sneakoscope 0.9.9 → 0.9.11

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "sneakoscope",
   "displayName": "ㅅㅋㅅ",
-  "version": "0.9.9",
+  "version": "0.9.11",
   "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

@@ -3,12 +3,13 @@ import os from 'node:os';
 import fsp from 'node:fs/promises';
 import readline from 'node:readline/promises';
 import { stdin as input, stdout as output } from 'node:process';
-import { ensureDir, exists, globalSksRoot, packageRoot, readText, runProcess, tmpdir, which, writeTextAtomic } from '../core/fsx.mjs';
+import { ensureDir, exists, globalSksRoot, packageRoot, PACKAGE_VERSION, readText, runProcess, tmpdir, which, writeTextAtomic } from '../core/fsx.mjs';
 import { getCodexInfo } from '../core/codex-adapter.mjs';
 import { formatHarnessConflictReport, llmHarnessCleanupPrompt, scanHarnessConflicts } from '../core/harness-conflicts.mjs';
 import { initProject, installSkills } from '../core/init.mjs';
 import { context7ConfigToml, DOLLAR_SKILL_NAMES, GETDESIGN_REFERENCE, hasContext7ConfigText, RECOMMENDED_SKILLS } from '../core/routes.mjs';
 import { codexLaunchCommand, platformTmuxInstallHint, tmuxReadiness } from '../core/tmux-ui.mjs';
+import { reconcileCodexAppUpgradeProcesses } from '../core/codex-app.mjs';
 
 const DEFAULT_CODEX_APP_PLUGINS = [
   ['browser', 'openai-bundled'],
@@ -31,6 +32,7 @@ export async function postinstall({ bootstrap }) {
   console.log('\nSKS installed.');
   const shim = await ensureSksCommandDuringInstall();
   if (shim.status === 'present') console.log(`SKS command: available (${shim.command}).`);
+  else if (shim.status === 'repaired') console.log(`SKS command: stale PATH shim repaired (${shim.command}).`);
   else if (shim.status === 'created') console.log(`SKS command: shim created at ${shim.command}.`);
   else if (shim.status === 'created_not_on_path') console.log(`SKS command: shim created at ${shim.command}. Add ${path.dirname(shim.command)} to PATH, or run npx -y -p sneakoscope sks.`);
   else if (shim.status === 'skipped') console.log(`SKS command: skipped (${shim.reason}).`);
@@ -46,6 +48,11 @@ export async function postinstall({ bootstrap }) {
   else if (fastModeRepair.status === 'present') console.log('Codex App Fast mode: config already compatible.');
   else if (fastModeRepair.status === 'skipped') console.log(`Codex App Fast mode: skipped (${fastModeRepair.reason}).`);
   else if (fastModeRepair.status === 'failed') console.log(`Codex App Fast mode: auto repair failed. Run \`sks setup\`. ${fastModeRepair.error || ''}`.trim());
+  const appProcessRepair = await reconcileCodexAppUpgradeProcesses();
+  if (appProcessRepair.status === 'repaired') console.log(`Codex App reconnect repair: stopped ${appProcessRepair.killed.length} stale orphan app-server process(es). Restart Codex App to reconnect cleanly.`);
+  else if (appProcessRepair.status === 'partial') console.log(`Codex App reconnect repair: stopped ${appProcessRepair.killed.length} stale orphan app-server process(es); ${appProcessRepair.failed.length} could not be stopped. Restart Codex App if reconnecting continues.`);
+  else if (appProcessRepair.status === 'skipped' && appProcessRepair.reason !== 'platform') console.log(`Codex App reconnect repair: skipped (${appProcessRepair.reason}).`);
+  else if (appProcessRepair.status === 'failed') console.log(`Codex App reconnect repair: skipped (${appProcessRepair.error || appProcessRepair.reason || 'process check failed'}).`);
   const globalSkills = await ensureGlobalCodexSkillsDuringInstall();
   if (globalSkills.status === 'installed') {
     const removed = globalSkills.removed_stale_generated_skills || [];
@@ -1361,10 +1368,13 @@ function escapeRegExp(value) {
 export async function ensureSksCommandDuringInstall(opts = {}) {
   if (process.env.SKS_SKIP_POSTINSTALL_SHIM === '1' && !opts.force) return { status: 'skipped', reason: 'SKS_SKIP_POSTINSTALL_SHIM=1' };
   const pathEnv = opts.pathEnv ?? process.env.PATH ?? '';
-  const existing = await findCommandOnPath('sks', pathEnv);
-  if (isStableSksBin(existing)) return { status: 'present', command: existing };
   const nodeBin = opts.nodeBin || process.execPath;
   const target = opts.target || path.join(packageRoot(), 'bin', 'sks.mjs');
+  const repair = await reconcileSksPathShimsDuringInstall({ ...opts, pathEnv, nodeBin, target });
+  if (repair.status === 'repaired') return { ...repair, command: repair.command || repair.repaired?.[0]?.path || target };
+  if (repair.status === 'failed') return repair;
+  const existing = await findCommandOnPath('sks', pathEnv);
+  if (isStableSksBin(existing)) return { status: 'present', command: existing };
   const dirs = candidateShimDirs(pathEnv, opts.home || process.env.HOME);
   const script = process.platform === 'win32'
     ? `@echo off\r\n"${nodeBin}" "${target}" %*\r\n`
@@ -1388,6 +1398,80 @@ export async function ensureSksCommandDuringInstall(opts = {}) {
   return { status: 'failed', error: lastError };
 }
 
+export async function selftestSksShimRepair() {
+  const staleShimTmp = tmpdir();
+  const staleBin = path.join(staleShimTmp, 'old-prefix', 'bin');
+  const stalePkg = path.join(staleShimTmp, 'old-prefix', 'lib', 'node_modules', 'sneakoscope');
+  await ensureDir(path.join(stalePkg, 'bin'));
+  await ensureDir(staleBin);
+  await writeTextAtomic(path.join(stalePkg, 'package.json'), JSON.stringify({ name: 'sneakoscope', version: '0.0.1' }, null, 2));
+  await writeTextAtomic(path.join(stalePkg, 'bin', 'sks.mjs'), '#!/usr/bin/env node\nconsole.log("sneakoscope 0.0.1");\n');
+  await fsp.chmod(path.join(stalePkg, 'bin', 'sks.mjs'), 0o755).catch(() => {});
+  await fsp.symlink(path.join(stalePkg, 'bin', 'sks.mjs'), path.join(staleBin, 'sks'));
+  const repair = await ensureSksCommandDuringInstall({ force: true, pathEnv: staleBin, home: path.join(staleShimTmp, 'home') });
+  if (repair.status !== 'repaired') throw new Error(`selftest: stale global sks shim was not repaired (${repair.status})`);
+  const run = await runProcess(path.join(staleBin, 'sks'), ['--version'], { timeoutMs: 10000, maxOutputBytes: 16 * 1024 });
+  if (run.code !== 0 || !String(run.stdout || '').includes(PACKAGE_VERSION)) throw new Error('selftest: repaired stale sks shim does not run current package version');
+  return { ok: true, repaired: repair.repaired || [] };
+}
+
+async function reconcileSksPathShimsDuringInstall(opts = {}) {
+  if (process.env.SKS_SKIP_POSTINSTALL_SHIM_REPAIR === '1' && !opts.force) return { status: 'skipped', reason: 'SKS_SKIP_POSTINSTALL_SHIM_REPAIR=1' };
+  const target = opts.target || path.join(packageRoot(), 'bin', 'sks.mjs');
+  const nodeBin = opts.nodeBin || process.execPath;
+  const currentVersion = await installedPackageVersion(packageRoot());
+  const commands = await findCommandsOnPath(['sks', 'sneakoscope'], opts.pathEnv ?? process.env.PATH ?? '');
+  const repaired = [];
+  const failed = [];
+  for (const command of commands) {
+    const info = await inspectSksPathShim(command.path, { target, currentVersion });
+    if (!info.repairable) continue;
+    const script = process.platform === 'win32'
+      ? `@echo off\r\n"${nodeBin}" "${target}" %*\r\n`
+      : `#!/bin/sh\nexec "${nodeBin}" "${target}" "$@"\n`;
+    try {
+      await writeTextAtomic(command.path, script);
+      if (process.platform !== 'win32') await fsp.chmod(command.path, 0o755).catch(() => {});
+      repaired.push({ path: command.path, name: command.name, previous_version: info.version || null, target });
+    } catch (err) {
+      failed.push({ path: command.path, name: command.name, previous_version: info.version || null, error: err.message });
+    }
+  }
+  if (repaired.length) return { status: 'repaired', command: repaired[0].path, repaired, failed };
+  if (failed.length) return { status: 'failed', error: failed.map((entry) => `${entry.path}: ${entry.error}`).join('; '), failed };
+  return { status: 'present' };
+}
+
+async function inspectSksPathShim(candidate, opts = {}) {
+  if (!candidate || isTransientNpmBinPath(candidate)) return { repairable: false, reason: 'transient_or_missing' };
+  const target = path.resolve(opts.target || path.join(packageRoot(), 'bin', 'sks.mjs'));
+  const resolved = await fsp.realpath(candidate).catch(() => candidate);
+  if (path.resolve(resolved) === target) return { repairable: false, reason: 'current_target' };
+  const packageDir = sksPackageRootForBin(resolved) || sksPackageRootForBin(candidate);
+  if (!packageDir) return { repairable: false, reason: 'not_sneakoscope_bin' };
+  const version = await installedPackageVersion(packageDir);
+  const currentVersion = opts.currentVersion || await installedPackageVersion(packageRoot());
+  if (!version || !currentVersion || compareVersions(version, currentVersion) >= 0) return { repairable: false, reason: 'not_older', version, current_version: currentVersion };
+  return { repairable: true, version, current_version: currentVersion, package_dir: packageDir, resolved };
+}
+
+function sksPackageRootForBin(file) {
+  const normalized = String(file || '').split(path.sep).join('/');
+  const marker = '/node_modules/sneakoscope/bin/';
+  const idx = normalized.lastIndexOf(marker);
+  if (idx < 0) return null;
+  return normalized.slice(0, idx + '/node_modules/sneakoscope'.length).split('/').join(path.sep);
+}
+
+async function installedPackageVersion(root) {
+  const pkg = await readJsonMaybe(path.join(root, 'package.json'));
+  return pkg?.version || (root === packageRoot() ? PACKAGE_VERSION : null);
+}
+
+async function readJsonMaybe(file) {
+  try { return JSON.parse(await fsp.readFile(file, 'utf8')); } catch { return null; }
+}
+
 function candidateShimDirs(pathEnv, home) {
   const seen = new Set();
   const out = [];
@@ -1407,14 +1491,26 @@ function candidateShimDirs(pathEnv, home) {
 }
 
 async function findCommandOnPath(name, pathEnv) {
+  const found = await findCommandsOnPath([name], pathEnv);
+  return found[0]?.path || null;
+}
+
+async function findCommandsOnPath(names, pathEnv) {
   const suffixes = process.platform === 'win32' ? ['.cmd', '.exe', ''] : [''];
+  const out = [];
+  const seen = new Set();
   for (const dir of String(pathEnv || '').split(path.delimiter).filter(Boolean)) {
-    for (const suffix of suffixes) {
-      const candidate = path.join(dir, `${name}${suffix}`);
-      if (await exists(candidate)) return candidate;
+    for (const name of names) {
+      for (const suffix of suffixes) {
+        const candidate = path.join(dir, `${name}${suffix}`);
+        const key = path.resolve(candidate);
+        if (seen.has(key) || !await exists(candidate)) continue;
+        seen.add(key);
+        out.push({ name, path: candidate });
+      }
     }
   }
-  return null;
+  return out;
 }
 
 async function ensureGlobalContext7DuringInstall() {
@@ -1766,6 +1862,7 @@ function codexLbPostinstallEnv(baseEnv, overrides = {}) {
     SKS_SKIP_POSTINSTALL_GLOBAL_SKILLS: '1',
     SKS_SKIP_POSTINSTALL_CODEX_LB_AUTH: '0',
     SKS_SKIP_CODEX_LB_LAUNCH_ENV: '1',
+    SKS_SKIP_CODEX_APP_UPGRADE_REPAIR: '1',
     ...overrides
   };
 }
@@ -1838,7 +1935,7 @@ export async function selftestCodexLb(tmp) {
   const codexLbPostinstallAuth = await safeReadText(path.join(codexLbHome, '.codex', 'auth.json'));
   const codexLbLoginCallsAfterPostinstall = await codexLbLoginCallCount(codexLbHome);
   if (!String(codexLbPostinstall.stdout || '').includes('codex-lb auth: preserved') || !codexLbPostinstallAuth.includes('"auth_mode":"browser"') || codexLbPostinstallAuth.includes('sk-test') || codexLbLoginCallsAfterPostinstall !== codexLbLoginCallsBeforePostinstall) throw new Error('selftest: postinstall auth');
-  const postinstallEnvKeys = ['HOME', 'PATH', 'INIT_CWD', 'SKS_GLOBAL_ROOT', 'SKS_POSTINSTALL_BOOTSTRAP', 'SKS_POSTINSTALL_NO_BOOTSTRAP', 'SKS_SKIP_POSTINSTALL_SHIM', 'SKS_SKIP_POSTINSTALL_CONTEXT7', 'SKS_SKIP_POSTINSTALL_GETDESIGN', 'SKS_SKIP_POSTINSTALL_GLOBAL_SKILLS', 'SKS_SKIP_POSTINSTALL_CODEX_LB_AUTH', 'SKS_SKIP_CODEX_LB_LAUNCH_ENV', 'SKS_CODEX_LB_SYNC_CODEX_LOGIN'];
+  const postinstallEnvKeys = ['HOME', 'PATH', 'INIT_CWD', 'SKS_GLOBAL_ROOT', 'SKS_POSTINSTALL_BOOTSTRAP', 'SKS_POSTINSTALL_NO_BOOTSTRAP', 'SKS_SKIP_POSTINSTALL_SHIM', 'SKS_SKIP_POSTINSTALL_CONTEXT7', 'SKS_SKIP_POSTINSTALL_GETDESIGN', 'SKS_SKIP_POSTINSTALL_GLOBAL_SKILLS', 'SKS_SKIP_POSTINSTALL_CODEX_LB_AUTH', 'SKS_SKIP_CODEX_LB_LAUNCH_ENV', 'SKS_SKIP_CODEX_APP_UPGRADE_REPAIR', 'SKS_CODEX_LB_SYNC_CODEX_LOGIN'];
   const postinstallEnvBefore = Object.fromEntries(postinstallEnvKeys.map((key) => [key, process.env[key]]));
   const codexLbLoginCallsBeforeBootstrap = await codexLbLoginCallCount(codexLbHome);
   try {
@@ -1854,7 +1951,8 @@ export async function selftestCodexLb(tmp) {
       SKS_SKIP_POSTINSTALL_GETDESIGN: '1',
       SKS_SKIP_POSTINSTALL_GLOBAL_SKILLS: '1',
       SKS_SKIP_POSTINSTALL_CODEX_LB_AUTH: '0',
-      SKS_SKIP_CODEX_LB_LAUNCH_ENV: '1'
+      SKS_SKIP_CODEX_LB_LAUNCH_ENV: '1',
+      SKS_SKIP_CODEX_APP_UPGRADE_REPAIR: '1'
     });
     await postinstall({
       bootstrap: async () => {

package/src/cli/main.mjs

@@ -73,7 +73,7 @@ import { MISTAKE_RECALL_ARTIFACT, contractConsumesMistakeRecall } from '../core/
 import { buildPromptContext } from '../core/prompt-context-builder.mjs';
 import { renderTeamDashboardState, writeTeamDashboardState } from '../core/team-dashboard-renderer.mjs';
 import { GOAL_WORKFLOW_ARTIFACT } from '../core/goal-workflow.mjs';
-import { CODEX_APP_DOCS_URL, codexAccessTokenStatus, codexAppIntegrationStatus, formatCodexAppStatus } from '../core/codex-app.mjs';
+import { CODEX_APP_DOCS_URL, codexAccessTokenStatus, codexAppIntegrationStatus, findCodexAppUpgradeRepairTargets, formatCodexAppStatus, parseProcessRows } from '../core/codex-app.mjs';
 import { buildAllFeaturesSelftest, buildFeatureRegistry, validateFeatureRegistry } from '../core/feature-registry.mjs';
 import { codexAppRemoteControlCommand } from './codex-app-command.mjs';
 import { allFeaturesCommand, featuresCommand, hooksCommand, hooksExplainReport } from './feature-commands.mjs';
@@ -81,7 +81,7 @@ 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, sweepCodexLbTmuxSessions, sweepTmuxTeamSurfaces, 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, checkCodexLbResponseChain, checkContext7, checkRequiredSkills, codexLbChatgptBackupPath, codexLbStatus, configureCodexLb, ensureCodexCliTool, ensureGlobalCodexFastModeDuringInstall, ensureGlobalCodexSkillsDuringInstall, ensureProjectContext7Config, ensureRelatedCliTools, ensureSksCommandDuringInstall, ensureTmuxCliTool, formatCodexLbRepairResultText, formatCodexLbStatusText, globalCodexSkillsRoot, maybePromptCodexLbSetupForLaunch, maybePromptCodexUpdateForLaunch, postinstall, postinstallBootstrapDecision, releaseCodexLbAuthHold, repairCodexLbAuth, selftestCodexLb, shouldAutoApproveInstall, unselectCodexLbProvider } from './install-helpers.mjs';
+import { askPostinstallQuestion, checkCodexLbResponseChain, checkContext7, checkRequiredSkills, codexLbChatgptBackupPath, codexLbStatus, configureCodexLb, ensureCodexCliTool, ensureGlobalCodexFastModeDuringInstall, ensureGlobalCodexSkillsDuringInstall, ensureProjectContext7Config, ensureRelatedCliTools, ensureSksCommandDuringInstall, ensureTmuxCliTool, formatCodexLbRepairResultText, formatCodexLbStatusText, globalCodexSkillsRoot, maybePromptCodexLbSetupForLaunch, maybePromptCodexUpdateForLaunch, postinstall, postinstallBootstrapDecision, releaseCodexLbAuthHold, repairCodexLbAuth, selftestCodexLb, selftestSksShimRepair, shouldAutoApproveInstall, unselectCodexLbProvider } 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';
 import { recallPulseCommand } from './recallpulse-command.mjs';
@@ -2289,11 +2289,11 @@ async function selftest() {
   await ensureDir(path.join(conflictTmp, '.omx'));
   const conflictScan = await scanHarnessConflicts(conflictTmp, { home: path.join(conflictTmp, 'home') });
   if (!conflictScan.hard_block || !formatHarnessConflictReport(conflictScan).includes('GPT-5.5')) throw new Error('selftest: OMX conflict did not block with cleanup prompt');
-  const postinstallConflict = await runProcess(process.execPath, [path.join(packageRoot(), 'bin', 'sks.mjs'), 'postinstall'], { cwd: conflictTmp, env: { INIT_CWD: conflictTmp, HOME: path.join(conflictTmp, 'home'), SKS_SKIP_POSTINSTALL_SHIM: '1', SKS_SKIP_POSTINSTALL_CONTEXT7: '1', SKS_SKIP_POSTINSTALL_GETDESIGN: '1' }, timeoutMs: 15000, maxOutputBytes: 128 * 1024 });
+  const postinstallConflict = await runProcess(process.execPath, [path.join(packageRoot(), 'bin', 'sks.mjs'), 'postinstall'], { cwd: conflictTmp, env: { INIT_CWD: conflictTmp, HOME: path.join(conflictTmp, 'home'), SKS_SKIP_POSTINSTALL_SHIM: '1', SKS_SKIP_POSTINSTALL_CONTEXT7: '1', SKS_SKIP_POSTINSTALL_GETDESIGN: '1', SKS_SKIP_CODEX_APP_UPGRADE_REPAIR: '1' }, timeoutMs: 15000, maxOutputBytes: 128 * 1024 });
   if (postinstallConflict.code !== 0) throw new Error('selftest: postinstall conflict notice should not make npm install fail');
   const postinstallConflictOutput = String(`${postinstallConflict.stdout}\n${postinstallConflict.stderr}`);
   if (!postinstallConflictOutput.includes('SKS setup is blocked') || postinstallConflictOutput.includes('Cleanup prompt:')) throw new Error('selftest: postinstall conflict notice did not stay informational');
-  const postinstallConflictPrompt = await runProcess(process.execPath, [path.join(packageRoot(), 'bin', 'sks.mjs'), 'postinstall'], { cwd: conflictTmp, input: 'y\n', env: { INIT_CWD: conflictTmp, HOME: path.join(conflictTmp, 'home'), SKS_SKIP_POSTINSTALL_SHIM: '1', SKS_SKIP_POSTINSTALL_CONTEXT7: '1', SKS_SKIP_POSTINSTALL_GETDESIGN: '1', SKS_POSTINSTALL_PROMPT: '1' }, timeoutMs: 15000, maxOutputBytes: 128 * 1024 });
+  const postinstallConflictPrompt = await runProcess(process.execPath, [path.join(packageRoot(), 'bin', 'sks.mjs'), 'postinstall'], { cwd: conflictTmp, input: 'y\n', env: { INIT_CWD: conflictTmp, HOME: path.join(conflictTmp, 'home'), SKS_SKIP_POSTINSTALL_SHIM: '1', SKS_SKIP_POSTINSTALL_CONTEXT7: '1', SKS_SKIP_POSTINSTALL_GETDESIGN: '1', SKS_SKIP_CODEX_APP_UPGRADE_REPAIR: '1', SKS_POSTINSTALL_PROMPT: '1' }, timeoutMs: 15000, maxOutputBytes: 128 * 1024 });
   if (postinstallConflictPrompt.code !== 0 || !String(postinstallConflictPrompt.stdout || '').includes('Goal: completely remove the conflicting Codex harnesses')) throw new Error('selftest: conflict prompt');
   const postinstallSetupTmp = tmpdir();
   await writeJsonAtomic(path.join(postinstallSetupTmp, 'package.json'), { name: 'postinstall-setup-smoke', version: '0.0.0' });
@@ -2303,7 +2303,7 @@ async function selftest() {
     await ensureDir(path.join(postinstallSetupHome, '.agents', 'skills', name));
     await writeTextAtomic(path.join(postinstallSetupHome, '.agents', 'skills', name, 'SKILL.md'), stalePluginSkillContent(name));
   }
-  const postinstallSetup = await runProcess(process.execPath, [path.join(packageRoot(), 'bin', 'sks.mjs'), 'postinstall'], { cwd: postinstallSetupTmp, env: { INIT_CWD: postinstallSetupTmp, HOME: path.join(postinstallSetupTmp, 'home'), SKS_SKIP_POSTINSTALL_SHIM: '1', SKS_SKIP_POSTINSTALL_CONTEXT7: '1', SKS_SKIP_POSTINSTALL_GETDESIGN: '1', SKS_SKIP_CLI_TOOLS: '1' }, timeoutMs: 30000, maxOutputBytes: 256 * 1024 });
+  const postinstallSetup = await runProcess(process.execPath, [path.join(packageRoot(), 'bin', 'sks.mjs'), 'postinstall'], { cwd: postinstallSetupTmp, env: { INIT_CWD: postinstallSetupTmp, HOME: path.join(postinstallSetupTmp, 'home'), SKS_SKIP_POSTINSTALL_SHIM: '1', SKS_SKIP_POSTINSTALL_CONTEXT7: '1', SKS_SKIP_POSTINSTALL_GETDESIGN: '1', SKS_SKIP_CODEX_APP_UPGRADE_REPAIR: '1', SKS_SKIP_CLI_TOOLS: '1' }, timeoutMs: 30000, maxOutputBytes: 256 * 1024 });
   if (postinstallSetup.code !== 0) throw new Error(`selftest: postinstall setup exited ${postinstallSetup.code}: ${postinstallSetup.stderr}`);
   if (await exists(path.join(postinstallSetupTmp, '.agents', 'skills', 'agent-team', 'SKILL.md'))) throw new Error('selftest: postinstall installed deprecated agent-team fallback skill');
   if (!String(postinstallSetup.stdout || '').includes('SKS bootstrap: auto-running sks setup --bootstrap --install-scope global --force') || !String(postinstallSetup.stdout || '').includes('SKS Ready')) throw new Error('selftest: postinstall bootstrap');
@@ -2330,6 +2330,7 @@ async function selftest() {
     if (await exists(path.join(postinstallSetupHome, '.agents', 'skills', name, 'SKILL.md'))) throw new Error(`selftest: postinstall global skills shadow the first-party ${name} plugin`);
   }
   if (!(await exists(path.join(postinstallSetupTmp, 'home', '.agents', 'skills', 'getdesign-reference', 'SKILL.md')))) throw new Error('selftest: postinstall global getdesign-reference skill not installed');
+  await selftestSksShimRepair();
   const oldNoBootstrap = process.env.SKS_POSTINSTALL_NO_BOOTSTRAP;
   process.env.SKS_POSTINSTALL_NO_BOOTSTRAP = '1';
   const noBootstrapDecision = await postinstallBootstrapDecision(postinstallSetupTmp);
@@ -2341,7 +2342,7 @@ async function selftest() {
   const postinstallNoMarkerCwd = path.join(postinstallNoMarkerTmp, 'cwd');
   const postinstallNoMarkerGlobalRoot = path.join(postinstallNoMarkerTmp, 'global-root');
   await ensureDir(postinstallNoMarkerCwd);
-  const postinstallNoMarker = await runProcess(process.execPath, [path.join(packageRoot(), 'bin', 'sks.mjs'), 'postinstall'], { cwd: postinstallNoMarkerCwd, env: { INIT_CWD: postinstallNoMarkerCwd, HOME: postinstallNoMarkerHome, SKS_GLOBAL_ROOT: postinstallNoMarkerGlobalRoot, SKS_SKIP_POSTINSTALL_SHIM: '1', SKS_SKIP_POSTINSTALL_CONTEXT7: '1', SKS_SKIP_POSTINSTALL_GETDESIGN: '1', SKS_SKIP_CLI_TOOLS: '1' }, timeoutMs: 30000, maxOutputBytes: 256 * 1024 });
+  const postinstallNoMarker = await runProcess(process.execPath, [path.join(packageRoot(), 'bin', 'sks.mjs'), 'postinstall'], { cwd: postinstallNoMarkerCwd, env: { INIT_CWD: postinstallNoMarkerCwd, HOME: postinstallNoMarkerHome, SKS_GLOBAL_ROOT: postinstallNoMarkerGlobalRoot, SKS_SKIP_POSTINSTALL_SHIM: '1', SKS_SKIP_POSTINSTALL_CONTEXT7: '1', SKS_SKIP_POSTINSTALL_GETDESIGN: '1', SKS_SKIP_CODEX_APP_UPGRADE_REPAIR: '1', SKS_SKIP_CLI_TOOLS: '1' }, timeoutMs: 30000, maxOutputBytes: 256 * 1024 });
   if (postinstallNoMarker.code !== 0) throw new Error(`selftest: no-marker postinstall bootstrap exited ${postinstallNoMarker.code}: ${postinstallNoMarker.stderr}`);
   if (!String(postinstallNoMarker.stdout || '').includes('no project marker found; auto-running global SKS runtime bootstrap')) throw new Error('selftest: no-marker bootstrap');
   if (!(await exists(path.join(postinstallNoMarkerGlobalRoot, '.sneakoscope', 'manifest.json')))) throw new Error('selftest: no-marker postinstall did not bootstrap global runtime root');
@@ -3182,6 +3183,15 @@ async function selftest() {
   const codexAppFixtureOpts = { codex: { bin: fakeCodex, version: 'codex-cli 99.0.0' }, home: appFeatureTmp, cwd: appFeatureTmp, env: { SKS_CODEX_APP_PATH: fakeCodexApp } };
   const codexAppFeatureStatus = await codexAppIntegrationStatus(codexAppFixtureOpts);
   if (!codexAppFeatureStatus.ok || !codexAppFeatureStatus.features?.required_flags_ok || !codexAppFeatureStatus.features?.codex_git_commit || !codexAppFeatureStatus.features?.remote_control || !codexAppFeatureStatus.features?.git_actions?.ok || !codexAppFeatureStatus.features?.fast_mode_config?.ok) throw new Error('selftest: codex-app check did not accept required app feature flags, git actions, remote_control, and unlocked Fast UI config');
+  const codexAppProcessRows = parseProcessRows([
+    '101 1 /Applications/Codex.app/Contents/Resources/codex app-server --analytics-default-enabled',
+    '200 1 /Applications/Codex.app/Contents/MacOS/Codex',
+    '201 200 /Applications/Codex.app/Contents/Resources/codex app-server --analytics-default-enabled',
+    '202 1 /Applications/Codex.app/Contents/Resources/codex app-server --listen stdio://',
+    '203 1 /Users/me/.nvm/versions/node/bin/codex --model gpt-5.5'
+  ].join('\n'));
+  const codexAppRepairTargets = findCodexAppUpgradeRepairTargets(codexAppProcessRows);
+  if (codexAppRepairTargets.length !== 1 || codexAppRepairTargets[0].pid !== 101) throw new Error('selftest: Codex App upgrade repair target selection is not limited to orphan desktop app-server processes');
   const codexAppOldCliStatus = await codexAppIntegrationStatus({ codex: { bin: fakeCodex, version: 'codex-cli 0.129.0' }, home: appFeatureTmp, cwd: appFeatureTmp, env: { SKS_CODEX_APP_PATH: fakeCodexApp } });
   if (codexAppOldCliStatus.ok || codexAppOldCliStatus.features?.git_actions?.ok || !codexAppOldCliStatus.guidance.some((line) => line.includes('git commit/push actions are blocked'))) throw new Error('selftest: codex-app check did not block commit/push actions on old Codex CLI remote-control');
   const missingDefaultPluginTmp = tmpdir();

package/src/core/codex-app.mjs

@@ -238,6 +238,65 @@ export function codexSupportsRemoteControl(versionText) {
   return Boolean(current && compareVersions(current, CODEX_REMOTE_CONTROL_MIN_VERSION) >= 0);
 }
 
+export function parseProcessRows(text = '') {
+  return String(text || '')
+    .split(/\r?\n/)
+    .map((line) => line.trim())
+    .filter(Boolean)
+    .map((line) => {
+      const match = line.match(/^(\d+)\s+(\d+)\s+(.+)$/);
+      if (!match) return null;
+      return {
+        pid: Number.parseInt(match[1], 10),
+        ppid: Number.parseInt(match[2], 10),
+        command: match[3]
+      };
+    })
+    .filter((row) => Number.isFinite(row?.pid) && Number.isFinite(row?.ppid) && row.command);
+}
+
+export function findCodexAppUpgradeRepairTargets(rows = []) {
+  return rows.filter((row) => (
+    row?.ppid === 1
+    && /\/Codex\.app\/Contents\/Resources\/codex\s+app-server\s+--analytics-default-enabled(?:\s|$)/.test(String(row.command || ''))
+  ));
+}
+
+export async function reconcileCodexAppUpgradeProcesses(opts = {}) {
+  const platform = opts.platform || process.platform;
+  const env = opts.env || process.env;
+  if (platform !== 'darwin') return { status: 'skipped', reason: 'platform', killed: [] };
+  if (env.SKS_SKIP_CODEX_APP_UPGRADE_REPAIR === '1') return { status: 'skipped', reason: 'SKS_SKIP_CODEX_APP_UPGRADE_REPAIR=1', killed: [] };
+  const run = opts.runProcess || runProcess;
+  const ps = await run('ps', ['-axo', 'pid=', '-o', 'ppid=', '-o', 'command='], {
+    timeoutMs: opts.timeoutMs || 5000,
+    maxOutputBytes: opts.maxOutputBytes || 256 * 1024
+  }).catch((err) => ({ code: 1, stdout: '', stderr: err.message }));
+  if (ps.code !== 0) return { status: 'failed', reason: 'ps_failed', error: ps.stderr || ps.stdout || 'ps exited non-zero', killed: [] };
+  const rows = parseProcessRows(ps.stdout);
+  const targets = findCodexAppUpgradeRepairTargets(rows);
+  const killed = [];
+  const failed = [];
+  for (const target of targets) {
+    if (opts.dryRun) {
+      killed.push({ pid: target.pid, command: target.command, dry_run: true });
+      continue;
+    }
+    const kill = await run('kill', ['-TERM', String(target.pid)], {
+      timeoutMs: opts.timeoutMs || 5000,
+      maxOutputBytes: 8 * 1024
+    }).catch((err) => ({ code: 1, stdout: '', stderr: err.message }));
+    if (kill.code === 0) killed.push({ pid: target.pid, command: target.command });
+    else failed.push({ pid: target.pid, command: target.command, error: kill.stderr || kill.stdout || 'kill exited non-zero' });
+  }
+  return {
+    status: failed.length ? 'partial' : killed.length ? 'repaired' : 'clean',
+    killed,
+    failed,
+    checked: rows.length
+  };
+}
+
 export function formatCodexRemoteControlStatus(status) {
   const lines = [
     'Codex remote-control',

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 = '0.9.9';
+export const PACKAGE_VERSION = '0.9.11';
 export const DEFAULT_PROCESS_TAIL_BYTES = 256 * 1024;
 export const DEFAULT_PROCESS_TIMEOUT_MS = 30 * 60 * 1000;