aiox-core 5.0.7 → 5.0.8

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "aiox-core",
-  "version": "5.0.7",
+  "version": "5.0.8",
   "description": "Synkra AIOX: AI-Orchestrated System for Full Stack Development - Core Framework",
   "bin": {
     "aiox": "bin/aiox.js",
@@ -18,6 +18,8 @@
     "packages/",
     ".aiox-core/",
     ".claude/CLAUDE.md",
+    ".claude/commands/",
+    ".claude/skills/",
     ".claude/rules/",
     ".claude/hooks/",
     "pro/license/",
@@ -43,11 +45,16 @@
     "README.md",
     "LICENSE"
   ],
+  "exports": {
+    "./installer/pro-scaffolder": "./packages/installer/src/pro/pro-scaffolder.js",
+    "./package.json": "./package.json"
+  },
   "scripts": {
     "format": "prettier --write \"**/*.md\"",
     "test": "jest",
     "test:watch": "jest --watch",
     "test:coverage": "jest --coverage",
+    "test:e2e:installed-skills": "node scripts/e2e/installed-skills-smoke.js",
     "test:health-check": "mocha tests/health-check/**/*.test.js --timeout 30000",
     "lint": "eslint . --cache --cache-location .eslintcache",
     "typecheck": "tsc --noEmit",
@@ -75,7 +82,10 @@
     "validate:gemini-integration": "node .aiox-core/infrastructure/scripts/validate-gemini-integration.js",
     "sync:skills:codex": "node .aiox-core/infrastructure/scripts/codex-skills-sync/index.js",
     "sync:skills:codex:global": "node .aiox-core/infrastructure/scripts/codex-skills-sync/index.js --global --global-only",
+    "setup:codex-skills": "node .aiox-core/infrastructure/scripts/codex-skills-sync/bootstrap.js",
+    "setup:codex-skills:dry": "node .aiox-core/infrastructure/scripts/codex-skills-sync/bootstrap.js --dry-run",
     "validate:codex-skills": "node .aiox-core/infrastructure/scripts/codex-skills-sync/validate.js --strict",
+    "repair:agent-references": "node .aiox-core/infrastructure/scripts/repair-agent-references.js",
     "validate:paths": "node .aiox-core/infrastructure/scripts/validate-paths.js",
     "validate:parity": "node .aiox-core/infrastructure/scripts/validate-parity.js",
     "validate:semantic-lint": "node scripts/semantic-lint.js",
@@ -103,6 +113,7 @@
     "handlebars": "^4.7.8",
     "inquirer": "^8.2.6",
     "js-yaml": "^4.1.0",
+    "node-machine-id": "^1.1.12",
     "ora": "^5.4.1",
     "picocolors": "^1.1.1",
     "proper-lockfile": "^4.1.2",

package/packages/aiox-pro-cli/bin/aiox-pro.js

@@ -3,11 +3,12 @@
 /**
  * aiox-pro CLI
  *
- * Thin CLI wrapper for @aiox-fullstack/pro.
+ * Thin CLI wrapper for AIOX Pro packages.
  * Provides a clean npx interface: npx aiox-pro install
  *
  * Commands:
- *   install             Install @aiox-fullstack/pro in the current project
+ *   install             Install AIOX Pro in the current project
+ *   update              Update AIOX Pro and re-sync assets
  *   activate --key X    Activate a license key
  *   deactivate          Deactivate the current license
  *   status              Show license status
@@ -22,7 +23,10 @@ const path = require('path');
 const fs = require('fs');
 const { recoverLicense } = require('../src/recover');
 
-const PRO_PACKAGE = '@aiox-fullstack/pro';
+const PRO_PACKAGE_CANONICAL = '@aiox-squads/pro';
+const PRO_PACKAGE_FALLBACK = '@aiox-fullstack/pro';
+const PRO_PACKAGE_LEGACY = '@aios-fullstack/pro';
+const PRO_PACKAGES = [PRO_PACKAGE_CANONICAL, PRO_PACKAGE_FALLBACK, PRO_PACKAGE_LEGACY];
 const VERSION = require('../package.json').version;
 
 const args = process.argv.slice(2);
@@ -42,8 +46,11 @@ function run(cmd, options = {}) {
 
 function isProInstalled() {
   try {
-    const pkgPath = path.join(process.cwd(), 'node_modules', '@aiox-fullstack', 'pro', 'package.json');
-    return fs.existsSync(pkgPath);
+    return PRO_PACKAGES.some((packageName) => {
+      const scopeDir = packageName.split('/')[0];
+      const packageJson = path.join(process.cwd(), 'node_modules', scopeDir, 'pro', 'package.json');
+      return fs.existsSync(packageJson);
+    });
   } catch {
     return false;
   }
@@ -133,7 +140,8 @@ Usage:
   npx aiox-pro <command> [options]
 
 Commands:
-  install              Install ${PRO_PACKAGE} in the current project
+  install              Install AIOX Pro in the current project
+  update               Update AIOX Pro and re-sync assets
   install --wizard     Install and run the setup wizard
   setup, wizard        Run Pro setup wizard (license gate + scaffold + verify)
   activate --key KEY   Activate a license key
@@ -147,6 +155,7 @@ Commands:
 
 Examples:
   npx aiox-pro install
+  npx aiox-pro update
   npx aiox-pro setup
   npx aiox-pro wizard --key PRO-XXXX-XXXX-XXXX-XXXX
   npx aiox-pro activate --key PRO-XXXX-XXXX-XXXX-XXXX
@@ -158,16 +167,27 @@ Documentation: https://synkra.ai/pro/docs
 }
 
 function installPro() {
-  console.log(`\nInstalling ${PRO_PACKAGE}...\n`);
+  console.log('\nInstalling AIOX Pro...\n');
+
+  let installedPackage = null;
 
-  const exitCode = run(`npm install ${PRO_PACKAGE}`);
+  for (const packageName of PRO_PACKAGES) {
+    console.log(`Trying ${packageName}...`);
+    const exitCode = run(`npm install ${packageName}`);
+    if (exitCode === 0) {
+      installedPackage = packageName;
+      break;
+    }
+    console.log('');
+  }
 
-  if (exitCode !== 0) {
-    console.error(`\nFailed to install ${PRO_PACKAGE}`);
+  if (!installedPackage) {
+    console.error('\nFailed to install AIOX Pro.');
+    console.error(`Tried: ${PRO_PACKAGES.join(', ')}`);
     process.exit(1);
   }
 
-  console.log(`\n✅ ${PRO_PACKAGE} installed successfully!\n`);
+  console.log(`\n✅ ${installedPackage} installed successfully!\n`);
   console.log('Next steps:');
   console.log('  npx aiox-pro activate --key PRO-XXXX-XXXX-XXXX-XXXX');
   console.log('  npx aiox-pro status');
@@ -218,8 +238,9 @@ switch (command) {
   case 'status':
   case 'features':
   case 'validate':
+  case 'update':
     if (!isProInstalled()) {
-      console.error(`${PRO_PACKAGE} is not installed.`);
+      console.error('AIOX Pro is not installed.');
       console.error('Run first: npx aiox-pro install\n');
       process.exit(1);
     }

package/packages/installer/src/config/configure-environment.js

@@ -24,6 +24,68 @@ const {
 } = require('./validation/config-validator');
 const { getMergeStrategy, hasMergeStrategy } = require('../merger/index.js');
 
+function isBrownfieldProjectType(projectType) {
+  const normalized = String(projectType || '').toLowerCase();
+  return normalized === 'brownfield' || normalized === 'existing_aiox' || normalized === 'existing-aiox';
+}
+
+async function resolveFileAction(filePath, options = {}) {
+  const {
+    skipPrompts = false,
+    forceMerge = false,
+    noMerge = false,
+    projectType = 'greenfield',
+    message,
+  } = options;
+
+  const exists = await fs.pathExists(filePath);
+  if (!exists) {
+    return 'create';
+  }
+
+  const isBrownfield = isBrownfieldProjectType(projectType);
+  const canMerge = !noMerge && hasMergeStrategy(filePath);
+
+  if (forceMerge && canMerge) {
+    return 'merge';
+  }
+
+  if (skipPrompts) {
+    return isBrownfield && canMerge ? 'merge' : 'overwrite';
+  }
+
+  const choices = [];
+
+  if (canMerge) {
+    choices.push({
+      value: 'merge',
+      label: 'Merge (preserve existing customizations)',
+      hint: isBrownfield ? 'recommended' : '',
+    });
+  }
+
+  choices.push(
+    { value: 'backup', label: 'Backup and overwrite' },
+    { value: 'overwrite', label: 'Overwrite completely' },
+    { value: 'skip', label: 'Skip (keep existing)' },
+  );
+
+  let action = await select({
+    message,
+    options: choices,
+    initialValue: isBrownfield && canMerge ? 'merge' : 'backup',
+  });
+
+  if (action === 'backup') {
+    const backupPath = `${filePath}.backup.${Date.now()}`;
+    await fs.copy(filePath, backupPath);
+    console.log(`✅ Backup created: ${backupPath}`);
+    action = 'overwrite';
+  }
+
+  return action;
+}
+
 /**
  * Configure environment files (.env and core-config.yaml)
  *
@@ -62,50 +124,16 @@ async function configureEnvironment(options = {}) {
     // Step 1: Check for existing .env and handle with merge/backup/overwrite
     const envPath = path.join(targetDir, '.env');
     const envExists = await fs.pathExists(envPath);
-    let envAction = 'create'; // 'create', 'merge', 'overwrite', 'skip'
-    const isBrownfield = projectType === 'BROWNFIELD' || projectType === 'EXISTING_AIOX';
-    const canMerge = !noMerge && hasMergeStrategy(envPath);
-
-    if (envExists) {
-      // Story 9.4: Handle CLI flags for merge behavior
-      if (forceMerge && canMerge) {
-        // --merge flag: Force merge without prompting
-        envAction = 'merge';
-        console.log('🔀 Using merge mode (--merge flag)');
-      } else if (skipPrompts) {
-        // Quiet mode: default to merge for brownfield, overwrite for greenfield
-        envAction = isBrownfield && canMerge ? 'merge' : 'overwrite';
-      } else {
-        // Interactive mode: Offer merge option for brownfield projects
-        const choices = [];
-
-        if (canMerge) {
-          choices.push({
-            value: 'merge',
-            label: 'Merge (add new variables, keep existing)',
-            hint: isBrownfield ? 'recommended' : '',
-          });
-        }
-
-        choices.push(
-          { value: 'backup', label: 'Backup and overwrite' },
-          { value: 'overwrite', label: 'Overwrite completely' },
-          { value: 'skip', label: 'Skip (keep existing)' },
-        );
-
-        envAction = await select({
-          message: 'Found existing .env file. What would you like to do?',
-          options: choices,
-          initialValue: isBrownfield && canMerge ? 'merge' : 'backup',
-        });
-
-        if (envAction === 'backup') {
-          const backupPath = path.join(targetDir, `.env.backup.${Date.now()}`);
-          await fs.copy(envPath, backupPath);
-          console.log(`✅ Backup created: ${backupPath}`);
-          envAction = 'overwrite';
-        }
-      }
+    const envAction = await resolveFileAction(envPath, {
+      skipPrompts,
+      forceMerge,
+      noMerge,
+      projectType,
+      message: 'Found existing .env file. What would you like to do?',
+    });
+
+    if (envAction === 'merge' && envExists && forceMerge) {
+      console.log('🔀 Using merge mode (--merge flag)');
     }
 
     // Step 2: API keys are configured later via .env or aiox-master
@@ -158,9 +186,29 @@ async function configureEnvironment(options = {}) {
     // Step 4: Generate and write .env.example
     const envExamplePath = path.join(targetDir, '.env.example');
     const envExampleContent = generateEnvExample();
-    await fs.writeFile(envExamplePath, envExampleContent, { encoding: 'utf8' });
-    results.envExampleCreated = true;
-    console.log('✅ Created .env.example file');
+    const envExampleAction = await resolveFileAction(envExamplePath, {
+      skipPrompts,
+      forceMerge,
+      noMerge,
+      projectType,
+      message: 'Found existing .env.example file. What would you like to do?',
+    });
+
+    if (envExampleAction === 'skip') {
+      console.log('⏭️  Skipped .env.example file (keeping existing)');
+    } else if (envExampleAction === 'merge' && await fs.pathExists(envExamplePath)) {
+      const existingContent = await fs.readFile(envExamplePath, 'utf8');
+      const merger = getMergeStrategy(envExamplePath);
+      const mergeResult = await merger.merge(existingContent, envExampleContent);
+
+      await fs.writeFile(envExamplePath, mergeResult.content, { encoding: 'utf8' });
+      results.envExampleCreated = true;
+      console.log('✅ Merged .env.example file');
+    } else {
+      await fs.writeFile(envExamplePath, envExampleContent, { encoding: 'utf8' });
+      results.envExampleCreated = true;
+      console.log('✅ Created .env.example file');
+    }
 
     // Step 5: Update .gitignore
     await updateGitignore(targetDir);
@@ -194,9 +242,29 @@ async function configureEnvironment(options = {}) {
     }
 
     const coreConfigPath = path.join(coreConfigDir, 'core-config.yaml');
-    await fs.writeFile(coreConfigPath, coreConfigContent, { encoding: 'utf8' });
-    results.coreConfigCreated = true;
-    console.log('✅ Created .aiox-core/core-config.yaml');
+    const coreConfigAction = await resolveFileAction(coreConfigPath, {
+      skipPrompts,
+      forceMerge,
+      noMerge,
+      projectType,
+      message: 'Found existing .aiox-core/core-config.yaml. What would you like to do?',
+    });
+
+    if (coreConfigAction === 'skip') {
+      console.log('⏭️  Skipped .aiox-core/core-config.yaml (keeping existing)');
+    } else if (coreConfigAction === 'merge' && await fs.pathExists(coreConfigPath)) {
+      const existingContent = await fs.readFile(coreConfigPath, 'utf8');
+      const merger = getMergeStrategy(coreConfigPath);
+      const mergeResult = await merger.merge(coreConfigContent, existingContent);
+
+      await fs.writeFile(coreConfigPath, mergeResult.content, { encoding: 'utf8' });
+      results.coreConfigCreated = true;
+      console.log('✅ Merged .aiox-core/core-config.yaml');
+    } else {
+      await fs.writeFile(coreConfigPath, coreConfigContent, { encoding: 'utf8' });
+      results.coreConfigCreated = true;
+      console.log('✅ Created .aiox-core/core-config.yaml');
+    }
 
     return results;
   } catch (error) {

package/packages/installer/src/installer/aiox-core-installer.js

@@ -12,6 +12,7 @@ const fs = require('fs-extra');
 const path = require('path');
 const ora = require('ora');
 const { hashFile } = require('./file-hasher');
+const { loadSourceManifest, updateInstalledManifest } = require('./brownfield-upgrader');
 
 /**
  * Get the path to the source .aiox-core directory in the package
@@ -70,6 +71,59 @@ const ROOT_FILES_TO_COPY = [
   'working-in-the-brownfield.md',
 ];
 
+const BROWNFIELD_PRESERVE_PATTERNS = [
+  /^core-config\.yaml$/,
+  /^development\/agents\/[^/]+\/MEMORY\.md$/,
+];
+
+function isBrownfieldProjectType(projectType = '') {
+  const normalized = String(projectType).toLowerCase();
+  return normalized === 'brownfield' || normalized === 'existing_aiox' || normalized === 'existing-aiox';
+}
+
+function shouldPreserveExistingFile(relativePath, options = {}) {
+  if (!options.preserveExisting) {
+    return false;
+  }
+
+  return BROWNFIELD_PRESERVE_PATTERNS.some((pattern) => pattern.test(relativePath));
+}
+
+function extractManifestFileHashes(manifest) {
+  if (!manifest || !Array.isArray(manifest.files)) {
+    return {};
+  }
+
+  const fileHashes = {};
+  for (const entry of manifest.files) {
+    if (entry && entry.path && entry.hash) {
+      fileHashes[entry.path] = entry.hash;
+    }
+  }
+
+  return fileHashes;
+}
+
+async function copyManifestArtifacts(sourceDir, targetAioxCore) {
+  const manifestPath = path.join(sourceDir, 'install-manifest.yaml');
+  const signaturePath = manifestPath + '.minisig';
+  const targetSignaturePath = path.join(targetAioxCore, 'install-manifest.yaml.minisig');
+
+  if (await fs.pathExists(manifestPath)) {
+    await fs.copy(manifestPath, path.join(targetAioxCore, 'install-manifest.yaml'), {
+      overwrite: true,
+    });
+  }
+
+  if (await fs.pathExists(signaturePath)) {
+    await fs.copy(signaturePath, targetSignaturePath, {
+      overwrite: true,
+    });
+  } else if (await fs.pathExists(targetSignaturePath)) {
+    await fs.remove(targetSignaturePath);
+  }
+}
+
 /**
  * Replace {root} placeholder in file content
  * @param {string} content - File content
@@ -128,9 +182,10 @@ async function generateVersionJson(options) {
     version,
     installedFiles,
     mode = 'project-development',
+    fileHashes: providedFileHashes = null,
   } = options;
 
-  const fileHashes = await generateFileHashes(targetAioxCore, installedFiles);
+  const fileHashes = providedFileHashes || await generateFileHashes(targetAioxCore, installedFiles);
 
   const versionJson = {
     version,
@@ -153,8 +208,14 @@ async function generateVersionJson(options) {
  * @param {boolean} replaceRoot - Whether to replace {root} placeholders
  * @returns {Promise<boolean>} Success status
  */
-async function copyFileWithRootReplacement(sourcePath, destPath, replaceRoot = true) {
+async function copyFileWithRootReplacement(sourcePath, destPath, replaceRoot = true, options = {}) {
   try {
+    if (options.relativePath && shouldPreserveExistingFile(options.relativePath, options)) {
+      if (await fs.pathExists(destPath)) {
+        return { copied: false, preserved: true, relativePath: options.relativePath };
+      }
+    }
+
     await fs.ensureDir(path.dirname(destPath));
 
     // Check if file needs {root} replacement (.md, .yaml, .yml)
@@ -169,10 +230,10 @@ async function copyFileWithRootReplacement(sourcePath, destPath, replaceRoot = t
       await fs.copy(sourcePath, destPath);
     }
 
-    return true;
+    return { copied: true, preserved: false, relativePath: options.relativePath || null };
   } catch (error) {
     console.error(`Failed to copy ${sourcePath}: ${error.message}`);
-    return false;
+    return { copied: false, preserved: false, relativePath: options.relativePath || null };
   }
 }
 
@@ -183,7 +244,7 @@ async function copyFileWithRootReplacement(sourcePath, destPath, replaceRoot = t
  * @param {Function} onProgress - Progress callback
  * @returns {Promise<string[]>} List of copied files (relative paths)
  */
-async function copyDirectoryWithRootReplacement(sourceDir, destDir, onProgress = null) {
+async function copyDirectoryWithRootReplacement(sourceDir, destDir, onProgress = null, options = {}) {
   const copiedFiles = [];
 
   if (!await fs.pathExists(sourceDir)) {
@@ -205,15 +266,28 @@ async function copyDirectoryWithRootReplacement(sourceDir, destDir, onProgress =
     }
 
     if (item.isDirectory()) {
-      const subFiles = await copyDirectoryWithRootReplacement(sourcePath, destPath, onProgress);
+      const subFiles = await copyDirectoryWithRootReplacement(sourcePath, destPath, onProgress, {
+        ...options,
+        baseDir: options.baseDir || destDir,
+      });
       copiedFiles.push(...subFiles);
     } else {
-      const success = await copyFileWithRootReplacement(sourcePath, destPath);
-      if (success) {
-        copiedFiles.push(path.relative(destDir, destPath));
+      const baseDir = options.baseDir || destDir;
+      const relativePath = path.relative(baseDir, destPath).replace(/\\/g, '/');
+      const fullRelativePath = options.pathPrefix
+        ? path.posix.join(options.pathPrefix, relativePath)
+        : relativePath;
+      const result = await copyFileWithRootReplacement(sourcePath, destPath, true, {
+        ...options,
+        relativePath: fullRelativePath,
+      });
+      if (result.copied) {
+        copiedFiles.push(relativePath);
         if (onProgress) {
           onProgress({ file: item.name, copied: true });
         }
+      } else if (result.preserved && onProgress) {
+        onProgress({ file: item.name, copied: false, preserved: true });
       }
     }
   }
@@ -237,6 +311,9 @@ async function installAioxCore(options = {}) {
   const {
     targetDir = process.cwd(),
     onProgress = null,
+    projectType = 'greenfield',
+    sourceDir: providedSourceDir = null,
+    packageVersion: providedPackageVersion = null,
   } = options;
 
   const result = {
@@ -249,8 +326,9 @@ async function installAioxCore(options = {}) {
   const spinner = ora('Installing AIOX core framework...').start();
 
   try {
-    const sourceDir = getAioxCoreSourcePath();
+    const sourceDir = providedSourceDir || getAioxCoreSourcePath();
     const targetAioxCore = path.join(targetDir, '.aiox-core');
+    const preserveExisting = isBrownfieldProjectType(projectType);
 
     // Check if source exists
     if (!await fs.pathExists(sourceDir)) {
@@ -272,6 +350,11 @@ async function installAioxCore(options = {}) {
           folderSource,
           folderDest,
           onProgress,
+          {
+            baseDir: folderDest,
+            pathPrefix: folder,
+            preserveExisting,
+          },
         );
 
         if (copiedFiles.length > 0) {
@@ -288,28 +371,37 @@ async function installAioxCore(options = {}) {
 
       if (await fs.pathExists(fileSource)) {
         spinner.text = `Copying ${file}...`;
-        const success = await copyFileWithRootReplacement(fileSource, fileDest);
-        if (success) {
+        const relativePath = file;
+        const copyResult = await copyFileWithRootReplacement(fileSource, fileDest, true, {
+          relativePath,
+          preserveExisting,
+        });
+        if (copyResult.copied) {
           result.installedFiles.push(file);
         }
       }
     }
 
-    // Create install manifest
-    spinner.text = 'Creating installation manifest...';
-    const packageVersion = require('../../../../package.json').version;
-    const manifest = {
-      version: packageVersion,
-      installed_at: new Date().toISOString(),
-      install_type: 'full',
-      files: result.installedFiles,
-    };
-
-    await fs.writeFile(
-      path.join(targetAioxCore, 'install-manifest.yaml'),
-      require('js-yaml').dump(manifest),
-      'utf8',
-    );
+    const sourceManifest = loadSourceManifest(sourceDir);
+    const manifestFileHashes = extractManifestFileHashes(sourceManifest);
+    const packageVersion = providedPackageVersion || require('../../../../package.json').version;
+
+    spinner.text = 'Copying installation manifest...';
+    await copyManifestArtifacts(sourceDir, targetAioxCore);
+    if (!sourceManifest) {
+      const manifest = {
+        version: packageVersion,
+        installed_at: new Date().toISOString(),
+        install_type: 'full',
+        files: result.installedFiles,
+      };
+
+      await fs.writeFile(
+        path.join(targetAioxCore, 'install-manifest.yaml'),
+        require('js-yaml').dump(manifest),
+        'utf8',
+      );
+    }
 
     // Story 7.2: Create version.json with file hashes for update tracking
     spinner.text = 'Generating version tracking info...';
@@ -318,9 +410,14 @@ async function installAioxCore(options = {}) {
       version: packageVersion,
       installedFiles: result.installedFiles,
       mode: 'project-development',
+      fileHashes: Object.keys(manifestFileHashes).length > 0 ? manifestFileHashes : null,
     });
     result.versionInfo = versionInfo;
 
+    if (sourceManifest) {
+      updateInstalledManifest(targetDir, sourceManifest, `aiox-core@${packageVersion}`);
+    }
+
     // BUG-2 fix (INS-1): Install .aiox-core dependencies after copy
     // The copied .aiox-core/package.json has dependencies (js-yaml, execa, etc.)
     // that must be installed for the activation pipeline to work