aios-core 4.0.4 → 4.2.0

package/.aios-core/cli/commands/migrate/analyze.js

@@ -2,11 +2,11 @@
  * Migration Structure Analysis Module
  *
  * Detects v2.0 structure and generates migration plan
- * for v2.0 → v2.1 migration.
+ * for v2.0 → v4.0.4 migration.
  *
  * @module cli/commands/migrate/analyze
  * @version 1.0.0
- * @story 2.14 - Migration Script v2.0 → v2.1
+ * @story 2.14 - Migration Script v2.0 → v4.0.4
  */
 
 const fs = require('fs');
@@ -14,7 +14,7 @@ const path = require('path');
 const { getAllFiles } = require('./backup');
 
 /**
- * Module mapping configuration for v2.0 → v2.1 migration
+ * Module mapping configuration for v2.0 → v4.0.4 migration
  */
 const MODULE_MAPPING = {
   core: {
@@ -81,7 +81,7 @@ async function detectV2Structure(projectRoot) {
     };
   }
 
-  // Check for v2.1 modular structure (core, development, product, infrastructure dirs)
+  // Check for v4.0.4 modular structure (core, development, product, infrastructure dirs)
   const v21Modules = ['core', 'development', 'product', 'infrastructure'];
   const hasV21Structure = v21Modules.every(module =>
     fs.existsSync(path.join(aiosCoreDir, module)),
@@ -92,7 +92,7 @@ async function detectV2Structure(projectRoot) {
       isV2: false,
       isV21: true,
       version: '2.1',
-      message: 'Project already has v2.1 modular structure',
+      message: 'Project already has v4.0.4 modular structure',
     };
   }
 
@@ -211,7 +211,7 @@ async function analyzeMigrationPlan(projectRoot, options = {}) {
     plan.totalSize += stats.size;
   }
 
-  // Check for potential conflicts (existing v2.1 directories)
+  // Check for potential conflicts (existing v4.0.4 directories)
   for (const moduleName of Object.keys(plan.modules)) {
     const targetDir = path.join(aiosCoreDir, moduleName);
     if (fs.existsSync(targetDir)) {

package/.aios-core/cli/commands/migrate/backup.js

@@ -2,11 +2,11 @@
  * Migration Backup Module
  *
  * Handles backup creation, verification, and manifest generation
- * for v2.0 → v2.1 migration.
+ * for v2.0 → v4.0.4 migration.
  *
  * @module cli/commands/migrate/backup
  * @version 1.0.0
- * @story 2.14 - Migration Script v2.0 → v2.1
+ * @story 2.14 - Migration Script v2.0 → v4.0.4
  */
 
 const fs = require('fs');

package/.aios-core/cli/commands/migrate/execute.js

@@ -1,11 +1,11 @@
 /**
  * Migration Execution Module
  *
- * Executes the migration from v2.0 → v2.1 structure.
+ * Executes the migration from v2.0 → v4.0.4 structure.
  *
  * @module cli/commands/migrate/execute
  * @version 1.0.0
- * @story 2.14 - Migration Script v2.0 → v2.1
+ * @story 2.14 - Migration Script v2.0 → v4.0.4
  */
 
 const fs = require('fs');
@@ -14,7 +14,7 @@ const { copyFileWithMetadata } = require('./backup');
 const { MODULE_MAPPING } = require('./analyze');
 
 /**
- * Create module directories for v2.1 structure
+ * Create module directories for v4.0.4 structure
  * @param {string} aiosCoreDir - Path to .aios-core
  * @param {Object} options - Options
  * @returns {Promise<Object>} Created directories
@@ -102,7 +102,7 @@ async function migrateModule(moduleData, moduleName, aiosCoreDir, options = {})
 }
 
 /**
- * Execute full migration from v2.0 to v2.1
+ * Execute full migration from v2.0 to v4.0.4
  * @param {Object} plan - Migration plan from analyzeMigrationPlan
  * @param {Object} options - Execution options
  * @returns {Promise<Object>} Migration result

package/.aios-core/cli/commands/migrate/index.js

@@ -1,11 +1,11 @@
 /**
  * AIOS Migration Command
  *
- * CLI command for migrating from v2.0 to v2.1 modular structure.
+ * CLI command for migrating from v2.0 to v4.0.4 modular structure.
  *
  * @module cli/commands/migrate
  * @version 1.0.0
- * @story 2.14 - Migration Script v2.0 → v2.1
+ * @story 2.14 - Migration Script v2.0 → v4.0.4
  */
 
 const { Command } = require('commander');
@@ -91,7 +91,7 @@ async function runMigration(options) {
 
   if (!versionInfo.isV2) {
     if (versionInfo.isV21) {
-      console.log('ℹ️  Project already has v2.1 structure. No migration needed.');
+      console.log('ℹ️  Project already has v4.0.4 structure. No migration needed.');
       return;
     }
     console.error(`❌ ${versionInfo.error || 'Cannot detect AIOS version'}`);
@@ -118,7 +118,7 @@ async function runMigration(options) {
   // Check for conflicts
   if (plan.conflicts.length > 0) {
     console.log('');
-    console.log('⚠️  Conflicts detected. Some v2.1 directories already exist.');
+    console.log('⚠️  Conflicts detected. Some v4.0.4 directories already exist.');
 
     if (!yes) {
       const proceed = await askConfirmation('Continue anyway?');
@@ -363,7 +363,7 @@ function createMigrateCommand() {
   const migrate = new Command('migrate');
 
   migrate
-    .description('Migrate AIOS from v2.0 to v2.1 modular structure')
+    .description('Migrate AIOS from v2.0 to v4.0.4 modular structure')
     .option('--from <version>', 'Source version', '2.0')
     .option('--to <version>', 'Target version', '2.1')
     .option('--dry-run', 'Show migration plan without executing')

package/.aios-core/cli/commands/migrate/rollback.js

@@ -1,11 +1,11 @@
 /**
  * Migration Rollback Module
  *
- * Handles rollback from v2.1 back to v2.0 structure using backup.
+ * Handles rollback from v4.0.4 back to v2.0 structure using backup.
  *
  * @module cli/commands/migrate/rollback
  * @version 1.0.0
- * @story 2.14 - Migration Script v2.0 → v2.1
+ * @story 2.14 - Migration Script v2.0 → v4.0.4
  */
 
 const fs = require('fs');
@@ -14,7 +14,7 @@ const { findLatestBackup, verifyBackup, copyFileWithMetadata } = require('./back
 const { clearMigrationState } = require('./execute');
 
 /**
- * Remove v2.1 module directories
+ * Remove v4.0.4 module directories
  * @param {string} aiosCoreDir - Path to .aios-core
  * @param {Object} options - Options
  * @returns {Promise<Object>} Removal result
@@ -28,7 +28,7 @@ async function removeV21Structure(aiosCoreDir, options = {}) {
     errors: [],
   };
 
-  onProgress({ phase: 'remove', message: '✓ Removing v2.1 structure...' });
+  onProgress({ phase: 'remove', message: '✓ Removing v4.0.4 structure...' });
 
   for (const moduleName of v21Modules) {
     const moduleDir = path.join(aiosCoreDir, moduleName);
@@ -182,7 +182,7 @@ async function executeRollback(projectRoot, options = {}) {
     },
   });
 
-  // Step 1: Remove v2.1 structure
+  // Step 1: Remove v4.0.4 structure
   const aiosCoreDir = path.join(projectRoot, '.aios-core');
   result.removal = await removeV21Structure(aiosCoreDir, { onProgress });
 
@@ -273,7 +273,7 @@ function formatRollbackSummary(result) {
   }
 
   if (result.removal?.removed?.length > 0) {
-    lines.push(`Removed: ${result.removal.removed.length} v2.1 directories`);
+    lines.push(`Removed: ${result.removal.removed.length} v4.0.4 directories`);
   }
 
   return lines.join('\n');

package/.aios-core/cli/commands/migrate/update-imports.js

@@ -5,7 +5,7 @@
  *
  * @module cli/commands/migrate/update-imports
  * @version 1.0.0
- * @story 2.14 - Migration Script v2.0 → v2.1
+ * @story 2.14 - Migration Script v2.0 → v4.0.4
  */
 
 const fs = require('fs');
@@ -86,7 +86,7 @@ async function scanFileImports(filePath) {
 }
 
 /**
- * Transform an import path from v2.0 to v2.1 structure
+ * Transform an import path from v2.0 to v4.0.4 structure
  * @param {string} importPath - Original import path
  * @param {string} currentFileModule - Module of the file containing the import
  * @param {string} currentFilePath - Path of the file containing the import

package/.aios-core/cli/commands/migrate/validate.js

@@ -5,7 +5,7 @@
  *
  * @module cli/commands/migrate/validate
  * @version 1.0.0
- * @story 2.14 - Migration Script v2.0 → v2.1
+ * @story 2.14 - Migration Script v2.0 → v4.0.4
  */
 
 const fs = require('fs');
@@ -17,7 +17,7 @@ const { verifyImports } = require('./update-imports');
 // const { formatSize } = require('./analyze');
 
 /**
- * Validate the v2.1 module structure exists
+ * Validate the v4.0.4 module structure exists
  * @param {string} aiosCoreDir - Path to .aios-core
  * @returns {Promise<Object>} Validation result
  */

package/.aios-core/cli/commands/pro/index.js

@@ -214,6 +214,58 @@ async function activateAction(options) {
     console.log(`  Cache:        ${result.cacheValidDays} days offline operation`);
     console.log('');
 
+    // Scaffold pro content into project (Story INS-3.1)
+    // Lazy-load to avoid crashing if pro-scaffolder or js-yaml is unavailable
+    const projectRoot = path.resolve(__dirname, '..', '..', '..', '..');
+    const proSourceDir = path.join(projectRoot, 'node_modules', '@aios-fullstack', 'pro');
+
+    if (fs.existsSync(proSourceDir)) {
+      let scaffoldProContent;
+      try {
+        ({ scaffoldProContent } = require('../../../../packages/installer/src/pro/pro-scaffolder'));
+      } catch {
+        console.log('Note: Pro scaffolder not available. Skipping content scaffolding.');
+        console.log('');
+      }
+
+      if (scaffoldProContent) {
+        console.log('Scaffolding pro content...');
+        const scaffoldResult = await scaffoldProContent(projectRoot, proSourceDir, {
+          onProgress: ({ item, status, message }) => {
+            if (status === 'done') {
+              console.log(`  + ${message}`);
+            } else if (status === 'warning') {
+              console.log(`  ! ${message}`);
+            }
+          },
+        });
+
+        if (scaffoldResult.success) {
+          console.log(`\nPro content installed (${scaffoldResult.copiedFiles.length} files)`);
+          if (scaffoldResult.skippedFiles.length > 0) {
+            console.log(`  ${scaffoldResult.skippedFiles.length} files unchanged (already up to date)`);
+          }
+          if (scaffoldResult.warnings.length > 0) {
+            for (const warning of scaffoldResult.warnings) {
+              console.log(`  Warning: ${warning}`);
+            }
+          }
+        } else {
+          console.error('\nWarning: Pro content scaffolding failed.');
+          for (const err of scaffoldResult.errors) {
+            console.error(`  ${err}`);
+          }
+          console.error('Pro features are activated but content was not copied.');
+          console.error('Try running "aios pro activate" again to retry scaffolding.');
+        }
+        console.log('');
+      }
+    } else {
+      console.log('Note: @aios-fullstack/pro package not found in node_modules.');
+      console.log('Pro content will be scaffolded when the package is installed.');
+      console.log('');
+    }
+
   } catch (error) {
     if (error instanceof LicenseActivationError) {
       console.error(`\nActivation failed: ${error.message}`);

package/.aios-core/cli/index.js

@@ -54,7 +54,7 @@ Commands:
   config            Manage layered configuration (show, diff, migrate, validate)
   pro               AIOS Pro license management (activate, status, deactivate, features)
   mcp               Manage global MCP configuration
-  migrate           Migrate from v2.0 to v2.1 structure
+  migrate           Migrate from v2.0 to v4.0.4 structure
   generate          Generate documents from templates (prd, adr, pmdr, etc.)
   install           Install AIOS in current project
   init <name>       Create new AIOS project

package/.aios-core/core/ids/registry-updater.js

@@ -47,7 +47,14 @@ const EXCLUDE_PATTERNS = [
 class RegistryUpdater {
   constructor(options = {}) {
     this._registryPath = options.registryPath || REGISTRY_PATH;
-    this._repoRoot = options.repoRoot || REPO_ROOT;
+    // Resolve repoRoot to real path to handle macOS /var -> /private/var symlink
+    // This ensures path.relative() works correctly with resolved file paths
+    const rawRepoRoot = options.repoRoot || REPO_ROOT;
+    try {
+      this._repoRoot = fs.realpathSync(rawRepoRoot);
+    } catch {
+      this._repoRoot = rawRepoRoot;
+    }
     this._debounceMs = options.debounceMs ?? DEBOUNCE_MS;
     this._auditLogPath = options.auditLogPath || AUDIT_LOG_PATH;
     this._lockFile = options.lockFile || LOCK_FILE;
@@ -126,9 +133,28 @@ class RegistryUpdater {
         const abs = path.isAbsolute(c.filePath)
           ? c.filePath
           : path.resolve(this._repoRoot, c.filePath);
-        return { action: c.action, filePath: this._resolveSymlink(abs) };
+        // For unlink, file doesn't exist so _resolveSymlink returns original path
+        // We need to manually resolve the path to match _repoRoot format on macOS
+        let resolved = this._resolveSymlink(abs);
+        if (c.action === 'unlink' && resolved === abs) {
+          // File doesn't exist - normalize path manually for macOS /var -> /private/var
+          // This ensures path.relative() works correctly with _repoRoot
+          resolved = abs.replace(/^\/var\//, '/private/var/');
+        }
+        return { action: c.action, filePath: resolved };
       })
-      .filter((c) => !this._isExcluded(c.filePath) && this._isIncluded(c.filePath));
+      .filter((c) => {
+        // For unlink (delete), skip file existence checks - the file no longer exists
+        // We only need to verify the path would be in scope and not excluded
+        if (c.action === 'unlink') {
+          if (this._isExcluded(c.filePath)) return false;
+          // For deletions, check if path matches any known category pattern
+          const relPath = path.relative(this._repoRoot, c.filePath).replace(/\\/g, '/');
+          return this._detectCategory(relPath) !== null;
+        }
+        // For add/change, use standard inclusion check
+        return !this._isExcluded(c.filePath) && this._isIncluded(c.filePath);
+      });
 
     if (validChanges.length === 0) return { updated: 0, errors: [] };
 

package/.aios-core/core/migration/migration-config.yaml

@@ -1,5 +1,5 @@
 # AIOS Migration Configuration
-# Story 2.14 - Migration Script v2.0 → v2.1
+# Story 2.14 - Migration Script v2.0 → v4.0.4
 
 version: "1.0.0"
 story: "2.14"
@@ -29,7 +29,7 @@ backup:
     algorithm: "md5"
     parallel: true
 
-# Module configuration for v2.1
+# Module configuration for v4.0.4
 modules:
   core:
     description: "Core framework utilities and runtime"

package/.aios-core/core/migration/module-mapping.yaml

@@ -1,9 +1,9 @@
-# AIOS Module Mapping v2.0 → v2.1
+# AIOS Module Mapping v2.0 → v4.0.4
 # Story 2.14 - Migration Script
 
 version: "1.0.0"
 
-# Mapping of v2.0 directories to v2.1 modules
+# Mapping of v2.0 directories to v4.0.4 modules
 mapping:
   core:
     source: ".aios-core/"

package/.aios-core/core/registry/README.md

@@ -172,8 +172,8 @@ The registry integrates with:
 
 ## Story Reference
 
-Created in [Story 2.6 - Service Registry Creation](../../../../docs/stories/v2.1/sprint-2/story-2.6-service-registry.md)
+Created in [Story 2.6 - Service Registry Creation](../../../../docs/stories/v4.0.4/sprint-2/story-2.6-service-registry.md)
 
 ---
 
-*Generated by AIOS Framework v2.1*
+*Generated by AIOS Framework v4.0.4*

package/.aios-core/core/synapse/context/context-builder.js

@@ -0,0 +1,34 @@
+'use strict';
+
+/**
+ * Build a normalized context payload for SYNAPSE layer execution.
+ *
+ * Centralizing this shape avoids drift between engine callers and ensures
+ * all layers always receive the same contract.
+ *
+ * @param {Object} params
+ * @param {string} params.prompt
+ * @param {Object} params.session
+ * @param {Object} params.config
+ * @param {string} params.synapsePath
+ * @param {Object} [params.manifest]
+ * @param {Array<Object>} [params.previousLayers]
+ * @returns {{prompt: string, session: Object, config: Object, previousLayers: Array<Object>}}
+ */
+function buildLayerContext(params) {
+  const safeParams = params || {};
+  return {
+    prompt: safeParams.prompt || '',
+    session: safeParams.session || {},
+    config: {
+      ...(safeParams.config || {}),
+      synapsePath: safeParams.synapsePath,
+      manifest: safeParams.manifest || {},
+    },
+    previousLayers: Array.isArray(safeParams.previousLayers) ? safeParams.previousLayers : [],
+  };
+}
+
+module.exports = {
+  buildLayerContext,
+};

package/.aios-core/core/synapse/diagnostics/collectors/consistency-collector.js

@@ -0,0 +1,168 @@
+/**
+ * Consistency Collector — Cross-validates UAP and Hook metrics for coherence.
+ *
+ * Performs 4 consistency checks between the two pipeline metrics files:
+ * 1. Bracket consistency — Hook bracket matches expected for session state
+ * 2. Agent consistency — UAP agentId matches Hook session active_agent
+ * 3. Timestamp consistency — Both metrics from same activation window
+ * 4. Quality consistency — UAP quality aligns with Hook layer count
+ *
+ * @module core/synapse/diagnostics/collectors/consistency-collector
+ * @version 1.0.0
+ * @created Story SYN-14
+ */
+
+'use strict';
+
+const path = require('path');
+const { safeReadJson } = require('./safe-read-json');
+
+/** Maximum time gap (ms) between UAP and Hook timestamps to be considered consistent.
+ * UAP writes once at activation; Hook writes every prompt. Gaps of several minutes are normal.
+ */
+const MAX_TIMESTAMP_GAP_MS = 10 * 60 * 1000;
+
+/**
+ * Collect cross-pipeline consistency checks.
+ *
+ * @param {string} projectRoot - Absolute path to project root
+ * @returns {{
+ *   available: boolean,
+ *   checks: Array<{ name: string, status: string, detail: string }>,
+ *   score: number,
+ *   maxScore: number
+ * }}
+ */
+function collectConsistencyMetrics(projectRoot) {
+  const metricsDir = path.join(projectRoot, '.synapse', 'metrics');
+
+  const uapData = safeReadJson(path.join(metricsDir, 'uap-metrics.json'));
+  const hookData = safeReadJson(path.join(metricsDir, 'hook-metrics.json'));
+
+  if (!uapData && !hookData) {
+    return { available: false, checks: [], score: 0, maxScore: 0 };
+  }
+
+  // If only one side exists, partial consistency is possible
+  if (!uapData || !hookData) {
+    return {
+      available: true,
+      checks: [{
+        name: 'data-completeness',
+        status: 'WARN',
+        detail: !uapData ? 'UAP metrics missing — only Hook available' : 'Hook metrics missing — only UAP available',
+      }],
+      score: 0,
+      maxScore: 4,
+    };
+  }
+
+  const checks = [];
+  let score = 0;
+  const maxScore = 4;
+
+  // Check 1: Bracket consistency
+  const bracketCheck = _checkBracket(hookData);
+  checks.push(bracketCheck);
+  if (bracketCheck.status === 'PASS') score++;
+
+  // Check 2: Agent consistency
+  const agentCheck = _checkAgent(uapData, projectRoot);
+  checks.push(agentCheck);
+  if (agentCheck.status === 'PASS') score++;
+
+  // Check 3: Timestamp consistency
+  const timestampCheck = _checkTimestamp(uapData, hookData);
+  checks.push(timestampCheck);
+  if (timestampCheck.status === 'PASS') score++;
+
+  // Check 4: Quality consistency
+  const qualityCheck = _checkQuality(uapData, hookData);
+  checks.push(qualityCheck);
+  if (qualityCheck.status === 'PASS') score++;
+
+  return { available: true, checks, score, maxScore };
+}
+
+/**
+ * Check 1: Bracket is a known value.
+ * @param {Object} hookData
+ * @returns {{ name: string, status: string, detail: string }}
+ */
+function _checkBracket(hookData) {
+  const validBrackets = ['FRESH', 'MODERATE', 'DEPLETED', 'CRITICAL'];
+  const bracket = hookData.bracket;
+  if (validBrackets.includes(bracket)) {
+    return { name: 'bracket', status: 'PASS', detail: `Hook bracket: ${bracket}` };
+  }
+  return { name: 'bracket', status: 'FAIL', detail: `Unknown bracket: ${bracket || 'undefined'}` };
+}
+
+/**
+ * Check 2: UAP agentId matches _active-agent.json bridge file.
+ * @param {Object} uapData
+ * @param {string} projectRoot
+ * @returns {{ name: string, status: string, detail: string }}
+ */
+function _checkAgent(uapData, projectRoot) {
+  const bridgePath = path.join(projectRoot, '.synapse', 'sessions', '_active-agent.json');
+  const bridgeData = safeReadJson(bridgePath);
+
+  if (!bridgeData || !bridgeData.id) {
+    return { name: 'agent', status: 'WARN', detail: 'No active-agent bridge file found' };
+  }
+  if (uapData.agentId === bridgeData.id) {
+    return { name: 'agent', status: 'PASS', detail: `Agent match: ${uapData.agentId}` };
+  }
+  return {
+    name: 'agent',
+    status: 'FAIL',
+    detail: `UAP agent (${uapData.agentId}) != bridge agent (${bridgeData.id})`,
+  };
+}
+
+/**
+ * Check 3: UAP and Hook timestamps are within MAX_TIMESTAMP_GAP_MS.
+ * @param {Object} uapData
+ * @param {Object} hookData
+ * @returns {{ name: string, status: string, detail: string }}
+ */
+function _checkTimestamp(uapData, hookData) {
+  if (!uapData.timestamp || !hookData.timestamp) {
+    return { name: 'timestamp', status: 'WARN', detail: 'Missing timestamp in one or both metrics' };
+  }
+  const gap = Math.abs(new Date(uapData.timestamp).getTime() - new Date(hookData.timestamp).getTime());
+  if (gap <= MAX_TIMESTAMP_GAP_MS) {
+    return { name: 'timestamp', status: 'PASS', detail: `Gap: ${Math.round(gap / 1000)}s (within ${MAX_TIMESTAMP_GAP_MS / 1000}s)` };
+  }
+  return {
+    name: 'timestamp',
+    status: 'FAIL',
+    detail: `Gap: ${Math.round(gap / 1000)}s (exceeds ${MAX_TIMESTAMP_GAP_MS / 1000}s threshold)`,
+  };
+}
+
+/**
+ * Check 4: UAP quality aligns with Hook layer count.
+ * 'full' quality should have layers loaded; 'fallback' may have zero.
+ * @param {Object} uapData
+ * @param {Object} hookData
+ * @returns {{ name: string, status: string, detail: string }}
+ */
+function _checkQuality(uapData, hookData) {
+  const quality = uapData.quality;
+  const layersLoaded = hookData.layersLoaded || 0;
+
+  if (quality === 'fallback' && layersLoaded > 0) {
+    return { name: 'quality', status: 'PASS', detail: `UAP fallback but Hook loaded ${layersLoaded} layers (Hook independent)` };
+  }
+  if (quality === 'full' && layersLoaded === 0) {
+    return { name: 'quality', status: 'WARN', detail: 'UAP full quality but Hook loaded 0 layers' };
+  }
+  if (quality === 'full' && layersLoaded > 0) {
+    return { name: 'quality', status: 'PASS', detail: `UAP ${quality}, Hook ${layersLoaded} layers` };
+  }
+  return { name: 'quality', status: 'PASS', detail: `UAP ${quality || 'unknown'}, Hook ${layersLoaded} layers` };
+}
+
+module.exports = { collectConsistencyMetrics, MAX_TIMESTAMP_GAP_MS };