixScope, globalCommand, localOnly: flag(args, '--local-only') || Boolean(existingManifest?.git?.local_only), force: true, repair: true });
+    if (!flag(args, '--local-only')) globalCodexConfigRepair = await ensureGlobalCodexFastModeDuringInstall();
     if (!flag(args, '--local-only')) globalSkillsRepair = await ensureGlobalCodexSkillsDuringInstall({ force: true });
     codexLbRepair = await repairCodexLbAuth();
     repairApplied = true;
@@ -1695,7 +1697,7 @@ async function doctor(args) {
   const result = {
     node: { ok: nodeOk, version: process.version }, root, codex, rust,
     install,
-    repair: { applied: repairApplied, project: projectRepair, global_skills: globalSkillsRepair, codex_lb: codexLbRepair, blocked_by_other_harness: flag(args, '--fix') && conflictScan.hard_block },
+    repair: { applied: repairApplied, project: projectRepair, global_codex_config: globalCodexConfigRepair, global_skills: globalSkillsRepair, codex_lb: codexLbRepair, blocked_by_other_harness: flag(args, '--fix') && conflictScan.hard_block },
     harness_conflicts: {
       ok: conflictScan.ok,
       hard_block: conflictScan.hard_block,
@@ -1729,6 +1731,7 @@ async function doctor(args) {
   console.log(`Install:   ${install.ok ? 'ok' : 'missing'} ${install.scope} (${install.command_prefix})`);
   console.log(`Conflicts: ${result.harness_conflicts.hard_block ? 'blocked' : 'ok'} ${result.harness_conflicts.conflicts.length} finding(s)`);
   if (repairApplied) console.log('Repair:    regenerated SKS managed files from the installed package template');
+  if (globalCodexConfigRepair) console.log(`Global Codex config: ${globalCodexConfigRepair.status} ${globalCodexConfigRepair.config_path || ''}`.trimEnd());
   if (globalSkillsRepair) {
     const removed = globalSkillsRepair.removed_stale_generated_skills || [];
     const cleanup = removed.length ? ` removed stale generated skill shadow(s): ${removed.join(', ')}` : '';
@@ -1925,34 +1928,6 @@ async function safeReadText(file, fallback = '') {
   try { return await fsp.readFile(file, 'utf8'); } catch { return fallback; }
 }
 
-function hasTopLevelCodexModeLock(text = '') {
-  const lines = String(text || '').split('\n');
-  const firstTable = lines.findIndex((x) => /^\s*\[.+\]\s*$/.test(x));
-  const top = (firstTable === -1 ? lines : lines.slice(0, firstTable)).join('\n');
-  const model = top.match(/^model\s*=\s*"([^"]+)"/m)?.[1];
-  return (Boolean(model) && model !== 'gpt-5.5') || /^model_reasoning_effort\s*=/m.test(top);
-}
-
-function hasDeprecatedCodexHooksFeatureFlag(text = '') {
-  const lines = String(text || '').split('\n');
-  const start = lines.findIndex((line) => line.trim() === '[features]');
-  if (start === -1) return false;
-  let end = lines.length;
-  for (let i = start + 1; i < lines.length; i += 1) {
-    if (/^\s*\[.+\]\s*$/.test(lines[i])) {
-      end = i;
-      break;
-    }
-  }
-  return lines.slice(start + 1, end).some((line) => /^\s*codex_hooks\s*=/.test(line));
-}
-
-const REQUIRED_GENERATED_CODEX_APP_FEATURE_FLAGS = ['hooks', 'multi_agent', 'fast_mode', 'fast_mode_ui', 'codex_git_commit', 'computer_use', 'apps', 'plugins'];
-
-function missingGeneratedCodexAppFeatureFlags(text = '') {
-  return REQUIRED_GENERATED_CODEX_APP_FEATURE_FLAGS.filter((name) => !String(text || '').includes(`${name} = true`));
-}
-
 async function resolveMissionId(root, arg) { return (!arg || arg === 'latest') ? findLatestMission(root) : arg; }
 function readMaxCycles(args, fallback) {
   const i = args.indexOf('--max-cycles');
@@ -1963,7 +1938,7 @@ function readMaxCycles(args, fallback) {
 
 function positionalArgs(args = []) {
   const out = [];
-  const valueFlags = new Set(['--format', '--iterations', '--out', '--baseline', '--candidate', '--install-scope', '--max-cycles', '--depth', '--scope', '--transport', '--query', '--topic', '--tokens', '--timeout-ms', '--sql', '--command', '--project-ref', '--agent', '--phase', '--message', '--role', '--max-anchors', '--lines', '--dir']);
+  const valueFlags = new Set(['--format', '--iterations', '--out', '--baseline', '--candidate', '--install-scope', '--max-cycles', '--cycle-timeout-minutes', '--depth', '--scope', '--transport', '--query', '--topic', '--tokens', '--timeout-ms', '--sql', '--command', '--project-ref', '--agent', '--phase', '--message', '--role', '--max-anchors', '--lines', '--dir']);
   for (let i = 0; i < args.length; i++) {
     const arg = String(args[i]);
     if (valueFlags.has(arg)) {
@@ -2118,6 +2093,8 @@ async function selftest() {
   if (!doctorRepairJson.repair?.applied || doctorRepairJson.install?.scope !== 'project' || !doctorRepairJson.install?.ok || !doctorRepairJson.install?.source_project) throw new Error('selftest: doctor scope');
   const repairedManifest = await readJson(path.join(repairTmp, '.sneakoscope', 'manifest.json'));
   if (repairedManifest.installation?.scope !== 'project' || repairedManifest.installation?.hook_command_prefix !== 'node ./bin/sks.mjs') throw new Error('selftest: manifest scope');
+  const repairedCodexConfig = await safeReadText(path.join(repairTmp, '.codex', 'config.toml'));
+  assertCodexWarn(repairedCodexConfig, 'doctor project config');
   const repairedTeamSkill = await safeReadText(path.join(repairTmp, '.agents', 'skills', 'team', 'SKILL.md'));
   if (!repairedTeamSkill.includes('SKS Team orchestration') || repairedTeamSkill.includes('tampered')) throw new Error('selftest: doctor repair did not regenerate team skill');
   if (await exists(path.join(repairTmp, '.agents', 'skills', 'agent-team', 'SKILL.md'))) throw new Error('selftest: doctor repair did not remove deprecated agent-team alias skill');
@@ -2153,6 +2130,9 @@ async function selftest() {
   });
   if (doctorGlobalRepair.code !== 0) throw new Error(`selftest: doctor --fix global skill repair exited ${doctorGlobalRepair.code}: ${doctorGlobalRepair.stderr}`);
   const doctorGlobalRepairJson = JSON.parse(doctorGlobalRepair.stdout || '{}');
+  const doctorGlobalCodexConfig = await safeReadText(path.join(doctorGlobalHome, '.codex', 'config.toml'));
+  if (!doctorGlobalRepairJson.repair?.global_codex_config) throw new Error('selftest: doctor global config repair missing');
+  assertCodexWarn(doctorGlobalCodexConfig, 'doctor global config');
   for (const name of stalePluginSkillNames) {
     if (await exists(path.join(doctorGlobalHome, '.agents', 'skills', name, 'SKILL.md'))) throw new Error(`selftest: doctor --fix did not remove global generated ${name} plugin shadow skill`);
   }
@@ -2185,6 +2165,7 @@ async function selftest() {
   if (!(await exists(path.join(postinstallSetupTmp, '.codex', 'hooks.json')))) throw new Error('selftest: postinstall did not create project hooks during automatic bootstrap');
   const postinstallSetupConfig = await safeReadText(path.join(postinstallSetupTmp, '.codex', 'config.toml'));
   if (missingGeneratedCodexAppFeatureFlags(postinstallSetupConfig).length || hasDeprecatedCodexHooksFeatureFlag(postinstallSetupConfig)) throw new Error('selftest: postinstall flags');
+  assertCodexWarn(postinstallSetupConfig, 'postinstall project config');
   if (!String(postinstallSetup.stdout || '').includes('Codex App global $ skills: installed')) throw new Error('selftest: postinstall did not report automatic global Codex App skills');
   if (!String(postinstallSetup.stdout || '').includes('Removed stale generated skill shadow(s):')) throw new Error('selftest: postinstall did not report stale first-party plugin shadow cleanup');
   const postinstallSetupManifest = await readJson(path.join(postinstallSetupTmp, '.sneakoscope', 'manifest.json'));
@@ -2221,6 +2202,7 @@ async function selftest() {
   if (!(await exists(path.join(postinstallNoMarkerGlobalRoot, '.sneakoscope', 'manifest.json')))) throw new Error('selftest: no-marker postinstall did not bootstrap global runtime root');
   const postinstallNoMarkerConfig = await safeReadText(path.join(postinstallNoMarkerGlobalRoot, '.codex', 'config.toml'));
   if (missingGeneratedCodexAppFeatureFlags(postinstallNoMarkerConfig).length || hasDeprecatedCodexHooksFeatureFlag(postinstallNoMarkerConfig)) throw new Error('selftest: no-marker flags');
+  assertCodexWarn(postinstallNoMarkerConfig, 'postinstall global runtime config');
   if (await exists(path.join(postinstallNoMarkerCwd, '.sneakoscope'))) throw new Error('selftest: no-marker postinstall polluted install cwd');
   if (await exists(path.join(postinstallNoMarkerGlobalRoot, '.gitignore'))) throw new Error('selftest: global runtime bootstrap without project git wrote shared .gitignore');
   const bootstrapJsonTmp = tmpdir();
@@ -2647,19 +2629,21 @@ async function selftest() {
   const hookResearchTeamResult = await runProcess(process.execPath, [hookBin, 'hook', 'user-prompt-submit'], { cwd: hookResearchMarkdownTmp, input: hookResearchTeamPayload, env: { SKS_DISABLE_UPDATE_CHECK: '1' }, timeoutMs: 15000, maxOutputBytes: 256 * 1024 });
   if (hookResearchTeamResult.code !== 0) throw new Error(`selftest: active Team setup before markdown $Research hook exited ${hookResearchTeamResult.code}: ${hookResearchTeamResult.stderr}`);
   const hookResearchTeamState = await readJson(stateFile(hookResearchMarkdownTmp), {});
-  const hookResearchMarkdownPayload = JSON.stringify({ cwd: hookResearchMarkdownTmp, prompt: '[$research](/tmp/research/SKILL.md) Codex Computer Use 도구 노출 문제를 QA루프 관점에서 연구' });
+  const hookResearchMarkdownPayload = JSON.stringify({ cwd: hookResearchMarkdownTmp, prompt: '논문 [$research](x) 팀 커밋 푸쉬 연구' });
   const hookResearchMarkdownResult = await runProcess(process.execPath, [hookBin, 'hook', 'user-prompt-submit'], { cwd: hookResearchMarkdownTmp, input: hookResearchMarkdownPayload, env: { SKS_DISABLE_UPDATE_CHECK: '1' }, timeoutMs: 15000, maxOutputBytes: 256 * 1024 });
   if (hookResearchMarkdownResult.code !== 0) throw new Error(`selftest: markdown $Research hook exited ${hookResearchMarkdownResult.code}: ${hookResearchMarkdownResult.stderr}`);
   const hookResearchMarkdownJson = JSON.parse(hookResearchMarkdownResult.stdout);
   const hookResearchMarkdownContext = hookResearchMarkdownJson.hookSpecificOutput?.additionalContext || '';
-  if (!hookResearchMarkdownContext.includes('$Research route prepared')) throw new Error('selftest: markdown $Research hook did not prepare Research route');
-  if (hookResearchMarkdownContext.includes(`Active Team mission ${hookResearchTeamState.mission_id}`)) throw new Error('selftest: markdown $Research hook retained stale active Team context');
-  if (!String(hookResearchMarkdownJson.systemMessage || '').includes('Research route') || String(hookResearchMarkdownJson.systemMessage || '').includes('QA-LOOP route')) throw new Error('selftest: markdown $Research visible hook message was hijacked by QA-LOOP policy text');
+  if (!hookResearchMarkdownContext.includes('$Research route prepared')) throw new Error('selftest: markdown research hook');
+  if (hookResearchMarkdownContext.includes(`Active Team mission ${hookResearchTeamState.mission_id}`)) throw new Error('selftest: stale Team context');
+  if (!String(hookResearchMarkdownJson.systemMessage || '').includes('Research route') || String(hookResearchMarkdownJson.systemMessage || '').includes('QA-LOOP route')) throw new Error('selftest: research hook message');
   const hookResearchMarkdownState = await readJson(stateFile(hookResearchMarkdownTmp), {});
-  if (hookResearchMarkdownState.mode !== 'RESEARCH' || hookResearchMarkdownState.route !== 'Research' || hookResearchMarkdownState.mission_id === hookResearchTeamState.mission_id || hookResearchMarkdownState.stop_gate !== 'research-gate.json' || !hookResearchMarkdownState.pipeline_plan_ready) throw new Error('selftest: markdown $Research hook did not replace active Team with prepared Research mission state');
+  if (hookResearchMarkdownState.mode !== 'RESEARCH' || hookResearchMarkdownState.route !== 'Research' || hookResearchMarkdownState.mission_id === hookResearchTeamState.mission_id || hookResearchMarkdownState.stop_gate !== 'research-gate.json' || !hookResearchMarkdownState.pipeline_plan_ready) throw new Error('selftest: research hook state');
   const hookResearchMissionDir = missionDir(hookResearchMarkdownTmp, hookResearchMarkdownState.mission_id);
-  if (!(await exists(path.join(hookResearchMissionDir, PIPELINE_PLAN_ARTIFACT)))) throw new Error('selftest: markdown $Research hook did not write pipeline plan');
-  for (const artifact of ['source-ledger.json', 'scout-ledger.json', 'debate-ledger.json', 'falsification-ledger.json']) {
+  if (!(await exists(path.join(hookResearchMissionDir, PIPELINE_PLAN_ARTIFACT)))) throw new Error('selftest: research hook plan');
+  const rss = 'research-source-skill.md';
+  const gos = 'genius-opinion-summary.md';
+  for (const artifact of [rss, 'source-ledger.json', 'scout-ledger.json', 'debate-ledger.json', 'falsification-ledger.json']) {
     if (!(await exists(path.join(hookResearchMissionDir, artifact)))) throw new Error(`selftest: hook research ${artifact}`);
   }
   const hookPayload = JSON.stringify({ cwd: hookGoalTmp, prompt: '$Goal 로그인 세션 만료 UX 개선' });
@@ -2999,6 +2983,7 @@ async function selftest() {
   const codexConfigText = await safeReadText(path.join(tmp, '.codex', 'config.toml'));
   const missingCodexConfigFlags = missingGeneratedCodexAppFeatureFlags(codexConfigText);
   if (missingCodexConfigFlags.length || hasDeprecatedCodexHooksFeatureFlag(codexConfigText)) throw new Error(`selftest: generated Codex App feature flags missing or deprecated: ${missingCodexConfigFlags.join(', ')}`);
+  assertCodexWarn(codexConfigText, 'generated Codex App config');
   if (!hasContext7ConfigText(codexConfigText)) throw new Error('selftest: Context7 MCP not configured');
   if (!codexConfigText.includes('[profiles.sks-task-low]') || !codexConfigText.includes('[profiles.sks-task-medium]') || !codexConfigText.includes('[profiles.sks-logic-high]') || !codexConfigText.includes('[profiles.sks-fast-high]') || !codexConfigText.includes('[profiles.sks-research-xhigh]') || !codexConfigText.includes('[profiles.sks-mad-high]')) throw new Error('selftest: GPT-5.5 reasoning profiles not configured');
   if (!/\[profiles\.sks-mad-high\][\s\S]*?approval_policy = "never"[\s\S]*?sandbox_mode = "danger-full-access"/.test(codexConfigText)) throw new Error('selftest: generated sks-mad-high profile is not full access');
@@ -3010,6 +2995,7 @@ async function selftest() {
   await initProject(preservedConfigTmp, {});
   const preservedConfig = await safeReadText(path.join(preservedConfigTmp, '.codex', 'config.toml'));
   if (!/^model = "gpt-5\.5"/m.test(preservedConfig) || !preservedConfig.includes('service_tier = "fast"') || !preservedConfig.includes('fast_mode = true') || !preservedConfig.includes('fast_mode_ui = true') || !preservedConfig.includes('[user.fast_mode]') || !preservedConfig.includes('visible = true') || !preservedConfig.includes('enabled = true') || !preservedConfig.includes('default_profile = "sks-fast-high"') || !/\[profiles\.sks-fast-high\][\s\S]*?service_tier = "fast"/.test(preservedConfig)) throw new Error('selftest: Codex config merge dropped or failed to enable Fast mode defaults and GPT-5.5');
+  assertCodexWarn(preservedConfig, 'merged Codex config');
   if (preservedConfig.includes('fast_default_opt_out = true') || !preservedConfig.includes('keep = true')) throw new Error('selftest: Codex config merge did not remove stale Fast opt-out notice while preserving other notice keys');
   const missingPreservedFlags = missingGeneratedCodexAppFeatureFlags(preservedConfig);
   if (missingPreservedFlags.length || hasDeprecatedCodexHooksFeatureFlag(preservedConfig) || !preservedConfig.includes('custom_preview = true') || !preservedConfig.includes('[profiles.sks-fast-high]')) throw new Error(`selftest: Codex config merge did not add required app feature flags, preserve existing feature flags, or remove deprecated codex_hooks: ${missingPreservedFlags.join(', ')}`);
@@ -3245,7 +3231,7 @@ async function selftest() {
   if (teamPlan.agent_session_count !== 5) throw new Error('selftest: team default sessions not 5');
   if (teamPlan.role_counts.executor !== 3 || teamPlan.role_counts.user !== 1 || teamPlan.role_counts.reviewer !== 5) throw new Error('selftest: team default role counts invalid');
   const teamPlanFeatureFlags = teamPlan.codex_config_required?.features || {};
-  const missingTeamPlanFeatureFlags = REQUIRED_GENERATED_CODEX_APP_FEATURE_FLAGS.filter((name) => teamPlanFeatureFlags[name] !== true);
+  const missingTeamPlanFeatureFlags = missingGeneratedCodexAppFeatureFlags(teamPlanFeatureFlags);
   if (missingTeamPlanFeatureFlags.length || teamPlanFeatureFlags.codex_hooks === true) throw new Error(`selftest: team plan Codex config missing required app flags or still uses deprecated codex_hooks: ${missingTeamPlanFeatureFlags.join(', ')}`);
   if (!teamPlan.review_gate?.passed || teamPlan.review_gate.required_reviewer_lanes !== 5) throw new Error('selftest: team review policy gate did not pass default plan');
   if (teamPlan.codex_config_required?.service_tier !== 'fast' || teamPlan.reasoning?.service_tier !== 'fast') throw new Error('selftest: team plan did not require Fast service tier');
@@ -3476,7 +3462,7 @@ async function selftest() {
   if (!(await readTeamTranscriptTail(teamDir, 1)).join('\n').includes('selftest mapped options')) throw new Error('selftest: team transcript tail missing event');
   const teamLane = await renderTeamAgentLane(teamDir, { missionId: teamId, agent: 'analysis_scout_1', lines: 4 });
   if (!teamLane.includes('selftest mapped repo slice')) throw new Error('selftest: team agent lane missing event context');
-  if (!teamLane.includes('## Live Chat') || !teamLane.includes('selftest mapped repo slice') || teamLane.includes('## Global Tail')) throw new Error('selftest:cht');
+  if (!teamLane.includes('## Codex Chat') || !teamLane.includes('+-- me [status]') || !teamLane.includes('selftest mapped repo slice') || teamLane.includes('## Global Tail')) throw new Error('selftest: chat lane');
   const teamLaneCli = await runProcess(process.execPath, [hookBin, 'team', 'lane', teamId, '--agent', 'analysis_scout_1', '--lines', '4'], { cwd: tmp, env: { SKS_DISABLE_UPDATE_CHECK: '1' }, timeoutMs: 15000, maxOutputBytes: 64 * 1024 });
   if (teamLaneCli.code !== 0 || !String(teamLaneCli.stdout || '').includes('SKS Team Agent Lane') || !String(teamLaneCli.stdout || '').includes('analysis_scout_1')) throw new Error('selftest: sks team lane CLI did not render an agent lane');
   await writeTextAtomic(path.join(teamDir, 'team-analysis.md'), '- claim: analysis scout mapped route registry | source: src/core/routes.mjs | risk: high | confidence: supported\n');
@@ -3782,15 +3768,16 @@ async function selftest() {
   if (wikiPruneDryRun.candidates < 1 || !wikiPruneDryRun.actions.some((action) => action.reason === 'low_wiki_trust')) throw new Error('selftest: wiki prune did not flag low-trust artifact');
   const { dir: researchDir, mission: researchMission } = await createMission(tmp, { mode: 'research', prompt: '새로운 코드 리뷰 방법론 연구' });
   const researchPlan = await writeResearchPlan(researchDir, researchMission.prompt, {});
-  if (researchPlan.methodology !== 'genius-scout-council-frontier-discovery-loop' || researchPlan.web_research_policy?.mode !== 'maximum_source_retrieval') throw new Error('selftest: research plan contract');
+  if (researchPlan.methodology !== 'genius-scout-council-frontier-discovery-loop' || researchPlan.web_research_policy?.mode !== 'layered_source_retrieval_and_triangulation') throw new Error('selftest: research plan contract');
   const rArts = researchPlan.required_artifacts || [];
-  for (const a of ['source-ledger.json', 'scout-ledger.json', 'debate-ledger.json', 'falsification-ledger.json']) if (!rArts.includes(a) || !(await exists(path.join(researchDir, a)))) throw new Error('selftest: research artifact');
-  if (!rArts.includes('research-paper.md')) throw new Error('selftest: research paper');
+  for (const a of [rss, 'source-ledger.json', 'scout-ledger.json', 'debate-ledger.json', 'falsification-ledger.json']) if (!rArts.includes(a) || !(await exists(path.join(researchDir, a)))) throw new Error('selftest: research artifact');
+  if (!rArts.includes('research-paper.md') || !rArts.includes(gos)) throw new Error('selftest: research paper');
   const initialResearchGate = await evaluateResearchGate(researchDir);
   if (initialResearchGate.passed || ['web_search_pass_missing', 'eureka_missing', 'debate_exchanges_missing', 'research_paper_missing'].some((r) => !initialResearchGate.reasons.includes(r))) throw new Error('selftest: research gate');
   const researchGate = await writeMockResearchResult(researchDir, researchPlan);
   if (!researchGate.passed) throw new Error('selftest: mock research gate did not pass');
-  if (['independent_scouts', 'xhigh_scouts', 'eureka_moments', 'debate_participants'].some((m) => researchGate.metrics?.[m] < 5) || researchGate.metrics?.counterevidence_sources < 1 || researchGate.metrics?.paper_sections < 8 || researchGate.metrics?.citation_coverage !== true || researchGate.metrics?.falsification_cases < 1) throw new Error('selftest: research metrics');
+  const rm = researchGate.metrics || {};
+  if (['independent_scouts', 'xhigh_scouts', 'eureka_moments', 'debate_participants', 'genius_opinion_summaries'].some((m) => rm[m] < 5) || ['counterevidence_sources', 'falsification_cases', 'triangulation_checks'].some((m) => rm[m] < 1) || rm.paper_sections < 8 || rm.citation_coverage !== true || rm.source_layers_covered < 7) throw new Error('selftest: research metrics');
   await writeJsonAtomic(path.join(dir, 'done-gate.json'), { passed: true, unsupported_critical_claims: 0, database_safety_violation: false, database_safety_reviewed: true, visual_drift: 'low', wiki_drift: 'low', tests_required: false });
   const gate = await evaluateDoneGate(tmp, id);
   if (!gate.passed) throw new Error('selftest: done gate');

package/src/cli/maintenance-commands.mjs

@@ -8,14 +8,14 @@ import { buildQuestionSchema, writeQuestions } from '../core/questions.mjs';
 import { sealContract } from '../core/decision-contract.mjs';
 import { buildQaLoopQuestionSchema, buildQaLoopPrompt, evaluateQaGate, qaStatus, writeMockQaResult, writeQaLoopArtifacts } from '../core/qa-loop.mjs';
 import { containsUserQuestion, noQuestionContinuationReason } from '../core/no-question-guard.mjs';
-import { RESEARCH_PAPER_ARTIFACT, countResearchPaperSections, buildResearchPrompt, evaluateResearchGate, writeMockResearchResult, writeResearchPlan } from '../core/research.mjs';
+import { RESEARCH_GENIUS_SUMMARY_ARTIFACT, RESEARCH_PAPER_ARTIFACT, RESEARCH_SOURCE_SKILL_ARTIFACT, countGeniusOpinionSummaries, countResearchPaperSections, buildResearchPrompt, evaluateResearchGate, writeMockResearchResult, writeResearchPlan } from '../core/research.mjs';
 import { storageReport, enforceRetention, pruneWikiArtifacts } from '../core/retention.mjs';
 import { evaluateDoneGate } from '../core/hproof.mjs';
 import { renderCartridge, validateCartridge, driftCartridge, snapshotCartridge } from '../core/gx-renderer.mjs';
 import { DEFAULT_EVAL_THRESHOLDS, compareEvaluationReports, runEvaluationBenchmark } from '../core/evaluation.mjs';
 import { contextCapsule } from '../core/triwiki-attention.mjs';
 import { rgbaKey, rgbaToWikiCoord, validateWikiCoordinateIndex } from '../core/wiki-coordinate.mjs';
-import { ALLOWED_REASONING_EFFORTS, CODEX_COMPUTER_USE_ONLY_POLICY, DOLLAR_SKILL_NAMES, FROM_CHAT_IMG_CHECKLIST_ARTIFACT, FROM_CHAT_IMG_COVERAGE_ARTIFACT, FROM_CHAT_IMG_QA_LOOP_ARTIFACT, FROM_CHAT_IMG_SOURCE_INVENTORY_ARTIFACT, FROM_CHAT_IMG_TEMP_TRIWIKI_ARTIFACT, FROM_CHAT_IMG_TEMP_TRIWIKI_SESSIONS, FROM_CHAT_IMG_VISUAL_MAP_ARTIFACT, FROM_CHAT_IMG_WORK_ORDER_ARTIFACT, RECOMMENDED_SKILLS, ROUTES, hasFromChatImgSignal, reflectionRequiredForRoute, routePrompt, routeReasoning, routeRequiresSubagents, stackCurrentDocsPolicy, stripVisibleDecisionAnswerBlocks, triwikiContextTracking } from '../core/routes.mjs';
+import { ALLOWED_REASONING_EFFORTS, CODEX_COMPUTER_USE_ONLY_POLICY, DOLLAR_SKILL_NAMES, FROM_CHAT_IMG_CHECKLIST_ARTIFACT, FROM_CHAT_IMG_COVERAGE_ARTIFACT, FROM_CHAT_IMG_QA_LOOP_ARTIFACT, FROM_CHAT_IMG_SOURCE_INVENTORY_ARTIFACT, FROM_CHAT_IMG_TEMP_TRIWIKI_ARTIFACT, FROM_CHAT_IMG_TEMP_TRIWIKI_SESSIONS, FROM_CHAT_IMG_VISUAL_MAP_ARTIFACT, FROM_CHAT_IMG_WORK_ORDER_ARTIFACT, RECOMMENDED_SKILLS, ROUTES, hasFromChatImgSignal, reflectionRequiredForRoute, routeNeedsContext7, routePrompt, routeReasoning, routeRequiresSubagents, stackCurrentDocsPolicy, stripVisibleDecisionAnswerBlocks, triwikiContextTracking } from '../core/routes.mjs';
 import { TEAM_DECOMPOSITION_ARTIFACT, TEAM_GRAPH_ARTIFACT, TEAM_INBOX_DIR, TEAM_RUNTIME_TASKS_ARTIFACT, teamRuntimePlanMetadata, teamRuntimeRequiredArtifacts, writeTeamRuntimeArtifacts } from '../core/team-dag.mjs';
 import { appendTeamEvent, formatAgentReasoning, formatRoleCounts, initTeamLive, normalizeTeamSpec, parseTeamSpecArgs, readTeamControl, readTeamDashboard, readTeamLive, readTeamTranscriptTail, renderTeamAgentLane, renderTeamCleanupSummary, renderTeamWatch, requestTeamSessionCleanup, teamCleanupRequested, teamReasoningPolicy } from '../core/team-live.mjs';
 import { evaluateTeamReviewPolicyGate, MIN_TEAM_REVIEWER_LANES, MIN_TEAM_REVIEW_POLICY_TEXT, teamReviewPolicy } from '../core/team-review-policy.mjs';
@@ -42,6 +42,10 @@ const flag = (args, name) => args.includes(name);
 const promptOf = (args) => args.filter((x) => !String(x).startsWith('--')).join(' ').trim();
 const TEAM_SESSION_CLEANUP_ARTIFACT = 'team-session-cleanup.json';
 const REPOSITORY_URL = 'https://github.com/mandarange/Sneakoscope-Codex.git';
+const RESEARCH_DEFAULT_MAX_CYCLES = 3;
+const RESEARCH_DEFAULT_CYCLE_TIMEOUT_MINUTES = 120;
+const RESEARCH_MIN_CYCLE_TIMEOUT_MINUTES = 15;
+const RESEARCH_MAX_CYCLE_TIMEOUT_MINUTES = 240;
 
 async function resolveMissionId(root, arg) { return (!arg || arg === 'latest') ? findLatestMission(root) : arg; }
 
@@ -429,7 +433,7 @@ async function researchPrepare(args) {
   if (!prompt) throw new Error('Missing research topic.');
   const { id, dir } = await createMission(root, { mode: 'research', prompt });
   const route = ROUTES.find((entry) => entry.id === 'Research') || routePrompt('$Research');
-  const context7Required = true;
+  const context7Required = routeNeedsContext7(route, prompt);
   const reasoning = routeReasoning(route, prompt);
   const plan = await writeResearchPlan(dir, prompt, { depth: readFlagValue(args, '--depth', 'frontier') });
   const pipelinePlan = await writePipelinePlan(dir, { missionId: id, route, task: prompt, required: context7Required, ambiguity: { required: false, status: 'direct_research_cli' } });
@@ -457,7 +461,7 @@ async function researchPrepare(args) {
     mode: route.mode,
     phase: 'RESEARCH_PREPARED',
     questions_allowed: false,
-    implementation_allowed: true,
+    implementation_allowed: false,
     context7_required: context7Required,
     context7_verified: false,
     subagents_required: routeRequiresSubagents(route, prompt),
@@ -480,14 +484,16 @@ async function researchPrepare(args) {
   console.log(`Plan: ${path.relative(root, path.join(dir, 'research-plan.md'))}`);
   console.log(`Pipeline: ${path.relative(root, path.join(dir, PIPELINE_PLAN_ARTIFACT))}`);
   console.log(`Paper: ${RESEARCH_PAPER_ARTIFACT}`);
+  console.log(`Genius summary: ${RESEARCH_GENIUS_SUMMARY_ARTIFACT}`);
+  console.log(`Source skill: ${RESEARCH_SOURCE_SKILL_ARTIFACT}`);
   console.log('Ledgers: source-ledger.json, scout-ledger.json, debate-ledger.json, novelty-ledger.json, falsification-ledger.json');
-  console.log(`Run: sks research run ${id} --max-cycles 3`);
+  console.log(`Run: sks research run ${id} --max-cycles ${RESEARCH_DEFAULT_MAX_CYCLES} --cycle-timeout-minutes ${RESEARCH_DEFAULT_CYCLE_TIMEOUT_MINUTES}`);
 }
 
 async function researchRun(args) {
   const root = await sksRoot();
   const id = await resolveMissionId(root, args[0]);
-  if (!id) throw new Error('Usage: sks research run <mission-id|latest> [--mock] [--max-cycles N]');
+  if (!id) throw new Error('Usage: sks research run <mission-id|latest> [--mock] [--max-cycles N] [--cycle-timeout-minutes N]');
   const { dir, mission } = await loadMission(root, id);
   const planPath = path.join(dir, 'research-plan.json');
   if (!(await exists(planPath))) await writeResearchPlan(dir, mission.prompt || '', {});
@@ -499,32 +505,46 @@ async function researchRun(args) {
     process.exitCode = 2;
     return;
   }
-  const maxCycles = readMaxCycles(args, 3);
+  const maxCycles = readMaxCycles(args, RESEARCH_DEFAULT_MAX_CYCLES);
+  const cycleTimeoutMinutes = readResearchCycleTimeoutMinutes(args);
+  const cycleTimeoutMs = cycleTimeoutMinutes * 60 * 1000;
   const mock = flag(args, '--mock');
-  await setCurrent(root, { mission_id: id, mode: 'RESEARCH', phase: 'RESEARCH_RUNNING_NO_QUESTIONS', questions_allowed: false });
-  await appendJsonlBounded(path.join(dir, 'events.jsonl'), { ts: nowIso(), type: 'research.run.started', maxCycles, mock });
+  await setCurrent(root, { mission_id: id, mode: 'RESEARCH', phase: 'RESEARCH_RUNNING_NO_QUESTIONS', questions_allowed: false, implementation_allowed: false, research_real_run_required: !mock, research_cycle_timeout_minutes: cycleTimeoutMinutes });
+  await appendJsonlBounded(path.join(dir, 'events.jsonl'), { ts: nowIso(), type: 'research.run.started', maxCycles, mock, cycleTimeoutMinutes, real_run_required: !mock });
   if (mock) {
     const gate = await writeMockResearchResult(dir, plan);
-    await setCurrent(root, { mission_id: id, mode: 'RESEARCH', phase: gate.passed ? 'RESEARCH_DONE' : 'RESEARCH_PAUSED', questions_allowed: true });
+    await setCurrent(root, { mission_id: id, mode: 'RESEARCH', phase: gate.passed ? 'RESEARCH_DONE' : 'RESEARCH_PAUSED', questions_allowed: true, implementation_allowed: false });
     console.log(`Mock research done: ${id}`);
     console.log(`Gate: ${gate.passed ? 'passed' : 'blocked'}`);
     return;
   }
   const codex = await getCodexInfo();
   if (!codex.bin) {
-    console.error('Codex CLI not found. Running mock research instead.');
-    const gate = await writeMockResearchResult(dir, plan);
-    await setCurrent(root, { mission_id: id, mode: 'RESEARCH', phase: gate.passed ? 'RESEARCH_DONE' : 'RESEARCH_PAUSED', questions_allowed: true });
-    console.log(`Mock research done: ${id}`);
+    const blocker = {
+      schema_version: 1,
+      mission_id: id,
+      ts: nowIso(),
+      phase: 'RESEARCH_BLOCKED_REAL_RUN_REQUIRED',
+      reason: 'Codex CLI not found; normal Research cannot fall back to mock output.',
+      required_action: 'Install/configure the Codex CLI or set SKS_CODEX_BIN to a valid executable, then rerun sks research run without --mock.',
+      mock_policy: '--mock is allowed only for selftests and dry harness checks.',
+      implementation_allowed: false
+    };
+    await writeJsonAtomic(path.join(dir, 'research-blocker.json'), blocker);
+    await appendJsonlBounded(path.join(dir, 'events.jsonl'), { ts: blocker.ts, type: 'research.blocked.real_run_required', reason: blocker.reason, blocker: 'research-blocker.json' });
+    await setCurrent(root, { mission_id: id, mode: 'RESEARCH', phase: 'RESEARCH_BLOCKED_REAL_RUN_REQUIRED', questions_allowed: true, implementation_allowed: false, research_real_run_required: true, blocker: 'research-blocker.json' });
+    console.error('Research cannot run real sources: Codex CLI not found.');
+    console.error('Mock fallback is disabled for normal Research. Use --mock only for selftests, or install/configure Codex CLI/SKS_CODEX_BIN.');
+    process.exitCode = 2;
     return;
   }
   let last = '';
   for (let cycle = 1; cycle <= maxCycles; cycle++) {
     const cycleDir = path.join(dir, 'research', `cycle-${cycle}`);
     const outputFile = path.join(cycleDir, 'final.md');
-    await appendJsonlBounded(path.join(dir, 'events.jsonl'), { ts: nowIso(), type: 'research.cycle.start', cycle });
+    await appendJsonlBounded(path.join(dir, 'events.jsonl'), { ts: nowIso(), type: 'research.cycle.start', cycle, timeoutMinutes: cycleTimeoutMinutes });
     const prompt = buildResearchPrompt({ id, mission, plan, cycle, previous: last });
-    const result = await runCodexExec({ root, prompt, outputFile, json: true, profile: 'sks-research', logDir: cycleDir, timeoutMs: 45 * 60 * 1000 });
+    const result = await runCodexExec({ root, prompt, outputFile, json: true, profile: 'sks-research', logDir: cycleDir, timeoutMs: cycleTimeoutMs });
     await writeJsonAtomic(path.join(cycleDir, 'process.json'), { code: result.code, stdout_tail: result.stdout, stderr_tail: result.stderr, stdout_bytes: result.stdoutBytes, stderr_bytes: result.stderrBytes, truncated: result.truncated, timed_out: result.timedOut });
     last = await safeReadText(outputFile, result.stdout || result.stderr || '');
     if (containsUserQuestion(last)) {
@@ -534,7 +554,7 @@ async function researchRun(args) {
     }
     const gate = await evaluateResearchGate(dir);
     if (gate.passed) {
-      await setCurrent(root, { mission_id: id, mode: 'RESEARCH', phase: 'RESEARCH_DONE', questions_allowed: true });
+      await setCurrent(root, { mission_id: id, mode: 'RESEARCH', phase: 'RESEARCH_DONE', questions_allowed: true, implementation_allowed: false });
       await appendJsonlBounded(path.join(dir, 'events.jsonl'), { ts: nowIso(), type: 'research.done', cycle });
       await enforceRetention(root).catch(() => {});
       console.log(`Research done: ${id}`);
@@ -542,7 +562,7 @@ async function researchRun(args) {
     }
     await appendJsonlBounded(path.join(dir, 'events.jsonl'), { ts: nowIso(), type: 'research.cycle.continue', cycle, reasons: gate.reasons });
   }
-  await setCurrent(root, { mission_id: id, mode: 'RESEARCH', phase: 'RESEARCH_PAUSED_MAX_CYCLES', questions_allowed: true });
+  await setCurrent(root, { mission_id: id, mode: 'RESEARCH', phase: 'RESEARCH_PAUSED_MAX_CYCLES', questions_allowed: true, implementation_allowed: false });
   console.log(`Research paused after max cycles: ${id}`);
 }
 
@@ -558,19 +578,29 @@ async function researchStatus(args) {
   const scoutLedger = await readJson(path.join(dir, 'scout-ledger.json'), null);
   const debateLedger = await readJson(path.join(dir, 'debate-ledger.json'), null);
   const falsificationLedger = await readJson(path.join(dir, 'falsification-ledger.json'), null);
+  const sourceSkillText = await readText(path.join(dir, RESEARCH_SOURCE_SKILL_ARTIFACT), '');
+  const geniusSummaryText = await readText(path.join(dir, RESEARCH_GENIUS_SUMMARY_ARTIFACT), '');
   const paperText = await readText(path.join(dir, RESEARCH_PAPER_ARTIFACT), '');
   const scoutRows = Array.isArray(scoutLedger?.scouts) ? scoutLedger.scouts : [];
+  const sourceLayerRows = Array.isArray(sourceLedger?.source_layers) ? sourceLedger.source_layers : [];
+  const sourceLayersCovered = sourceLayerRows.filter((layer) => layer.status === 'covered' && ((Array.isArray(layer.source_ids) && layer.source_ids.length) || (Array.isArray(layer.counterevidence_ids) && layer.counterevidence_ids.length))).length;
   console.log(JSON.stringify({
     mission,
     state,
     gate,
     novelty_entries: ledger?.entries?.length ?? null,
     source_entries: sourceLedger?.sources?.length ?? null,
+    source_layers_required: sourceLayerRows.length || gate?.metrics?.source_layers_required || gate?.source_layers_required || null,
+    source_layers_covered: gate?.metrics?.source_layers_covered ?? gate?.source_layers_covered ?? (sourceLayerRows.length ? sourceLayersCovered : null),
+    triangulation_checks: sourceLedger?.triangulation?.cross_layer_checks?.length ?? gate?.metrics?.triangulation_checks ?? gate?.triangulation_checks ?? null,
+    genius_opinion_summaries: gate?.metrics?.genius_opinion_summaries ?? gate?.genius_opinion_summaries ?? (geniusSummaryText.trim() ? countGeniusOpinionSummaries(geniusSummaryText) : null),
     counterevidence_sources: sourceLedger?.counterevidence_sources?.length ?? null,
     xhigh_scouts: scoutRows.length ? scoutRows.filter((scout) => scout.effort === 'xhigh').length : null,
     eureka_moments: scoutRows.length ? scoutRows.filter((scout) => scout.eureka?.exclamation === 'Eureka!' && String(scout.eureka?.idea || '').trim()).length : null,
     scout_findings: scoutRows.length ? scoutRows.reduce((sum, scout) => sum + (Array.isArray(scout.findings) ? scout.findings.length : 0), 0) : null,
     debate_exchanges: debateLedger?.exchanges?.length ?? null,
+    research_source_skill_present: Boolean(sourceSkillText.trim()),
+    genius_opinion_summary_present: Boolean(geniusSummaryText.trim()),
     paper_present: Boolean(paperText.trim()),
     paper_sections: countResearchPaperSections(paperText),
     falsification_cases: falsificationLedger?.cases?.length ?? null
@@ -625,11 +655,19 @@ async function safeReadText(file, fallback = '') {
   try { return await fsp.readFile(file, 'utf8'); } catch { return fallback; }
 }
 
-function readMaxCycles(args, fallback) {
-  const i = args.indexOf('--max-cycles');
+function readBoundedIntegerFlag(args, name, fallback, min, max) {
+  const i = args.indexOf(name);
   const raw = i >= 0 && args[i + 1] ? Number(args[i + 1]) : Number(fallback);
-  if (!Number.isFinite(raw)) return Math.max(1, Number.parseInt(fallback, 10) || 1);
-  return Math.max(1, Math.min(50, Math.floor(raw)));
+  if (!Number.isFinite(raw)) return Math.max(min, Number.parseInt(fallback, 10) || min);
+  return Math.max(min, Math.min(max, Math.floor(raw)));
+}
+
+function readMaxCycles(args, fallback) {
+  return readBoundedIntegerFlag(args, '--max-cycles', fallback, 1, 50);
+}
+
+function readResearchCycleTimeoutMinutes(args) {
+  return readBoundedIntegerFlag(args, '--cycle-timeout-minutes', RESEARCH_DEFAULT_CYCLE_TIMEOUT_MINUTES, RESEARCH_MIN_CYCLE_TIMEOUT_MINUTES, RESEARCH_MAX_CYCLE_TIMEOUT_MINUTES);
 }
 
 export async function goalCommand(sub, args) {
@@ -1580,7 +1618,7 @@ export async function statsCommand(args) {
 
 function positionalArgs(args = []) {
   const out = [];
-  const valueFlags = new Set(['--format', '--iterations', '--out', '--baseline', '--candidate', '--install-scope', '--max-cycles', '--depth', '--scope', '--transport', '--query', '--topic', '--tokens', '--timeout-ms', '--sql', '--command', '--project-ref', '--agent', '--phase', '--message', '--role', '--max-anchors', '--lines', '--intent', '--changed', '--route', '--skills', '--prompt-signature']);
+  const valueFlags = new Set(['--format', '--iterations', '--out', '--baseline', '--candidate', '--install-scope', '--max-cycles', '--cycle-timeout-minutes', '--depth', '--scope', '--transport', '--query', '--topic', '--tokens', '--timeout-ms', '--sql', '--command', '--project-ref', '--agent', '--phase', '--message', '--role', '--max-anchors', '--lines', '--intent', '--changed', '--route', '--skills', '--prompt-signature']);
   for (let i = 0; i < args.length; i++) {
     const arg = String(args[i]);
     if (valueFlags.has(arg)) {

package/src/core/fsx.mjs

@@ -5,7 +5,7 @@ import os from 'node:os';
 import crypto from 'node:crypto';
 import { spawn } from 'node:child_process';
 
-export const PACKAGE_VERSION = '0.7.69';
+export const PACKAGE_VERSION = '0.7.74';
 export const DEFAULT_PROCESS_TAIL_BYTES = 256 * 1024;
 export const DEFAULT_PROCESS_TIMEOUT_MS = 30 * 60 * 1000;
 

package/src/core/hooks-runtime.mjs

@@ -7,7 +7,7 @@ import { checkHarnessModification, harnessGuardBlockReason } from './harness-gua
 import { activeRouteContext, evaluateStop, prepareRoute, promptPipelineContext as routePipelineContext, recordContext7Evidence, recordSubagentEvidence, routePrompt } from './pipeline.mjs';
 import { classifyToolError } from './evaluation.mjs';
 import { REQUIRED_CODEX_MODEL, isForbiddenCodexModel } from './codex-model-guard.mjs';
-import { stripVisibleDecisionAnswerBlocks } from './routes.mjs';
+import { dollarCommand, stripVisibleDecisionAnswerBlocks } from './routes.mjs';
 
 const TEAM_DIGEST_MAX_EVENTS = 4;
 const TEAM_DIGEST_MESSAGE_CHARS = 180;
@@ -77,13 +77,6 @@ function toolFailed(payload = {}) {
   return false;
 }
 
-function dollarCommand(prompt) {
-  const text = String(prompt || '').trim();
-  const match = text.match(/^\$([A-Za-z][A-Za-z0-9_-]*)(?:\s|:|$)/)
-    || text.match(/^\[\$([A-Za-z][A-Za-z0-9_-]*)\]\([^)]+\)(?:\s|:|$)/);
-  return match ? match[1].toUpperCase() : null;
-}
-
 function looksLikeUpdateDecline(prompt) {
   return /^(no|nope|skip|later|not now|don't|dont|아니|아니요|안해|안 함|나중에|건너뛰|스킵)/i.test(String(prompt || '').trim());
 }