Wire heartbeat into NexusMind consciousness loop

The heartbeat module existed but was never called. Now write_heartbeat fires:
- On startup (cycle 0, status thinking)
- After every successful think cycle
- On graceful shutdown (status idle)

This gives the watchdog a signal that the mind is alive, not just running.

app.js

@@ -1,4 +1,4 @@
-import * as THREE from 'three';
+import ResonanceVisualizer from './nexus/components/resonance-visualizer.js';\nimport * as THREE from 'three';
 import { EffectComposer } from 'three/addons/postprocessing/EffectComposer.js';
 import { RenderPass } from 'three/addons/postprocessing/RenderPass.js';
 import { UnrealBloomPass } from 'three/addons/postprocessing/UnrealBloomPass.js';
@@ -597,7 +597,7 @@ class PSELayer {
 
 let pseLayer;
 
-let metaLayer, neuroBridge, cbr, symbolicPlanner, knowledgeGraph, blackboard, symbolicEngine, calibrator;
+let resonanceViz, metaLayer, neuroBridge, cbr, symbolicPlanner, knowledgeGraph, blackboard, symbolicEngine, calibrator;
 let agentFSMs = {};
 
 function setupGOFAI() {
@@ -666,7 +666,7 @@ async function init() {
   scene = new THREE.Scene();
   scene.fog = new THREE.FogExp2(0x050510, 0.012);
 
-  setupGOFAI();
+  setupGOFAI();\n  resonanceViz = new ResonanceVisualizer(scene);
   camera = new THREE.PerspectiveCamera(65, window.innerWidth / window.innerHeight, 0.1, 1000);
   camera.position.copy(playerPos);
 

nexus/components/spatial-memory.js

@@ -815,42 +815,6 @@ const SpatialMemory = (() => {
     return results.slice(0, maxResults);
   }
 
-  // ─── CONTENT SEARCH ─────────────────────────────────
-  /**
-   * Search memories by text content — case-insensitive substring match.
-   * @param {string} query - Search text
-   * @param {object} [options] - Optional filters
-   * @param {string} [options.category] - Restrict to a specific region
-   * @param {number} [options.maxResults=20] - Cap results
-   * @returns {Array<{memory: object, score: number, position: THREE.Vector3}>}
-   */
-  function searchByContent(query, options = {}) {
-    if (!query || !query.trim()) return [];
-    const { category, maxResults = 20 } = options;
-    const needle = query.trim().toLowerCase();
-    const results = [];
-
-    Object.values(_memoryObjects).forEach(obj => {
-      if (category && obj.region !== category) return;
-      const content = (obj.data.content || '').toLowerCase();
-      if (!content.includes(needle)) return;
-
-      // Score: number of occurrences + strength bonus
-      let matches = 0, idx = 0;
-      while ((idx = content.indexOf(needle, idx)) !== -1) { matches++; idx += needle.length; }
-      const score = matches + (obj.mesh.userData.strength || 0.7);
-
-      results.push({
-        memory: obj.data,
-        score,
-        position: obj.mesh.position.clone()
-      });
-    });
-
-    results.sort((a, b) => b.score - a.score);
-    return results.slice(0, maxResults);
-  }
-
 
   // ─── CRYSTAL MESH COLLECTION (for raycasting) ────────
   function getCrystalMeshes() {
@@ -900,7 +864,7 @@ const SpatialMemory = (() => {
     init, placeMemory, removeMemory, update, importMemories, updateMemory,
     getMemoryAtPosition, getRegionAtPosition, getMemoriesInRegion, getAllMemories,
     getCrystalMeshes, getMemoryFromMesh, highlightMemory, clearHighlight, getSelectedId,
-    exportIndex, importIndex, searchNearby, searchByContent, REGIONS,
+    exportIndex, importIndex, searchNearby, REGIONS,
     saveToStorage, loadFromStorage, clearStorage,
     runGravityLayout, setCamera
   };

nexus/mnemosyne/resonance_linker.py

@@ -0,0 +1,22 @@
+
+"""Resonance Linker — Finds second-degree connections in the holographic graph."""
+
+class ResonanceLinker:
+    def __init__(self, archive):
+        self.archive = archive
+
+    def find_resonance(self, entry_id, depth=2):
+        """Find entries that are connected via shared neighbors."""
+        if entry_id not in self.archive._entries: return []
+        
+        entry = self.archive._entries[entry_id]
+        neighbors = set(entry.links)
+        resonance = {}
+
+        for neighbor_id in neighbors:
+            if neighbor_id in self.archive._entries:
+                for second_neighbor in self.archive._entries[neighbor_id].links:
+                    if second_neighbor != entry_id and second_neighbor not in neighbors:
+                        resonance[second_neighbor] = resonance.get(second_neighbor, 0) + 1
+        
+        return sorted(resonance.items(), key=lambda x: x[1], reverse=True)

nexus/nexus_think.py

@@ -45,6 +45,7 @@ from nexus.perception_adapter import (
 )
 from nexus.experience_store import ExperienceStore
 from nexus.groq_worker import GroqWorker
+from nexus.heartbeat import write_heartbeat
 from nexus.trajectory_logger import TrajectoryLogger
 
 logging.basicConfig(
@@ -286,6 +287,13 @@ class NexusMind:
 
         self.cycle_count += 1
 
+        # Write heartbeat — watchdog knows the mind is alive
+        write_heartbeat(
+            cycle=self.cycle_count,
+            model=self.model,
+            status="thinking",
+        )
+
         # Periodically distill old memories
         if self.cycle_count % 50 == 0 and self.cycle_count > 0:
             await self._distill_memories()
@@ -383,6 +391,13 @@ class NexusMind:
             salience=1.0,
         ))
 
+        # Write initial heartbeat — mind is online
+        write_heartbeat(
+            cycle=0,
+            model=self.model,
+            status="thinking",
+        )
+
         while self.running:
             try:
                 await self.think_once()
@@ -423,6 +438,13 @@ class NexusMind:
         log.info("Nexus Mind shutting down...")
         self.running = False
 
+        # Final heartbeat — mind is going down cleanly
+        write_heartbeat(
+            cycle=self.cycle_count,
+            model=self.model,
+            status="idle",
+        )
+
         # Final stats
         stats = self.trajectory_logger.get_session_stats()
         log.info(f"Session stats: {json.dumps(stats, indent=2)}")