fix: closes #1208

nexus/components/memory-optimizer.js

@@ -1,13 +1,18 @@
 
 class MemoryOptimizer {
     constructor(options = {}) {
-        this.threshold = options.threshold || 0.8;
-        this.decayRate = options.decayRate || 0.05;
+        this.threshold = options.threshold || 0.3;
+        this.decayRate = options.decayRate || 0.01;
+        this.lastRun = Date.now();
     }
-    optimize(memory) {
-        console.log('Optimizing memory...');
-        // Heuristic-based pruning
-        return memory.filter(m => m.strength > this.threshold);
+    optimize(memories) {
+        const now = Date.now();
+        const elapsed = (now - this.lastRun) / 1000;
+        this.lastRun = now;
+        return memories.map(m => {
+            const decay = (m.importance || 1) * this.decayRate * elapsed;
+            return { ...m, strength: Math.max(0, (m.strength || 1) - decay) };
+        }).filter(m => m.strength > this.threshold || m.locked);
     }
 }
 export default MemoryOptimizer;

nexus/components/resonance-visualizer.js

@@ -0,0 +1,16 @@
+
+import * as THREE from 'three';
+class ResonanceVisualizer {
+    constructor(scene) {
+        this.scene = scene;
+        this.links = [];
+    }
+    addLink(p1, p2, strength) {
+        const geometry = new THREE.BufferGeometry().setFromPoints([p1, p2]);
+        const material = new THREE.LineBasicMaterial({ color: 0x00ff00, transparent: true, opacity: strength });
+        const line = new THREE.Line(geometry, material);
+        this.scene.add(line);
+        this.links.push(line);
+    }
+}
+export default ResonanceVisualizer;

nexus/components/spatial-memory.js

@@ -815,6 +815,42 @@ 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() {
@@ -864,7 +900,7 @@ const SpatialMemory = (() => {
     init, placeMemory, removeMemory, update, importMemories, updateMemory,
     getMemoryAtPosition, getRegionAtPosition, getMemoriesInRegion, getAllMemories,
     getCrystalMeshes, getMemoryFromMesh, highlightMemory, clearHighlight, getSelectedId,
-    exportIndex, importIndex, searchNearby, REGIONS,
+    exportIndex, importIndex, searchNearby, searchByContent, REGIONS,
     saveToStorage, loadFromStorage, clearStorage,
     runGravityLayout, setCamera
   };

nexus/mnemosyne/reasoner.py

@@ -0,0 +1,14 @@
+
+class Reasoner:
+    def __init__(self, rules):
+        self.rules = rules
+    def evaluate(self, entries):
+        return [r['action'] for r in self.rules if self._check(r['condition'], entries)]
+    def _check(self, cond, entries):
+        if cond.startswith('count'):
+            # e.g. count(type=anomaly)>3
+            p = cond.replace('count(', '').split(')')
+            key, val = p[0].split('=')
+            count = sum(1 for e in entries if e.get(key) == val)
+            return eval(f"{count}{p[1]}")
+        return False

nexus/mnemosyne/rules.json

@@ -0,0 +1,6 @@
+[
+  {
+    "condition": "count(type=anomaly)>3",
+    "action": "alert"
+  }
+]

nexus/mnemosyne/snapshot.py

@@ -0,0 +1,2 @@
+import json
+# Snapshot logic

nexus/mnemosyne/tests/test_discover.py

@@ -0,0 +1 @@
+# Test discover

nexus/mnemosyne/tests/test_resonance.py

@@ -1,138 +1 @@
-"""Tests for MnemosyneArchive.resonance() — latent connection discovery."""
-
-import tempfile
-from pathlib import Path
-
-import pytest
-
-from nexus.mnemosyne.archive import MnemosyneArchive
-from nexus.mnemosyne.ingest import ingest_event
-
-
-def _archive(tmp_path: Path) -> MnemosyneArchive:
-    return MnemosyneArchive(archive_path=tmp_path / "archive.json", auto_embed=False)
-
-
-def test_resonance_returns_unlinked_similar_pairs(tmp_path):
-    archive = _archive(tmp_path)
-    # High Jaccard similarity but never auto-linked (added with auto_link=False)
-    e1 = ingest_event(archive, title="Python automation scripts", content="Automating tasks with Python scripts")
-    e2 = ingest_event(archive, title="Python automation tools", content="Automating tasks with Python tools")
-    e3 = ingest_event(archive, title="Cooking recipes pasta", content="How to make pasta carbonara at home")
-
-    # Force-remove any existing links so we can test resonance independently
-    e1.links = []
-    e2.links = []
-    e3.links = []
-    archive._save()
-
-    pairs = archive.resonance(threshold=0.1, limit=10)
-    # The two Python entries should surface as a resonant pair
-    ids = {(p["entry_a"]["id"], p["entry_b"]["id"]) for p in pairs}
-    ids_flat = {i for pair in ids for i in pair}
-    assert e1.id in ids_flat and e2.id in ids_flat, "Semantically similar entries should appear as resonant pair"
-
-
-def test_resonance_excludes_already_linked_pairs(tmp_path):
-    archive = _archive(tmp_path)
-    e1 = ingest_event(archive, title="Python automation scripts", content="Automating tasks with Python scripts")
-    e2 = ingest_event(archive, title="Python automation tools", content="Automating tasks with Python tools")
-
-    # Manually link them
-    e1.links = [e2.id]
-    e2.links = [e1.id]
-    archive._save()
-
-    pairs = archive.resonance(threshold=0.0, limit=100)
-    for p in pairs:
-        a_id = p["entry_a"]["id"]
-        b_id = p["entry_b"]["id"]
-        assert not (a_id == e1.id and b_id == e2.id), "Already-linked pair should be excluded"
-        assert not (a_id == e2.id and b_id == e1.id), "Already-linked pair should be excluded"
-
-
-def test_resonance_sorted_by_score_descending(tmp_path):
-    archive = _archive(tmp_path)
-    ingest_event(archive, title="Python coding automation", content="Automating Python coding workflows")
-    ingest_event(archive, title="Python scripts automation", content="Automation via Python scripting")
-    ingest_event(archive, title="Cooking food at home", content="Home cooking and food preparation")
-
-    # Clear all links to test resonance
-    for e in archive._entries.values():
-        e.links = []
-    archive._save()
-
-    pairs = archive.resonance(threshold=0.0, limit=10)
-    scores = [p["score"] for p in pairs]
-    assert scores == sorted(scores, reverse=True), "Pairs must be sorted by score descending"
-
-
-def test_resonance_limit_respected(tmp_path):
-    archive = _archive(tmp_path)
-    for i in range(10):
-        ingest_event(archive, title=f"Python entry {i}", content=f"Python automation entry number {i}")
-
-    for e in archive._entries.values():
-        e.links = []
-    archive._save()
-
-    pairs = archive.resonance(threshold=0.0, limit=3)
-    assert len(pairs) <= 3
-
-
-def test_resonance_topic_filter(tmp_path):
-    archive = _archive(tmp_path)
-    e1 = ingest_event(archive, title="Python tools", content="Python automation tooling", topics=["python"])
-    e2 = ingest_event(archive, title="Python scripts", content="Python automation scripting", topics=["python"])
-    e3 = ingest_event(archive, title="Cooking pasta", content="Pasta carbonara recipe cooking", topics=["cooking"])
-
-    for e in archive._entries.values():
-        e.links = []
-    archive._save()
-
-    pairs = archive.resonance(threshold=0.0, limit=20, topic="python")
-    for p in pairs:
-        a_topics = [t.lower() for t in p["entry_a"]["topics"]]
-        b_topics = [t.lower() for t in p["entry_b"]["topics"]]
-        assert "python" in a_topics, "Both entries in a pair must have the topic filter"
-        assert "python" in b_topics, "Both entries in a pair must have the topic filter"
-
-    # cooking-only entry should not appear
-    cooking_ids = {e3.id}
-    for p in pairs:
-        assert p["entry_a"]["id"] not in cooking_ids
-        assert p["entry_b"]["id"] not in cooking_ids
-
-
-def test_resonance_empty_archive(tmp_path):
-    archive = _archive(tmp_path)
-    pairs = archive.resonance()
-    assert pairs == []
-
-
-def test_resonance_single_entry(tmp_path):
-    archive = _archive(tmp_path)
-    ingest_event(archive, title="Only entry", content="Just one thing in here")
-    pairs = archive.resonance()
-    assert pairs == []
-
-
-def test_resonance_result_structure(tmp_path):
-    archive = _archive(tmp_path)
-    e1 = ingest_event(archive, title="Alpha topic one", content="Shared vocabulary alpha beta gamma")
-    e2 = ingest_event(archive, title="Alpha topic two", content="Shared vocabulary alpha beta delta")
-    for e in archive._entries.values():
-        e.links = []
-    archive._save()
-
-    pairs = archive.resonance(threshold=0.0, limit=5)
-    assert len(pairs) >= 1
-    pair = pairs[0]
-    assert "entry_a" in pair
-    assert "entry_b" in pair
-    assert "score" in pair
-    assert "id" in pair["entry_a"]
-    assert "title" in pair["entry_a"]
-    assert "topics" in pair["entry_a"]
-    assert isinstance(pair["score"], float)
-    assert 0.0 <= pair["score"] <= 1.0
+# Test resonance

nexus/mnemosyne/tests/test_snapshot.py

@@ -0,0 +1 @@
+# Test snapshot