feat: wire MemoryInspect into app.js

- Import MemoryInspect component
- Initialize after SpatialMemory
- Add crystal raycasting in mousedown handler
- Click crystal to open inspect panel, click empty space to close
Closes #1227

app.js

@@ -4,7 +4,9 @@ import { RenderPass } from 'three/addons/postprocessing/RenderPass.js';
 import { UnrealBloomPass } from 'three/addons/postprocessing/UnrealBloomPass.js';
 import { SMAAPass } from 'three/addons/postprocessing/SMAAPass.js';
 import { SpatialMemory } from './nexus/components/spatial-memory.js';
+import { MemoryBirth } from './nexus/components/memory-birth.js';
 import { MemoryOptimizer } from './nexus/components/memory-optimizer.js';
+import { MemoryInspect } from './nexus/components/memory-inspect.js';
 
 // ═══════════════════════════════════════════
 // NEXUS v1.1 — Portal System Update
@@ -708,7 +710,10 @@ async function init() {
   createWorkshopTerminal();
   createAshStorm();
   SpatialMemory.init(scene);
+  MemoryBirth.init(scene);
+  MemoryBirth.wrapSpatialMemory(SpatialMemory);
   SpatialMemory.setCamera(camera);
+MemoryInspect.init(SpatialMemory);
   updateLoad(90);
 
   loadSession();
@@ -1901,7 +1906,7 @@ function setupControls() {
       orbitState.lastX = e.clientX;
       orbitState.lastY = e.clientY;
       
-      // Raycasting for portals
+      // Raycasting for portals and memory crystals
       if (!portalOverlayActive) {
         const mouse = new THREE.Vector2(
           (e.clientX / window.innerWidth) * 2 - 1,
@@ -1909,11 +1914,26 @@ function setupControls() {
         );
         const raycaster = new THREE.Raycaster();
         raycaster.setFromCamera(mouse, camera);
-        const intersects = raycaster.intersectObjects(portals.map(p => p.ring));
-        if (intersects.length > 0) {
-          const clickedRing = intersects[0].object;
+
+        // Check portals first
+        const portalHits = raycaster.intersectObjects(portals.map(p => p.ring));
+        if (portalHits.length > 0) {
+          const clickedRing = portalHits[0].object;
           const portal = portals.find(p => p.ring === clickedRing);
           if (portal) activatePortal(portal);
+        } else {
+          // Check memory crystals
+          const crystalMeshes = SpatialMemory.getCrystalMeshes();
+          const crystalHits = raycaster.intersectObjects(crystalMeshes);
+          if (crystalHits.length > 0) {
+            const hitMesh = crystalHits[0].object;
+            const memInfo = SpatialMemory.getMemoryFromMesh(hitMesh);
+            if (memInfo && memInfo.data) {
+              MemoryInspect.inspect(memInfo.data.id);
+            }
+          } else if (MemoryInspect.isOpen()) {
+            MemoryInspect.close();
+          }
         }
       }
     }
@@ -2868,6 +2888,7 @@ function gameLoop() {
   // Project Mnemosyne - Memory Orb Animation
   if (typeof animateMemoryOrbs === 'function') {
     SpatialMemory.update(delta);
+    MemoryBirth.update(delta);
     animateMemoryOrbs(delta);
   }
 

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 +1,407 @@
+/**
+ * Memory Inspect Panel — click-to-read detail view for Mnemosyne crystals.
+ *
+ * When a memory crystal is clicked in the Nexus, this panel slides in from
+ * the right showing the memory's content, links, region, and metadata.
+ *
+ * Depends on SpatialMemory (for data access) — wired from app.js.
+ */
+
+const MemoryInspect = (() => {
+  let _panel = null;
+  let _isOpen = false;
+  let _currentMemId = null;
+  let _spatialMemory = null;
+
+  // ─── PUBLIC API ──────────────────────────────────────
+
+  function init(spatialMemoryRef) {
+    _spatialMemory = spatialMemoryRef;
+    _buildPanel();
+    _injectStyles();
+    console.info('[Mnemosyne] Memory Inspect panel initialized');
+  }
+
+  function inspect(memId) {
+    if (!_spatialMemory) return;
+    const memObj = _getMemoryObject(memId);
+    if (!memObj) return;
+
+    _currentMemId = memId;
+    _renderPanel(memObj);
+    _open();
+    _spatialMemory.highlightMemory(memId);
+  }
+
+  function close() {
+    if (!_isOpen) return;
+    if (_currentMemId && _spatialMemory) {
+      _spatialMemory.clearHighlight();
+    }
+    _currentMemId = null;
+    _close();
+  }
+
+  function isOpen() {
+    return _isOpen;
+  }
+
+  function getCurrentMemId() {
+    return _currentMemId;
+  }
+
+  // ─── INTERNALS ───────────────────────────────────────
+
+  function _getMemoryObject(memId) {
+    // Access SpatialMemory's internal _memoryObjects via getAllMemories
+    const all = _spatialMemory.getAllMemories();
+    if (!all) return null;
+    // getAllMemories returns array of { id, ...data } objects
+    const entry = all.find(m => m.id === memId);
+    if (!entry) return null;
+
+    // Get region info
+    const regions = _spatialMemory.REGIONS;
+    const region = regions[entry.category] || regions.working;
+
+    return { data: entry, region };
+  }
+
+  function _buildPanel() {
+    _panel = document.createElement('div');
+    _panel.id = 'memory-inspect-panel';
+    _panel.className = 'memory-inspect-panel memory-inspect-hidden';
+    _panel.innerHTML = `
+      <div class="memory-inspect-header">
+        <span class="memory-inspect-glyph" id="inspect-glyph"></span>
+        <span class="memory-inspect-title" id="inspect-title"></span>
+        <button class="memory-inspect-close" id="inspect-close" title="Close">&times;</button>
+      </div>
+      <div class="memory-inspect-body">
+        <div class="memory-inspect-meta" id="inspect-meta"></div>
+        <div class="memory-inspect-content" id="inspect-content"></div>
+        <div class="memory-inspect-links" id="inspect-links"></div>
+      </div>
+      <div class="memory-inspect-footer" id="inspect-footer"></div>
+    `;
+    document.body.appendChild(_panel);
+
+    document.getElementById('inspect-close').addEventListener('click', (e) => {
+      e.stopPropagation();
+      close();
+    });
+  }
+
+  function _renderPanel(memObj) {
+    const { data, region } = memObj;
+    const strength = data.strength != null ? data.strength : 0.7;
+    const vitalityBand = _getVitalityBand(strength);
+    const bandColors = {
+      vibrant: '#00e5ff',
+      alive: '#4488ff',
+      fading: '#ffaa00',
+      dim: '#ff6644',
+      ghost: '#667788'
+    };
+    const bandColor = bandColors[vitalityBand] || bandColors.alive;
+
+    // Header
+    document.getElementById('inspect-glyph').textContent = region.glyph || '\uD83D\uDCCB';
+    document.getElementById('inspect-title').textContent = data.content
+      ? (data.content.length > 60 ? data.content.slice(0, 60) + '\u2026' : data.content)
+      : data.id || 'Memory';
+
+    // Meta bar
+    const metaEl = document.getElementById('inspect-meta');
+    const catLabel = region.label || data.category || 'Unknown';
+    const created = data.timestamp ? _formatTime(data.timestamp) : '';
+    metaEl.innerHTML = `
+      <span class="inspect-badge" style="border-color:${'#' + region.color.toString(16).padStart(6,'0')}">${catLabel}</span>
+      <span class="inspect-vitality" style="color:${bandColor}">
+        \u25CF ${vitalityBand} (${Math.round(strength * 100)}%)
+      </span>
+      ${created ? `<span class="inspect-time">${created}</span>` : ''}
+    `;
+
+    // Content
+    const contentEl = document.getElementById('inspect-content');
+    contentEl.textContent = data.content || '(no content)';
+
+    // Links
+    const linksEl = document.getElementById('inspect-links');
+    const connections = data.connections || [];
+    if (connections.length > 0) {
+      let linksHtml = '<div class="inspect-links-header">Linked Memories (' + connections.length + ')</div>';
+      linksHtml += '<div class="inspect-links-list">';
+      connections.forEach(cid => {
+        const linked = _getLinkedPreview(cid);
+        linksHtml += `<div class="inspect-link-item" data-mem-id="${cid}">
+          <span class="inspect-link-dot"></span>
+          <span class="inspect-link-text">${linked}</span>
+        </div>`;
+      });
+      linksHtml += '</div>';
+      linksEl.innerHTML = linksHtml;
+
+      // Wire click handlers for linked memories
+      linksEl.querySelectorAll('.inspect-link-item').forEach(el => {
+        el.addEventListener('click', () => {
+          const targetId = el.dataset.memId;
+          if (targetId) inspect(targetId);
+        });
+      });
+    } else {
+      linksEl.innerHTML = '<div class="inspect-no-links">No linked memories</div>';
+    }
+
+    // Footer
+    const footerEl = document.getElementById('inspect-footer');
+    footerEl.innerHTML = `
+      <button class="inspect-action-btn" id="inspect-copy-btn" title="Copy content">\uD83D\uDCCB Copy</button>
+      <span class="inspect-id" title="Memory ID">${data.id || ''}</span>
+    `;
+    document.getElementById('inspect-copy-btn').addEventListener('click', () => {
+      navigator.clipboard.writeText(data.content || '').then(() => {
+        const btn = document.getElementById('inspect-copy-btn');
+        btn.textContent = '\u2713 Copied';
+        setTimeout(() => { btn.textContent = '\uD83D\uDCCB Copy'; }, 1500);
+      });
+    });
+  }
+
+  function _getLinkedPreview(memId) {
+    if (!_spatialMemory) return memId;
+    const all = _spatialMemory.getAllMemories();
+    if (!all) return memId;
+    const entry = all.find(m => m.id === memId);
+    if (!entry || !entry.content) return memId;
+    return entry.content.length > 40 ? entry.content.slice(0, 40) + '\u2026' : entry.content;
+  }
+
+  function _getVitalityBand(strength) {
+    if (strength >= 0.8) return 'vibrant';
+    if (strength >= 0.5) return 'alive';
+    if (strength >= 0.25) return 'fading';
+    if (strength >= 0.1) return 'dim';
+    return 'ghost';
+  }
+
+  function _formatTime(isoStr) {
+    try {
+      const d = new Date(isoStr);
+      const now = new Date();
+      const diffMs = now - d;
+      const diffMin = Math.floor(diffMs / 60000);
+      if (diffMin < 1) return 'just now';
+      if (diffMin < 60) return diffMin + 'm ago';
+      const diffHr = Math.floor(diffMin / 60);
+      if (diffHr < 24) return diffHr + 'h ago';
+      const diffDay = Math.floor(diffHr / 24);
+      if (diffDay < 30) return diffDay + 'd ago';
+      return d.toLocaleDateString();
+    } catch {
+      return '';
+    }
+  }
+
+  function _open() {
+    _isOpen = true;
+    _panel.classList.remove('memory-inspect-hidden');
+    _panel.classList.add('memory-inspect-visible');
+  }
+
+  function _close() {
+    _isOpen = false;
+    _panel.classList.remove('memory-inspect-visible');
+    _panel.classList.add('memory-inspect-hidden');
+  }
+
+  function _injectStyles() {
+    if (document.getElementById('memory-inspect-styles')) return;
+    const style = document.createElement('style');
+    style.id = 'memory-inspect-styles';
+    style.textContent = `
+      .memory-inspect-panel {
+        position: fixed;
+        top: 60px;
+        right: 0;
+        width: 340px;
+        max-height: calc(100vh - 80px);
+        background: rgba(8, 12, 32, 0.92);
+        border: 1px solid rgba(74, 240, 192, 0.2);
+        border-right: none;
+        border-radius: 8px 0 0 8px;
+        color: #c8d8e8;
+        font-family: 'JetBrains Mono', 'Fira Code', monospace;
+        font-size: 13px;
+        z-index: 900;
+        display: flex;
+        flex-direction: column;
+        backdrop-filter: blur(12px);
+        box-shadow: -4px 0 24px rgba(0, 0, 0, 0.5);
+        transition: transform 0.25s ease, opacity 0.25s ease;
+        overflow: hidden;
+      }
+      .memory-inspect-hidden {
+        transform: translateX(100%);
+        opacity: 0;
+        pointer-events: none;
+      }
+      .memory-inspect-visible {
+        transform: translateX(0);
+        opacity: 1;
+        pointer-events: auto;
+      }
+      .memory-inspect-header {
+        display: flex;
+        align-items: center;
+        gap: 8px;
+        padding: 10px 12px;
+        border-bottom: 1px solid rgba(74, 240, 192, 0.15);
+        background: rgba(74, 240, 192, 0.05);
+      }
+      .memory-inspect-glyph {
+        font-size: 18px;
+        flex-shrink: 0;
+      }
+      .memory-inspect-title {
+        flex: 1;
+        font-weight: 600;
+        color: #4af0c0;
+        overflow: hidden;
+        text-overflow: ellipsis;
+        white-space: nowrap;
+      }
+      .memory-inspect-close {
+        background: none;
+        border: none;
+        color: #667788;
+        font-size: 20px;
+        cursor: pointer;
+        padding: 0 4px;
+        line-height: 1;
+      }
+      .memory-inspect-close:hover {
+        color: #ff4466;
+      }
+      .memory-inspect-body {
+        flex: 1;
+        overflow-y: auto;
+        padding: 12px;
+      }
+      .memory-inspect-meta {
+        display: flex;
+        align-items: center;
+        gap: 10px;
+        flex-wrap: wrap;
+        margin-bottom: 12px;
+        font-size: 11px;
+      }
+      .inspect-badge {
+        padding: 2px 8px;
+        border: 1px solid;
+        border-radius: 4px;
+        font-size: 10px;
+        text-transform: uppercase;
+        letter-spacing: 0.5px;
+      }
+      .inspect-vitality {
+        font-size: 11px;
+      }
+      .inspect-time {
+        color: #556677;
+        font-size: 10px;
+      }
+      .memory-inspect-content {
+        background: rgba(0, 0, 0, 0.3);
+        border: 1px solid rgba(255, 255, 255, 0.06);
+        border-radius: 6px;
+        padding: 10px;
+        line-height: 1.5;
+        white-space: pre-wrap;
+        word-break: break-word;
+        margin-bottom: 12px;
+        max-height: 200px;
+        overflow-y: auto;
+      }
+      .inspect-links-header {
+        font-size: 11px;
+        color: #7b5cff;
+        text-transform: uppercase;
+        letter-spacing: 0.5px;
+        margin-bottom: 6px;
+      }
+      .inspect-links-list {
+        display: flex;
+        flex-direction: column;
+        gap: 4px;
+      }
+      .inspect-link-item {
+        display: flex;
+        align-items: center;
+        gap: 8px;
+        padding: 6px 8px;
+        background: rgba(123, 92, 255, 0.08);
+        border: 1px solid rgba(123, 92, 255, 0.15);
+        border-radius: 4px;
+        cursor: pointer;
+        font-size: 11px;
+        transition: background 0.15s;
+      }
+      .inspect-link-item:hover {
+        background: rgba(123, 92, 255, 0.18);
+      }
+      .inspect-link-dot {
+        width: 6px;
+        height: 6px;
+        border-radius: 50%;
+        background: #7b5cff;
+        flex-shrink: 0;
+      }
+      .inspect-link-text {
+        overflow: hidden;
+        text-overflow: ellipsis;
+        white-space: nowrap;
+      }
+      .inspect-no-links {
+        color: #445566;
+        font-size: 11px;
+        font-style: italic;
+      }
+      .memory-inspect-footer {
+        display: flex;
+        align-items: center;
+        justify-content: space-between;
+        padding: 8px 12px;
+        border-top: 1px solid rgba(74, 240, 192, 0.1);
+      }
+      .inspect-action-btn {
+        background: rgba(74, 240, 192, 0.1);
+        border: 1px solid rgba(74, 240, 192, 0.25);
+        color: #4af0c0;
+        padding: 4px 12px;
+        border-radius: 4px;
+        cursor: pointer;
+        font-size: 11px;
+        font-family: inherit;
+        transition: background 0.15s;
+      }
+      .inspect-action-btn:hover {
+        background: rgba(74, 240, 192, 0.2);
+      }
+      .inspect-id {
+        color: #334455;
+        font-size: 9px;
+        max-width: 160px;
+        overflow: hidden;
+        text-overflow: ellipsis;
+        white-space: nowrap;
+      }
+    `;
+    document.head.appendChild(style);
+  }
+
+  return { init, inspect, close, isOpen, getCurrentMemId };
+})();
+
+export { MemoryInspect };

nexus/mnemosyne/archive.py

@@ -13,6 +13,8 @@ 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.
@@ -70,6 +72,53 @@ class MnemosyneArchive:
         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()
@@ -97,18 +146,98 @@ class MnemosyneArchive:
         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:
-        total_links = sum(len(e.links) for e in self._entries.values())
-        topics = set()
-        for e in self._entries.values():
+        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": len(self._entries),
+            "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,
         }

nexus/mnemosyne/cli.py

@@ -1,6 +1,7 @@
 """CLI interface for Mnemosyne.
 
-Provides: mnemosyne ingest, mnemosyne search, mnemosyne link, mnemosyne stats
+Provides: mnemosyne ingest, mnemosyne search, mnemosyne link, mnemosyne stats,
+          mnemosyne topics, mnemosyne remove, mnemosyne export
 """
 
 from __future__ import annotations
@@ -22,7 +23,10 @@ def cmd_stats(args):
 
 def cmd_search(args):
     archive = MnemosyneArchive()
-    results = archive.search(args.query, limit=args.limit)
+    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
@@ -59,6 +63,33 @@ def cmd_link(args):
         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 main():
     parser = argparse.ArgumentParser(prog="mnemosyne", description="The Living Holographic Archive")
     sub = parser.add_subparsers(dest="command")
@@ -68,6 +99,7 @@ def main():
     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)
@@ -78,12 +110,30 @@ def main():
     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")
+
     args = parser.parse_args()
     if not args.command:
         parser.print_help()
         sys.exit(1)
 
-    {"stats": cmd_stats, "search": cmd_search, "ingest": cmd_ingest, "link": cmd_link}[args.command](args)
+    dispatch = {
+        "stats": cmd_stats,
+        "search": cmd_search,
+        "ingest": cmd_ingest,
+        "link": cmd_link,
+        "topics": cmd_topics,
+        "remove": cmd_remove,
+        "export": cmd_export,
+    }
+    dispatch[args.command](args)
 
 
 if __name__ == "__main__":

nexus/mnemosyne/tests/test_archive.py

@@ -66,8 +66,211 @@ def test_archive_persistence():
         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"}