aios-core 4.2.15 → 4.4.0

package/.aios-core/core/health-check/checks/local/index.js

@@ -4,7 +4,7 @@
  * Checks for local development environment health.
  * Domain: local
  *
- * @module @synkra/aios-core/health-check/checks/local
+ * @module aios-core/health-check/checks/local
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/local/memory.js

@@ -3,7 +3,7 @@
  *
  * Verifies sufficient memory is available.
  *
- * @module @synkra/aios-core/health-check/checks/local/memory
+ * @module aios-core/health-check/checks/local/memory
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/local/network.js

@@ -3,7 +3,7 @@
  *
  * Verifies network connectivity for development tools.
  *
- * @module @synkra/aios-core/health-check/checks/local/network
+ * @module aios-core/health-check/checks/local/network
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/local/npm-install.js

@@ -3,7 +3,7 @@
  *
  * Verifies npm is installed and working.
  *
- * @module @synkra/aios-core/health-check/checks/local/npm-install
+ * @module aios-core/health-check/checks/local/npm-install
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/local/shell-environment.js

@@ -3,7 +3,7 @@
  *
  * Verifies shell environment is properly configured.
  *
- * @module @synkra/aios-core/health-check/checks/local/shell-environment
+ * @module aios-core/health-check/checks/local/shell-environment
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/project/agent-config.js

@@ -3,7 +3,7 @@
  *
  * Verifies agent configuration files are valid YAML.
  *
- * @module @synkra/aios-core/health-check/checks/project/agent-config
+ * @module aios-core/health-check/checks/project/agent-config
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/project/aios-directory.js

@@ -3,7 +3,7 @@
  *
  * Verifies .aios/ directory structure and permissions.
  *
- * @module @synkra/aios-core/health-check/checks/project/aios-directory
+ * @module aios-core/health-check/checks/project/aios-directory
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/project/dependencies.js

@@ -3,7 +3,7 @@
  *
  * Verifies that required dependencies are present and installed.
  *
- * @module @synkra/aios-core/health-check/checks/project/dependencies
+ * @module aios-core/health-check/checks/project/dependencies
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/project/framework-config.js

@@ -3,7 +3,7 @@
  *
  * Verifies that AIOS framework configuration files are present.
  *
- * @module @synkra/aios-core/health-check/checks/project/framework-config
+ * @module aios-core/health-check/checks/project/framework-config
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/project/index.js

@@ -4,7 +4,7 @@
  * Checks for project configuration coherence and structure.
  * Domain: project
  *
- * @module @synkra/aios-core/health-check/checks/project
+ * @module aios-core/health-check/checks/project
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/project/node-version.js

@@ -3,7 +3,7 @@
  *
  * Verifies Node.js version compatibility with project requirements.
  *
- * @module @synkra/aios-core/health-check/checks/project/node-version
+ * @module aios-core/health-check/checks/project/node-version
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/project/package-json.js

@@ -3,7 +3,7 @@
  *
  * Verifies that package.json exists and is valid JSON.
  *
- * @module @synkra/aios-core/health-check/checks/project/package-json
+ * @module aios-core/health-check/checks/project/package-json
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/project/task-definitions.js

@@ -3,7 +3,7 @@
  *
  * Verifies task definition files are valid.
  *
- * @module @synkra/aios-core/health-check/checks/project/task-definitions
+ * @module aios-core/health-check/checks/project/task-definitions
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/project/workflow-dependencies.js

@@ -3,7 +3,7 @@
  *
  * Verifies workflow files have valid dependencies.
  *
- * @module @synkra/aios-core/health-check/checks/project/workflow-dependencies
+ * @module aios-core/health-check/checks/project/workflow-dependencies
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/repository/branch-protection.js

@@ -3,7 +3,7 @@
  *
  * Verifies branch protection best practices.
  *
- * @module @synkra/aios-core/health-check/checks/repository/branch-protection
+ * @module aios-core/health-check/checks/repository/branch-protection
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/repository/commit-history.js

@@ -3,7 +3,7 @@
  *
  * Verifies commit history quality and patterns.
  *
- * @module @synkra/aios-core/health-check/checks/repository/commit-history
+ * @module aios-core/health-check/checks/repository/commit-history
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/repository/conflicts.js

@@ -3,7 +3,7 @@
  *
  * Checks for merge conflicts in the repository.
  *
- * @module @synkra/aios-core/health-check/checks/repository/conflicts
+ * @module aios-core/health-check/checks/repository/conflicts
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/repository/git-repo.js

@@ -3,7 +3,7 @@
  *
  * Verifies the project is a valid Git repository.
  *
- * @module @synkra/aios-core/health-check/checks/repository/git-repo
+ * @module aios-core/health-check/checks/repository/git-repo
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/repository/git-status.js

@@ -3,7 +3,7 @@
  *
  * Verifies working directory status and uncommitted changes.
  *
- * @module @synkra/aios-core/health-check/checks/repository/git-status
+ * @module aios-core/health-check/checks/repository/git-status
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/repository/gitignore.js

@@ -3,7 +3,7 @@
  *
  * Verifies .gitignore has required patterns.
  *
- * @module @synkra/aios-core/health-check/checks/repository/gitignore
+ * @module aios-core/health-check/checks/repository/gitignore
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/repository/index.js

@@ -4,7 +4,7 @@
  * Checks for git repository health and configuration.
  * Domain: repository
  *
- * @module @synkra/aios-core/health-check/checks/repository
+ * @module aios-core/health-check/checks/repository
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/repository/large-files.js

@@ -3,7 +3,7 @@
  *
  * Checks for large files that shouldn't be in git.
  *
- * @module @synkra/aios-core/health-check/checks/repository/large-files
+ * @module aios-core/health-check/checks/repository/large-files
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/repository/lockfile-integrity.js

@@ -3,7 +3,7 @@
  *
  * Verifies package-lock.json integrity and sync with package.json.
  *
- * @module @synkra/aios-core/health-check/checks/repository/lockfile-integrity
+ * @module aios-core/health-check/checks/repository/lockfile-integrity
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/services/api-endpoints.js

@@ -3,7 +3,7 @@
  *
  * Verifies external API endpoint connectivity.
  *
- * @module @synkra/aios-core/health-check/checks/services/api-endpoints
+ * @module aios-core/health-check/checks/services/api-endpoints
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/services/claude-code.js

@@ -3,7 +3,7 @@
  *
  * Verifies Claude Code CLI installation and configuration.
  *
- * @module @synkra/aios-core/health-check/checks/services/claude-code
+ * @module aios-core/health-check/checks/services/claude-code
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/services/gemini-cli.js

@@ -4,7 +4,7 @@
  * Verifies Gemini CLI installation, authentication, and configuration.
  * Detects available features including Preview features, Extensions, and Hooks.
  *
- * @module @synkra/aios-core/health-check/checks/services/gemini-cli
+ * @module aios-core/health-check/checks/services/gemini-cli
  * @version 1.0.0
  * @story GEMINI-INT Story 1 - Gemini CLI Health Check & Detection
  */

package/.aios-core/core/health-check/checks/services/github-cli.js

@@ -3,7 +3,7 @@
  *
  * Verifies GitHub CLI (gh) integration.
  *
- * @module @synkra/aios-core/health-check/checks/services/github-cli
+ * @module aios-core/health-check/checks/services/github-cli
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/services/index.js

@@ -4,7 +4,7 @@
  * Checks for external service integrations.
  * Domain: services
  *
- * @module @synkra/aios-core/health-check/checks/services
+ * @module aios-core/health-check/checks/services
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/checks/services/mcp-integration.js

@@ -3,7 +3,7 @@
  *
  * Verifies MCP (Model Context Protocol) server integration.
  *
- * @module @synkra/aios-core/health-check/checks/services/mcp-integration
+ * @module aios-core/health-check/checks/services/mcp-integration
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/engine.js

@@ -4,7 +4,7 @@
  * Core execution engine for health checks. Handles parallel execution,
  * caching, timeout management, and result aggregation.
  *
- * @module @synkra/aios-core/health-check/engine
+ * @module aios-core/health-check/engine
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/healers/backup-manager.js

@@ -4,7 +4,7 @@
  * Manages file backups for self-healing operations.
  * Ensures safe rollback capability before any modifications.
  *
- * @module @synkra/aios-core/health-check/healers/backup-manager
+ * @module aios-core/health-check/healers/backup-manager
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/healers/index.js

@@ -4,7 +4,7 @@
  * Manages self-healing operations for health check failures.
  * Implements three-tier safety model for auto-fixes.
  *
- * @module @synkra/aios-core/health-check/healers
+ * @module aios-core/health-check/healers
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/index.js

@@ -1,13 +1,20 @@
 /**
- * Health Check System - Main Entry Point
+ * Health Check System - Main Entry Point (HCS-2)
  *
  * Provides comprehensive health checking capabilities for AIOS projects.
  * Supports 5 domains: Project Coherence, Local Environment, Repository Health,
  * Deployment Environment, and Service Integration.
  *
- * @module @synkra/aios-core/health-check
+ * NOTE (INS-4.8): This is a SEPARATE system from `core/doctor/` (INS-4.1).
+ * The primary diagnostic interface is `aios doctor` (bin/aios.js → core/doctor/).
+ * The agent-facing task `*health-check` now delegates to `aios doctor --json`
+ * and no longer calls this module. This module is preserved for potential
+ * programmatic use but is NOT the primary health check mechanism.
+ *
+ * @module aios-core/health-check
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
+ * @see core/doctor/ for the primary diagnostic system (15 checks)
  */
 
 const HealthCheckEngine = require('./engine');

package/.aios-core/core/health-check/reporters/console.js

@@ -4,7 +4,7 @@
  * Generates formatted console output for health check results.
  * Supports colors and various verbosity levels.
  *
- * @module @synkra/aios-core/health-check/reporters/console
+ * @module aios-core/health-check/reporters/console
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/reporters/index.js

@@ -4,7 +4,7 @@
  * Manages report generation for health check results.
  * Supports multiple output formats: Console, Markdown, JSON.
  *
- * @module @synkra/aios-core/health-check/reporters
+ * @module aios-core/health-check/reporters
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/reporters/json.js

@@ -4,7 +4,7 @@
  * Generates JSON-formatted health check reports.
  * Suitable for CI/CD integration, dashboards, and programmatic consumption.
  *
- * @module @synkra/aios-core/health-check/reporters/json
+ * @module aios-core/health-check/reporters/json
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/health-check/reporters/markdown.js

@@ -4,7 +4,7 @@
  * Generates Markdown-formatted health check reports.
  * Suitable for documentation, GitHub, and static site hosting.
  *
- * @module @synkra/aios-core/health-check/reporters/markdown
+ * @module aios-core/health-check/reporters/markdown
  * @version 1.0.0
  * @story HCS-2 - Health Check System Implementation
  */

package/.aios-core/core/ids/layer-classifier.js

@@ -0,0 +1,65 @@
+/**
+ * Layer Classifier — Entity Registry Layer Classification (L1-L4)
+ *
+ * Pure function module that classifies entity paths into boundary layers.
+ * Used by: populate-entity-registry.js, registry-updater.js
+ *
+ * Layer Model:
+ *   L1 (Framework Core)      — .aios-core/core/, bin/, constitution.md
+ *   L2 (Framework Templates)  — .aios-core/development/, infrastructure/, product/
+ *   L3 (Project Config)       — .aios-core/data/, MEMORY.md, .claude/, *-config.yaml
+ *   L4 (Project Runtime)      — docs/, tests/, packages/, everything else (fallback)
+ *
+ * Rule ordering: most specific first. First match wins.
+ *
+ * @module layer-classifier
+ * @see Story BM-5
+ */
+
+const LAYER_RULES = [
+  // --- L1: Framework Core ---
+  { layer: 'L1', test: (p) => p.startsWith('.aios-core/core/') },
+  { layer: 'L1', test: (p) => p.startsWith('bin/') },
+  { layer: 'L1', test: (p) => p === '.aios-core/constitution.md' },
+
+  // --- L3: Project Config (before L2 to catch MEMORY.md inside agents/) ---
+  { layer: 'L3', test: (p) => p.startsWith('.aios-core/data/') },
+  { layer: 'L3', test: (p) => p.endsWith('/MEMORY.md') || p === 'MEMORY.md' },
+  { layer: 'L3', test: (p) => p.startsWith('.claude/') },
+  { layer: 'L3', test: (p) => p === 'core-config.yaml' || p === 'project-config.yaml' },
+  { layer: 'L3', test: (p) => p.endsWith('-config.yaml') && !p.includes('/') },
+
+  // --- L2: Framework Templates ---
+  { layer: 'L2', test: (p) => p.startsWith('.aios-core/development/') },
+  { layer: 'L2', test: (p) => p.startsWith('.aios-core/infrastructure/') },
+  { layer: 'L2', test: (p) => p.startsWith('.aios-core/product/') },
+
+  // --- L4: Project Runtime (fallback — safest default for unknown files) ---
+];
+
+/**
+ * Classify an entity path into a boundary layer (L1-L4).
+ *
+ * @param {string} entityPath — Relative path from repo root (forward slashes)
+ * @returns {'L1' | 'L2' | 'L3' | 'L4'} The boundary layer
+ */
+function classifyLayer(entityPath) {
+  if (typeof entityPath !== "string") return "L4";
+
+  // Normalize: forward slashes, no leading ./ or /
+  const normalized = entityPath
+    .replace(/\\/g, '/')
+    .replace(/^\.\//,'')
+    .replace(/^\//,'');
+
+  for (const rule of LAYER_RULES) {
+    if (rule.test(normalized)) {
+      return rule.layer;
+    }
+  }
+
+  // Fallback: L4 (Project Runtime)
+  return 'L4';
+}
+
+module.exports = { classifyLayer, LAYER_RULES };

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

@@ -18,6 +18,8 @@ const {
   REPO_ROOT,
   REGISTRY_PATH,
 } = require(path.resolve(__dirname, '../../development/scripts/populate-entity-registry.js'));
+const { enrichRegistryEntry } = require(path.resolve(__dirname, '../code-intel/helpers/creation-helper'));
+const { classifyLayer } = require(path.resolve(__dirname, 'layer-classifier'));
 
 const LOCK_FILE = path.resolve(REPO_ROOT, '.aios-core/data/.entity-registry.lock');
 const BACKUP_DIR = path.resolve(REPO_ROOT, '.aios-core/data/registry-backups');
@@ -278,6 +280,10 @@ class RegistryUpdater {
 
         if (updated > 0) {
           this._resolveAllUsedBy(registry);
+
+          // NOG-8: Apply code intelligence enrichment AFTER resolveAllUsedBy
+          // so that code-intel usedBy data is merged on top of static graph
+          await this._applyCodeIntelEnrichments(registry);
           registry.metadata.lastUpdated = new Date().toISOString();
           registry.metadata.entityCount = this._countEntities(registry);
           this._writeRegistry(registry);
@@ -327,6 +333,7 @@ class RegistryUpdater {
 
     registry.entities[category][entityId] = {
       path: relPath,
+      layer: classifyLayer(relPath),
       type: config.type,
       purpose,
       keywords,
@@ -340,6 +347,11 @@ class RegistryUpdater {
       checksum,
       lastVerified: new Date().toISOString(),
     };
+
+    // NOG-8: Enrich with code intelligence data (advisory, never blocks registration)
+    this._pendingEnrichments = this._pendingEnrichments || [];
+    this._pendingEnrichments.push({ entityId, category, relPath });
+
     return true;
   }
 
@@ -426,6 +438,43 @@ class RegistryUpdater {
     return found;
   }
 
+  // ─── Internal: Code Intelligence Enrichment (NOG-8) ────────────
+
+  /**
+   * Apply code intelligence enrichment to newly created entities.
+   * Advisory only — never blocks registration. Falls back gracefully.
+   * @param {Object} registry - Registry data
+   * @private
+   */
+  async _applyCodeIntelEnrichments(registry) {
+    const pending = this._pendingEnrichments || [];
+    this._pendingEnrichments = [];
+
+    for (const { entityId, category, relPath } of pending) {
+      try {
+        const entity = registry.entities[category]?.[entityId];
+        if (!entity) continue;
+
+        const enrichment = await enrichRegistryEntry(entityId, relPath);
+        if (!enrichment) continue;
+
+        // Pre-populate usedBy if code intel found references
+        if (enrichment.usedBy && enrichment.usedBy.length > 0) {
+          entity.usedBy = [...new Set([...(entity.usedBy || []), ...enrichment.usedBy])];
+        }
+
+        // Pre-populate dependencies if code intel found them
+        if (enrichment.dependencies && enrichment.dependencies.nodes && enrichment.dependencies.nodes.length > 0) {
+          const existingDeps = Array.isArray(entity.dependencies) ? entity.dependencies : [];
+          const newDeps = enrichment.dependencies.nodes.filter((n) => typeof n === 'string');
+          entity.dependencies = [...new Set([...existingDeps, ...newDeps])];
+        }
+      } catch {
+        // NOG-8 AC5: Fallback — enrichment failure never blocks registration
+      }
+    }
+  }
+
   // ─── Internal: Registry I/O ──────────────────────────────────────
 
   _loadRegistry() {

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

@@ -3,7 +3,7 @@
  *
  * Provides ES module exports for all core framework functionality.
  *
- * @module @synkra/aios-core/core
+ * @module aios-core/core
  * @version 2.0.0
  * @created Story 2.2 - Core Module Creation
  */

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

@@ -5,7 +5,7 @@
  * This module contains the essential runtime components that all other
  * modules depend on.
  *
- * @module @synkra/aios-core/core
+ * @module aios-core/core
  * @version 2.0.0
  * @created Story 2.2 - Core Module Creation
  */

package/.aios-core/core/session/context-detector.js

@@ -15,6 +15,7 @@
 
 const fs = require('fs');
 const path = require('path');
+const { atomicWriteSync } = require('../synapse/utils/atomic-write');
 
 const SESSION_STATE_PATH = path.join(process.cwd(), '.aios', 'session-state.json');
 const SESSION_TTL = 60 * 60 * 1000; // 1 hour
@@ -173,12 +174,6 @@ class ContextDetector {
    */
   updateSessionState(state, sessionFilePath = SESSION_STATE_PATH) {
     try {
-      // Ensure directory exists
-      const dir = path.dirname(sessionFilePath);
-      if (!fs.existsSync(dir)) {
-        fs.mkdirSync(dir, { recursive: true });
-      }
-
       const sessionData = {
         sessionId: state.sessionId || this._generateSessionId(),
         startTime: state.startTime || Date.now(),
@@ -191,7 +186,7 @@ class ContextDetector {
         currentStory: state.currentStory || null,
       };
 
-      fs.writeFileSync(sessionFilePath, JSON.stringify(sessionData, null, 2), 'utf8');
+      atomicWriteSync(sessionFilePath, JSON.stringify(sessionData, null, 2));
     } catch (error) {
       console.warn('[ContextDetector] Failed to update session state:', error.message);
     }

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

@@ -42,6 +42,13 @@ const TOKEN_BUDGETS = {
   CRITICAL: 2500,
 };
 
+/**
+ * Safety multiplier for XML-heavy output (SYNAPSE rules).
+ * chars/4 underestimates by 15-25% on XML; 1.2x corrects this.
+ * @see NOG-9 research C6-token-budget.md
+ */
+const XML_SAFETY_MULTIPLIER = 1.2;
+
 /**
  * Default configuration values.
  */
@@ -114,7 +121,7 @@ function estimateContextPercent(promptCount, options = {}) {
     return 0;
   }
 
-  const usedTokens = promptCount * avgTokensPerPrompt;
+  const usedTokens = promptCount * avgTokensPerPrompt * XML_SAFETY_MULTIPLIER;
   const percent = 100 - (usedTokens / maxContext * 100);
   return Math.max(0, Math.min(100, percent));
 }
@@ -187,4 +194,5 @@ module.exports = {
   BRACKETS,
   TOKEN_BUDGETS,
   DEFAULTS,
+  XML_SAFETY_MULTIPLIER,
 };