aios-core 4.0.4 → 4.2.0

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

@@ -1,7 +1,7 @@
 metadata:
   version: 1.0.0
-  lastUpdated: '2026-02-12T13:07:01.327Z'
-  entityCount: 487
+  lastUpdated: '2026-02-15T23:35:00.000Z'
+  entityCount: 498
   checksumAlgorithm: sha256
 entities:
   tasks:
@@ -1641,7 +1641,8 @@ entities:
         - quality
         - gate
         - pre-push-quality-gate.md
-      usedBy: []
+      usedBy:
+        - publish-npm
       dependencies:
         - repository-detector
         - N/A
@@ -2758,7 +2759,8 @@ entities:
         - manage
         - software
         - releases
-      usedBy: []
+      usedBy:
+        - publish-npm
       dependencies:
         - package
         - N/A
@@ -3887,6 +3889,27 @@ entities:
         extensionPoints: []
       checksum: sha256:093a9ee73e79ec5682d9161648f36710d635a0a7b074d45f4036c782bbc72bb2
       lastVerified: '2026-02-10T15:31:01.205Z'
+    publish-npm:
+      path: .aios-core/development/tasks/publish-npm.md
+      type: task
+      purpose: 'Safe, validated npm publishing using a two-phase release strategy:'
+      keywords:
+        - publish
+        - npm
+        - publishing
+        - 'pipeline:'
+        - preview
+        - latest
+      usedBy: []
+      dependencies:
+        - release-management
+        - github-devops-pre-push-quality-gate
+      adaptability:
+        score: 0.8
+        constraints: []
+        extensionPoints: []
+      checksum: sha256:f7a0bb8fed5663c88ad691b8871fdf7a861b6a7c02599f0c2db3eb9393d353c8
+      lastVerified: '2026-02-15T20:39:45.236Z'
   templates:
     activation-instructions-inline-greeting:
       path: .aios-core/product/templates/activation-instructions-inline-greeting.yaml
@@ -5618,8 +5641,8 @@ entities:
         score: 0.7
         constraints: []
         extensionPoints: []
-      checksum: sha256:11c9a7f19044ed38df9e47d26feb1ba5346efd15bd4ec856c871722386575f1b
-      lastVerified: '2026-02-10T14:51:55.740Z'
+      checksum: sha256:dd1ad8050ac6ea04ff634434be9b97f67239ee0a7342d669bc5618eb2b7a7f5b
+      lastVerified: '2026-02-15T20:39:45.236Z'
     usage-tracker:
       path: .aios-core/development/scripts/usage-tracker.js
       type: script
@@ -6506,14 +6529,15 @@ entities:
       usedBy: []
       dependencies:
         - context-tracker
+        - context-builder
         - formatter
         - memory-bridge
       adaptability:
         score: 0.4
         constraints: []
         extensionPoints: []
-      checksum: sha256:90572bd719491e1f57bc43cb29179ad8de34db9d752fff54bf8638d9fcf22bc7
-      lastVerified: '2026-02-12T13:07:01.326Z'
+      checksum: sha256:65e9c48d8ba7991fcd32bb1ea0bd087ce6d709ebf7f5bc4fd4b2e947ee5ddf0f
+      lastVerified: '2026-02-15T20:39:45.235Z'
     ideation-engine:
       path: .aios-core/core/ideation/ideation-engine.js
       type: module
@@ -8246,8 +8270,8 @@ 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
@@ -8491,6 +8515,137 @@ entities:
         extensionPoints: []
       checksum: sha256:3b927daec51d0a791f3fe4ef9aafc362773450e7cf50eb4b6d8ae9011d70df9a
       lastVerified: '2026-02-12T12:53:14.532Z'
+    consistency-collector:
+      path: .aios-core/core/synapse/diagnostics/collectors/consistency-collector.js
+      type: module
+      purpose: Entity at .aios-core\core\synapse\diagnostics\collectors\consistency-collector.js
+      keywords:
+        - consistency
+        - collector
+      usedBy: []
+      dependencies:
+        - safe-read-json
+      adaptability:
+        score: 0.4
+        constraints: []
+        extensionPoints: []
+      checksum: sha256:65f4255f87c9900400649dc8b9aedaac4851b5939d93e127778bd93cee99db12
+      lastVerified: '2026-02-15T20:39:45.229Z'
+    hook-collector:
+      path: .aios-core/core/synapse/diagnostics/collectors/hook-collector.js
+      type: module
+      purpose: Entity at .aios-core\core\synapse\diagnostics\collectors\hook-collector.js
+      keywords:
+        - hook
+        - collector
+      usedBy: []
+      dependencies: []
+      adaptability:
+        score: 0.4
+        constraints: []
+        extensionPoints: []
+      checksum: sha256:9cd342cc0c2253296f931a977b20408370c1e1bebe02a22a757418d4d0630884
+      lastVerified: '2026-02-15T20:39:45.231Z'
+    output-analyzer:
+      path: .aios-core/core/synapse/diagnostics/collectors/output-analyzer.js
+      type: module
+      purpose: string }>}
+      keywords:
+        - output
+        - analyzer
+      usedBy: []
+      dependencies:
+        - safe-read-json
+      adaptability:
+        score: 0.4
+        constraints: []
+        extensionPoints: []
+      checksum: sha256:e6846b1aba0a6cba17c297a871861d4f8199d7500220bff296a6a3291e32493e
+      lastVerified: '2026-02-15T20:39:45.232Z'
+    quality-collector:
+      path: .aios-core/core/synapse/diagnostics/collectors/quality-collector.js
+      type: module
+      purpose: Entity at .aios-core\core\synapse\diagnostics\collectors\quality-collector.js
+      keywords:
+        - quality
+        - collector
+      usedBy: []
+      dependencies:
+        - safe-read-json
+      adaptability:
+        score: 0.4
+        constraints: []
+        extensionPoints: []
+      checksum: sha256:30ae299eab6d569d09afe3530a5b2f1ff35ef75366a1ab56a9e2a57d39d3611c
+      lastVerified: '2026-02-15T20:39:45.232Z'
+    relevance-matrix:
+      path: .aios-core/core/synapse/diagnostics/collectors/relevance-matrix.js
+      type: module
+      purpose: Entity at .aios-core\core\synapse\diagnostics\collectors\relevance-matrix.js
+      keywords:
+        - relevance
+        - matrix
+      usedBy: []
+      dependencies:
+        - safe-read-json
+      adaptability:
+        score: 0.4
+        constraints: []
+        extensionPoints: []
+      checksum: sha256:f92c4f7061dc82eed4310a27b69eade33d3015f9beb1bed688601a2dccbad22e
+      lastVerified: '2026-02-15T20:39:45.233Z'
+    safe-read-json:
+      path: .aios-core/core/synapse/diagnostics/collectors/safe-read-json.js
+      type: module
+      purpose: Entity at .aios-core\core\synapse\diagnostics\collectors\safe-read-json.js
+      keywords:
+        - safe
+        - read
+        - json
+      usedBy:
+        - consistency-collector
+        - output-analyzer
+        - quality-collector
+        - relevance-matrix
+        - timing-collector
+      dependencies: []
+      adaptability:
+        score: 0.4
+        constraints: []
+        extensionPoints: []
+      checksum: sha256:dc7bcd13779207ad67b1c3929b7e1e0ccfa3563f3458c20cad28cb1922e9a74c
+      lastVerified: '2026-02-15T20:39:45.233Z'
+    timing-collector:
+      path: .aios-core/core/synapse/diagnostics/collectors/timing-collector.js
+      type: module
+      purpose: Entity at .aios-core\core\synapse\diagnostics\collectors\timing-collector.js
+      keywords:
+        - timing
+        - collector
+      usedBy: []
+      dependencies:
+        - safe-read-json
+      adaptability:
+        score: 0.4
+        constraints: []
+        extensionPoints: []
+      checksum: sha256:2523ce93f863a28f798d992c4f2fab041c91a09413b3186fd290e6035b391587
+      lastVerified: '2026-02-15T20:39:45.234Z'
+    report-formatter:
+      path: .aios-core/core/synapse/diagnostics/report-formatter.js
+      type: module
+      purpose: Entity at .aios-core\core\synapse\diagnostics\report-formatter.js
+      keywords:
+        - report
+        - formatter
+      usedBy: []
+      dependencies: []
+      adaptability:
+        score: 0.4
+        constraints: []
+        extensionPoints: []
+      checksum: sha256:33faf5820fbe2559e425707ff6ce19ce20b046d7222814d4040e739317ff998e
+      lastVerified: '2026-02-15T20:39:45.235Z'
   agents:
     aios-master:
       path: .aios-core/development/agents/aios-master.md
@@ -8864,6 +9019,51 @@ entities:
         extensionPoints: []
       checksum: sha256:1a7262912c8c8e264d307f0d38a1109bdb2b9bff9ea7d8855c768835201aa59b
       lastVerified: '2026-02-08T13:33:24.397Z'
+    code-intel-health-check:
+      path: scripts/code-intel-health-check.js
+      type: script
+      purpose: Health check and validation for Code Graph MCP provider. Outputs structured JSON with status, tools availability, and response time.
+      keywords:
+        - code-intelligence
+        - health-check
+        - mcp
+        - code-graph
+        - provider
+        - validation
+      usedBy:
+        - NOG-1
+      dependencies:
+        - code-graph-mcp
+      adaptability:
+        score: 0.8
+        constraints:
+          - Requires code-graph-mcp pip package installed
+        extensionPoints:
+          - Additional provider checks can be added
+      story: NOG-0
+      lastVerified: '2026-02-15T23:30:00.000Z'
+    code-graph-mcp-setup-guide:
+      path: docs/guides/code-graph-mcp-setup.md
+      type: guide
+      purpose: Setup guide for Code Graph MCP installation, configuration, verification and troubleshooting.
+      keywords:
+        - code-graph
+        - mcp
+        - setup
+        - installation
+        - troubleshooting
+        - guide
+      usedBy:
+        - NOG-0
+        - NOG-1
+      dependencies: []
+      adaptability:
+        score: 0.9
+        constraints: []
+        extensionPoints:
+          - Additional provider setup guides can follow same pattern
+      story: NOG-0
+      lastVerified: '2026-02-15T23:30:00.000Z'
 categories:
   - id: tasks
     description: Executable task workflows for agent operations

package/.aios-core/data/registry-update-log.jsonl

@@ -111,3 +111,55 @@
 {"timestamp":"2026-02-12T13:07:21.219Z","action":"change","path":".aios-core/core/synapse/engine.js","trigger":"watcher"}
 {"timestamp":"2026-02-12T13:07:21.219Z","action":"change","path":".aios-core/core/synapse/memory/memory-bridge.js","trigger":"watcher"}
 {"timestamp":"2026-02-13T00:49:51.580Z","action":"change","path":".aios-core/development/scripts/unified-activation-pipeline.js","trigger":"watcher"}
+{"timestamp":"2026-02-13T16:52:52.699Z","action":"add","path":".aios-core/core/synapse/diagnostics/collectors/hook-collector.js","trigger":"watcher"}
+{"timestamp":"2026-02-13T16:52:52.700Z","action":"add","path":".aios-core/core/synapse/diagnostics/collectors/manifest-collector.js","trigger":"watcher"}
+{"timestamp":"2026-02-13T16:52:52.701Z","action":"add","path":".aios-core/core/synapse/diagnostics/collectors/pipeline-collector.js","trigger":"watcher"}
+{"timestamp":"2026-02-13T16:52:52.701Z","action":"add","path":".aios-core/core/synapse/diagnostics/collectors/session-collector.js","trigger":"watcher"}
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