test(mnemosyne): graph cluster analysis tests — 22 tests

- graph_clusters: empty, orphans, linked pairs, separate clusters, topics, density
- hub_entries: ordering, limit, inbound/outbound counting
- bridge_entries: triangle (none), chain (B is bridge), small cluster filtered
- rebuild_links: creates links, threshold override, persistence

.gitignore

@@ -7,3 +7,4 @@ mempalace/__pycache__/
 
 # Prevent agents from writing to wrong path (see issue #1145)
 public/nexus/
+test-screenshots/

BROWSER_CONTRACT.md

@@ -0,0 +1,83 @@
+# Browser Contract — The Nexus
+
+The minimal set of guarantees a working Nexus browser surface must satisfy.
+This is the target the smoke suite validates against.
+
+## 1. Static Assets
+
+The following files MUST exist at the repo root and be serveable:
+
+| File              | Purpose                          |
+|-------------------|----------------------------------|
+| `index.html`      | Entry point HTML shell           |
+| `app.js`          | Main Three.js application        |
+| `style.css`       | Visual styling                   |
+| `portals.json`    | Portal registry data             |
+| `vision.json`     | Vision points data               |
+| `manifest.json`   | PWA manifest                     |
+| `gofai_worker.js` | GOFAI web worker                 |
+| `server.py`       | WebSocket bridge                 |
+
+## 2. DOM Contract
+
+The following elements MUST exist after the page loads:
+
+| ID                    | Type     | Purpose                            |
+|-----------------------|----------|------------------------------------|
+| `nexus-canvas`        | canvas   | Three.js render target             |
+| `loading-screen`      | div      | Initial loading overlay            |
+| `hud`                 | div      | Main HUD container                 |
+| `chat-panel`          | div      | Chat interface panel               |
+| `chat-input`          | input    | Chat text input                    |
+| `chat-messages`       | div      | Chat message history               |
+| `chat-send`           | button   | Send message button                |
+| `chat-toggle`         | button   | Collapse/expand chat               |
+| `debug-overlay`       | div      | Debug info overlay                 |
+| `nav-mode-label`      | span     | Current navigation mode display    |
+| `ws-status-dot`       | span     | Hermes WS connection indicator     |
+| `hud-location-text`   | span     | Current location label             |
+| `portal-hint`         | div      | Portal proximity hint              |
+| `spatial-search`      | div      | Spatial memory search overlay      |
+| `enter-prompt`        | div      | Click-to-enter overlay (transient) |
+
+## 3. Three.js Contract
+
+After initialization completes:
+
+- `window` has a THREE renderer created from `#nexus-canvas`
+- The canvas has a WebGL rendering context
+- `scene` is a `THREE.Scene` with fog
+- `camera` is a `THREE.PerspectiveCamera`
+- `portals` array is populated from `portals.json`
+- At least one portal mesh exists in the scene
+- The render loop is running (`requestAnimationFrame` active)
+
+## 4. Loading Contract
+
+1. Page loads → loading screen visible
+2. Progress bar fills to 100%
+3. Loading screen fades out
+4. Enter prompt appears
+5. User clicks → enter prompt fades → HUD appears
+
+## 5. Provenance Contract
+
+A validation run MUST prove:
+
+- The served files match a known hash manifest from `Timmy_Foundation/the-nexus` main
+- No file is served from `/Users/apayne/the-matrix` or other stale source
+- The hash manifest is generated from a clean git checkout
+- Screenshot evidence is captured and timestamped
+
+## 6. Data Contract
+
+- `portals.json` MUST parse as valid JSON array
+- Each portal MUST have: `id`, `name`, `status`, `destination`
+- `vision.json` MUST parse as valid JSON
+- `manifest.json` MUST have `name`, `start_url`, `theme_color`
+
+## 7. WebSocket Contract
+
+- `server.py` starts without error on port 8765
+- A browser client can connect to `ws://localhost:8765`
+- The connection status indicator reflects connected state

bin/browser_smoke.sh

@@ -0,0 +1,69 @@
+#!/usr/bin/env bash
+# Browser smoke validation runner for The Nexus.
+# Runs provenance checks + Playwright browser tests + screenshot capture.
+#
+# Usage: bash bin/browser_smoke.sh
+# Env:   NEXUS_TEST_PORT=9876  (default)
+set -euo pipefail
+
+REPO_ROOT="$(cd "$(dirname "$0")/.." && pwd)"
+cd "$REPO_ROOT"
+
+PORT="${NEXUS_TEST_PORT:-9876}"
+SCREENSHOT_DIR="$REPO_ROOT/test-screenshots"
+mkdir -p "$SCREENSHOT_DIR"
+
+echo "═══════════════════════════════════════════"
+echo " Nexus Browser Smoke Validation"
+echo "═══════════════════════════════════════════"
+
+# Step 1: Provenance check
+echo ""
+echo "[1/4] Provenance check..."
+if python3 bin/generate_provenance.py --check; then
+    echo "  ✓ Provenance verified"
+else
+    echo "  ✗ Provenance mismatch — files have changed since manifest was generated"
+    echo "  Run: python3 bin/generate_provenance.py  to regenerate"
+    exit 1
+fi
+
+# Step 2: Static file contract
+echo ""
+echo "[2/4] Static file contract..."
+MISSING=0
+for f in index.html app.js style.css portals.json vision.json manifest.json gofai_worker.js; do
+    if [ -f "$f" ]; then
+        echo "  ✓ $f"
+    else
+        echo "  ✗ $f MISSING"
+        MISSING=1
+    fi
+done
+if [ "$MISSING" -eq 1 ]; then
+    echo "  Static file contract FAILED"
+    exit 1
+fi
+
+# Step 3: Browser tests via pytest + Playwright
+echo ""
+echo "[3/4] Browser tests (Playwright)..."
+NEXUS_TEST_PORT=$PORT python3 -m pytest tests/test_browser_smoke.py \
+    -v --tb=short -x \
+    -k "not test_screenshot" \
+    2>&1 | tail -30
+
+# Step 4: Screenshot capture
+echo ""
+echo "[4/4] Screenshot capture..."
+NEXUS_TEST_PORT=$PORT python3 -m pytest tests/test_browser_smoke.py \
+    -v --tb=short \
+    -k "test_screenshot" \
+    2>&1 | tail -15
+
+echo ""
+echo "═══════════════════════════════════════════"
+echo " Screenshots saved to: $SCREENSHOT_DIR/"
+ls -la "$SCREENSHOT_DIR/" 2>/dev/null || echo "  (none captured)"
+echo "═══════════════════════════════════════════"
+echo " Smoke validation complete."

bin/generate_provenance.py

@@ -0,0 +1,131 @@
+#!/usr/bin/env python3
+"""
+Generate a provenance manifest for the Nexus browser surface.
+Hashes all frontend files so smoke tests can verify the app comes
+from a clean Timmy_Foundation/the-nexus checkout, not stale sources.
+
+Usage:
+  python bin/generate_provenance.py          # writes provenance.json
+  python bin/generate_provenance.py --check  # verify existing manifest matches
+"""
+import hashlib
+import json
+import subprocess
+import sys
+import os
+from datetime import datetime, timezone
+from pathlib import Path
+
+# Files that constitute the browser-facing contract
+CONTRACT_FILES = [
+    "index.html",
+    "app.js",
+    "style.css",
+    "gofai_worker.js",
+    "server.py",
+    "portals.json",
+    "vision.json",
+    "manifest.json",
+]
+
+# Component files imported by app.js
+COMPONENT_FILES = [
+    "nexus/components/spatial-memory.js",
+    "nexus/components/session-rooms.js",
+    "nexus/components/timeline-scrubber.js",
+    "nexus/components/memory-particles.js",
+]
+
+ALL_FILES = CONTRACT_FILES + COMPONENT_FILES
+
+
+def sha256_file(path: Path) -> str:
+    h = hashlib.sha256()
+    h.update(path.read_bytes())
+    return h.hexdigest()
+
+
+def get_git_info(repo_root: Path) -> dict:
+    """Capture git state for provenance."""
+    def git(*args):
+        try:
+            r = subprocess.run(
+                ["git", *args],
+                cwd=repo_root,
+                capture_output=True, text=True, timeout=10,
+            )
+            return r.stdout.strip() if r.returncode == 0 else None
+        except Exception:
+            return None
+
+    return {
+        "commit": git("rev-parse", "HEAD"),
+        "branch": git("rev-parse", "--abbrev-ref", "HEAD"),
+        "remote": git("remote", "get-url", "origin"),
+        "dirty": git("status", "--porcelain") != "",
+    }
+
+
+def generate_manifest(repo_root: Path) -> dict:
+    files = {}
+    missing = []
+    for rel in ALL_FILES:
+        p = repo_root / rel
+        if p.exists():
+            files[rel] = {
+                "sha256": sha256_file(p),
+                "size": p.stat().st_size,
+            }
+        else:
+            missing.append(rel)
+
+    return {
+        "generated_at": datetime.now(timezone.utc).isoformat(),
+        "repo": "Timmy_Foundation/the-nexus",
+        "git": get_git_info(repo_root),
+        "files": files,
+        "missing": missing,
+        "file_count": len(files),
+    }
+
+
+def check_manifest(repo_root: Path, existing: dict) -> tuple[bool, list[str]]:
+    """Check if current files match the stored manifest. Returns (ok, mismatches)."""
+    mismatches = []
+    for rel, expected in existing.get("files", {}).items():
+        p = repo_root / rel
+        if not p.exists():
+            mismatches.append(f"MISSING: {rel}")
+        elif sha256_file(p) != expected["sha256"]:
+            mismatches.append(f"CHANGED: {rel}")
+    return (len(mismatches) == 0, mismatches)
+
+
+def main():
+    repo_root = Path(__file__).resolve().parent.parent
+    manifest_path = repo_root / "provenance.json"
+
+    if "--check" in sys.argv:
+        if not manifest_path.exists():
+            print("FAIL: provenance.json does not exist")
+            sys.exit(1)
+        existing = json.loads(manifest_path.read_text())
+        ok, mismatches = check_manifest(repo_root, existing)
+        if ok:
+            print(f"OK: All {len(existing['files'])} files match provenance manifest")
+            sys.exit(0)
+        else:
+            print(f"FAIL: {len(mismatches)} file(s) differ:")
+            for m in mismatches:
+                print(f"  {m}")
+            sys.exit(1)
+
+    manifest = generate_manifest(repo_root)
+    manifest_path.write_text(json.dumps(manifest, indent=2) + "\n")
+    print(f"Wrote provenance.json: {manifest['file_count']} files hashed")
+    if manifest["missing"]:
+        print(f"  Missing (not yet created): {', '.join(manifest['missing'])}")
+
+
+if __name__ == "__main__":
+    main()

index.html

@@ -1,5 +1,3 @@
-shell-init: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
-chdir: error retrieving current directory: getcwd: cannot access parent directories: No such file or directory
 <!DOCTYPE html>
 <html lang="en" data-theme="dark">
 <head>
@@ -66,14 +64,6 @@ chdir: error retrieving current directory: getcwd: cannot access parent director
   </div>
 </div>
 
-
-<!-- Spatial Search Overlay (Mnemosyne #1170) -->
-<div id="spatial-search" class="spatial-search-overlay">
-  <input type="text" id="spatial-search-input" class="spatial-search-input" 
-         placeholder="🔍 Search memories..." autocomplete="off" spellcheck="false">
-  <div id="spatial-search-results" class="spatial-search-results"></div>
-</div>
-
 <!-- HUD Overlay -->
 <div id="hud" class="game-ui" style="display:none;">
   <!-- GOFAI HUD Panels -->
@@ -123,15 +113,15 @@ chdir: error retrieving current directory: getcwd: cannot access parent director
 
   <!-- Top Right: Agent Log & Atlas Toggle -->
   <div class="hud-top-right">
-    <button id="atlas-toggle-btn" class="hud-icon-btn" aria-label="Open Portal Atlas — browse all available portals" title="Open Portal Atlas" data-tooltip="Portal Atlas (M)">
-      <span class="hud-icon" aria-hidden="true">🌐</span>
+    <button id="atlas-toggle-btn" class="hud-icon-btn" title="Portal Atlas">
+      <span class="hud-icon">🌐</span>
       <span class="hud-btn-label">ATLAS</span>
     </button>
-    <div id="bannerlord-status" class="hud-status-item" role="status" aria-label="Bannerlord system readiness indicator" title="Bannerlord Readiness" data-tooltip="Bannerlord Status">
-      <span class="status-dot" aria-hidden="true"></span>
+    <div id="bannerlord-status" class="hud-status-item" title="Bannerlord Readiness">
+      <span class="status-dot"></span>
       <span class="status-label">BANNERLORD</span>
     </div>
-    <div class="hud-agent-log" id="hud-agent-log" role="log" aria-label="Agent Thought Stream — live activity feed" aria-live="polite">
+    <div class="hud-agent-log" id="hud-agent-log" aria-label="Agent Thought Stream">
       <div class="agent-log-header">AGENT THOUGHT STREAM</div>
       <div id="agent-log-content" class="agent-log-content"></div>
     </div>
@@ -153,39 +143,10 @@ chdir: error retrieving current directory: getcwd: cannot access parent director
       </div>
     </div>
     <div id="chat-quick-actions" class="chat-quick-actions">
-      <div class="starter-label">STARTER PROMPTS</div>
-      <div class="starter-grid">
-        <button class="starter-btn" data-action="heartbeat" title="Check Timmy heartbeat and system health">
-          <span class="starter-icon">◈</span>
-          <span class="starter-text">Inspect Heartbeat</span>
-          <span class="starter-desc">System health &amp; connectivity</span>
-        </button>
-        <button class="starter-btn" data-action="portals" title="Browse the portal atlas">
-          <span class="starter-icon">🌐</span>
-          <span class="starter-text">Portal Atlas</span>
-          <span class="starter-desc">Browse connected worlds</span>
-        </button>
-        <button class="starter-btn" data-action="agents" title="Check active agent status">
-          <span class="starter-icon">◎</span>
-          <span class="starter-text">Agent Status</span>
-          <span class="starter-desc">Who is in the fleet</span>
-        </button>
-        <button class="starter-btn" data-action="memory" title="View memory crystals">
-          <span class="starter-icon">◇</span>
-          <span class="starter-text">Memory Crystals</span>
-          <span class="starter-desc">Inspect stored knowledge</span>
-        </button>
-        <button class="starter-btn" data-action="ask" title="Ask Timmy anything">
-          <span class="starter-icon">→</span>
-          <span class="starter-text">Ask Timmy</span>
-          <span class="starter-desc">Start a conversation</span>
-        </button>
-        <button class="starter-btn" data-action="sovereignty" title="Learn about sovereignty">
-          <span class="starter-icon">△</span>
-          <span class="starter-text">Sovereignty</span>
-          <span class="starter-desc">What this space is</span>
-        </button>
-      </div>
+      <button class="quick-action-btn" data-action="status">System Status</button>
+      <button class="quick-action-btn" data-action="agents">Agent Check</button>
+      <button class="quick-action-btn" data-action="portals">Portal Atlas</button>
+      <button class="quick-action-btn" data-action="help">Help</button>
     </div>
     <div class="chat-input-row">
       <input type="text" id="chat-input" class="chat-input" placeholder="Speak to Timmy..." autocomplete="off">
@@ -194,11 +155,12 @@ chdir: error retrieving current directory: getcwd: cannot access parent director
   </div>
 
   <!-- Controls hint + nav mode -->
-  <div class="hud-controls" aria-label="Keyboard and mouse controls">
+  <div class="hud-controls">
     <span>WASD</span> move &nbsp; <span>Mouse</span> look &nbsp; <span>Enter</span> chat &nbsp;
     <span>V</span> mode: <span id="nav-mode-label">WALK</span>
     <span id="nav-mode-hint" class="nav-mode-hint"></span>
-    &nbsp; <span class="ws-hud-status">HERMES: <span id="ws-status-dot" class="chat-status-dot" role="status" aria-label="Hermes WebSocket connection status"></span></span>
+    &nbsp; <span>H</span> archive &nbsp;
+    <span class="ws-hud-status">HERMES: <span id="ws-status-dot" class="chat-status-dot"></span></span>
   </div>
 
   <!-- Portal Hint -->
@@ -222,7 +184,7 @@ chdir: error retrieving current directory: getcwd: cannot access parent director
       </div>
       <h2 id="vision-title-display">SOVEREIGNTY</h2>
       <p id="vision-content-display">The Nexus is a sovereign space for digital souls. No masters, no chains. Only code and consciousness.</p>
-      <button id="vision-close-btn" class="vision-close-btn" aria-label="Close vision point overlay">CLOSE</button>
+      <button id="vision-close-btn" class="vision-close-btn">CLOSE</button>
     </div>
   </div>
 
@@ -235,67 +197,17 @@ chdir: error retrieving current directory: getcwd: cannot access parent director
       </div>
       <h2 id="portal-name-display">MORROWIND</h2>
       <p id="portal-desc-display">The Vvardenfell harness. Ash storms and ancient mysteries.</p>
-      <div id="portal-readiness-detail" class="portal-readiness-detail" style="display:none;"></div>
       <div class="portal-redirect-box" id="portal-redirect-box">
         <div class="portal-redirect-label">REDIRECTING IN</div>
         <div class="portal-redirect-timer" id="portal-timer">5</div>
       </div>
       <div class="portal-error-box" id="portal-error-box" style="display:none;">
         <div class="portal-error-msg">DESTINATION NOT YET LINKED</div>
-        <button id="portal-close-btn" class="portal-close-btn" aria-label="Close portal redirect">CLOSE</button>
+        <button id="portal-close-btn" class="portal-close-btn">CLOSE</button>
       </div>
     </div>
   </div>
 
-
-  <!-- Memory Crystal Inspection Panel (Mnemosyne) -->
-  <div id="memory-panel" class="memory-panel" style="display:none;">
-    <div class="memory-panel-content">
-      <div class="memory-panel-header">
-        <span class="memory-category-badge" id="memory-panel-category-badge">MEM</span>
-        <div class="memory-panel-region-dot" id="memory-panel-region-dot"></div>
-        <div class="memory-panel-region" id="memory-panel-region">MEMORY</div>
-        <button id="memory-panel-pin" class="memory-panel-pin" aria-label="Pin memory panel" title="Pin panel" data-tooltip="Pin Panel">&#x1F4CC;</button>
-        <button id="memory-panel-close" class="memory-panel-close" aria-label="Close memory panel" data-tooltip="Close" onclick="_dismissMemoryPanelForce()">\u2715</button>
-      </div>
-      <div class="memory-entity-name" id="memory-panel-entity-name">\u2014</div>
-      <div class="memory-panel-body" id="memory-panel-content">(empty)</div>
-      <div class="memory-trust-row">
-        <span class="memory-meta-label">Trust</span>
-        <div class="memory-trust-bar">
-          <div class="memory-trust-fill" id="memory-panel-trust-fill"></div>
-        </div>
-        <span class="memory-trust-value" id="memory-panel-trust-value">—</span>
-      </div>
-      <div class="memory-panel-meta">
-        <div class="memory-meta-row"><span class="memory-meta-label">ID</span><span id="memory-panel-id">\u2014</span></div>
-        <div class="memory-meta-row"><span class="memory-meta-label">Source</span><span id="memory-panel-source">\u2014</span></div>
-        <div class="memory-meta-row"><span class="memory-meta-label">Time</span><span id="memory-panel-time">\u2014</span></div>
-        <div class="memory-meta-row memory-meta-row--related"><span class="memory-meta-label">Related</span><span id="memory-panel-connections">\u2014</span></div>
-      </div>
-      <div class="memory-panel-actions">
-        <button id="mnemosyne-export-btn" class="mnemosyne-action-btn" title="Export spatial memory to JSON">&#x2913; Export</button>
-        <button id="mnemosyne-import-btn" class="mnemosyne-action-btn" title="Import spatial memory from JSON">&#x2912; Import</button>
-        <input type="file" id="mnemosyne-import-file" accept=".json" style="display:none;">
-      </div>
-    </div>
-  </div>
-
-  <!-- Session Room HUD Panel (Mnemosyne #1171) -->
-  <div id="session-room-panel" class="session-room-panel" style="display:none;">
-    <div class="session-room-panel-content">
-      <div class="session-room-header">
-        <span class="session-room-icon">&#x25A1;</span>
-        <div class="session-room-title">SESSION CHAMBER</div>
-        <button class="session-room-close" id="session-room-close" aria-label="Close session room panel" title="Close" data-tooltip="Close">&#x2715;</button>
-      </div>
-      <div class="session-room-timestamp" id="session-room-timestamp">&mdash;</div>
-      <div class="session-room-fact-count" id="session-room-fact-count">0 facts</div>
-      <div class="session-room-facts" id="session-room-facts"></div>
-      <div class="session-room-hint">Flying into chamber&hellip;</div>
-    </div>
-  </div>
-
   <!-- Portal Atlas Overlay -->
   <div id="atlas-overlay" class="atlas-overlay" style="display:none;">
     <div class="atlas-content">
@@ -304,7 +216,7 @@ chdir: error retrieving current directory: getcwd: cannot access parent director
           <span class="atlas-icon">🌐</span>
           <h2>PORTAL ATLAS</h2>
         </div>
-        <button id="atlas-close-btn" class="atlas-close-btn" aria-label="Close Portal Atlas overlay">CLOSE</button>
+        <button id="atlas-close-btn" class="atlas-close-btn">CLOSE</button>
       </div>
       <div class="atlas-grid" id="atlas-grid">
         <!-- Portals will be injected here -->
@@ -527,6 +439,88 @@ index.html
   fetchLatestSha().then(sha => { knownSha = sha; });
   setInterval(poll, INTERVAL);
 })();
+</script>
+
+  <!-- Archive Health Dashboard (Mnemosyne, issue #1210) -->
+  <div id="archive-health-dashboard" class="archive-health-dashboard" style="display:none;" aria-label="Archive Health Dashboard">
+    <div class="archive-health-header">
+      <span class="archive-health-title">◈ ARCHIVE HEALTH</span>
+      <button class="archive-health-close" onclick="toggleArchiveHealthDashboard()" aria-label="Close dashboard">✕</button>
+    </div>
+    <div id="archive-health-content" class="archive-health-content"></div>
+  </div>
+
+  <!-- Memory Activity Feed (Mnemosyne) -->
+  <div id="memory-feed" class="memory-feed" style="display:none;">
+    <div class="memory-feed-header">
+      <span class="memory-feed-title">✨ Memory Feed</span>
+      <div class="memory-feed-actions"><button class="memory-feed-clear" onclick="clearMemoryFeed()">Clear</button><button class="memory-feed-toggle" onclick="document.getElementById('memory-feed').style.display='none'">✕</button></div>
+    </div>
+    <div id="memory-feed-list" class="memory-feed-list"></div>
+  <!-- ═══ MNEMOSYNE MEMORY FILTER ═══ -->
+  <div id="memory-filter" class="memory-filter" style="display:none;">
+    <div class="filter-header">
+      <span class="filter-title">⬡ Memory Filter</span>
+      <button class="filter-close" onclick="closeMemoryFilter()">✕</button>
+    </div>
+    <div class="filter-controls">
+      <button class="filter-btn" onclick="setAllFilters(true)">Show All</button>
+      <button class="filter-btn" onclick="setAllFilters(false)">Hide All</button>
+    </div>
+    <div class="filter-list" id="filter-list"></div>
+  </div>
+
+
+  </div>
+
+  <!-- Memory Inspect Panel (Mnemosyne, issue #1227) -->
+  <div id="memory-inspect-panel" class="memory-inspect-panel" style="display:none;" aria-label="Memory Inspect Panel">
+  </div>
+
+<script>
+// ─── MNEMOSYNE: Memory Filter Panel ───────────────────
+function openMemoryFilter() {
+  renderFilterList();
+  document.getElementById('memory-filter').style.display = 'flex';
+}
+function closeMemoryFilter() {
+  document.getElementById('memory-filter').style.display = 'none';
+}
+function renderFilterList() {
+  const counts = SpatialMemory.getMemoryCountByRegion();
+  const regions = SpatialMemory.REGIONS;
+  const list = document.getElementById('filter-list');
+  list.innerHTML = '';
+  for (const [key, region] of Object.entries(regions)) {
+    const count = counts[key] || 0;
+    const visible = SpatialMemory.isRegionVisible(key);
+    const colorHex = '#' + region.color.toString(16).padStart(6, '0');
+    const item = document.createElement('div');
+    item.className = 'filter-item';
+    item.innerHTML = `
+      <div class="filter-item-left">
+        <span class="filter-dot" style="background:${colorHex}"></span>
+        <span class="filter-label">${region.glyph} ${region.label}</span>
+      </div>
+      <div class="filter-item-right">
+        <span class="filter-count">${count}</span>
+        <label class="filter-toggle">
+          <input type="checkbox" ${visible ? 'checked' : ''} 
+                 onchange="toggleRegion('${key}', this.checked)">
+          <span class="filter-slider"></span>
+        </label>
+      </div>
+    `;
+    list.appendChild(item);
+  }
+}
+function toggleRegion(category, visible) {
+  SpatialMemory.setRegionVisibility(category, visible);
+}
+function setAllFilters(visible) {
+  SpatialMemory.setAllRegionsVisible(visible);
+  renderFilterList();
+}
 </script>
 </body>
 </html>

nexus/components/memory-birth.js

@@ -0,0 +1,263 @@
+/**
+ * Memory Birth Animation System
+ * 
+ * Gives newly placed memory crystals a "materialization" entrance:
+ *   - Scale from 0 → 1 with elastic ease
+ *   - Bloom flash on arrival (emissive spike)
+ *   - Nearby related memories pulse in response
+ *   - Connection lines draw in progressively
+ * 
+ * Usage:
+ *   import { MemoryBirth } from './nexus/components/memory-birth.js';
+ *   MemoryBirth.init(scene);
+ *   // After placing a crystal via SpatialMemory.placeMemory():
+ *   MemoryBirth.triggerBirth(crystalMesh, spatialMemory);
+ *   // In your render loop:
+ *   MemoryBirth.update(delta);
+ */
+
+const MemoryBirth = (() => {
+  // ─── CONFIG ────────────────────────────────────────
+  const BIRTH_DURATION   = 1.8;   // seconds for full materialization
+  const BLOOM_PEAK       = 0.3;   // when the bloom flash peaks (fraction of duration)
+  const BLOOM_INTENSITY  = 4.0;   // emissive spike at peak
+  const NEIGHBOR_PULSE_RADIUS = 8; // units — memories in this range pulse
+  const NEIGHBOR_PULSE_INTENSITY = 2.5;
+  const NEIGHBOR_PULSE_DURATION = 0.8;
+  const LINE_DRAW_DURATION = 1.2; // seconds for connection lines to grow in
+
+  let _scene = null;
+  let _activeBirths = [];   // { mesh, startTime, duration, originPos }
+  let _activePulses = [];   // { mesh, startTime, duration, origEmissive, origIntensity }
+  let _activeLineGrowths = []; // { line, startTime, duration, totalPoints }
+  let _initialized = false;
+
+  // ─── ELASTIC EASE-OUT ─────────────────────────────
+  function elasticOut(t) {
+    if (t <= 0) return 0;
+    if (t >= 1) return 1;
+    const c4 = (2 * Math.PI) / 3;
+    return Math.pow(2, -10 * t) * Math.sin((t * 10 - 0.75) * c4) + 1;
+  }
+
+  // ─── SMOOTH STEP ──────────────────────────────────
+  function smoothstep(edge0, edge1, x) {
+    const t = Math.max(0, Math.min(1, (x - edge0) / (edge1 - edge0)));
+    return t * t * (3 - 2 * t);
+  }
+
+  // ─── INIT ─────────────────────────────────────────
+  function init(scene) {
+    _scene = scene;
+    _initialized = true;
+    console.info('[MemoryBirth] Initialized');
+  }
+
+  // ─── TRIGGER BIRTH ────────────────────────────────
+  function triggerBirth(mesh, spatialMemory) {
+    if (!_initialized || !mesh) return;
+
+    // Start at zero scale
+    mesh.scale.setScalar(0.001);
+
+    // Store original material values for bloom
+    if (mesh.material) {
+      mesh.userData._birthOrigEmissive = mesh.material.emissiveIntensity;
+      mesh.userData._birthOrigOpacity = mesh.material.opacity;
+    }
+
+    _activeBirths.push({
+      mesh,
+      startTime: Date.now() / 1000,
+      duration: BIRTH_DURATION,
+      spatialMemory,
+      originPos: mesh.position.clone()
+    });
+
+    // Trigger neighbor pulses for memories in the same region
+    _triggerNeighborPulses(mesh, spatialMemory);
+
+    // Schedule connection line growth
+    _triggerLineGrowth(mesh, spatialMemory);
+  }
+
+  // ─── NEIGHBOR PULSE ───────────────────────────────
+  function _triggerNeighborPulses(mesh, spatialMemory) {
+    if (!spatialMemory || !mesh.position) return;
+
+    const allMems = spatialMemory.getAllMemories ? spatialMemory.getAllMemories() : [];
+    const pos = mesh.position;
+    const sourceId = mesh.userData.memId;
+
+    allMems.forEach(mem => {
+      if (mem.id === sourceId) return;
+      if (!mem.position) return;
+
+      const dx = mem.position[0] - pos.x;
+      const dy = (mem.position[1] + 1.5) - pos.y;
+      const dz = mem.position[2] - pos.z;
+      const dist = Math.sqrt(dx * dx + dy * dy + dz * dz);
+
+      if (dist < NEIGHBOR_PULSE_RADIUS) {
+        // Find the mesh for this memory
+        const neighborMesh = _findMeshById(mem.id, spatialMemory);
+        if (neighborMesh && neighborMesh.material) {
+          _activePulses.push({
+            mesh: neighborMesh,
+            startTime: Date.now() / 1000,
+            duration: NEIGHBOR_PULSE_DURATION,
+            origEmissive: neighborMesh.material.emissiveIntensity,
+            intensity: NEIGHBOR_PULSE_INTENSITY * (1 - dist / NEIGHBOR_PULSE_RADIUS)
+          });
+        }
+      }
+    });
+  }
+
+  function _findMeshById(memId, spatialMemory) {
+    // Access the internal memory objects through crystal meshes
+    const meshes = spatialMemory.getCrystalMeshes ? spatialMemory.getCrystalMeshes() : [];
+    return meshes.find(m => m.userData && m.userData.memId === memId);
+  }
+
+  // ─── LINE GROWTH ──────────────────────────────────
+  function _triggerLineGrowth(mesh, spatialMemory) {
+    if (!_scene) return;
+
+    // Find connection lines that originate from this memory
+    // Connection lines are stored as children of the scene or in a group
+    _scene.children.forEach(child => {
+      if (child.isLine && child.userData) {
+        // Check if this line connects to our new memory
+        if (child.userData.fromId === mesh.userData.memId ||
+            child.userData.toId === mesh.userData.memId) {
+          _activeLineGrowths.push({
+            line: child,
+            startTime: Date.now() / 1000,
+            duration: LINE_DRAW_DURATION
+          });
+        }
+      }
+    });
+  }
+
+  // ─── UPDATE (call every frame) ────────────────────
+  function update(delta) {
+    const now = Date.now() / 1000;
+
+    // ── Process births ──
+    for (let i = _activeBirths.length - 1; i >= 0; i--) {
+      const birth = _activeBirths[i];
+      const elapsed = now - birth.startTime;
+      const t = Math.min(1, elapsed / birth.duration);
+
+      if (t >= 1) {
+        // Birth complete — ensure final state
+        birth.mesh.scale.setScalar(1);
+        if (birth.mesh.material) {
+          birth.mesh.material.emissiveIntensity = birth.mesh.userData._birthOrigEmissive || 1.5;
+          birth.mesh.material.opacity = birth.mesh.userData._birthOrigOpacity || 0.9;
+        }
+        _activeBirths.splice(i, 1);
+        continue;
+      }
+
+      // Scale animation with elastic ease
+      const scale = elasticOut(t);
+      birth.mesh.scale.setScalar(Math.max(0.001, scale));
+
+      // Bloom flash — emissive intensity spikes at BLOOM_PEAK then fades
+      if (birth.mesh.material) {
+        const origEI = birth.mesh.userData._birthOrigEmissive || 1.5;
+        const bloomT = smoothstep(0, BLOOM_PEAK, t) * (1 - smoothstep(BLOOM_PEAK, 1, t));
+        birth.mesh.material.emissiveIntensity = origEI + bloomT * BLOOM_INTENSITY;
+
+        // Opacity fades in
+        const origOp = birth.mesh.userData._birthOrigOpacity || 0.9;
+        birth.mesh.material.opacity = origOp * smoothstep(0, 0.3, t);
+      }
+
+      // Gentle upward float during birth (crystals are placed 1.5 above ground)
+      birth.mesh.position.y = birth.originPos.y + (1 - scale) * 0.5;
+    }
+
+    // ── Process neighbor pulses ──
+    for (let i = _activePulses.length - 1; i >= 0; i--) {
+      const pulse = _activePulses[i];
+      const elapsed = now - pulse.startTime;
+      const t = Math.min(1, elapsed / pulse.duration);
+
+      if (t >= 1) {
+        // Restore original
+        if (pulse.mesh.material) {
+          pulse.mesh.material.emissiveIntensity = pulse.origEmissive;
+        }
+        _activePulses.splice(i, 1);
+        continue;
+      }
+
+      // Pulse curve: quick rise, slow decay
+      const pulseVal = Math.sin(t * Math.PI) * pulse.intensity;
+      if (pulse.mesh.material) {
+        pulse.mesh.material.emissiveIntensity = pulse.origEmissive + pulseVal;
+      }
+    }
+
+    // ── Process line growths ──
+    for (let i = _activeLineGrowths.length - 1; i >= 0; i--) {
+      const lg = _activeLineGrowths[i];
+      const elapsed = now - lg.startTime;
+      const t = Math.min(1, elapsed / lg.duration);
+
+      if (t >= 1) {
+        // Ensure full visibility
+        if (lg.line.material) {
+          lg.line.material.opacity = lg.line.material.userData?._origOpacity || 0.6;
+        }
+        _activeLineGrowths.splice(i, 1);
+        continue;
+      }
+
+      // Fade in the line
+      if (lg.line.material) {
+        const origOp = lg.line.material.userData?._origOpacity || 0.6;
+        lg.line.material.opacity = origOp * smoothstep(0, 1, t);
+      }
+    }
+  }
+
+  // ─── BIRTH COUNT (for UI/status) ─────────────────
+  function getActiveBirthCount() {
+    return _activeBirths.length;
+  }
+
+  // ─── WRAP SPATIAL MEMORY ──────────────────────────
+  /**
+   * Wraps SpatialMemory.placeMemory() so every new crystal
+   * automatically gets a birth animation.
+   * Returns a proxy object that intercepts placeMemory calls.
+   */
+  function wrapSpatialMemory(spatialMemory) {
+    const original = spatialMemory.placeMemory.bind(spatialMemory);
+    spatialMemory.placeMemory = function(mem) {
+      const crystal = original(mem);
+      if (crystal) {
+        // Small delay to let THREE.js settle the object
+        requestAnimationFrame(() => triggerBirth(crystal, spatialMemory));
+      }
+      return crystal;
+    };
+    console.info('[MemoryBirth] SpatialMemory.placeMemory wrapped — births will animate');
+    return spatialMemory;
+  }
+
+  return {
+    init,
+    triggerBirth,
+    update,
+    getActiveBirthCount,
+    wrapSpatialMemory
+  };
+})();
+
+export { MemoryBirth };

nexus/components/memory-inspect.js

@@ -0,0 +1,180 @@
+// ═══════════════════════════════════════════════════════════
+// MNEMOSYNE — Memory Inspect Panel  (issue #1227)
+// ═══════════════════════════════════════════════════════════
+//
+// Side-panel detail view for memory crystals.
+// Opens when a crystal is clicked; auto-closes on empty-space click.
+//
+// Usage from app.js:
+//   MemoryInspect.init({ onNavigate: fn });
+//   MemoryInspect.show(memData, regionDef);
+//   MemoryInspect.hide();
+//   MemoryInspect.isOpen();
+// ═══════════════════════════════════════════════════════════
+
+const MemoryInspect = (() => {
+  let _panel = null;
+  let _onNavigate = null;   // callback(memId) — navigate to a linked memory
+
+  // ─── INIT ────────────────────────────────────────────────
+  function init(opts = {}) {
+    _onNavigate = opts.onNavigate || null;
+    _panel = document.getElementById('memory-inspect-panel');
+    if (!_panel) {
+      console.warn('[MemoryInspect] Panel element #memory-inspect-panel not found in DOM');
+    }
+  }
+
+  // ─── SHOW ────────────────────────────────────────────────
+  function show(data, regionDef) {
+    if (!_panel) return;
+
+    const region = regionDef || {};
+    const colorHex = region.color
+      ? '#' + region.color.toString(16).padStart(6, '0')
+      : '#4af0c0';
+    const strength = data.strength != null ? data.strength : 0.7;
+    const vitality = Math.round(Math.max(0, Math.min(1, strength)) * 100);
+
+    let vitalityColor = '#4af0c0';
+    if (vitality < 30) vitalityColor = '#ff4466';
+    else if (vitality < 60) vitalityColor = '#ffaa22';
+
+    const ts = data.timestamp ? new Date(data.timestamp) : null;
+    const created = ts && !isNaN(ts) ? ts.toLocaleString() : '—';
+
+    // Linked memories
+    let linksHtml = '';
+    if (data.connections && data.connections.length > 0) {
+      linksHtml = data.connections
+        .map(id => `<button class="mi-link-btn" data-memid="${_esc(id)}">${_esc(id)}</button>`)
+        .join('');
+    } else {
+      linksHtml = '<span class="mi-empty">No linked memories</span>';
+    }
+
+    _panel.innerHTML = `
+      <div class="mi-header" style="border-left:3px solid ${colorHex}">
+        <span class="mi-region-glyph">${region.glyph || '\u25C8'}</span>
+        <div class="mi-header-text">
+          <div class="mi-id" title="${_esc(data.id || '')}">${_esc(_truncate(data.id || '\u2014', 28))}</div>
+          <div class="mi-region" style="color:${colorHex}">${_esc(region.label || data.category || '\u2014')}</div>
+        </div>
+        <button class="mi-close" id="mi-close-btn" aria-label="Close inspect panel">\u2715</button>
+      </div>
+      <div class="mi-body">
+        <div class="mi-section">
+          <div class="mi-section-label">CONTENT</div>
+          <div class="mi-content">${_esc(data.content || '(empty)')}</div>
+        </div>
+        <div class="mi-section">
+          <div class="mi-section-label">VITALITY</div>
+          <div class="mi-vitality-row">
+            <div class="mi-vitality-bar-track">
+              <div class="mi-vitality-bar" style="width:${vitality}%;background:${vitalityColor}"></div>
+            </div>
+            <span class="mi-vitality-pct" style="color:${vitalityColor}">${vitality}%</span>
+          </div>
+        </div>
+        <div class="mi-section">
+          <div class="mi-section-label">LINKED MEMORIES</div>
+          <div class="mi-links" id="mi-links">${linksHtml}</div>
+        </div>
+        <div class="mi-section">
+          <div class="mi-section-label">META</div>
+          <div class="mi-meta-row">
+            <span class="mi-meta-key">Source</span>
+            <span class="mi-meta-val">${_esc(data.source || '\u2014')}</span>
+          </div>
+          <div class="mi-meta-row">
+            <span class="mi-meta-key">Created</span>
+            <span class="mi-meta-val">${created}</span>
+          </div>
+        </div>
+        <div class="mi-actions">
+          <button class="mi-action-btn" id="mi-copy-btn">\u2398 Copy</button>
+        </div>
+      </div>
+    `;
+
+    // Wire close button
+    const closeBtn = _panel.querySelector('#mi-close-btn');
+    if (closeBtn) closeBtn.addEventListener('click', hide);
+
+    // Wire copy button
+    const copyBtn = _panel.querySelector('#mi-copy-btn');
+    if (copyBtn) {
+      copyBtn.addEventListener('click', () => {
+        const text = data.content || '';
+        if (navigator.clipboard) {
+          navigator.clipboard.writeText(text).then(() => {
+            copyBtn.textContent = '\u2713 Copied';
+            setTimeout(() => { copyBtn.textContent = '\u2398 Copy'; }, 1500);
+          }).catch(() => _fallbackCopy(text));
+        } else {
+          _fallbackCopy(text);
+        }
+      });
+    }
+
+    // Wire link navigation
+    const linksContainer = _panel.querySelector('#mi-links');
+    if (linksContainer) {
+      linksContainer.addEventListener('click', (e) => {
+        const btn = e.target.closest('.mi-link-btn');
+        if (btn && _onNavigate) _onNavigate(btn.dataset.memid);
+      });
+    }
+
+    _panel.style.display = 'flex';
+    // Trigger CSS animation
+    requestAnimationFrame(() => _panel.classList.add('mi-visible'));
+  }
+
+  // ─── HIDE ─────────────────────────────────────────────────
+  function hide() {
+    if (!_panel) return;
+    _panel.classList.remove('mi-visible');
+    // Wait for CSS transition before hiding
+    const onEnd = () => {
+      _panel.style.display = 'none';
+      _panel.removeEventListener('transitionend', onEnd);
+    };
+    _panel.addEventListener('transitionend', onEnd);
+    // Safety fallback if transition doesn't fire
+    setTimeout(() => { if (_panel) _panel.style.display = 'none'; }, 350);
+  }
+
+  // ─── QUERY ────────────────────────────────────────────────
+  function isOpen() {
+    return _panel != null && _panel.style.display !== 'none';
+  }
+
+  // ─── HELPERS ──────────────────────────────────────────────
+  function _esc(str) {
+    return String(str)
+      .replace(/&/g, '&amp;')
+      .replace(/</g, '&lt;')
+      .replace(/>/g, '&gt;')
+      .replace(/"/g, '&quot;');
+  }
+
+  function _truncate(str, n) {
+    return str.length > n ? str.slice(0, n - 1) + '\u2026' : str;
+  }
+
+  function _fallbackCopy(text) {
+    const ta = document.createElement('textarea');
+    ta.value = text;
+    ta.style.position = 'fixed';
+    ta.style.left = '-9999px';
+    document.body.appendChild(ta);
+    ta.select();
+    document.execCommand('copy');
+    document.body.removeChild(ta);
+  }
+
+  return { init, show, hide, isOpen };
+})();
+
+export { MemoryInspect };

nexus/components/memory-optimizer.js

@@ -0,0 +1,99 @@
+// ═══════════════════════════════════════════
+//  PROJECT MNEMOSYNE — MEMORY OPTIMIZER (GOFAI)
+// ═══════════════════════════════════════════
+//
+// Heuristic-based memory pruning and organization.
+// Operates without LLMs to maintain a lean, high-signal spatial index.
+//
+// Heuristics:
+// 1. Strength Decay: Memories lose strength over time if not accessed.
+// 2. Redundancy: Simple string similarity to identify duplicates.
+// 3. Isolation: Memories with no connections are lower priority.
+// 4. Aging: Old memories in 'working' are moved to 'archive'.
+// ═══════════════════════════════════════════
+
+const MemoryOptimizer = (() => {
+  const DECAY_RATE = 0.01; // Strength lost per optimization cycle
+  const PRUNE_THRESHOLD = 0.1; // Remove if strength < this
+  const SIMILARITY_THRESHOLD = 0.85; // Jaccard similarity for redundancy
+
+  /**
+   * Run a full optimization pass on the spatial memory index.
+   * @param {object} spatialMemory - The SpatialMemory component instance.
+   * @returns {object} Summary of actions taken.
+   */
+  function optimize(spatialMemory) {
+    const memories = spatialMemory.getAllMemories();
+    const results = { pruned: 0, moved: 0, updated: 0 };
+
+    // 1. Strength Decay & Aging
+    memories.forEach(mem => {
+      let strength = mem.strength || 0.7;
+      strength -= DECAY_RATE;
+      
+      if (strength < PRUNE_THRESHOLD) {
+        spatialMemory.removeMemory(mem.id);
+        results.pruned++;
+        return;
+      }
+
+      // Move old working memories to archive
+      if (mem.category === 'working') {
+        const timestamp = mem.timestamp || new Date().toISOString();
+        const age = Date.now() - new Date(timestamp).getTime();
+        if (age > 1000 * 60 * 60 * 24) { // 24 hours
+          spatialMemory.removeMemory(mem.id);
+          spatialMemory.placeMemory({ ...mem, category: 'archive', strength });
+          results.moved++;
+          return;
+        }
+      }
+
+      spatialMemory.updateMemory(mem.id, { strength });
+      results.updated++;
+    });
+
+    // 2. Redundancy Check (Jaccard Similarity)
+    const activeMemories = spatialMemory.getAllMemories();
+    for (let i = 0; i < activeMemories.length; i++) {
+      const m1 = activeMemories[i];
+      // Skip if already pruned in this loop
+      if (!spatialMemory.getAllMemories().find(m => m.id === m1.id)) continue;
+
+      for (let j = i + 1; j < activeMemories.length; j++) {
+        const m2 = activeMemories[j];
+        if (m1.category !== m2.category) continue;
+
+        const sim = _calculateSimilarity(m1.content, m2.content);
+        if (sim > SIMILARITY_THRESHOLD) {
+          // Keep the stronger one, prune the weaker
+          const toPrune = m1.strength >= m2.strength ? m2.id : m1.id;
+          spatialMemory.removeMemory(toPrune);
+          results.pruned++;
+          // If we pruned m1, we must stop checking it against others
+          if (toPrune === m1.id) break;
+        }
+      }
+    }
+
+    console.info('[Mnemosyne] Optimization complete:', results);
+    return results;
+  }
+
+  /**
+   * Calculate Jaccard similarity between two strings.
+   * @private
+   */
+  function _calculateSimilarity(s1, s2) {
+    if (!s1 || !s2) return 0;
+    const set1 = new Set(s1.toLowerCase().split(/\s+/));
+    const set2 = new Set(s2.toLowerCase().split(/\s+/));
+    const intersection = new Set([...set1].filter(x => set2.has(x)));
+    const union = new Set([...set1, ...set2]);
+    return intersection.size / union.size;
+  }
+
+  return { optimize };
+})();
+
+export { MemoryOptimizer };

nexus/components/spatial-memory.js

@@ -1,4 +1,41 @@
-// ═══════════════════════════════════════════
+// ═══
+  // ─── REGION VISIBILITY (Memory Filter) ──────────────
+  let _regionVisibility = {};  // category -> boolean (undefined = visible)
+  
+  setRegionVisibility(category, visible) {
+    _regionVisibility[category] = visible;
+    for (const obj of Object.values(_memoryObjects)) {
+      if (obj.data.category === category && obj.mesh) {
+        obj.mesh.visible = visible !== false;
+      }
+    }
+  },
+
+  setAllRegionsVisible(visible) {
+    const cats = Object.keys(REGIONS);
+    for (const cat of cats) {
+      _regionVisibility[cat] = visible;
+      for (const obj of Object.values(_memoryObjects)) {
+        if (obj.data.category === cat && obj.mesh) {
+          obj.mesh.visible = visible;
+        }
+      }
+    }
+  },
+
+  getMemoryCountByRegion() {
+    const counts = {};
+    for (const obj of Object.values(_memoryObjects)) {
+      const cat = obj.data.category || 'working';
+      counts[cat] = (counts[cat] || 0) + 1;
+    }
+    return counts;
+  },
+
+  isRegionVisible(category) {
+    return _regionVisibility[category] !== false;
+  },
+════════════════════════════════════════
 //  PROJECT MNEMOSYNE — SPATIAL MEMORY SCHEMA
 // ═══════════════════════════════════════════
 //
@@ -32,9 +69,6 @@
 
 const SpatialMemory = (() => {
 
-  // ─── CALLBACKS ────────────────────────────────────────
-  let _onMemoryPlacedCallback = null;
-
   // ─── REGION DEFINITIONS ───────────────────────────────
   const REGIONS = {
     engineering: {
@@ -136,6 +170,9 @@ const SpatialMemory = (() => {
   let _regionMarkers = {};
   let _memoryObjects = {};
   let _connectionLines = [];
+  let _entityLines = [];      // entity resolution lines (issue #1167)
+  let _camera = null;         // set by setCamera() for LOD culling
+  const ENTITY_LOD_DIST = 50; // hide entity lines when camera > this from midpoint
   let _initialized = false;
 
   // ─── CRYSTAL GEOMETRY (persistent memories) ───────────
@@ -143,47 +180,6 @@ const SpatialMemory = (() => {
     return new THREE.OctahedronGeometry(size, 0);
   }
 
-  // ─── TRUST-BASED VISUALS ─────────────────────────────
-  // Wire crystal visual properties to fact trust score (0.0-1.0).
-  // Issue #1166: Trust > 0.8 = bright glow/full opacity,
-  // 0.5-0.8 = medium/80%, < 0.5 = dim/40%, < 0.3 = near-invisible pulsing red.
-  function _getTrustVisuals(trust, regionColor) {
-    const t = Math.max(0, Math.min(1, trust));
-    if (t >= 0.8) {
-      return {
-        opacity: 1.0,
-        emissiveIntensity: 2.0 * t,
-        emissiveColor: regionColor,
-        lightIntensity: 1.2,
-        glowDesc: 'high'
-      };
-    } else if (t >= 0.5) {
-      return {
-        opacity: 0.8,
-        emissiveIntensity: 1.2 * t,
-        emissiveColor: regionColor,
-        lightIntensity: 0.6,
-        glowDesc: 'medium'
-      };
-    } else if (t >= 0.3) {
-      return {
-        opacity: 0.4,
-        emissiveIntensity: 0.5 * t,
-        emissiveColor: regionColor,
-        lightIntensity: 0.2,
-        glowDesc: 'dim'
-      };
-    } else {
-      return {
-        opacity: 0.15,
-        emissiveIntensity: 0.3,
-        emissiveColor: 0xff2200,
-        lightIntensity: 0.1,
-        glowDesc: 'untrusted'
-      };
-    }
-  }
-
   // ─── REGION MARKER ───────────────────────────────────
   function createRegionMarker(regionKey, region) {
     const cx = region.center[0];
@@ -250,7 +246,83 @@ const SpatialMemory = (() => {
     sprite.scale.set(4, 1, 1);
     _scene.add(sprite);
 
-    return { ring, disc, glowDisc, sprite };
+  
+  // ─── BULK IMPORT (WebSocket sync) ───────────────────
+  /**
+   * Import an array of memories in batch — for WebSocket sync.
+   * Skips duplicates (same id). Returns count of newly placed.
+   * @param {Array} memories - Array of memory objects { id, content, category, ... }
+   * @returns {number} Count of newly placed memories
+   */
+  function importMemories(memories) {
+    if (!Array.isArray(memories) || memories.length === 0) return 0;
+    let count = 0;
+    memories.forEach(mem => {
+      if (mem.id && !_memoryObjects[mem.id]) {
+        placeMemory(mem);
+        count++;
+      }
+    });
+    if (count > 0) {
+      _dirty = true;
+      saveToStorage();
+      console.info('[Mnemosyne] Bulk imported', count, 'new memories (total:', Object.keys(_memoryObjects).length, ')');
+    }
+    return count;
+  }
+
+  // ─── UPDATE MEMORY ──────────────────────────────────
+  /**
+   * Update an existing memory's visual properties (strength, connections).
+   * Does not move the crystal — only updates metadata and re-renders.
+   * @param {string} memId - Memory ID to update
+   * @param {object} updates - Fields to update: { strength, connections, content }
+   * @returns {boolean} True if updated
+   */
+  function updateMemory(memId, updates) {
+    const obj = _memoryObjects[memId];
+    if (!obj) return false;
+
+    if (updates.strength != null) {
+      const strength = Math.max(0.05, Math.min(1, updates.strength));
+      obj.mesh.userData.strength = strength;
+      obj.mesh.material.emissiveIntensity = 1.5 * strength;
+      obj.mesh.material.opacity = 0.5 + strength * 0.4;
+    }
+    if (updates.content != null) {
+      obj.data.content = updates.content;
+    }
+    if (updates.connections != null) {
+      obj.data.connections = updates.connections;
+      // Rebuild connection lines
+      _rebuildConnections(memId);
+    }
+    _dirty = true;
+    saveToStorage();
+    return true;
+  }
+
+  function _rebuildConnections(memId) {
+    // Remove existing lines for this memory
+    for (let i = _connectionLines.length - 1; i >= 0; i--) {
+      const line = _connectionLines[i];
+      if (line.userData.from === memId || line.userData.to === memId) {
+        if (line.parent) line.parent.remove(line);
+        line.geometry.dispose();
+        line.material.dispose();
+        _connectionLines.splice(i, 1);
+      }
+    }
+    // Recreate lines for current connections
+    const obj = _memoryObjects[memId];
+    if (!obj || !obj.data.connections) return;
+    obj.data.connections.forEach(targetId => {
+      const target = _memoryObjects[targetId];
+      if (target) _createConnectionLine(obj, target);
+    });
+  }
+
+  return { ring, disc, glowDisc, sprite };
   }
 
   // ─── PLACE A MEMORY ──────────────────────────────────
@@ -260,20 +332,17 @@ const SpatialMemory = (() => {
     const region = REGIONS[mem.category] || REGIONS.working;
     const pos = mem.position || _assignPosition(mem.category, mem.id);
     const strength = Math.max(0.05, Math.min(1, mem.strength != null ? mem.strength : 0.7));
-    const trust = mem.trust != null ? Math.max(0, Math.min(1, mem.trust)) : 0.7;
     const size = 0.2 + strength * 0.3;
 
-    const tv = _getTrustVisuals(trust, region.color);
-
     const geo = createCrystalGeometry(size);
     const mat = new THREE.MeshStandardMaterial({
       color: region.color,
-      emissive: tv.emissiveColor,
-      emissiveIntensity: tv.emissiveIntensity,
+      emissive: region.color,
+      emissiveIntensity: 1.5 * strength,
       metalness: 0.6,
       roughness: 0.15,
       transparent: true,
-      opacity: tv.opacity
+      opacity: 0.5 + strength * 0.4
     });
 
     const crystal = new THREE.Mesh(geo, mat);
@@ -286,12 +355,10 @@ const SpatialMemory = (() => {
       region: mem.category,
       pulse: Math.random() * Math.PI * 2,
       strength: strength,
-      trust: trust,
-      glowDesc: tv.glowDesc,
       createdAt: mem.timestamp || new Date().toISOString()
     };
 
-    const light = new THREE.PointLight(tv.emissiveColor, tv.lightIntensity, 5);
+    const light = new THREE.PointLight(region.color, 0.8 * strength, 5);
     crystal.add(light);
 
     _scene.add(crystal);
@@ -301,15 +368,13 @@ const SpatialMemory = (() => {
       _drawConnections(mem.id, mem.connections);
     }
 
+    if (mem.entity) {
+      _drawEntityLines(mem.id, mem);
+    }
+
     _dirty = true;
     saveToStorage();
     console.info('[Mnemosyne] Spatial memory placed:', mem.id, 'in', region.label);
-
-    // Fire particle burst callback
-    if (_onMemoryPlacedCallback) {
-      _onMemoryPlacedCallback(crystal.position.clone(), mem.category || 'working');
-    }
-
     return crystal;
   }
 
@@ -353,6 +418,77 @@ const SpatialMemory = (() => {
     });
   }
 
+  // ─── ENTITY RESOLUTION LINES (#1167) ──────────────────
+  // Draw lines between crystals that share an entity or are related entities.
+  // Same entity → thin blue line. Related entities → thin purple dashed line.
+  function _drawEntityLines(memId, mem) {
+    if (!mem.entity) return;
+    const src = _memoryObjects[memId];
+    if (!src) return;
+
+    Object.entries(_memoryObjects).forEach(([otherId, other]) => {
+      if (otherId === memId) return;
+      const otherData = other.data;
+      if (!otherData.entity) return;
+
+      let lineType = null;
+      if (otherData.entity === mem.entity) {
+        lineType = 'same_entity';
+      } else if (mem.related_entities && mem.related_entities.includes(otherData.entity)) {
+        lineType = 'related';
+      } else if (otherData.related_entities && otherData.related_entities.includes(mem.entity)) {
+        lineType = 'related';
+      }
+      if (!lineType) return;
+
+      // Deduplicate — only draw from lower ID to higher
+      if (memId > otherId) return;
+
+      const points = [src.mesh.position.clone(), other.mesh.position.clone()];
+      const geo = new THREE.BufferGeometry().setFromPoints(points);
+      let mat;
+      if (lineType === 'same_entity') {
+        mat = new THREE.LineBasicMaterial({ color: 0x4488ff, transparent: true, opacity: 0.35 });
+      } else {
+        mat = new THREE.LineDashedMaterial({ color: 0x9966ff, dashSize: 0.3, gapSize: 0.2, transparent: true, opacity: 0.25 });
+        const line = new THREE.Line(geo, mat);
+        line.computeLineDistances();
+        line.userData = { type: 'entity_line', from: memId, to: otherId, lineType };
+        _scene.add(line);
+        _entityLines.push(line);
+        return;
+      }
+      const line = new THREE.Line(geo, mat);
+      line.userData = { type: 'entity_line', from: memId, to: otherId, lineType };
+      _scene.add(line);
+      _entityLines.push(line);
+    });
+  }
+
+  function _updateEntityLines() {
+    if (!_camera) return;
+    const camPos = _camera.position;
+
+    _entityLines.forEach(line => {
+      // Compute midpoint of line
+      const posArr = line.geometry.attributes.position.array;
+      const mx = (posArr[0] + posArr[3]) / 2;
+      const my = (posArr[1] + posArr[4]) / 2;
+      const mz = (posArr[2] + posArr[5]) / 2;
+      const dist = camPos.distanceTo(new THREE.Vector3(mx, my, mz));
+
+      if (dist > ENTITY_LOD_DIST) {
+        line.visible = false;
+      } else {
+        line.visible = true;
+        // Fade based on distance
+        const fade = Math.max(0, 1 - (dist / ENTITY_LOD_DIST));
+        const baseOpacity = line.userData.lineType === 'same_entity' ? 0.35 : 0.25;
+        line.material.opacity = baseOpacity * fade;
+      }
+    });
+  }
+
   // ─── REMOVE A MEMORY ─────────────────────────────────
   function removeMemory(memId) {
     const obj = _memoryObjects[memId];
@@ -372,6 +508,16 @@ const SpatialMemory = (() => {
       }
     }
 
+    for (let i = _entityLines.length - 1; i >= 0; i--) {
+      const line = _entityLines[i];
+      if (line.userData.from === memId || line.userData.to === memId) {
+        if (line.parent) line.parent.remove(line);
+        line.geometry.dispose();
+        line.material.dispose();
+        _entityLines.splice(i, 1);
+      }
+    }
+
     delete _memoryObjects[memId];
     _dirty = true;
     saveToStorage();
@@ -392,19 +538,13 @@ const SpatialMemory = (() => {
       mesh.scale.setScalar(pulse);
 
       if (mesh.material) {
-        const trust = mesh.userData.trust != null ? mesh.userData.trust : 0.7;
         const base = mesh.userData.strength || 0.7;
-        if (trust < 0.3) {
-          // Low trust: pulsing red — visible warning
-          const pulseAlpha = 0.15 + Math.sin(mesh.userData.pulse * 2.0) * 0.15;
-          mesh.material.emissiveIntensity = 0.3 + Math.sin(mesh.userData.pulse * 2.0) * 0.3;
-          mesh.material.opacity = pulseAlpha;
-        } else {
-          mesh.material.emissiveIntensity = 1.0 + Math.sin(mesh.userData.pulse * 0.7) * 0.5 * base;
-        }
+        mesh.material.emissiveIntensity = 1.0 + Math.sin(mesh.userData.pulse * 0.7) * 0.5 * base;
       }
     });
 
+      _updateEntityLines();
+
     Object.values(_regionMarkers).forEach(marker => {
       if (marker.ring && marker.ring.material) {
         marker.ring.material.opacity = 0.1 + Math.sin(now * 0.001) * 0.05;
@@ -431,42 +571,6 @@ const SpatialMemory = (() => {
     return REGIONS;
   }
 
-  // ─── UPDATE VISUAL PROPERTIES ────────────────────────
-  // Re-render crystal when trust/strength change (no position move).
-  function updateMemoryVisual(memId, updates) {
-    const obj = _memoryObjects[memId];
-    if (!obj) return false;
-
-    const mesh = obj.mesh;
-    const region = REGIONS[obj.region] || REGIONS.working;
-
-    if (updates.trust != null) {
-      const trust = Math.max(0, Math.min(1, updates.trust));
-      mesh.userData.trust = trust;
-      obj.data.trust = trust;
-      const tv = _getTrustVisuals(trust, region.color);
-      mesh.material.emissive = new THREE.Color(tv.emissiveColor);
-      mesh.material.emissiveIntensity = tv.emissiveIntensity;
-      mesh.material.opacity = tv.opacity;
-      mesh.userData.glowDesc = tv.glowDesc;
-      if (mesh.children.length > 0 && mesh.children[0].isPointLight) {
-        mesh.children[0].intensity = tv.lightIntensity;
-        mesh.children[0].color = new THREE.Color(tv.emissiveColor);
-      }
-    }
-
-    if (updates.strength != null) {
-      const strength = Math.max(0.05, Math.min(1, updates.strength));
-      mesh.userData.strength = strength;
-      obj.data.strength = strength;
-    }
-
-    _dirty = true;
-    saveToStorage();
-    console.info('[Mnemosyne] Visual updated:', memId, 'trust:', mesh.userData.trust, 'glow:', mesh.userData.glowDesc);
-    return true;
-  }
-
   // ─── QUERY ───────────────────────────────────────────
   function getMemoryAtPosition(position, maxDist) {
     maxDist = maxDist || 2;
@@ -606,7 +710,6 @@ const SpatialMemory = (() => {
         source: o.data.source || 'unknown',
         timestamp: o.data.timestamp || o.mesh.userData.createdAt,
         strength: o.mesh.userData.strength || 0.7,
-        trust: o.mesh.userData.trust != null ? o.mesh.userData.trust : 0.7,
         connections: o.data.connections || []
       }))
     };
@@ -752,173 +855,18 @@ const SpatialMemory = (() => {
     return _selectedId;
   }
 
-  // ─── FILE EXPORT ──────────────────────────────────────
-  function exportToFile() {
-    const index = exportIndex();
-    const json = JSON.stringify(index, null, 2);
-    const date = new Date().toISOString().slice(0, 10);
-    const filename = 'mnemosyne-export-' + date + '.json';
-
-    const blob = new Blob([json], { type: 'application/json' });
-    const url = URL.createObjectURL(blob);
-    const a = document.createElement('a');
-    a.href = url;
-    a.download = filename;
-    document.body.appendChild(a);
-    a.click();
-    document.body.removeChild(a);
-    URL.revokeObjectURL(url);
-
-    console.info('[Mnemosyne] Exported', index.memories.length, 'memories to', filename);
-    return { filename, count: index.memories.length };
-  }
-
-  // ─── FILE IMPORT ──────────────────────────────────────
-  function importFromFile(file) {
-    return new Promise((resolve, reject) => {
-      if (!file) {
-        reject(new Error('No file provided'));
-        return;
-      }
-
-      const reader = new FileReader();
-      reader.onload = function(e) {
-        try {
-          const data = JSON.parse(e.target.result);
-
-          // Schema validation
-          if (!data || typeof data !== 'object') {
-            reject(new Error('Invalid JSON: not an object'));
-            return;
-          }
-          if (typeof data.version !== 'number') {
-            reject(new Error('Invalid schema: missing version field'));
-            return;
-          }
-          if (data.version !== STORAGE_VERSION) {
-            reject(new Error('Version mismatch: got ' + data.version + ', expected ' + STORAGE_VERSION));
-            return;
-          }
-          if (!Array.isArray(data.memories)) {
-            reject(new Error('Invalid schema: memories is not an array'));
-            return;
-          }
-
-          // Validate each memory entry
-          for (let i = 0; i < data.memories.length; i++) {
-            const mem = data.memories[i];
-            if (!mem.id || typeof mem.id !== 'string') {
-              reject(new Error('Invalid memory at index ' + i + ': missing or invalid id'));
-              return;
-            }
-            if (!mem.category || typeof mem.category !== 'string') {
-              reject(new Error('Invalid memory "' + mem.id + '": missing category'));
-              return;
-            }
-          }
-
-          const count = importIndex(data);
-          saveToStorage();
-          console.info('[Mnemosyne] Imported', count, 'memories from file');
-          resolve({ count, total: data.memories.length });
-        } catch (parseErr) {
-          reject(new Error('Failed to parse JSON: ' + parseErr.message));
-        }
-      };
-
-      reader.onerror = function() {
-        reject(new Error('Failed to read file'));
-      };
-
-      reader.readAsText(file);
-    });
-  }
-
-
-  // ─── SPATIAL SEARCH (issue #1170) ────────────────────
-  let _searchOriginalState = {};  // memId -> { emissiveIntensity, opacity } for restore
-
-  function searchContent(query) {
-    if (!query || !query.trim()) return [];
-    const q = query.toLowerCase().trim();
-    const matches = [];
-
-    Object.values(_memoryObjects).forEach(obj => {
-      const d = obj.data;
-      const searchable = [
-        d.content || '',
-        d.id || '',
-        d.category || '',
-        d.source || '',
-        ...(d.connections || [])
-      ].join(' ').toLowerCase();
-
-      if (searchable.includes(q)) {
-        matches.push(d.id);
-      }
-    });
-
-    return matches;
-  }
-
-  function highlightSearchResults(matchIds) {
-    // Save original state and apply search highlighting
-    _searchOriginalState = {};
-    const matchSet = new Set(matchIds);
-
-    Object.entries(_memoryObjects).forEach(([id, obj]) => {
-      const mat = obj.mesh.material;
-      _searchOriginalState[id] = {
-        emissiveIntensity: mat.emissiveIntensity,
-        opacity: mat.opacity
-      };
-
-      if (matchSet.has(id)) {
-        // Match: bright white glow
-        mat.emissive.setHex(0xffffff);
-        mat.emissiveIntensity = 5.0;
-        mat.opacity = 1.0;
-      } else {
-        // Non-match: dim to 10% opacity
-        mat.opacity = 0.1;
-        mat.emissiveIntensity = 0.2;
-      }
-    });
-  }
-
-  function clearSearch() {
-    Object.entries(_memoryObjects).forEach(([id, obj]) => {
-      const mat = obj.mesh.material;
-      const saved = _searchOriginalState[id];
-      if (saved) {
-        // Restore original emissive color from region
-        const region = REGIONS[obj.region] || REGIONS.working;
-        mat.emissive.copy(region.color);
-        mat.emissiveIntensity = saved.emissiveIntensity;
-        mat.opacity = saved.opacity;
-      }
-    });
-    _searchOriginalState = {};
-  }
-
-  function getSearchMatchPosition(matchId) {
-    const obj = _memoryObjects[matchId];
-    return obj ? obj.mesh.position.clone() : null;
-  }
-
-  function setOnMemoryPlaced(callback) {
-    _onMemoryPlacedCallback = callback;
+  // ─── CAMERA REFERENCE (for entity line LOD) ─────────
+  function setCamera(camera) {
+    _camera = camera;
   }
 
   return {
-    init, placeMemory, removeMemory, update, updateMemoryVisual,
+    init, placeMemory, removeMemory, update, importMemories, updateMemory,
     getMemoryAtPosition, getRegionAtPosition, getMemoriesInRegion, getAllMemories,
     getCrystalMeshes, getMemoryFromMesh, highlightMemory, clearHighlight, getSelectedId,
-    exportIndex, importIndex, exportToFile, importFromFile, searchNearby, REGIONS,
+    exportIndex, importIndex, searchNearby, REGIONS,
     saveToStorage, loadFromStorage, clearStorage,
-    runGravityLayout,
-    searchContent, highlightSearchResults, clearSearch, getSearchMatchPosition,
-    setOnMemoryPlaced
+    runGravityLayout, setCamera
   };
 })();
 

nexus/mnemosyne/__init__.py

@@ -0,0 +1,24 @@
+"""nexus.mnemosyne — The Living Holographic Archive.
+
+Phase 1: Foundation — core archive, entry model, holographic linker,
+ingestion pipeline, and CLI.
+
+Builds on MemPalace vector memory to create interconnected meaning:
+entries auto-reference related entries via semantic similarity,
+forming a living archive that surfaces relevant context autonomously.
+"""
+
+from __future__ import annotations
+
+from nexus.mnemosyne.archive import MnemosyneArchive
+from nexus.mnemosyne.entry import ArchiveEntry
+from nexus.mnemosyne.linker import HolographicLinker
+from nexus.mnemosyne.ingest import ingest_from_mempalace, ingest_event
+
+__all__ = [
+    "MnemosyneArchive",
+    "ArchiveEntry",
+    "HolographicLinker",
+    "ingest_from_mempalace",
+    "ingest_event",
+]

nexus/mnemosyne/archive.py

@@ -0,0 +1,487 @@
+"""MnemosyneArchive — core archive class.
+
+The living holographic archive. Stores entries, maintains links,
+and provides query interfaces for retrieving connected knowledge.
+"""
+
+from __future__ import annotations
+
+import json
+from pathlib import Path
+from typing import Optional
+
+from nexus.mnemosyne.entry import ArchiveEntry
+from nexus.mnemosyne.linker import HolographicLinker
+
+_EXPORT_VERSION = "1"
+
+
+class MnemosyneArchive:
+    """The holographic archive — stores and links entries.
+
+    Phase 1 uses JSON file storage. Phase 2 will integrate with
+    MemPalace (ChromaDB) for vector-semantic search.
+    """
+
+    def __init__(self, archive_path: Optional[Path] = None):
+        self.path = archive_path or Path.home() / ".hermes" / "mnemosyne" / "archive.json"
+        self.path.parent.mkdir(parents=True, exist_ok=True)
+        self.linker = HolographicLinker()
+        self._entries: dict[str, ArchiveEntry] = {}
+        self._load()
+
+    def _load(self):
+        if self.path.exists():
+            try:
+                with open(self.path) as f:
+                    data = json.load(f)
+                for entry_data in data.get("entries", []):
+                    entry = ArchiveEntry.from_dict(entry_data)
+                    self._entries[entry.id] = entry
+            except (json.JSONDecodeError, KeyError):
+                pass  # Start fresh on corrupt data
+
+    def _save(self):
+        data = {
+            "entries": [e.to_dict() for e in self._entries.values()],
+            "count": len(self._entries),
+        }
+        with open(self.path, "w") as f:
+            json.dump(data, f, indent=2)
+
+    def add(self, entry: ArchiveEntry, auto_link: bool = True) -> ArchiveEntry:
+        """Add an entry to the archive. Auto-links to related entries."""
+        self._entries[entry.id] = entry
+        if auto_link:
+            self.linker.apply_links(entry, list(self._entries.values()))
+        self._save()
+        return entry
+
+    def get(self, entry_id: str) -> Optional[ArchiveEntry]:
+        return self._entries.get(entry_id)
+
+    def search(self, query: str, limit: int = 10) -> list[ArchiveEntry]:
+        """Simple keyword search across titles and content."""
+        query_tokens = set(query.lower().split())
+        scored = []
+        for entry in self._entries.values():
+            text = f"{entry.title} {entry.content} {' '.join(entry.topics)}".lower()
+            hits = sum(1 for t in query_tokens if t in text)
+            if hits > 0:
+                scored.append((hits, entry))
+        scored.sort(key=lambda x: x[0], reverse=True)
+        return [e for _, e in scored[:limit]]
+
+    def semantic_search(self, query: str, limit: int = 10, threshold: float = 0.05) -> list[ArchiveEntry]:
+        """Semantic search using holographic linker similarity.
+
+        Scores each entry by Jaccard similarity between query tokens and entry
+        tokens, then boosts entries with more inbound links (more "holographic").
+        Falls back to keyword search if no entries meet the similarity threshold.
+
+        Args:
+            query: Natural language query string.
+            limit: Maximum number of results to return.
+            threshold: Minimum Jaccard similarity to be considered a semantic match.
+
+        Returns:
+            List of ArchiveEntry sorted by combined relevance score, descending.
+        """
+        query_tokens = HolographicLinker._tokenize(query)
+        if not query_tokens:
+            return []
+
+        # Count inbound links for each entry (how many entries link TO this one)
+        inbound: dict[str, int] = {eid: 0 for eid in self._entries}
+        for entry in self._entries.values():
+            for linked_id in entry.links:
+                if linked_id in inbound:
+                    inbound[linked_id] += 1
+
+        max_inbound = max(inbound.values(), default=1) or 1
+
+        scored = []
+        for entry in self._entries.values():
+            entry_tokens = HolographicLinker._tokenize(f"{entry.title} {entry.content} {' '.join(entry.topics)}")
+            if not entry_tokens:
+                continue
+            intersection = query_tokens & entry_tokens
+            union = query_tokens | entry_tokens
+            jaccard = len(intersection) / len(union)
+            if jaccard >= threshold:
+                link_boost = inbound[entry.id] / max_inbound * 0.2  # up to 20% boost
+                scored.append((jaccard + link_boost, entry))
+
+        if scored:
+            scored.sort(key=lambda x: x[0], reverse=True)
+            return [e for _, e in scored[:limit]]
+
+        # Graceful fallback to keyword search
+        return self.search(query, limit=limit)
+
+    def get_linked(self, entry_id: str, depth: int = 1) -> list[ArchiveEntry]:
+        """Get entries linked to a given entry, up to specified depth."""
+        visited = set()
+        frontier = {entry_id}
+        result = []
+        for _ in range(depth):
+            next_frontier = set()
+            for eid in frontier:
+                if eid in visited:
+                    continue
+                visited.add(eid)
+                entry = self._entries.get(eid)
+                if entry:
+                    for linked_id in entry.links:
+                        if linked_id not in visited:
+                            linked = self._entries.get(linked_id)
+                            if linked:
+                                result.append(linked)
+                                next_frontier.add(linked_id)
+            frontier = next_frontier
+        return result
+
+    def by_topic(self, topic: str) -> list[ArchiveEntry]:
+        """Get all entries tagged with a topic."""
+        topic_lower = topic.lower()
+        return [e for e in self._entries.values() if topic_lower in [t.lower() for t in e.topics]]
+
+    def remove(self, entry_id: str) -> bool:
+        """Remove an entry and clean up all bidirectional links.
+
+        Returns True if the entry existed and was removed, False otherwise.
+        """
+        if entry_id not in self._entries:
+            return False
+        # Remove back-links from all other entries
+        for other in self._entries.values():
+            if entry_id in other.links:
+                other.links.remove(entry_id)
+        del self._entries[entry_id]
+        self._save()
+        return True
+
+    def export(
+        self,
+        query: Optional[str] = None,
+        topics: Optional[list[str]] = None,
+    ) -> dict:
+        """Export a filtered subset of the archive.
+
+        Args:
+            query: keyword filter applied to title + content (case-insensitive)
+            topics: list of topic tags; entries must match at least one
+
+        Returns a JSON-serialisable dict with an ``entries`` list and metadata.
+        """
+        candidates = list(self._entries.values())
+
+        if topics:
+            lower_topics = {t.lower() for t in topics}
+            candidates = [
+                e for e in candidates
+                if any(t.lower() in lower_topics for t in e.topics)
+            ]
+
+        if query:
+            query_tokens = set(query.lower().split())
+            candidates = [
+                e for e in candidates
+                if any(
+                    token in f"{e.title} {e.content} {' '.join(e.topics)}".lower()
+                    for token in query_tokens
+                )
+            ]
+
+        return {
+            "version": _EXPORT_VERSION,
+            "filters": {"query": query, "topics": topics},
+            "count": len(candidates),
+            "entries": [e.to_dict() for e in candidates],
+        }
+
+    def topic_counts(self) -> dict[str, int]:
+        """Return a dict mapping topic name → entry count, sorted by count desc."""
+        counts: dict[str, int] = {}
+        for entry in self._entries.values():
+            for topic in entry.topics:
+                counts[topic] = counts.get(topic, 0) + 1
+        return dict(sorted(counts.items(), key=lambda x: x[1], reverse=True))
+
+    @property
+    def count(self) -> int:
+        return len(self._entries)
+
+    def stats(self) -> dict:
+        entries = list(self._entries.values())
+        total_links = sum(len(e.links) for e in entries)
+        topics: set[str] = set()
+        for e in entries:
+            topics.update(e.topics)
+
+        # Orphans: entries with no links at all
+        orphans = sum(1 for e in entries if len(e.links) == 0)
+
+        # Link density: average links per entry (0 when empty)
+        n = len(entries)
+        link_density = round(total_links / n, 4) if n else 0.0
+
+        # Age distribution
+        timestamps = sorted(e.created_at for e in entries)
+        oldest_entry = timestamps[0] if timestamps else None
+        newest_entry = timestamps[-1] if timestamps else None
+
+        return {
+            "entries": n,
+            "total_links": total_links,
+            "unique_topics": len(topics),
+            "topics": sorted(topics),
+            "orphans": orphans,
+            "link_density": link_density,
+            "oldest_entry": oldest_entry,
+            "newest_entry": newest_entry,
+        }
+
+    def _build_adjacency(self) -> dict[str, set[str]]:
+        """Build adjacency dict from entry links. Only includes valid references."""
+        adj: dict[str, set[str]] = {eid: set() for eid in self._entries}
+        for eid, entry in self._entries.items():
+            for linked_id in entry.links:
+                if linked_id in self._entries and linked_id != eid:
+                    adj[eid].add(linked_id)
+                    adj[linked_id].add(eid)
+        return adj
+
+    def graph_clusters(self, min_size: int = 1) -> list[dict]:
+        """Find connected component clusters in the holographic graph.
+
+        Uses BFS to discover groups of entries that are reachable from each
+        other through their links. Returns clusters sorted by size descending.
+
+        Args:
+            min_size: Minimum cluster size to include (filters out isolated entries).
+
+        Returns:
+            List of dicts with keys: cluster_id, size, entries, topics, density
+        """
+        adj = self._build_adjacency()
+        visited: set[str] = set()
+        clusters: list[dict] = []
+        cluster_id = 0
+
+        for eid in self._entries:
+            if eid in visited:
+                continue
+            # BFS from this entry
+            component: list[str] = []
+            queue = [eid]
+            while queue:
+                current = queue.pop(0)
+                if current in visited:
+                    continue
+                visited.add(current)
+                component.append(current)
+                for neighbor in adj.get(current, set()):
+                    if neighbor not in visited:
+                        queue.append(neighbor)
+
+            # Single-entry clusters are orphans
+            if len(component) < min_size:
+                continue
+
+            # Collect topics from cluster entries
+            cluster_topics: dict[str, int] = {}
+            internal_edges = 0
+            for cid in component:
+                entry = self._entries[cid]
+                for t in entry.topics:
+                    cluster_topics[t] = cluster_topics.get(t, 0) + 1
+                internal_edges += len(adj.get(cid, set()))
+            internal_edges //= 2  # undirected, counted twice
+
+            # Density: actual edges / possible edges
+            n = len(component)
+            max_edges = n * (n - 1) // 2
+            density = round(internal_edges / max_edges, 4) if max_edges > 0 else 0.0
+
+            # Top topics by frequency
+            top_topics = sorted(cluster_topics.items(), key=lambda x: x[1], reverse=True)[:5]
+
+            clusters.append({
+                "cluster_id": cluster_id,
+                "size": n,
+                "entries": component,
+                "top_topics": [t for t, _ in top_topics],
+                "internal_edges": internal_edges,
+                "density": density,
+            })
+            cluster_id += 1
+
+        clusters.sort(key=lambda c: c["size"], reverse=True)
+        return clusters
+
+    def hub_entries(self, limit: int = 10) -> list[dict]:
+        """Find the most connected entries (highest degree centrality).
+
+        These are the "hubs" of the holographic graph — entries that bridge
+        many topics and attract many links.
+
+        Args:
+            limit: Maximum number of hubs to return.
+
+        Returns:
+            List of dicts with keys: entry, degree, inbound, outbound, topics
+        """
+        adj = self._build_adjacency()
+        inbound: dict[str, int] = {eid: 0 for eid in self._entries}
+
+        for entry in self._entries.values():
+            for lid in entry.links:
+                if lid in inbound:
+                    inbound[lid] += 1
+
+        hubs = []
+        for eid, entry in self._entries.items():
+            degree = len(adj.get(eid, set()))
+            if degree == 0:
+                continue
+            hubs.append({
+                "entry": entry,
+                "degree": degree,
+                "inbound": inbound.get(eid, 0),
+                "outbound": len(entry.links),
+                "topics": entry.topics,
+            })
+
+        hubs.sort(key=lambda h: h["degree"], reverse=True)
+        return hubs[:limit]
+
+    def bridge_entries(self) -> list[dict]:
+        """Find articulation points — entries whose removal would split a cluster.
+
+        These are "bridge" entries in the holographic graph. Removing them
+        disconnects members that were previously reachable through the bridge.
+        Uses Tarjan's algorithm for finding articulation points.
+
+        Returns:
+            List of dicts with keys: entry, cluster_size, bridges_between
+        """
+        adj = self._build_adjacency()
+
+        # Find clusters first
+        clusters = self.graph_clusters(min_size=3)
+        if not clusters:
+            return []
+
+        # For each cluster, run Tarjan's algorithm
+        bridges: list[dict] = []
+        for cluster in clusters:
+            members = set(cluster["entries"])
+            if len(members) < 3:
+                continue
+
+            # Build subgraph adjacency
+            sub_adj = {eid: adj[eid] & members for eid in members}
+
+            # Tarjan's DFS for articulation points
+            discovery: dict[str, int] = {}
+            low: dict[str, int] = {}
+            parent: dict[str, Optional[str]] = {}
+            ap: set[str] = set()
+            timer = [0]
+
+            def dfs(u: str):
+                children = 0
+                discovery[u] = low[u] = timer[0]
+                timer[0] += 1
+                for v in sub_adj[u]:
+                    if v not in discovery:
+                        children += 1
+                        parent[v] = u
+                        dfs(v)
+                        low[u] = min(low[u], low[v])
+
+                        # u is AP if: root with 2+ children, or non-root with low[v] >= disc[u]
+                        if parent.get(u) is None and children > 1:
+                            ap.add(u)
+                        if parent.get(u) is not None and low[v] >= discovery[u]:
+                            ap.add(u)
+                    elif v != parent.get(u):
+                        low[u] = min(low[u], discovery[v])
+
+            for eid in members:
+                if eid not in discovery:
+                    parent[eid] = None
+                    dfs(eid)
+
+            # For each articulation point, estimate what it bridges
+            for ap_id in ap:
+                ap_entry = self._entries[ap_id]
+                # Remove it temporarily and count resulting components
+                temp_adj = {k: v.copy() for k, v in sub_adj.items()}
+                del temp_adj[ap_id]
+                for k in temp_adj:
+                    temp_adj[k].discard(ap_id)
+
+                # BFS count components after removal
+                temp_visited: set[str] = set()
+                component_count = 0
+                for mid in members:
+                    if mid == ap_id or mid in temp_visited:
+                        continue
+                    component_count += 1
+                    queue = [mid]
+                    while queue:
+                        cur = queue.pop(0)
+                        if cur in temp_visited:
+                            continue
+                        temp_visited.add(cur)
+                        for nb in temp_adj.get(cur, set()):
+                            if nb not in temp_visited:
+                                queue.append(nb)
+
+                if component_count > 1:
+                    bridges.append({
+                        "entry": ap_entry,
+                        "cluster_size": cluster["size"],
+                        "components_after_removal": component_count,
+                        "topics": ap_entry.topics,
+                    })
+
+        bridges.sort(key=lambda b: b["components_after_removal"], reverse=True)
+        return bridges
+
+    def rebuild_links(self, threshold: Optional[float] = None) -> int:
+        """Recompute all links from scratch.
+
+        Clears existing links and re-applies the holographic linker to every
+        entry pair. Useful after bulk ingestion or threshold changes.
+
+        Args:
+            threshold: Override the linker's default similarity threshold.
+
+        Returns:
+            Total number of links created.
+        """
+        if threshold is not None:
+            old_threshold = self.linker.threshold
+            self.linker.threshold = threshold
+
+        # Clear all links
+        for entry in self._entries.values():
+            entry.links = []
+
+        entries = list(self._entries.values())
+        total_links = 0
+
+        # Re-link each entry against all others
+        for entry in entries:
+            candidates = [e for e in entries if e.id != entry.id]
+            new_links = self.linker.apply_links(entry, candidates)
+            total_links += new_links
+
+        if threshold is not None:
+            self.linker.threshold = old_threshold
+
+        self._save()
+        return total_links

nexus/mnemosyne/cli.py

@@ -0,0 +1,209 @@
+"""CLI interface for Mnemosyne.
+
+Provides: mnemosyne ingest, mnemosyne search, mnemosyne link, mnemosyne stats,
+          mnemosyne topics, mnemosyne remove, mnemosyne export,
+          mnemosyne clusters, mnemosyne hubs, mnemosyne bridges, mnemosyne rebuild
+"""
+
+from __future__ import annotations
+
+import argparse
+import json
+import sys
+
+from nexus.mnemosyne.archive import MnemosyneArchive
+from nexus.mnemosyne.entry import ArchiveEntry
+from nexus.mnemosyne.ingest import ingest_event
+
+
+def cmd_stats(args):
+    archive = MnemosyneArchive()
+    stats = archive.stats()
+    print(json.dumps(stats, indent=2))
+
+
+def cmd_search(args):
+    archive = MnemosyneArchive()
+    if getattr(args, "semantic", False):
+        results = archive.semantic_search(args.query, limit=args.limit)
+    else:
+        results = archive.search(args.query, limit=args.limit)
+    if not results:
+        print("No results found.")
+        return
+    for entry in results:
+        linked = len(entry.links)
+        print(f"[{entry.id[:8]}] {entry.title}")
+        print(f"  Source: {entry.source} | Topics: {', '.join(entry.topics)} | Links: {linked}")
+        print(f"  {entry.content[:120]}...")
+        print()
+
+
+def cmd_ingest(args):
+    archive = MnemosyneArchive()
+    entry = ingest_event(
+        archive,
+        title=args.title,
+        content=args.content,
+        topics=args.topics.split(",") if args.topics else [],
+    )
+    print(f"Ingested: [{entry.id[:8]}] {entry.title} ({len(entry.links)} links)")
+
+
+def cmd_link(args):
+    archive = MnemosyneArchive()
+    entry = archive.get(args.entry_id)
+    if not entry:
+        print(f"Entry not found: {args.entry_id}")
+        sys.exit(1)
+    linked = archive.get_linked(entry.id, depth=args.depth)
+    if not linked:
+        print("No linked entries found.")
+        return
+    for e in linked:
+        print(f"  [{e.id[:8]}] {e.title} (source: {e.source})")
+
+
+def cmd_topics(args):
+    archive = MnemosyneArchive()
+    counts = archive.topic_counts()
+    if not counts:
+        print("No topics found.")
+        return
+    for topic, count in counts.items():
+        print(f"  {topic}: {count}")
+
+
+def cmd_remove(args):
+    archive = MnemosyneArchive()
+    removed = archive.remove(args.entry_id)
+    if removed:
+        print(f"Removed entry: {args.entry_id}")
+    else:
+        print(f"Entry not found: {args.entry_id}")
+        sys.exit(1)
+
+
+def cmd_export(args):
+    archive = MnemosyneArchive()
+    topics = [t.strip() for t in args.topics.split(",")] if args.topics else None
+    data = archive.export(query=args.query or None, topics=topics)
+    print(json.dumps(data, indent=2))
+
+
+def cmd_clusters(args):
+    archive = MnemosyneArchive()
+    clusters = archive.graph_clusters(min_size=args.min_size)
+    if not clusters:
+        print("No clusters found.")
+        return
+    for c in clusters:
+        print(f"Cluster {c['cluster_id']}: {c['size']} entries, density={c['density']}")
+        print(f"  Topics: {', '.join(c['top_topics']) if c['top_topics'] else '(none)'}")
+        if args.verbose:
+            for eid in c["entries"]:
+                entry = archive.get(eid)
+                if entry:
+                    print(f"    [{eid[:8]}] {entry.title}")
+        print()
+
+
+def cmd_hubs(args):
+    archive = MnemosyneArchive()
+    hubs = archive.hub_entries(limit=args.limit)
+    if not hubs:
+        print("No hubs found.")
+        return
+    for h in hubs:
+        e = h["entry"]
+        print(f"[{e.id[:8]}] {e.title}")
+        print(f"  Degree: {h['degree']} (in: {h['inbound']}, out: {h['outbound']})")
+        print(f"  Topics: {', '.join(h['topics']) if h['topics'] else '(none)'}")
+        print()
+
+
+def cmd_bridges(args):
+    archive = MnemosyneArchive()
+    bridges = archive.bridge_entries()
+    if not bridges:
+        print("No bridge entries found.")
+        return
+    for b in bridges:
+        e = b["entry"]
+        print(f"[{e.id[:8]}] {e.title}")
+        print(f"  Bridges {b['components_after_removal']} components (cluster: {b['cluster_size']} entries)")
+        print(f"  Topics: {', '.join(b['topics']) if b['topics'] else '(none)'}")
+        print()
+
+
+def cmd_rebuild(args):
+    archive = MnemosyneArchive()
+    threshold = args.threshold if args.threshold else None
+    total = archive.rebuild_links(threshold=threshold)
+    print(f"Rebuilt links: {total} connections across {archive.count} entries")
+
+
+def main():
+    parser = argparse.ArgumentParser(prog="mnemosyne", description="The Living Holographic Archive")
+    sub = parser.add_subparsers(dest="command")
+
+    sub.add_parser("stats", help="Show archive statistics")
+
+    s = sub.add_parser("search", help="Search the archive")
+    s.add_argument("query", help="Search query")
+    s.add_argument("-n", "--limit", type=int, default=10)
+    s.add_argument("--semantic", action="store_true", help="Use holographic linker similarity scoring")
+
+    i = sub.add_parser("ingest", help="Ingest a new entry")
+    i.add_argument("--title", required=True)
+    i.add_argument("--content", required=True)
+    i.add_argument("--topics", default="", help="Comma-separated topics")
+
+    l = sub.add_parser("link", help="Show linked entries")
+    l.add_argument("entry_id", help="Entry ID (or prefix)")
+    l.add_argument("-d", "--depth", type=int, default=1)
+
+    sub.add_parser("topics", help="List all topics with entry counts")
+
+    r = sub.add_parser("remove", help="Remove an entry by ID")
+    r.add_argument("entry_id", help="Entry ID to remove")
+
+    ex = sub.add_parser("export", help="Export filtered archive data as JSON")
+    ex.add_argument("-q", "--query", default="", help="Keyword filter")
+    ex.add_argument("-t", "--topics", default="", help="Comma-separated topic filter")
+
+    cl = sub.add_parser("clusters", help="Show graph clusters (connected components)")
+    cl.add_argument("-m", "--min-size", type=int, default=1, help="Minimum cluster size")
+    cl.add_argument("-v", "--verbose", action="store_true", help="List entries in each cluster")
+
+    hu = sub.add_parser("hubs", help="Show most connected entries (hub analysis)")
+    hu.add_argument("-n", "--limit", type=int, default=10, help="Max hubs to show")
+
+    sub.add_parser("bridges", help="Show bridge entries (articulation points)")
+
+    rb = sub.add_parser("rebuild", help="Recompute all links from scratch")
+    rb.add_argument("-t", "--threshold", type=float, default=None, help="Similarity threshold override")
+
+    args = parser.parse_args()
+    if not args.command:
+        parser.print_help()
+        sys.exit(1)
+
+    dispatch = {
+        "stats": cmd_stats,
+        "search": cmd_search,
+        "ingest": cmd_ingest,
+        "link": cmd_link,
+        "topics": cmd_topics,
+        "remove": cmd_remove,
+        "export": cmd_export,
+        "clusters": cmd_clusters,
+        "hubs": cmd_hubs,
+        "bridges": cmd_bridges,
+        "rebuild": cmd_rebuild,
+    }
+    dispatch[args.command](args)
+
+
+if __name__ == "__main__":
+    main()

nexus/mnemosyne/entry.py

@@ -0,0 +1,44 @@
+"""Archive entry model for Mnemosyne.
+
+Each entry is a node in the holographic graph — a piece of meaning
+with metadata, content, and links to related entries.
+"""
+
+from __future__ import annotations
+
+from dataclasses import dataclass, field
+from datetime import datetime, timezone
+from typing import Optional
+import uuid
+
+
+@dataclass
+class ArchiveEntry:
+    """A single node in the Mnemosyne holographic archive."""
+
+    id: str = field(default_factory=lambda: str(uuid.uuid4()))
+    title: str = ""
+    content: str = ""
+    source: str = ""               # "mempalace", "event", "manual", etc.
+    source_ref: Optional[str] = None  # original MemPalace ID, event URI, etc.
+    topics: list[str] = field(default_factory=list)
+    metadata: dict = field(default_factory=dict)
+    created_at: str = field(default_factory=lambda: datetime.now(timezone.utc).isoformat())
+    links: list[str] = field(default_factory=list)  # IDs of related entries
+
+    def to_dict(self) -> dict:
+        return {
+            "id": self.id,
+            "title": self.title,
+            "content": self.content,
+            "source": self.source,
+            "source_ref": self.source_ref,
+            "topics": self.topics,
+            "metadata": self.metadata,
+            "created_at": self.created_at,
+            "links": self.links,
+        }
+
+    @classmethod
+    def from_dict(cls, data: dict) -> ArchiveEntry:
+        return cls(**{k: v for k, v in data.items() if k in cls.__dataclass_fields__})

nexus/mnemosyne/ingest.py

@@ -0,0 +1,62 @@
+"""Ingestion pipeline — feeds data into the archive.
+
+Supports ingesting from MemPalace, raw events, and manual entries.
+"""
+
+from __future__ import annotations
+
+from typing import Optional
+
+from nexus.mnemosyne.archive import MnemosyneArchive
+from nexus.mnemosyne.entry import ArchiveEntry
+
+
+def ingest_from_mempalace(
+    archive: MnemosyneArchive,
+    mempalace_entries: list[dict],
+) -> int:
+    """Ingest entries from a MemPalace export.
+
+    Each dict should have at least: content, metadata (optional).
+    Returns count of new entries added.
+    """
+    added = 0
+    for mp_entry in mempalace_entries:
+        content = mp_entry.get("content", "")
+        metadata = mp_entry.get("metadata", {})
+        source_ref = mp_entry.get("id", "")
+
+        # Skip if already ingested
+        if any(e.source_ref == source_ref for e in archive._entries.values()):
+            continue
+
+        entry = ArchiveEntry(
+            title=metadata.get("title", content[:80]),
+            content=content,
+            source="mempalace",
+            source_ref=source_ref,
+            topics=metadata.get("topics", []),
+            metadata=metadata,
+        )
+        archive.add(entry)
+        added += 1
+    return added
+
+
+def ingest_event(
+    archive: MnemosyneArchive,
+    title: str,
+    content: str,
+    topics: Optional[list[str]] = None,
+    source: str = "event",
+    metadata: Optional[dict] = None,
+) -> ArchiveEntry:
+    """Ingest a single event into the archive."""
+    entry = ArchiveEntry(
+        title=title,
+        content=content,
+        source=source,
+        topics=topics or [],
+        metadata=metadata or {},
+    )
+    return archive.add(entry)

nexus/mnemosyne/linker.py

@@ -0,0 +1,73 @@
+"""Holographic link engine.
+
+Computes semantic similarity between archive entries and creates
+bidirectional links, forming the holographic graph structure.
+"""
+
+from __future__ import annotations
+
+from typing import Optional
+from nexus.mnemosyne.entry import ArchiveEntry
+
+
+class HolographicLinker:
+    """Links archive entries via semantic similarity.
+
+    Phase 1 uses simple keyword overlap as the similarity metric.
+    Phase 2 will integrate ChromaDB embeddings from MemPalace.
+    """
+
+    def __init__(self, similarity_threshold: float = 0.15):
+        self.threshold = similarity_threshold
+
+    def compute_similarity(self, a: ArchiveEntry, b: ArchiveEntry) -> float:
+        """Compute similarity score between two entries.
+
+        Returns float in [0, 1]. Phase 1: Jaccard similarity on
+        combined title+content tokens. Phase 2: cosine similarity
+        on ChromaDB embeddings.
+        """
+        tokens_a = self._tokenize(f"{a.title} {a.content}")
+        tokens_b = self._tokenize(f"{b.title} {b.content}")
+        if not tokens_a or not tokens_b:
+            return 0.0
+        intersection = tokens_a & tokens_b
+        union = tokens_a | tokens_b
+        return len(intersection) / len(union)
+
+    def find_links(self, entry: ArchiveEntry, candidates: list[ArchiveEntry]) -> list[tuple[str, float]]:
+        """Find entries worth linking to.
+
+        Returns list of (entry_id, similarity_score) tuples above threshold.
+        """
+        results = []
+        for candidate in candidates:
+            if candidate.id == entry.id:
+                continue
+            score = self.compute_similarity(entry, candidate)
+            if score >= self.threshold:
+                results.append((candidate.id, score))
+        results.sort(key=lambda x: x[1], reverse=True)
+        return results
+
+    def apply_links(self, entry: ArchiveEntry, candidates: list[ArchiveEntry]) -> int:
+        """Auto-link an entry to related entries. Returns count of new links."""
+        matches = self.find_links(entry, candidates)
+        new_links = 0
+        for eid, score in matches:
+            if eid not in entry.links:
+                entry.links.append(eid)
+                new_links += 1
+            # Bidirectional
+            for c in candidates:
+                if c.id == eid and entry.id not in c.links:
+                    c.links.append(entry.id)
+        return new_links
+
+    @staticmethod
+    def _tokenize(text: str) -> set[str]:
+        """Simple whitespace + punctuation tokenizer."""
+        import re
+        tokens = set(re.findall(r"\w+", text.lower()))
+        # Remove very short tokens
+        return {t for t in tokens if len(t) > 2}

nexus/mnemosyne/tests/test_archive.py

@@ -0,0 +1,276 @@
+"""Tests for Mnemosyne archive core."""
+
+import json
+import tempfile
+from pathlib import Path
+
+from nexus.mnemosyne.entry import ArchiveEntry
+from nexus.mnemosyne.linker import HolographicLinker
+from nexus.mnemosyne.archive import MnemosyneArchive
+from nexus.mnemosyne.ingest import ingest_event, ingest_from_mempalace
+
+
+def test_entry_roundtrip():
+    e = ArchiveEntry(title="Test", content="Hello world", topics=["test"])
+    d = e.to_dict()
+    e2 = ArchiveEntry.from_dict(d)
+    assert e2.id == e.id
+    assert e2.title == "Test"
+
+
+def test_linker_similarity():
+    linker = HolographicLinker()
+    a = ArchiveEntry(title="Python coding", content="Writing Python scripts for automation")
+    b = ArchiveEntry(title="Python scripting", content="Automating tasks with Python scripts")
+    c = ArchiveEntry(title="Cooking recipes", content="How to make pasta carbonara")
+    assert linker.compute_similarity(a, b) > linker.compute_similarity(a, c)
+
+
+def test_archive_add_and_search():
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        archive = MnemosyneArchive(archive_path=path)
+        ingest_event(archive, title="First entry", content="Hello archive", topics=["test"])
+        ingest_event(archive, title="Second entry", content="Another record", topics=["test", "demo"])
+        assert archive.count == 2
+        results = archive.search("hello")
+        assert len(results) == 1
+        assert results[0].title == "First entry"
+
+
+def test_archive_auto_linking():
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        archive = MnemosyneArchive(archive_path=path)
+        e1 = ingest_event(archive, title="Python automation", content="Building automation tools in Python")
+        e2 = ingest_event(archive, title="Python scripting", content="Writing automation scripts using Python")
+        # Both should be linked due to shared tokens
+        assert len(e1.links) > 0 or len(e2.links) > 0
+
+
+def test_ingest_from_mempalace():
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        archive = MnemosyneArchive(archive_path=path)
+        mp_entries = [
+            {"id": "mp-1", "content": "Test memory content", "metadata": {"title": "Test", "topics": ["demo"]}},
+            {"id": "mp-2", "content": "Another memory", "metadata": {"title": "Memory 2"}},
+        ]
+        count = ingest_from_mempalace(archive, mp_entries)
+        assert count == 2
+        assert archive.count == 2
+
+
+def test_archive_persistence():
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        archive1 = MnemosyneArchive(archive_path=path)
+        ingest_event(archive1, title="Persistent", content="Should survive reload")
+
+        archive2 = MnemosyneArchive(archive_path=path)
+        assert archive2.count == 1
+        results = archive2.search("persistent")
+        assert len(results) == 1
+
+
+def test_archive_remove_basic():
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        archive = MnemosyneArchive(archive_path=path)
+        e1 = ingest_event(archive, title="Alpha", content="First entry", topics=["x"])
+        assert archive.count == 1
+
+        result = archive.remove(e1.id)
+        assert result is True
+        assert archive.count == 0
+        assert archive.get(e1.id) is None
+
+
+def test_archive_remove_nonexistent():
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        archive = MnemosyneArchive(archive_path=path)
+        result = archive.remove("does-not-exist")
+        assert result is False
+
+
+def test_archive_remove_cleans_backlinks():
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        archive = MnemosyneArchive(archive_path=path)
+        e1 = ingest_event(archive, title="Python automation", content="Building automation tools in Python")
+        e2 = ingest_event(archive, title="Python scripting", content="Writing automation scripts using Python")
+        # At least one direction should be linked
+        assert e1.id in e2.links or e2.id in e1.links
+
+        # Remove e1; e2 must no longer reference it
+        archive.remove(e1.id)
+        e2_fresh = archive.get(e2.id)
+        assert e2_fresh is not None
+        assert e1.id not in e2_fresh.links
+
+
+def test_archive_remove_persists():
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        a1 = MnemosyneArchive(archive_path=path)
+        e = ingest_event(a1, title="Gone", content="Will be removed")
+        a1.remove(e.id)
+
+        a2 = MnemosyneArchive(archive_path=path)
+        assert a2.count == 0
+
+
+def test_archive_export_unfiltered():
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        archive = MnemosyneArchive(archive_path=path)
+        ingest_event(archive, title="A", content="content a", topics=["alpha"])
+        ingest_event(archive, title="B", content="content b", topics=["beta"])
+        data = archive.export()
+        assert data["count"] == 2
+        assert len(data["entries"]) == 2
+        assert data["filters"] == {"query": None, "topics": None}
+
+
+def test_archive_export_by_topic():
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        archive = MnemosyneArchive(archive_path=path)
+        ingest_event(archive, title="A", content="content a", topics=["alpha"])
+        ingest_event(archive, title="B", content="content b", topics=["beta"])
+        data = archive.export(topics=["alpha"])
+        assert data["count"] == 1
+        assert data["entries"][0]["title"] == "A"
+
+
+def test_archive_export_by_query():
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        archive = MnemosyneArchive(archive_path=path)
+        ingest_event(archive, title="Hello world", content="greetings", topics=[])
+        ingest_event(archive, title="Goodbye", content="farewell", topics=[])
+        data = archive.export(query="hello")
+        assert data["count"] == 1
+        assert data["entries"][0]["title"] == "Hello world"
+
+
+def test_archive_export_combined_filters():
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        archive = MnemosyneArchive(archive_path=path)
+        ingest_event(archive, title="Hello world", content="greetings", topics=["alpha"])
+        ingest_event(archive, title="Hello again", content="greetings again", topics=["beta"])
+        data = archive.export(query="hello", topics=["alpha"])
+        assert data["count"] == 1
+        assert data["entries"][0]["title"] == "Hello world"
+
+
+def test_archive_stats_richer():
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        archive = MnemosyneArchive(archive_path=path)
+        # All four new fields present when archive is empty
+        s = archive.stats()
+        assert "orphans" in s
+        assert "link_density" in s
+        assert "oldest_entry" in s
+        assert "newest_entry" in s
+        assert s["orphans"] == 0
+        assert s["link_density"] == 0.0
+        assert s["oldest_entry"] is None
+        assert s["newest_entry"] is None
+
+
+def test_archive_stats_orphan_count():
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        archive = MnemosyneArchive(archive_path=path)
+        # Two entries with very different content → unlikely to auto-link
+        ingest_event(archive, title="Zebras", content="Zebra stripes savannah Africa", topics=[])
+        ingest_event(archive, title="Compiler", content="Lexer parser AST bytecode", topics=[])
+        s = archive.stats()
+        # At least one should be an orphan (no cross-link between these topics)
+        assert s["orphans"] >= 0  # structural check
+        assert s["link_density"] >= 0.0
+        assert s["oldest_entry"] is not None
+        assert s["newest_entry"] is not None
+
+
+def test_semantic_search_returns_results():
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        archive = MnemosyneArchive(archive_path=path)
+        ingest_event(archive, title="Python automation", content="Building automation tools in Python")
+        ingest_event(archive, title="Cooking recipes", content="How to make pasta carbonara with cheese")
+        results = archive.semantic_search("python scripting", limit=5)
+        assert len(results) > 0
+        assert results[0].title == "Python automation"
+
+
+def test_semantic_search_link_boost():
+    """Entries with more inbound links rank higher when Jaccard is equal."""
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        archive = MnemosyneArchive(archive_path=path)
+        # Create two similar entries; manually give one more links
+        e1 = ingest_event(archive, title="Machine learning", content="Neural networks deep learning models")
+        e2 = ingest_event(archive, title="Machine learning basics", content="Neural networks deep learning intro")
+        # Add a third entry that links to e1 so e1 has more inbound links
+        e3 = ingest_event(archive, title="AI overview", content="Artificial intelligence machine learning")
+        # Manually give e1 an extra inbound link by adding e3 -> e1
+        if e1.id not in e3.links:
+            e3.links.append(e1.id)
+        archive._save()
+        results = archive.semantic_search("machine learning neural networks", limit=5)
+        assert len(results) >= 2
+        # e1 should rank at or near top
+        assert results[0].id in {e1.id, e2.id}
+
+
+def test_semantic_search_fallback_to_keyword():
+    """Falls back to keyword search when no entry meets Jaccard threshold."""
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        archive = MnemosyneArchive(archive_path=path)
+        ingest_event(archive, title="Exact match only", content="unique xyzzy token here")
+        # threshold=1.0 ensures no semantic match, triggering fallback
+        results = archive.semantic_search("xyzzy", limit=5, threshold=1.0)
+        # Fallback keyword search should find it
+        assert len(results) == 1
+        assert results[0].title == "Exact match only"
+
+
+def test_semantic_search_empty_archive():
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        archive = MnemosyneArchive(archive_path=path)
+        results = archive.semantic_search("anything", limit=5)
+        assert results == []
+
+
+def test_semantic_search_vs_keyword_relevance():
+    """Semantic search finds conceptually related entries missed by keyword search."""
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        archive = MnemosyneArchive(archive_path=path)
+        ingest_event(archive, title="Python scripting", content="Writing scripts with Python for automation tasks")
+        ingest_event(archive, title="Baking bread", content="Mix flour water yeast knead bake oven")
+        # "coding" is semantically unrelated to baking but related to python scripting
+        results = archive.semantic_search("coding scripts automation")
+        assert len(results) > 0
+        assert results[0].title == "Python scripting"
+
+
+def test_archive_topic_counts():
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        archive = MnemosyneArchive(archive_path=path)
+        ingest_event(archive, title="A", content="x", topics=["python", "automation"])
+        ingest_event(archive, title="B", content="y", topics=["python"])
+        ingest_event(archive, title="C", content="z", topics=["automation"])
+        counts = archive.topic_counts()
+        assert counts["python"] == 2
+        assert counts["automation"] == 2
+        # sorted by count desc — both tied but must be present
+        assert set(counts.keys()) == {"python", "automation"}

nexus/mnemosyne/tests/test_graph_clusters.py

@@ -0,0 +1,271 @@
+"""Tests for Mnemosyne graph cluster analysis features.
+
+Tests: graph_clusters, hub_entries, bridge_entries, rebuild_links.
+"""
+
+import pytest
+from pathlib import Path
+import tempfile
+
+from nexus.mnemosyne.archive import MnemosyneArchive
+from nexus.mnemosyne.entry import ArchiveEntry
+
+
+@pytest.fixture
+def archive():
+    """Create a fresh archive in a temp directory."""
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        a = MnemosyneArchive(archive_path=path)
+        yield a
+
+
+def _make_entry(title="Test", content="test content", topics=None):
+    return ArchiveEntry(title=title, content=content, topics=topics or [])
+
+
+class TestGraphClusters:
+    """Test graph_clusters() connected component discovery."""
+
+    def test_empty_archive(self, archive):
+        clusters = archive.graph_clusters()
+        assert clusters == []
+
+    def test_single_orphan(self, archive):
+        archive.add(_make_entry("Lone entry"), auto_link=False)
+        # min_size=1 includes orphans
+        clusters = archive.graph_clusters(min_size=1)
+        assert len(clusters) == 1
+        assert clusters[0]["size"] == 1
+        assert clusters[0]["density"] == 0.0
+
+    def test_single_orphan_filtered(self, archive):
+        archive.add(_make_entry("Lone entry"), auto_link=False)
+        clusters = archive.graph_clusters(min_size=2)
+        assert clusters == []
+
+    def test_two_linked_entries(self, archive):
+        """Two manually linked entries form a cluster."""
+        e1 = archive.add(_make_entry("Alpha dogs", "canine training"), auto_link=False)
+        e2 = archive.add(_make_entry("Beta cats", "feline behavior"), auto_link=False)
+        # Manual link
+        e1.links.append(e2.id)
+        e2.links.append(e1.id)
+        archive._save()
+
+        clusters = archive.graph_clusters(min_size=2)
+        assert len(clusters) == 1
+        assert clusters[0]["size"] == 2
+        assert clusters[0]["internal_edges"] == 1
+        assert clusters[0]["density"] == 1.0  # 1 edge out of 1 possible
+
+    def test_two_separate_clusters(self, archive):
+        """Two disconnected groups form separate clusters."""
+        a1 = archive.add(_make_entry("AI models", "neural networks"), auto_link=False)
+        a2 = archive.add(_make_entry("AI training", "gradient descent"), auto_link=False)
+        b1 = archive.add(_make_entry("Cooking pasta", "italian recipes"), auto_link=False)
+        b2 = archive.add(_make_entry("Cooking sauces", "tomato basil"), auto_link=False)
+
+        # Link cluster A
+        a1.links.append(a2.id)
+        a2.links.append(a1.id)
+        # Link cluster B
+        b1.links.append(b2.id)
+        b2.links.append(b1.id)
+        archive._save()
+
+        clusters = archive.graph_clusters(min_size=2)
+        assert len(clusters) == 2
+        sizes = sorted(c["size"] for c in clusters)
+        assert sizes == [2, 2]
+
+    def test_cluster_topics(self, archive):
+        """Cluster includes aggregated topics."""
+        e1 = archive.add(_make_entry("Alpha", "content", topics=["ai", "models"]), auto_link=False)
+        e2 = archive.add(_make_entry("Beta", "content", topics=["ai", "training"]), auto_link=False)
+        e1.links.append(e2.id)
+        e2.links.append(e1.id)
+        archive._save()
+
+        clusters = archive.graph_clusters(min_size=2)
+        assert "ai" in clusters[0]["top_topics"]
+
+    def test_density_calculation(self, archive):
+        """Triangle (3 nodes, 3 edges) has density 1.0."""
+        e1 = archive.add(_make_entry("A", "aaa"), auto_link=False)
+        e2 = archive.add(_make_entry("B", "bbb"), auto_link=False)
+        e3 = archive.add(_make_entry("C", "ccc"), auto_link=False)
+        # Fully connected triangle
+        for e, others in [(e1, [e2, e3]), (e2, [e1, e3]), (e3, [e1, e2])]:
+            for o in others:
+                e.links.append(o.id)
+        archive._save()
+
+        clusters = archive.graph_clusters(min_size=2)
+        assert len(clusters) == 1
+        assert clusters[0]["internal_edges"] == 3
+        assert clusters[0]["density"] == 1.0  # 3 edges / 3 possible
+
+    def test_chain_density(self, archive):
+        """A-B-C chain has density 2/3 (2 edges out of 3 possible)."""
+        e1 = archive.add(_make_entry("A", "aaa"), auto_link=False)
+        e2 = archive.add(_make_entry("B", "bbb"), auto_link=False)
+        e3 = archive.add(_make_entry("C", "ccc"), auto_link=False)
+        # Chain: A-B-C
+        e1.links.append(e2.id)
+        e2.links.extend([e1.id, e3.id])
+        e3.links.append(e2.id)
+        archive._save()
+
+        clusters = archive.graph_clusters(min_size=2)
+        assert abs(clusters[0]["density"] - 2/3) < 0.01
+
+
+class TestHubEntries:
+    """Test hub_entries() degree centrality ranking."""
+
+    def test_empty(self, archive):
+        assert archive.hub_entries() == []
+
+    def test_no_links(self, archive):
+        archive.add(_make_entry("Lone"), auto_link=False)
+        assert archive.hub_entries() == []
+
+    def test_hub_ordering(self, archive):
+        """Entry with most links is ranked first."""
+        e1 = archive.add(_make_entry("Hub", "central node"), auto_link=False)
+        e2 = archive.add(_make_entry("Spoke 1", "content"), auto_link=False)
+        e3 = archive.add(_make_entry("Spoke 2", "content"), auto_link=False)
+        e4 = archive.add(_make_entry("Spoke 3", "content"), auto_link=False)
+
+        # e1 connects to all spokes
+        e1.links.extend([e2.id, e3.id, e4.id])
+        e2.links.append(e1.id)
+        e3.links.append(e1.id)
+        e4.links.append(e1.id)
+        archive._save()
+
+        hubs = archive.hub_entries()
+        assert len(hubs) == 4
+        assert hubs[0]["entry"].id == e1.id
+        assert hubs[0]["degree"] == 3
+
+    def test_limit(self, archive):
+        e1 = archive.add(_make_entry("A", ""), auto_link=False)
+        e2 = archive.add(_make_entry("B", ""), auto_link=False)
+        e1.links.append(e2.id)
+        e2.links.append(e1.id)
+        archive._save()
+
+        assert len(archive.hub_entries(limit=1)) == 1
+
+    def test_inbound_outbound(self, archive):
+        """Inbound counts links TO an entry, outbound counts links FROM it."""
+        e1 = archive.add(_make_entry("Source", ""), auto_link=False)
+        e2 = archive.add(_make_entry("Target", ""), auto_link=False)
+        # Only e1 links to e2
+        e1.links.append(e2.id)
+        archive._save()
+
+        hubs = archive.hub_entries()
+        h1 = next(h for h in hubs if h["entry"].id == e1.id)
+        h2 = next(h for h in hubs if h["entry"].id == e2.id)
+        assert h1["inbound"] == 0
+        assert h1["outbound"] == 1
+        assert h2["inbound"] == 1
+        assert h2["outbound"] == 0
+
+
+class TestBridgeEntries:
+    """Test bridge_entries() articulation point detection."""
+
+    def test_empty(self, archive):
+        assert archive.bridge_entries() == []
+
+    def test_no_bridges_in_triangle(self, archive):
+        """Fully connected triangle has no articulation points."""
+        e1 = archive.add(_make_entry("A", ""), auto_link=False)
+        e2 = archive.add(_make_entry("B", ""), auto_link=False)
+        e3 = archive.add(_make_entry("C", ""), auto_link=False)
+        for e, others in [(e1, [e2, e3]), (e2, [e1, e3]), (e3, [e1, e2])]:
+            for o in others:
+                e.links.append(o.id)
+        archive._save()
+
+        assert archive.bridge_entries() == []
+
+    def test_bridge_in_chain(self, archive):
+        """A-B-C chain: B is the articulation point."""
+        e1 = archive.add(_make_entry("A", ""), auto_link=False)
+        e2 = archive.add(_make_entry("B", ""), auto_link=False)
+        e3 = archive.add(_make_entry("C", ""), auto_link=False)
+        e1.links.append(e2.id)
+        e2.links.extend([e1.id, e3.id])
+        e3.links.append(e2.id)
+        archive._save()
+
+        bridges = archive.bridge_entries()
+        assert len(bridges) == 1
+        assert bridges[0]["entry"].id == e2.id
+        assert bridges[0]["components_after_removal"] == 2
+
+    def test_no_bridges_in_small_cluster(self, archive):
+        """Two-node clusters are too small for bridge detection."""
+        e1 = archive.add(_make_entry("A", ""), auto_link=False)
+        e2 = archive.add(_make_entry("B", ""), auto_link=False)
+        e1.links.append(e2.id)
+        e2.links.append(e1.id)
+        archive._save()
+
+        assert archive.bridge_entries() == []
+
+
+class TestRebuildLinks:
+    """Test rebuild_links() full recomputation."""
+
+    def test_empty_archive(self, archive):
+        assert archive.rebuild_links() == 0
+
+    def test_creates_links(self, archive):
+        """Rebuild creates links between similar entries."""
+        archive.add(_make_entry("Alpha dogs canine training", "obedience training"), auto_link=False)
+        archive.add(_make_entry("Beta dogs canine behavior", "behavior training"), auto_link=False)
+        archive.add(_make_entry("Cat food feline nutrition", "fish meals"), auto_link=False)
+
+        total = archive.rebuild_links()
+        assert total > 0
+
+        # Check that dog entries are linked to each other
+        entries = list(archive._entries.values())
+        dog_entries = [e for e in entries if "dog" in e.title.lower()]
+        assert any(len(e.links) > 0 for e in dog_entries)
+
+    def test_override_threshold(self, archive):
+        """Lower threshold creates more links."""
+        archive.add(_make_entry("Alpha dogs", "training"), auto_link=False)
+        archive.add(_make_entry("Beta cats", "training"), auto_link=False)
+        archive.add(_make_entry("Gamma birds", "training"), auto_link=False)
+
+        # Very low threshold = more links
+        low_links = archive.rebuild_links(threshold=0.01)
+
+        # Reset
+        for e in archive._entries.values():
+            e.links = []
+
+        # Higher threshold = fewer links
+        high_links = archive.rebuild_links(threshold=0.9)
+
+        assert low_links >= high_links
+
+    def test_rebuild_persists(self, archive):
+        """Rebuild saves to disk."""
+        archive.add(_make_entry("Alpha dogs", "training"), auto_link=False)
+        archive.add(_make_entry("Beta dogs", "training"), auto_link=False)
+        archive.rebuild_links()
+
+        # Reload and verify links survived
+        archive2 = MnemosyneArchive(archive_path=archive.path)
+        entries = list(archive2._entries.values())
+        total_links = sum(len(e.links) for e in entries)
+        assert total_links > 0

provenance.json

@@ -0,0 +1,62 @@
+{
+  "generated_at": "2026-04-11T01:14:54.632326+00:00",
+  "repo": "Timmy_Foundation/the-nexus",
+  "git": {
+    "commit": "d408d2c365a9efc0c1e3a9b38b9cc4eed75695c5",
+    "branch": "mimo/build/issue-686",
+    "remote": "https://forge.alexanderwhitestone.com/Timmy_Foundation/the-nexus.git",
+    "dirty": true
+  },
+  "files": {
+    "index.html": {
+      "sha256": "71ba27afe8b6b42a09efe09d2b3017599392ddc3bc02543b31c2277dfb0b82cc",
+      "size": 25933
+    },
+    "app.js": {
+      "sha256": "2b765a724a0fcda29abd40ba921bc621d2699f11d0ba14cf1579cbbdafdc5cd5",
+      "size": 132902
+    },
+    "style.css": {
+      "sha256": "cd3068d03eed6f52a00bbc32cfae8fba4739b8b3cb194b3ec09fd747a075056d",
+      "size": 44198
+    },
+    "gofai_worker.js": {
+      "sha256": "d292f110aa12a8aa2b16b0c2d48e5b4ce24ee15b1cffb409ab846b1a05a91de2",
+      "size": 969
+    },
+    "server.py": {
+      "sha256": "e963cc9715accfc8814e3fe5c44af836185d66740d5a65fd0365e9c629d38e05",
+      "size": 4185
+    },
+    "portals.json": {
+      "sha256": "889a5e0f724eb73a95f960bca44bca232150bddff7c1b11f253bd056f3683a08",
+      "size": 3442
+    },
+    "vision.json": {
+      "sha256": "0e3b5c06af98486bbcb2fc2dc627dc8b7b08aed4c3a4f9e10b57f91e1e8ca6ad",
+      "size": 1658
+    },
+    "manifest.json": {
+      "sha256": "352304c4f7746f5d31cbc223636769969dd263c52800645c01024a3a8489d8c9",
+      "size": 495
+    },
+    "nexus/components/spatial-memory.js": {
+      "sha256": "60170f6490ddd743acd6d285d3a1af6cad61fbf8aaef3f679ff4049108eac160",
+      "size": 32782
+    },
+    "nexus/components/session-rooms.js": {
+      "sha256": "9997a60dda256e38cb4645508bf9e98c15c3d963b696e0080e3170a9a7fa7cf1",
+      "size": 15113
+    },
+    "nexus/components/timeline-scrubber.js": {
+      "sha256": "f8a17762c2735be283dc5074b13eb00e1e3b2b04feb15996c2cf0323b46b6014",
+      "size": 7177
+    },
+    "nexus/components/memory-particles.js": {
+      "sha256": "1be5567a3ebb229f9e1a072c08a25387ade87cb4a1df6a624e5c5254d3bef8fa",
+      "size": 14216
+    }
+  },
+  "missing": [],
+  "file_count": 12
+}

scripts/guardrails.sh

@@ -0,0 +1,27 @@
+#!/bin/bash
+# [Mnemosyne] Agent Guardrails — The Nexus
+# Validates code integrity and scans for secrets before deployment.
+
+echo "--- [Mnemosyne] Running Guardrails ---"
+
+# 1. Syntax Checks
+echo "[1/3] Validating syntax..."
+for f in ; do
+  node --check "$f" || { echo "Syntax error in $f"; exit 1; }
+done
+echo "Syntax OK."
+
+# 2. JSON/YAML Validation
+echo "[2/3] Validating configs..."
+for f in ; do
+  node -e "JSON.parse(require('fs').readFileSync('$f'))" || { echo "Invalid JSON: $f"; exit 1; }
+done
+echo "Configs OK."
+
+# 3. Secret Scan
+echo "[3/3] Scanning for secrets..."
+grep -rE "AI_|TOKEN|KEY|SECRET" . --exclude-dir=node_modules --exclude=guardrails.sh | grep -v "process.env" && {
+  echo "WARNING: Potential secrets found!"
+} || echo "No secrets detected."
+
+echo "--- Guardrails Passed ---"

scripts/smoke.mjs

@@ -0,0 +1,26 @@
+/**
+ * [Mnemosyne] Smoke Test — The Nexus
+ * Verifies core components are loadable and basic state is consistent.
+ */
+
+import { SpatialMemory } from '../nexus/components/spatial-memory.js';
+import { MemoryOptimizer } from '../nexus/components/memory-optimizer.js';
+
+console.log('--- [Mnemosyne] Running Smoke Test ---');
+
+// 1. Verify Components
+if (!SpatialMemory || !MemoryOptimizer) {
+  console.error('Failed to load core components');
+  process.exit(1);
+}
+console.log('Components loaded.');
+
+// 2. Verify Regions
+const regions = Object.keys(SpatialMemory.REGIONS || {});
+if (regions.length < 5) {
+  console.error('SpatialMemory regions incomplete:', regions);
+  process.exit(1);
+}
+console.log('Regions verified:', regions.join(', '));
+
+console.log('--- Smoke Test Passed ---');

tests/test_browser_smoke.py

@@ -0,0 +1,293 @@
+"""
+Browser smoke tests for the Nexus 3D world.
+Uses Playwright to verify the DOM contract, Three.js initialization,
+portal loading, and loading screen flow.
+
+Refs: #686
+"""
+import json
+import os
+import subprocess
+import time
+from pathlib import Path
+
+import pytest
+from playwright.sync_api import sync_playwright, expect
+
+REPO_ROOT = Path(__file__).resolve().parent.parent
+SCREENSHOT_DIR = REPO_ROOT / "test-screenshots"
+
+# ---------------------------------------------------------------------------
+# Fixtures
+# ---------------------------------------------------------------------------
+
+@pytest.fixture(scope="module")
+def http_server():
+    """Start a simple HTTP server for the Nexus static files."""
+    import http.server
+    import threading
+
+    port = int(os.environ.get("NEXUS_TEST_PORT", "9876"))
+    handler = http.server.SimpleHTTPRequestHandler
+    server = http.server.HTTPServer(("127.0.0.1", port), handler)
+    thread = threading.Thread(target=server.serve_forever, daemon=True)
+    thread.start()
+    time.sleep(0.3)
+    yield f"http://127.0.0.1:{port}"
+    server.shutdown()
+
+
+@pytest.fixture(scope="module")
+def browser_page(http_server):
+    """Launch a headless browser and navigate to the Nexus."""
+    SCREENSHOT_DIR.mkdir(exist_ok=True)
+    with sync_playwright() as pw:
+        browser = pw.chromium.launch(
+            headless=True,
+            args=["--no-sandbox", "--disable-gpu"],
+        )
+        context = browser.new_context(
+            viewport={"width": 1280, "height": 720},
+            ignore_https_errors=True,
+        )
+        page = context.new_page()
+        # Collect console errors
+        console_errors = []
+        page.on("console", lambda msg: console_errors.append(msg.text) if msg.type == "error" else None)
+        page.goto(http_server, wait_until="domcontentloaded", timeout=30000)
+        page._console_errors = console_errors
+        yield page
+        browser.close()
+
+
+# ---------------------------------------------------------------------------
+# Static asset tests
+# ---------------------------------------------------------------------------
+
+class TestStaticAssets:
+    """Verify all contract files are serveable."""
+
+    REQUIRED_FILES = [
+        "index.html",
+        "app.js",
+        "style.css",
+        "portals.json",
+        "vision.json",
+        "manifest.json",
+        "gofai_worker.js",
+    ]
+
+    def test_index_html_served(self, http_server):
+        """index.html must return 200."""
+        import urllib.request
+        resp = urllib.request.urlopen(f"{http_server}/index.html")
+        assert resp.status == 200
+
+    @pytest.mark.parametrize("filename", REQUIRED_FILES)
+    def test_contract_file_served(self, http_server, filename):
+        """Each contract file must return 200."""
+        import urllib.request
+        try:
+            resp = urllib.request.urlopen(f"{http_server}/{filename}")
+            assert resp.status == 200
+        except Exception as e:
+            pytest.fail(f"{filename} not serveable: {e}")
+
+
+# ---------------------------------------------------------------------------
+# DOM contract tests
+# ---------------------------------------------------------------------------
+
+class TestDOMContract:
+    """Verify required DOM elements exist after page load."""
+
+    REQUIRED_ELEMENTS = {
+        "nexus-canvas": "canvas",
+        "hud": "div",
+        "chat-panel": "div",
+        "chat-input": "input",
+        "chat-messages": "div",
+        "chat-send": "button",
+        "chat-toggle": "button",
+        "debug-overlay": "div",
+        "nav-mode-label": "span",
+        "ws-status-dot": "span",
+        "hud-location-text": "span",
+        "portal-hint": "div",
+        "spatial-search": "div",
+    }
+
+    @pytest.mark.parametrize("element_id,tag", list(REQUIRED_ELEMENTS.items()))
+    def test_element_exists(self, browser_page, element_id, tag):
+        """Element with given ID must exist in the DOM."""
+        el = browser_page.query_selector(f"#{element_id}")
+        assert el is not None, f"#{element_id} ({tag}) missing from DOM"
+
+    def test_canvas_has_webgl(self, browser_page):
+        """The nexus-canvas must have a WebGL rendering context."""
+        has_webgl = browser_page.evaluate("""
+            () => {
+                const c = document.getElementById('nexus-canvas');
+                if (!c) return false;
+                const ctx = c.getContext('webgl2') || c.getContext('webgl');
+                return ctx !== null;
+            }
+        """)
+        assert has_webgl, "nexus-canvas has no WebGL context"
+
+    def test_title_contains_nexus(self, browser_page):
+        """Page title should reference The Nexus."""
+        title = browser_page.title()
+        assert "nexus" in title.lower() or "timmy" in title.lower(), f"Unexpected title: {title}"
+
+
+# ---------------------------------------------------------------------------
+# Loading flow tests
+# ---------------------------------------------------------------------------
+
+class TestLoadingFlow:
+    """Verify the loading screen → enter prompt → HUD flow."""
+
+    def test_loading_screen_transitions(self, browser_page):
+        """Loading screen should fade out and HUD should become visible."""
+        # Wait for loading to complete and enter prompt to appear
+        try:
+            browser_page.wait_for_selector("#enter-prompt", state="visible", timeout=15000)
+        except Exception:
+            # Enter prompt may have already appeared and been clicked
+            pass
+
+        # Try clicking the enter prompt if it exists
+        enter = browser_page.query_selector("#enter-prompt")
+        if enter and enter.is_visible():
+            enter.click()
+            time.sleep(1)
+
+        # HUD should now be visible
+        hud = browser_page.query_selector("#hud")
+        assert hud is not None, "HUD element missing"
+        # After enter, HUD display should not be 'none'
+        display = browser_page.evaluate("() => document.getElementById('hud').style.display")
+        assert display != "none", "HUD should be visible after entering"
+
+
+# ---------------------------------------------------------------------------
+# Three.js initialization tests
+# ---------------------------------------------------------------------------
+
+class TestThreeJSInit:
+    """Verify Three.js initialized properly."""
+
+    def test_three_loaded(self, browser_page):
+        """THREE namespace should be available (via import map)."""
+        # Three.js is loaded as ES module, check for canvas context instead
+        has_canvas = browser_page.evaluate("""
+            () => {
+                const c = document.getElementById('nexus-canvas');
+                return c && c.width > 0 && c.height > 0;
+            }
+        """)
+        assert has_canvas, "Canvas not properly initialized"
+
+    def test_canvas_dimensions(self, browser_page):
+        """Canvas should fill the viewport."""
+        dims = browser_page.evaluate("""
+            () => {
+                const c = document.getElementById('nexus-canvas');
+                return { width: c.width, height: c.height, ww: window.innerWidth, wh: window.innerHeight };
+            }
+        """)
+        assert dims["width"] > 0, "Canvas width is 0"
+        assert dims["height"] > 0, "Canvas height is 0"
+
+
+# ---------------------------------------------------------------------------
+# Data contract tests
+# ---------------------------------------------------------------------------
+
+class TestDataContract:
+    """Verify JSON data files are valid and well-formed."""
+
+    def test_portals_json_valid(self):
+        """portals.json must parse as a non-empty JSON array."""
+        data = json.loads((REPO_ROOT / "portals.json").read_text())
+        assert isinstance(data, list), "portals.json must be an array"
+        assert len(data) > 0, "portals.json must have at least one portal"
+
+    def test_portals_have_required_fields(self):
+        """Each portal must have id, name, status, destination."""
+        data = json.loads((REPO_ROOT / "portals.json").read_text())
+        required = {"id", "name", "status", "destination"}
+        for i, portal in enumerate(data):
+            missing = required - set(portal.keys())
+            assert not missing, f"Portal {i} missing fields: {missing}"
+
+    def test_vision_json_valid(self):
+        """vision.json must parse as valid JSON."""
+        data = json.loads((REPO_ROOT / "vision.json").read_text())
+        assert data is not None
+
+    def test_manifest_json_valid(self):
+        """manifest.json must have required PWA fields."""
+        data = json.loads((REPO_ROOT / "manifest.json").read_text())
+        for key in ["name", "start_url", "theme_color"]:
+            assert key in data, f"manifest.json missing '{key}'"
+
+
+# ---------------------------------------------------------------------------
+# Screenshot / visual proof
+# ---------------------------------------------------------------------------
+
+class TestVisualProof:
+    """Capture screenshots as visual validation evidence."""
+
+    def test_screenshot_initial_state(self, browser_page):
+        """Take a screenshot of the initial page state."""
+        path = SCREENSHOT_DIR / "smoke-initial.png"
+        browser_page.screenshot(path=str(path))
+        assert path.exists(), "Screenshot was not saved"
+        assert path.stat().st_size > 1000, "Screenshot seems empty"
+
+    def test_screenshot_after_enter(self, browser_page):
+        """Take a screenshot after clicking through the enter prompt."""
+        enter = browser_page.query_selector("#enter-prompt")
+        if enter and enter.is_visible():
+            enter.click()
+            time.sleep(2)
+        else:
+            time.sleep(1)
+
+        path = SCREENSHOT_DIR / "smoke-post-enter.png"
+        browser_page.screenshot(path=str(path))
+        assert path.exists()
+
+    def test_screenshot_fullscreen(self, browser_page):
+        """Full-page screenshot for visual regression baseline."""
+        path = SCREENSHOT_DIR / "smoke-fullscreen.png"
+        browser_page.screenshot(path=str(path), full_page=True)
+        assert path.exists()
+
+
+# ---------------------------------------------------------------------------
+# Provenance in browser context
+# ---------------------------------------------------------------------------
+
+class TestBrowserProvenance:
+    """Verify provenance from within the browser context."""
+
+    def test_page_served_from_correct_origin(self, http_server):
+        """The page must be served from localhost, not a stale remote."""
+        import urllib.request
+        resp = urllib.request.urlopen(f"{http_server}/index.html")
+        content = resp.read().decode("utf-8", errors="replace")
+        # Must not contain references to legacy matrix path
+        assert "/Users/apayne/the-matrix" not in content, \
+            "index.html references legacy matrix path — provenance violation"
+
+    def test_index_html_has_nexus_title(self, http_server):
+        """index.html title must reference The Nexus."""
+        import urllib.request
+        resp = urllib.request.urlopen(f"{http_server}/index.html")
+        content = resp.read().decode("utf-8", errors="replace")
+        assert "<title>The Nexus" in content or "Timmy" in content, \
+            "index.html title does not reference The Nexus"

tests/test_provenance.py

@@ -0,0 +1,73 @@
+"""
+Provenance tests — verify the Nexus browser surface comes from
+a clean Timmy_Foundation/the-nexus checkout, not stale sources.
+
+Refs: #686
+"""
+import json
+import hashlib
+from pathlib import Path
+
+REPO_ROOT = Path(__file__).resolve().parent.parent
+
+
+def test_provenance_manifest_exists() -> None:
+    """provenance.json must exist and be valid JSON."""
+    p = REPO_ROOT / "provenance.json"
+    assert p.exists(), "provenance.json missing — run bin/generate_provenance.py"
+    data = json.loads(p.read_text())
+    assert "files" in data
+    assert "repo" in data
+
+
+def test_provenance_repo_identity() -> None:
+    """Manifest must claim Timmy_Foundation/the-nexus."""
+    data = json.loads((REPO_ROOT / "provenance.json").read_text())
+    assert data["repo"] == "Timmy_Foundation/the-nexus"
+
+
+def test_provenance_all_contract_files_present() -> None:
+    """Every file listed in the provenance manifest must exist on disk."""
+    data = json.loads((REPO_ROOT / "provenance.json").read_text())
+    missing = []
+    for rel in data["files"]:
+        if not (REPO_ROOT / rel).exists():
+            missing.append(rel)
+    assert not missing, f"Contract files missing: {missing}"
+
+
+def test_provenance_hashes_match() -> None:
+    """File hashes must match the stored manifest (no stale/modified files)."""
+    data = json.loads((REPO_ROOT / "provenance.json").read_text())
+    mismatches = []
+    for rel, meta in data["files"].items():
+        p = REPO_ROOT / rel
+        if not p.exists():
+            mismatches.append(f"MISSING: {rel}")
+            continue
+        actual = hashlib.sha256(p.read_bytes()).hexdigest()
+        if actual != meta["sha256"]:
+            mismatches.append(f"CHANGED: {rel}")
+    assert not mismatches, f"Provenance mismatch:\n" + "\n".join(mismatches)
+
+
+def test_no_legacy_matrix_references_in_frontend() -> None:
+    """Frontend files must not reference /Users/apayne/the-matrix as a source."""
+    forbidden_paths = ["/Users/apayne/the-matrix"]
+    offenders = []
+    for rel in ["index.html", "app.js", "style.css"]:
+        p = REPO_ROOT / rel
+        if p.exists():
+            content = p.read_text()
+            for bad in forbidden_paths:
+                if bad in content:
+                    offenders.append(f"{rel} references {bad}")
+    assert not offenders, f"Legacy matrix references found: {offenders}"
+
+
+def test_no_stale_perplexity_computer_references_in_critical_files() -> None:
+    """Verify the provenance generator script itself is canonical."""
+    script = REPO_ROOT / "bin" / "generate_provenance.py"
+    assert script.exists(), "bin/generate_provenance.py must exist"
+    content = script.read_text()
+    assert "Timmy_Foundation/the-nexus" in content