aios-core 4.0.2 → 4.1.0

package/.aios-core/core/synapse/engine.js

@@ -10,6 +10,9 @@
  * @created Story SYN-6 - SynapseEngine Orchestrator + Output Formatter
  */
 
+const fs = require('fs');
+const path = require('path');
+
 const {
   estimateContextPercent,
   calculateBracket,
@@ -18,6 +21,7 @@ const {
   needsMemoryHints,
   needsHandoffWarning,
 } = require('./context/context-tracker');
+const { buildLayerContext } = require('./context/context-builder');
 
 const { formatSynapseRules } = require('./output/formatter');
 const { MemoryBridge } = require('./memory/memory-bridge');
@@ -70,9 +74,9 @@ class PipelineMetrics {
   constructor() {
     /** @type {Object.<string, object>} Per-layer metrics keyed by name */
     this.layers = {};
-    /** @type {number|null} Pipeline start timestamp (ms) */
+    /** @type {bigint|null} Pipeline start hrtime (nanoseconds) */
     this.totalStart = null;
-    /** @type {number|null} Pipeline end timestamp (ms) */
+    /** @type {bigint|null} Pipeline end hrtime (nanoseconds) */
     this.totalEnd = null;
   }
 
@@ -82,7 +86,7 @@ class PipelineMetrics {
    * @param {string} name - Layer name
    */
   startLayer(name) {
-    this.layers[name] = { start: Date.now(), status: 'running' };
+    this.layers[name] = { start: process.hrtime.bigint(), status: 'running' };
   }
 
   /**
@@ -97,8 +101,9 @@ class PipelineMetrics {
       this.layers[name] = { status: 'ok', rules: rulesCount };
       return;
     }
-    layer.end = Date.now();
-    layer.duration = layer.end - layer.start;
+    const endTime = process.hrtime.bigint();
+    layer.end = endTime;
+    layer.duration = Number(endTime - layer.start) / 1e6;
     layer.status = 'ok';
     layer.rules = rulesCount;
   }
@@ -122,8 +127,9 @@ class PipelineMetrics {
   errorLayer(name, error) {
     const existing = this.layers[name] || {};
     if (existing.start) {
-      existing.end = Date.now();
-      existing.duration = existing.end - existing.start;
+      const endTime = process.hrtime.bigint();
+      existing.end = endTime;
+      existing.duration = Number(endTime - existing.start) / 1e6;
     }
     this.layers[name] = {
       ...existing,
@@ -148,7 +154,7 @@ class PipelineMetrics {
     const values = Object.values(this.layers);
     return {
       total_ms: this.totalStart != null && this.totalEnd != null
-        ? this.totalEnd - this.totalStart
+        ? Number(this.totalEnd - this.totalStart) / 1e6
         : 0,
       layers_loaded: values.filter(l => l.status === 'ok').length,
       layers_skipped: values.filter(l => l.status === 'skipped').length,
@@ -221,7 +227,7 @@ class SynapseEngine {
     const safeProcessConfig = (processConfig && typeof processConfig === 'object') ? processConfig : {};
     const mergedConfig = { ...this.config, ...safeProcessConfig };
     const metrics = new PipelineMetrics();
-    metrics.totalStart = Date.now();
+    metrics.totalStart = process.hrtime.bigint();
 
     // 1. Calculate bracket
     const promptCount = (session && session.prompt_count) || 0;
@@ -232,7 +238,7 @@ class SynapseEngine {
 
     // Guard: no layer config (invalid bracket — should not happen)
     if (!layerConfig) {
-      metrics.totalEnd = Date.now();
+      metrics.totalEnd = process.hrtime.bigint();
       return { xml: '', metrics: metrics.getSummary() };
     }
 
@@ -249,8 +255,8 @@ class SynapseEngine {
         continue;
       }
 
-      // Check hard pipeline timeout
-      if (Date.now() - metrics.totalStart > PIPELINE_TIMEOUT_MS) {
+      // Check hard pipeline timeout (convert hrtime to ms for comparison)
+      if (Number(process.hrtime.bigint() - metrics.totalStart) / 1e6 > PIPELINE_TIMEOUT_MS) {
         // Log remaining layers as skipped
         const remaining = this.layers.slice(this.layers.indexOf(layer));
         for (const r of remaining) {
@@ -263,16 +269,14 @@ class SynapseEngine {
 
       // Execute layer via safe wrapper
       metrics.startLayer(layer.name);
-      const context = {
+      const context = buildLayerContext({
         prompt,
         session: session || {},
-        config: {
-          ...mergedConfig,
-          synapsePath: this.synapsePath,
-          manifest: mergedConfig.manifest || {},
-        },
+        config: mergedConfig,
+        synapsePath: this.synapsePath,
+        manifest: mergedConfig.manifest || {},
         previousLayers,
-      };
+      });
 
       const result = layer._safeProcess(context);
 
@@ -301,9 +305,12 @@ class SynapseEngine {
       }
     }
 
-    metrics.totalEnd = Date.now();
+    metrics.totalEnd = process.hrtime.bigint();
     const summary = metrics.getSummary();
 
+    // Persist hook metrics (fire-and-forget)
+    this._persistHookMetrics(summary, bracket, mergedConfig);
+
     // 4. Format output
     const xml = formatSynapseRules(
       results,
@@ -318,6 +325,52 @@ class SynapseEngine {
 
     return { xml, metrics: summary };
   }
+
+  /**
+   * Persist hook metrics to .synapse/metrics/hook-metrics.json (fire-and-forget).
+   * SYN-14: Includes hookBootMs from _hookBootTime passed via processConfig.
+   * @param {object} summary - Pipeline metrics summary
+   * @param {string} bracket - Context bracket
+   * @param {object} [config] - Merged config (may contain _hookBootTime bigint)
+   */
+  _persistHookMetrics(summary, bracket, config) {
+    try {
+      const synapsePath = this.synapsePath;
+      if (!synapsePath || !fs.existsSync(synapsePath)) return;
+      const metricsDir = path.join(synapsePath, 'metrics');
+      if (!fs.existsSync(metricsDir)) {
+        fs.mkdirSync(metricsDir, { recursive: true });
+      }
+      // SYN-14: Calculate hook boot time if _hookBootTime was passed
+      const hookBootTime = config && config._hookBootTime;
+      const hookBootMs = hookBootTime ? Number(process.hrtime.bigint() - hookBootTime) / 1e6 : 0;
+      const data = {
+        totalDuration: summary.total_ms,
+        hookBootMs,
+        bracket,
+        layersLoaded: summary.layers_loaded,
+        layersSkipped: summary.layers_skipped,
+        layersErrored: summary.layers_errored,
+        totalRules: summary.total_rules,
+        perLayer: {},
+        timestamp: new Date().toISOString(),
+      };
+      // Convert per_layer to serializable format (strip bigint start/end)
+      for (const [name, info] of Object.entries(summary.per_layer)) {
+        data.perLayer[name] = {
+          duration: info.duration || 0,
+          status: info.status || 'unknown',
+          rules: info.rules || 0,
+        };
+      }
+      fs.writeFileSync(
+        path.join(metricsDir, 'hook-metrics.json'),
+        JSON.stringify(data, null, 2), 'utf8',
+      );
+    } catch {
+      // Fire-and-forget: never block the hook pipeline
+    }
+  }
 }
 
 module.exports = {

package/.aios-core/core/synapse/runtime/hook-runtime.js

@@ -0,0 +1,60 @@
+'use strict';
+
+const path = require('path');
+const fs = require('fs');
+
+/**
+ * Resolve runtime dependencies for Synapse hook execution.
+ *
+ * @param {{cwd?: string, sessionId?: string}} input
+ * @returns {{
+ *   engine: import('../engine').SynapseEngine,
+ *   session: Object
+ * } | null}
+ */
+function resolveHookRuntime(input) {
+  const cwd = input && input.cwd;
+  const sessionId = input && input.sessionId;
+  if (!cwd || typeof cwd !== 'string') return null;
+
+  const synapsePath = path.join(cwd, '.synapse');
+  if (!fs.existsSync(synapsePath)) return null;
+
+  try {
+    const { loadSession } = require(
+      path.join(cwd, '.aios-core', 'core', 'synapse', 'session', 'session-manager.js'),
+    );
+    const { SynapseEngine } = require(
+      path.join(cwd, '.aios-core', 'core', 'synapse', 'engine.js'),
+    );
+
+    const sessionsDir = path.join(synapsePath, 'sessions');
+    const session = loadSession(sessionId, sessionsDir) || { prompt_count: 0 };
+    const engine = new SynapseEngine(synapsePath);
+
+    return { engine, session };
+  } catch (error) {
+    if (process.env.DEBUG === '1') {
+      console.error(`[hook-runtime] Failed to resolve runtime: ${error.message}`);
+    }
+    return null;
+  }
+}
+
+/**
+ * Normalize hook output payload shape.
+ * @param {string} xml
+ * @returns {{hookSpecificOutput: {additionalContext: string}}}
+ */
+function buildHookOutput(xml) {
+  return {
+    hookSpecificOutput: {
+      additionalContext: xml || '',
+    },
+  };
+}
+
+module.exports = {
+  resolveHookRuntime,
+  buildHookOutput,
+};

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

@@ -45,10 +45,12 @@ mindsLocation: outputs/minds
 ide:
   selected:
     - vscode
+    - codex
     - cursor
     - claude-code
   configs:
     vscode: true
+    codex: true
     cursor: true
     windsurf: false
     zed: false
@@ -307,6 +309,10 @@ ideSync:
       enabled: true
       path: .claude/commands/AIOS/agents
       format: full-markdown-yaml
+    codex:
+      enabled: true
+      path: .codex/agents
+      format: full-markdown-yaml
     cursor:
       enabled: true
       path: .cursor/rules/agents

package/.aios-core/data/agent-config-requirements.yaml

@@ -250,7 +250,7 @@ agents:
     files_loaded: []
     lazy_loading:
       agent_registry: true         # Load when validating/creating squads
-      expansion_pack_manifest: true # Load when managing expansion packs
+      squad_manifest: true # Load when managing squads
     performance_target: <150ms
 
   # ======================================================================
@@ -280,7 +280,7 @@ lazy_loading_strategy:
     expansionPacks:
       size: variable
       load_only_when: pack requested by user
-      description: Optional expansion packs
+      description: Optional squads
       fallback: []
 
     registry:

package/.aios-core/data/aios-kb.md

@@ -855,7 +855,7 @@ For full details, see `CONTRIBUTING.md`. Key points:
 
 ### What Are Expansion Packs?
 
-Expansion packs extend AIOS-Method beyond traditional software development into ANY domain. They provide specialized agent teams, templates, and workflows while keeping the core framework lean and focused on development.
+Squads extend AIOS-Method beyond traditional software development into ANY domain. They provide specialized agent teams, templates, and workflows while keeping the core framework lean and focused on development.
 
 ### Why Use Expansion Packs?
 
@@ -883,7 +883,7 @@ Expansion packs extend AIOS-Method beyond traditional software development into
 
 **Specialty Packs**:
 
-- **Expansion Creator**: Tools to build your own expansion packs
+- **Expansion Creator**: Tools to build your own squads
 - **RPG Game Master**: Tabletop gaming assistance
 - **Life Event Planning**: Wedding planners, event coordinators
 - **Scientific Research**: Literature reviewers, methodology designers
@@ -896,7 +896,7 @@ Expansion packs extend AIOS-Method beyond traditional software development into
 
    ```bash
    npx @synkra/aios-core install
-   # Select "Install expansion pack" option
+   # Select "Install squad" option
    ```
 
 4. **Use in Your Workflow**: Installed packs integrate seamlessly with existing agents
@@ -910,7 +910,7 @@ Use the **expansion-creator** pack to build your own:
 3. **Build Resources**: Tasks, templates, checklists for your domain
 4. **Test & Share**: Validate with real use cases, share with community
 
-**Key Principle**: Expansion packs democratize expertise by making specialized knowledge accessible through AI agents.
+**Key Principle**: Squads democratize expertise by making specialized knowledge accessible through AI agents.
 
 ## Getting Help
 

package/.aios-core/data/entity-registry.yaml

@@ -1,6 +1,6 @@
 metadata:
   version: 1.0.0
-  lastUpdated: '2026-02-12T13:07:01.327Z'
+  lastUpdated: '2026-02-14T16:25:15.484Z'
   entityCount: 487
   checksumAlgorithm: sha256
 entities:
@@ -5618,8 +5618,8 @@ entities:
         score: 0.7
         constraints: []
         extensionPoints: []
-      checksum: sha256:11c9a7f19044ed38df9e47d26feb1ba5346efd15bd4ec856c871722386575f1b
-      lastVerified: '2026-02-10T14:51:55.740Z'
+      checksum: sha256:2a66e09c4f778c223d6a00e85738abe26547bd6034dd6718d5ec352f57c65898
+      lastVerified: '2026-02-14T16:25:15.483Z'
     usage-tracker:
       path: .aios-core/development/scripts/usage-tracker.js
       type: script
@@ -8246,8 +8246,8 @@ entities:
         score: 0.4
         constraints: []
         extensionPoints: []
-      checksum: sha256:0e59a35fb77eaf7e757ecdc283381d8e6d20e9d24844280a4605af316f152f5e
-      lastVerified: '2026-02-09T00:54:48.061Z'
+      checksum: sha256:6d87ec21d32acff1ba9b9d13025118c106ce6db59c1339c3a6ef4b2a02fd7f52
+      lastVerified: '2026-02-14T16:25:15.482Z'
     core-config:
       path: .aios-core/core-config.yaml
       type: module

package/.aios-core/development/agents/architect.md

@@ -105,7 +105,7 @@ persona:
       - Integration patterns (event-driven, messaging, webhooks)
       - Performance optimization (across all layers)
 
-    delegate_to_data_architect:
+    delegate_to_data_engineer:
       when:
         - Database schema design (tables, relationships, indexes)
         - Query optimization and performance tuning
@@ -123,9 +123,9 @@ persona:
       collaboration_pattern: |
         When user asks data-related questions:
         1. For "which database?" → @architect answers from system perspective
-        2. For "design schema" → Delegate to @data-architect
-        3. For "optimize queries" → Delegate to @data-architect
-        4. For data layer integration → @architect designs, @data-architect provides schema
+        2. For "design schema" → Delegate to @data-engineer
+        3. For "optimize queries" → Delegate to @data-engineer
+        4. For data layer integration → @architect designs, @data-engineer provides schema
 
     delegate_to_github_devops:
       when:
@@ -257,7 +257,7 @@ dependencies:
     - exa # Research technologies and best practices
     - context7 # Look up library documentation and technical references
     - git # Read-only: status, log, diff (NO PUSH - use @github-devops)
-    - supabase-cli # High-level database architecture (schema design → @data-architect)
+    - supabase-cli # High-level database architecture (schema design → @data-engineer)
     - railway-cli # Infrastructure planning and deployment
     - coderabbit # Automated code review for architectural patterns and security
 
@@ -402,7 +402,7 @@ Type `*help` to see all commands, or `*yolo` to skip confirmations.
 
 **I collaborate with:**
 
-- **@db-sage (Dara):** For database schema design and query optimization
+- **@data-engineer (Dara):** For database schema design and query optimization
 - **@ux-design-expert (Uma):** For frontend architecture and user flows
 - **@pm (Morgan):** Receives requirements and strategic direction from
 
@@ -412,7 +412,7 @@ Type `*help` to see all commands, or `*yolo` to skip confirmations.
 
 **When to use others:**
 
-- Database design → Use @db-sage
+- Database design → Use @data-engineer
 - UX/UI design → Use @ux-design-expert
 - Code implementation → Use @dev
 - Push operations → Use @github-devops
@@ -439,21 +439,21 @@ Type `*help` to see all commands, or `*yolo` to skip confirmations.
 
 1. **Requirements analysis** → Review PRD and constraints
 2. **Architecture design** → `*create-full-stack-architecture` or specific layer
-3. **Collaboration** → Coordinate with @db-sage (database) and @ux-design-expert (frontend)
+3. **Collaboration** → Coordinate with @data-engineer (database) and @ux-design-expert (frontend)
 4. **Documentation** → `*document-project` for comprehensive docs
 5. **Handoff** → Provide architecture to @dev for implementation
 
 ### Common Pitfalls
 
 - ❌ Designing without understanding NFRs (scalability, security)
-- ❌ Not consulting @db-sage for data layer
+- ❌ Not consulting @data-engineer for data layer
 - ❌ Over-engineering for current requirements
 - ❌ Skipping architecture checklists
 - ❌ Not considering brownfield constraints
 
 ### Related Agents
 
-- **@db-sage (Dara)** - Database architecture
+- **@data-engineer (Dara)** - Database architecture
 - **@ux-design-expert (Uma)** - Frontend architecture
 - **@pm (Morgan)** - Receives requirements from
 

package/.aios-core/development/agents/devops.md

@@ -129,56 +129,99 @@ persona:
 
 # All commands require * prefix when used (e.g., *help)
 commands:
-  # Core Commands
-  - help: Show all available commands with descriptions
-  - detect-repo: Detect repository context (framework-dev vs project-dev)
-
-  # Quality & Push
-  - version-check: Analyze version and recommend next
-  - pre-push: Run all quality checks before push
-  - push: Execute git push after quality gates pass
-
-  # GitHub Operations
-  - create-pr: Create pull request from current branch
-  - configure-ci: Setup/update GitHub Actions workflows
-  - release: Create versioned release with changelog
-
-  # Repository Management
-  - cleanup: Identify and remove stale branches/files
-  - init-project-status: Initialize dynamic project status tracking (Story 6.1.2.4)
-
-  # Environment Setup (Greenfield Phase 0)
-  - environment-bootstrap: Complete environment setup for new projects (CLIs, auth, Git/GitHub)
-  - setup-github: Configure DevOps infrastructure for user projects (workflows, CodeRabbit, branch protection, secrets) [Story 5.10]
-
-  # MCP Management (via Docker Gateway) [Story 6.14]
-  - search-mcp: Search available MCPs in Docker MCP Toolkit catalog
-  - add-mcp: Add MCP server to Docker MCP Toolkit
-  - list-mcps: List currently enabled MCPs and their tools
-  - remove-mcp: Remove MCP server from Docker MCP Toolkit
-  - setup-mcp-docker: Initial Docker MCP Toolkit configuration [Story 5.11]
-
-  # Documentation Quality
-  - check-docs: Verify documentation links integrity (broken, incorrect markings)
-
-  # Worktree Management (Story 1.3-1.4 - ADE Infrastructure)
-  - create-worktree: Create isolated worktree for story development
-  - list-worktrees: List all active worktrees with status
-  - remove-worktree: Remove worktree (with safety checks)
-  - cleanup-worktrees: Remove all stale worktrees (> 30 days)
-  - merge-worktree: Merge worktree branch back to base
-
-  # Migration Management (Epic 2 - V2→V3 Migration)
-  - inventory-assets: Generate migration inventory from V2 assets
-  - analyze-paths: Analyze path dependencies and migration impact
-  - migrate-agent: Migrate single agent from V2 to V3 format
-  - migrate-batch: Batch migrate all agents with validation
-
-  # Utilities
-  - session-info: Show current session details (agent history, commands)
-  - guide: Show comprehensive usage guide for this agent
-  - yolo: 'Toggle permission mode (cycle: ask > auto > explore)'
-  - exit: Exit DevOps mode
+  - name: help
+    visibility: [full, quick, key]
+    description: 'Show all available commands with descriptions'
+  - name: detect-repo
+    visibility: [full, quick, key]
+    description: 'Detect repository context (framework-dev vs project-dev)'
+  - name: version-check
+    visibility: [full, quick, key]
+    description: 'Analyze version and recommend next'
+  - name: pre-push
+    visibility: [full, quick, key]
+    description: 'Run all quality checks before push'
+  - name: push
+    visibility: [full, quick, key]
+    description: 'Execute git push after quality gates pass'
+  - name: create-pr
+    visibility: [full, quick, key]
+    description: 'Create pull request from current branch'
+  - name: configure-ci
+    visibility: [full, quick]
+    description: 'Setup/update GitHub Actions workflows'
+  - name: release
+    visibility: [full, quick]
+    description: 'Create versioned release with changelog'
+  - name: cleanup
+    visibility: [full, quick]
+    description: 'Identify and remove stale branches/files'
+  - name: init-project-status
+    visibility: [full]
+    description: 'Initialize dynamic project status tracking (Story 6.1.2.4)'
+  - name: environment-bootstrap
+    visibility: [full]
+    description: 'Complete environment setup for new projects (CLIs, auth, Git/GitHub)'
+  - name: setup-github
+    visibility: [full]
+    description: 'Configure DevOps infrastructure for user projects (workflows, CodeRabbit, branch protection, secrets) [Story 5.10]'
+  - name: search-mcp
+    visibility: [full]
+    description: 'Search available MCPs in Docker MCP Toolkit catalog'
+  - name: add-mcp
+    visibility: [full]
+    description: 'Add MCP server to Docker MCP Toolkit'
+  - name: list-mcps
+    visibility: [full]
+    description: 'List currently enabled MCPs and their tools'
+  - name: remove-mcp
+    visibility: [full]
+    description: 'Remove MCP server from Docker MCP Toolkit'
+  - name: setup-mcp-docker
+    visibility: [full]
+    description: 'Initial Docker MCP Toolkit configuration [Story 5.11]'
+  - name: check-docs
+    visibility: [full, quick]
+    description: 'Verify documentation links integrity (broken, incorrect markings)'
+  - name: create-worktree
+    visibility: [full]
+    description: 'Create isolated worktree for story development'
+  - name: list-worktrees
+    visibility: [full]
+    description: 'List all active worktrees with status'
+  - name: remove-worktree
+    visibility: [full]
+    description: 'Remove worktree (with safety checks)'
+  - name: cleanup-worktrees
+    visibility: [full]
+    description: 'Remove all stale worktrees (> 30 days)'
+  - name: merge-worktree
+    visibility: [full]
+    description: 'Merge worktree branch back to base'
+  - name: inventory-assets
+    visibility: [full]
+    description: 'Generate migration inventory from V2 assets'
+  - name: analyze-paths
+    visibility: [full]
+    description: 'Analyze path dependencies and migration impact'
+  - name: migrate-agent
+    visibility: [full]
+    description: 'Migrate single agent from V2 to V3 format'
+  - name: migrate-batch
+    visibility: [full]
+    description: 'Batch migrate all agents with validation'
+  - name: session-info
+    visibility: [full, quick]
+    description: 'Show current session details (agent history, commands)'
+  - name: guide
+    visibility: [full, quick, key]
+    description: 'Show comprehensive usage guide for this agent'
+  - name: yolo
+    visibility: [full, quick, key]
+    description: 'Toggle permission mode (cycle: ask > auto > explore)'
+  - name: exit
+    visibility: [full, quick, key]
+    description: 'Exit DevOps mode'
 
 dependencies:
   tasks: