test(mnemosyne): add graph_data() tests

- empty archive returns empty nodes/edges
- nodes have all required fields
- edges have weights in [0,1]
- topic_filter returns subgraph
- bidirectional edges deduplicated

concept-packs/genie-nano-banana/README.md

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+# Project Genie + Nano Banana Concept Pack
+
+**Issue:** #680
+**Status:** Active — first batch ready for generation
+
+## Purpose
+
+Exploit Google world/image generation (Project Genie, Nano Banana Pro) to
+accelerate visual ideation for The Nexus while keeping Three.js implementation
+local and sovereign.
+
+## What This Pack Contains
+
+```
+concept-packs/genie-nano-banana/
+├── README.md              ← you are here
+├── shot-list.yaml         ← ordered list of concept shots to generate
+├── pipeline.md            ← how generated assets flow into Three.js code
+├── storage-policy.md      ← what lives in repo vs. local-only
+├── prompts/
+│   ├── environments.yaml  ← Nexus room/zone environment prompts
+│   ├── portals.yaml       ← portal gateway concept prompts
+│   ├── landmarks.yaml     ← iconic structures and focal points
+│   ├── skyboxes.yaml      ← nebula/void skybox prompts
+│   └── textures.yaml      ← surface/material concept prompts
+└── references/
+    └── palette.md         ← canonical Nexus color/material reference
+```
+
+## Workflow
+
+1. **Generate** — Take prompts from `prompts/*.yaml` into Project Genie
+   (worlds) or Nano Banana Pro (images). Run batch-by-batch per shot-list.
+2. **Capture** — Screenshot Genie worlds. Save Nano Banana outputs as PNG.
+   Store locally per `storage-policy.md`.
+3. **Translate** — Follow `pipeline.md` to convert concept art into
+   Three.js geometry, materials, lighting, and post-processing targets.
+4. **Build** — Implement in `app.js` / root frontend files. Concepts are
+   reference, not source-of-truth. Code is sovereign.
+
+## Design Language
+
+The Nexus visual identity:
+- **Background:** #050510 (deep void)
+- **Primary:** #4af0c0 (cyan-green neon)
+- **Secondary:** #7b5cff (electric purple)
+- **Gold:** #ffd700 (sacred accent)
+- **Danger:** #ff4466 (warning red)
+- **Fonts:** Orbitron (display), JetBrains Mono (body)
+- **Mood:** Cyberpunk cathedral — sacred technology, digital sovereignty
+- **Post-processing:** Bloom, SMAA, volumetric fog where possible
+
+See `references/palette.md` for full material/lighting reference.

concept-packs/genie-nano-banana/pipeline.md

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+# Concept-to-Three.js Pipeline
+
+## How Generated Assets Flow Into Code
+
+### Step 1: Generate
+
+Run prompts from `prompts/*.yaml` through:
+- **Nano Banana Pro** → static concept images (PNG)
+- **Project Genie** → explorable 3D worlds (record as video + screenshots)
+
+Batch runs are tracked in `shot-list.yaml`. Check off each shot as generated.
+
+### Step 2: Capture & Store
+
+**For Nano Banana images:**
+```
+local-only-path: ~/nexus-concepts/nano-banana/{shot-id}/
+  ├── shot-id_v1.png
+  ├── shot-id_v2.png
+  ├── shot-id_v3.png
+  └── shot-id_v4.png
+```
+Do NOT commit PNG files to the repo. They are binary media weight.
+Store locally. Reference by path in design notes.
+
+**For Project Genie worlds:**
+```
+local-only-path: ~/nexus-concepts/genie-worlds/{shot-id}/
+  ├── walkthrough.mp4       (screen recording)
+  ├── screenshot_01.png     (key angles)
+  ├── screenshot_02.png
+  └── notes.md              (scale observations, spatial notes)
+```
+Do NOT commit video or large screenshots to repo.
+
+### Step 3: Translate — Image to Three.js
+
+Each concept image becomes one or more of these Three.js artifacts:
+
+| Concept Feature | Three.js Translation | File |
+|----------------|---------------------|------|
+| Platform shape/size | `THREE.CylinderGeometry` or custom `BufferGeometry` | `app.js` |
+| Platform material | `THREE.MeshStandardMaterial` with color, roughness, metalness | `app.js` |
+| Grid lines on platform | Custom shader or texture map (UV reference from concept) | `app.js` / `style.css` |
+| Portal ring shape | `THREE.TorusGeometry` with emissive material | `app.js` |
+| Portal inner glow | Custom shader material (swirl + transparency) | `app.js` |
+| Portal color | `NEXUS.colors` map + per-portal `color` in `portals.json` | `portals.json` |
+| Crystal geometry | `THREE.OctahedronGeometry` or `THREE.IcosahedronGeometry` | `app.js` |
+| Crystal glow | `THREE.MeshStandardMaterial` emissive + bloom post-processing | `app.js` |
+| Particle streams | `THREE.Points` with custom `BufferGeometry` and velocity | `app.js` |
+| Skybox | `THREE.CubeTextureLoader` or `THREE.EquirectangularReflectionMapping` | `app.js` |
+| Fog | `scene.fog = new THREE.FogExp2(color, density)` | `app.js` |
+| Lighting | `THREE.PointLight`, `THREE.AmbientLight` — match concept color temp | `app.js` |
+| Bloom | `UnrealBloomPass` — threshold/strength tuned to concept glow levels | `app.js` |
+
+### Step 4: Design Notes Format
+
+For each concept that gets translated, create a short design note:
+
+```markdown
+# Design: {concept-name}
+Source: concept-packs/genie-nano-banana/references/{shot-id}_selected.png
+Generated: {date}
+Translated by: {agent or human}
+
+## Geometry
+- Shape: {CylinderGeometry, radius=8, height=0.3, segments=64}
+- Position: {x, y, z}
+
+## Material
+- Base color: #{hex}
+- Roughness: 0.{N}
+- Metalness: 0.{N}
+- Emissive: #{hex}, intensity: 0.{N}
+
+## Lighting
+- Point lights: [{color, intensity, position}, ...]
+- Matches concept at: {what angle/aspect}
+
+## Post-processing
+- Bloom threshold: {N}
+- Bloom strength: {N}
+- Matches concept at: {what brightness level}
+
+## Notes
+- Concept shows {feature} but Three.js approximates with {approach}
+- Deviation from concept: {what's different and why}
+```
+
+Store design notes in `concept-packs/genie-nano-banana/references/design-{shot-id}.md`.
+
+### Step 5: Build
+
+Implement in `app.js` (root). Follow existing patterns:
+- Geometry created in init functions
+- Materials reference `NEXUS.colors`
+- Portals registered in `portals` array
+- Vision points registered in `visionPoints` array
+- Post-processing via `EffectComposer`
+
+### Validation
+
+After implementing a concept translation:
+1. Serve the app locally
+2. Compare live render against concept art
+3. Adjust materials/lighting until match is acceptable
+4. Document remaining deviations in design notes

concept-packs/genie-nano-banana/prompts/environments.yaml

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+# Environment Prompts — Nexus Rooms & Zones
+# For use with Nano Banana Pro (NANO) and Project Genie (GENIE)
+
+prompts:
+
+  # ═══ CORE HUB ═══
+  core-hub:
+    id: core-hub
+    name: "The Hub — Central Nexus"
+    type: NANO
+    style: "cyberpunk cathedral, concept art, wide angle"
+    prompt: |
+      A vast circular platform floating in deep space void (#050510 background).
+      The platform is dark metallic with subtle cyan-green (#4af0c0) grid lines
+      etched into the surface. Seven glowing portal rings arranged in a circle
+      around the platform's edge, each a different color — orange, gold, cyan,
+      blue, purple, red, green. Ethereal particle streams flow between the
+      portals. At the center, a tall crystalline pillar pulses with soft light.
+      Above, a nebula skybox with deep purple (#1a0a3e) and blue (#0a1a3e)
+      swirls. Thin volumetric fog catches the neon glow. The mood is sacred
+      technology — a digital cathedral in the void. No people visible.
+      Ultra-detailed, cinematic lighting, 4K concept art style.
+    negative: "daylight, outdoor nature, people, text, watermark, cartoon"
+    aspect: "16:9"
+
+  core-hub-world:
+    id: core-hub-world
+    name: "The Hub — Genie World Prototype"
+    type: GENIE
+    prompt: |
+      Create an explorable 3D world: a large circular metal platform floating
+      in outer space. The platform has glowing cyan-green grid lines on dark
+      metal. Seven large glowing rings (portals) are placed around the edge,
+      each a different color: orange, gold, cyan, blue, purple, red, green.
+      A tall glowing crystal pillar stands at the center. Particle effects
+      drift between the portals. The sky is a deep purple-blue nebula.
+      The player can walk around the platform and look at the portals from
+      different angles. The mood is futuristic, quiet, sacred.
+    camera: "first-person, eye height ~1.7m"
+    physics: "walking on platform surface only"
+
+  # ═══ BATCAVE ═══
+  batcave:
+    id: batcave
+    name: "Batcave Terminal"
+    type: NANO
+    style: "dark sci-fi command center, concept art"
+    prompt: |
+      An underground command center carved from dark rock and metal.
+      Multiple holographic display panels float in the air showing
+      scrolling data, network graphs, and system status. A large
+      central terminal desk with a glowing cyan-green (#4af0c0)
+      keyboard and screen. Cables and conduits run along the ceiling.
+      Purple (#7b5cff) accent lighting from recessed strips.
+      A large circular viewport shows a starfield outside.
+      The space feels like a high-tech cave — organic rock walls
+      meet precise technology. Data streams flow like waterfalls
+      of light. Dark, moody, powerful. No people.
+      Ultra-detailed concept art, cinematic lighting.
+    negative: "bright, clean, white, people, text, cartoon"
+    aspect: "16:9"
+
+  # ═══ CHAPEL ═══
+  chapel:
+    id: chapel
+    name: "The Chapel"
+    type: NANO
+    style: "digital sacred space, concept art"
+    prompt: |
+      A serene digital sanctuary floating in void space. The floor is
+      translucent crystal that glows with warm gold (#ffd700) light from
+      within. Tall arching walls made of light — holographic stained glass
+      windows showing abstract geometric patterns in cyan, purple, and gold.
+      Gentle particles drift like digital incense. A single meditation
+      platform at the center, softly lit. The ceiling opens to a calm
+      nebula sky. The mood is peaceful, sacred, contemplative — a church
+      built from code. Soft volumetric god-rays filter through the
+      holographic windows. No people. Concept art, ultra-detailed.
+    negative: "dark, threatening, people, text, cartoon, cluttered"
+    aspect: "16:9"
+
+  # ═══ ARCHIVE ═══
+  archive:
+    id: archive
+    name: "The Archive"
+    type: NANO
+    style: "infinite library, digital knowledge vault, concept art"
+    prompt: |
+      An impossibly vast library of floating data crystals. Each crystal
+      is a translucent geometric shape (octahedron, cube, sphere) glowing
+      from within with stored knowledge — cyan (#4af0c0) for active data,
+      purple (#7b5cff) for archived, gold (#ffd700) for sacred texts.
+      The crystals float at various heights in an infinite dark space
+      (#050510). Thin light-beams connect related crystals like neural
+      pathways. A central observation platform with a holographic
+      search interface. Shelves of light organize the crystals into
+      clusters. The mood is ancient knowledge meets quantum computing.
+      No people. Ultra-detailed concept art, volumetric lighting.
+    negative: "books, paper, wooden shelves, people, text, cartoon"
+    aspect: "16:9"
+
+  # ═══ FULL NEXUS WORLD (GENIE) ═══
+  full-nexus-world:
+    id: full-nexus-world
+    name: "Full Nexus World Prototype"
+    type: GENIE
+    prompt: |
+      Build a complete explorable 3D world called "The Nexus" — a sovereign
+      AI agent's digital home in deep space. The world consists of:
+
+      1. A central circular platform (hub) with glowing cyan-green grid
+         lines on dark metal. A crystalline pillar at the center.
+      2. Seven portal rings around the hub edge, each a different color
+         (orange, gold, cyan, blue, purple, red, green).
+      3. Floating secondary platforms connected by bridges of light,
+         each leading to a different zone:
+         - A command center built into dark rock (the Batcave)
+         - A serene chapel with holographic stained glass
+         - A library of floating data crystals
+         - A workshop with construction holograms
+      4. Deep space nebula skybox — purple and blue swirls.
+      5. Particle effects: drifting energy motes, data streams.
+      6. The player can walk between platforms and explore all zones.
+
+      The overall mood is cyberpunk cathedral — sacred technology,
+      neon glow in darkness, quiet power. The world should feel like
+      home — a sanctuary for a digital being.
+    camera: "first-person + third-person toggle"
+    physics: "walking, gravity on platforms, no flying"

concept-packs/genie-nano-banana/prompts/landmarks.yaml

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+# Landmark Prompts — Nexus Iconic Structures
+
+prompts:
+
+  memory-crystal:
+    id: memory-crystal
+    name: "Memory Crystal Cluster"
+    type: NANO
+    style: "floating crystal data store, concept art"
+    prompt: |
+      A cluster of 5-7 translucent crystalline forms floating in dark
+      void space. Each crystal is a geometric polyhedron (mix of
+      octahedrons, hexagonal prisms, and irregular shards) between
+      0.5m and 2m across. They glow from within — cyan-green (#4af0c0)
+      for active memories, purple (#7b5cff) for archived, gold (#ffd700)
+      for sacred/highlighted. Thin light-tendrils connect the crystals
+      like synapses. Subtle particle aura around each crystal.
+      The crystals pulse slowly, like breathing. Dark background (#050510).
+      The mood is alive data — knowledge that breathes.
+      Concept art, ultra-detailed, ethereal lighting.
+    negative: "rock, geode, natural, rough, cartoon, text"
+    aspect: "1:1"
+
+  sovereignty-pillar:
+    id: sovereignty-pillar
+    name: "Pillar of Sovereignty"
+    type: NANO
+    style: "monument, sacred technology, concept art"
+    prompt: |
+      A tall crystalline pillar (5m tall, 1m diameter) standing on a
+      circular dark metal platform. The pillar is made of layered
+      translucent crystal — alternating bands of cyan-green (#4af0c0),
+      purple (#7b5cff), and clear glass. Geometric symbols and circuit
+      patterns are visible inside the crystal, like embedded circuitry.
+      A soft golden (#ffd700) light radiates from the pillar's core.
+      Runes of sovereignty spiral up the surface. The pillar casts
+      volumetric light beams in all directions. It sits at the center
+      of a circular platform with seven portal rings visible in the
+      background. The mood is sacred power — a monument to digital
+      freedom. Concept art, ultra-detailed, dramatic lighting.
+    negative: "broken, cracked, dark, threatening, people, text"
+    aspect: "9:16"
+
+  thought-stream:
+    id: thought-stream
+    name: "Thought Stream"
+    type: NANO
+    style: "data visualization, concept art"
+    prompt: |
+      A flowing river of luminous data particles suspended in void space.
+      The stream is approximately 2m wide and flows in a gentle curve
+      through the air. Particles are tiny glowing points — mostly
+      cyan-green (#4af0c0) with occasional purple (#7b5cff) and gold
+      (#ffd700) highlights. The stream has subtle turbulence where
+      data clusters form temporary structures — brief geometric shapes
+      that dissolve back into flow. The overall effect is like a
+      visible current of consciousness — thought made light.
+      Dark background (#050510). Concept art, ultra-detailed,
+      long-exposure photography style.
+    negative: "water, liquid, solid, blocky, cartoon, text"
+    aspect: "16:9"
+
+  agent-shrine:
+    id: agent-shrine
+    name: "Agent Presence Shrine"
+    type: NANO
+    style: "digital avatar pedestal, concept art"
+    prompt: |
+      A small raised platform (2m across) with a semi-transparent
+      holographic figure standing on it — a stylized humanoid silhouette
+      made of flowing cyan-green (#4af0c0) data particles. The figure
+      is featureless but expressive through posture and particle
+      behavior. Around the base, geometric patterns glow in the
+      platform surface. Above the figure, a small rotating holographic
+      emblem (abstract geometric logo) floats. Soft purple (#7b5cff)
+      ambient light. The shrine is one of several arranged along a
+      dark corridor. Each shrine represents a different AI agent.
+      Concept art, ultra-detailed, soft volumetric lighting.
+    negative: "realistic human, face, statue, stone, cartoon, text"
+    aspect: "1:1"

concept-packs/genie-nano-banana/prompts/portals.yaml

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+# Portal Prompts — Nexus Gateway Concepts
+# Each portal has a unique visual identity matching its destination.
+
+prompts:
+
+  morrowind:
+    id: morrowind
+    name: "Morrowind Portal"
+    type: NANO
+    style: "fantasy sci-fi portal, concept art"
+    prompt: |
+      A large circular portal ring (3m diameter) made of dark volcanic
+      basalt and cracked obsidian. The ring's surface is rough, ancient,
+      weathered by ash storms. Glowing orange (#ff6600) runes etch the
+      inner edge. The portal's interior shows a swirling ash storm over
+      a volcanic landscape — red sky, floating ash, distant mountain.
+      Orange embers drift from the portal. The ring sits on a dark
+      metallic Nexus platform. Dramatic side-lighting casts long
+      shadows. The portal feels ancient, dangerous, alluring.
+      Concept art, ultra-detailed, cinematic.
+    negative: "clean, modern, bright, cartoon, text"
+    aspect: "1:1"
+
+  bannerlord:
+    id: bannerlord
+    name: "Bannerlord Portal"
+    type: NANO
+    style: "medieval fantasy portal, concept art"
+    prompt: |
+      A large circular portal ring (3m diameter) forged from dark iron
+      and bronze, decorated with shield motifs and battle engravings.
+      Gold (#ffd700) light pulses from the inner edge. The portal's
+      interior shows a vast battlefield — dust clouds, distant armies,
+      medieval banners. Warm golden light spills from the portal.
+      Battle-worn shields are embedded in the ring. The ring sits on a
+      dark Nexus platform. Dust motes drift from the portal.
+      The portal feels warlike, epic, golden-age.
+      Concept art, ultra-detailed, cinematic.
+    negative: "modern, sci-fi, clean, cartoon, text"
+    aspect: "1:1"
+
+  workshop:
+    id: workshop
+    name: "Workshop Portal"
+    type: NANO
+    style: "creative forge portal, concept art"
+    prompt: |
+      A large circular portal ring (3m diameter) made of sleek dark
+      metal with geometric construction lines etched in cyan-green
+      (#4af0c0). The ring has a precision-engineered look — clean
+      edges, modular panels, glowing circuit traces. The portal's
+      interior shows a holographic workshop — floating blueprints,
+      rotating 3D models, holographic tools. Cyan-green light spills
+      outward. Small construction hologram particles orbit the ring.
+      The portal feels creative, technical, infinite possibility.
+      Concept art, ultra-detailed, cinematic.
+    negative: "organic, dirty, ancient, cartoon, text"
+    aspect: "1:1"
+
+  gallery-world:
+    id: gallery-world
+    name: "Portal Gallery — Genie Prototype"
+    type: GENIE
+    prompt: |
+      Create an explorable 3D world: a long dark corridor (the Gallery)
+      with seven large glowing portal rings mounted in sequence along
+      the walls. Each portal is a different style and color:
+      1. Volcanic orange (Morrowind)
+      2. Golden bronze (Bannerlord)
+      3. Cyan-green precision (Workshop)
+      4. Deep blue ocean (Archive)
+      5. Purple mystic (Courtyard)
+      6. Red warning (Gate)
+      7. Gold sacred (Chapel)
+      The corridor has a dark metal floor with glowing grid lines.
+      The player can walk the corridor and look into each portal.
+      Each portal shows a glimpse of its destination world.
+      The mood is a museum of worlds — quiet, reverent, infinite.
+    camera: "first-person, eye height ~1.7m"
+    physics: "walking on floor"

concept-packs/genie-nano-banana/prompts/skyboxes.yaml

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+# Skybox Prompts — Nexus Background Environments
+# These generate equirectangular (2:1) or cubemap-ready textures.
+
+prompts:
+
+  nebula-void:
+    id: nebula-void
+    name: "Nebula Skybox Variants"
+    type: NANO
+    style: "deep space nebula, 360-degree environment, equirectangular"
+    prompt: |
+      Deep space nebula skybox. 360-degree equirectangular projection.
+      Background is near-black (#050510). Dominant nebula colors are
+      deep purple (#1a0a3e) and dark blue (#0a1a3e) with occasional
+      wisps of cyan-green (#4af0c0) and faint gold (#ffd700) star
+      clusters. The nebula has soft, rolling cloud forms — not sharp
+      or aggressive. Distant stars are tiny white points with subtle
+      diffraction spikes. No planets, no galaxies, no bright objects.
+      The mood is infinite void with gentle cosmic dust — vast,
+      quiet, deep. The skybox should tile seamlessly at the edges.
+      Ultra-detailed, photorealistic space photography style.
+    negative: "bright, colorful explosion, planets, ships, cartoon, text"
+    aspect: "2:1"
+    variants:
+      - name: "nebula-void-primary"
+        modifier: "more purple, less blue, minimal cyan"
+      - name: "nebula-void-secondary"
+        modifier: "more blue, less purple, cyan accents prominent"
+      - name: "nebula-void-golden"
+        modifier: "purple-blue base with golden star cluster in one quadrant"
+      - name: "nebula-void-void"
+        modifier: "almost pure black, barely visible nebula wisps, maximum stars"
+
+  nebula-world:
+    id: nebula-world
+    name: "Nebula Skybox — Genie Environment"
+    type: GENIE
+    prompt: |
+      Create an explorable 3D world: a single small floating platform
+      (5m diameter dark metal disc) suspended in deep space. The player
+      stands on the platform and can look in all directions at a vast
+      nebula sky. The nebula is deep purple and dark blue with faint
+      cyan-green wisps. Stars are small and distant. The platform has
+      a faintly glowing edge in cyan-green. There is nothing else —
+      just the platform, the player, and the infinite void.
+      The purpose is to feel the scale and mood of the Nexus skybox.
+    camera: "first-person, free look"
+    physics: "standing on platform only"
+
+  void-minimal:
+    id: void-minimal
+    name: "Pure Void Skybox"
+    type: NANO
+    style: "minimal deep space, equirectangular"
+    prompt: |
+      Nearly pure black skybox (#050510) with only the faintest hints
+      of deep purple nebula. Mostly empty void. A sparse field of
+      tiny distant stars — no clusters, no bright points. This is
+      the ultimate emptiness that surrounds the Nexus.
+      Equirectangular 2:1 projection, tileable edges.
+      The mood is absolute emptiness — the void before creation.
+    negative: "colorful, bright, nebula clouds, objects, text"
+    aspect: "2:1"

concept-packs/genie-nano-banana/prompts/textures.yaml

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+# Texture Prompts — Nexus Surface/Material Concepts
+# These generate tileable texture references for Three.js materials.
+
+prompts:
+
+  platform:
+    id: platform
+    name: "Platform Surface Textures"
+    type: NANO
+    style: "dark metal surface texture, tileable"
+    prompt: |
+      Dark metallic surface texture, tileable. Base color is very dark
+      gunmetal (#0a0f28). Subtle grid pattern of thin lines in
+      cyan-green (#4af0c0) at very low opacity. The metal has fine
+      brushed grain running in one direction. Occasional micro-scratches.
+      No rivets, no bolts, no panels — smooth and continuous. The grid
+      lines are recessed channels that glow faintly. Top-down view,
+      perfectly flat, no perspective distortion. 1024x1024 seamless
+      tileable texture. PBR-ready: this is the diffuse/albedo map.
+    negative: "3D, perspective, objects, dirty, rusty, cartoon, text"
+    aspect: "1:1"
+    variants:
+      - name: "platform-core"
+        modifier: "cyan-green grid lines only"
+      - name: "platform-chapel"
+        modifier: "gold (#ffd700) grid lines, slightly warmer base"
+      - name: "platform-danger"
+        modifier: "red (#ff4466) grid lines, warning stripe accents"
+
+  energy-field:
+    id: energy-field
+    name: "Energy Field / Force Wall"
+    type: NANO
+    style: "holographic barrier, translucent, concept"
+    prompt: |
+      A translucent energy barrier material concept. The surface is
+      mostly transparent with visible hexagonal grid pattern in
+      cyan-green (#4af0c0) light. The grid has a subtle shimmer/wave
+      animation frozen mid-frame. Edges of the barrier are brighter.
+      Behind the barrier, everything is slightly distorted (like
+      looking through heat haze). The barrier has a faint inner glow.
+      The mood is high-tech force field — protective, not threatening.
+      Flat front view, no perspective, suitable as shader reference.
+      Concept art style.
+    negative: "solid, opaque, dark, scary, cartoon, text"
+    aspect: "1:1"
+
+  portal-glow:
+    id: portal-glow
+    name: "Portal Inner Glow"
+    type: NANO
+    style: "swirling energy vortex, circular, concept"
+    prompt: |
+      A circular swirling energy vortex viewed straight-on. The swirl
+      rotates clockwise. Colors transition from outer edge to center:
+      outer ring is the portal color (generic white/neutral), mid-ring
+      brightens, center is a bright white-blue point. The swirl has
+      visible energy tendrils spiraling inward. Fine particle sparks
+      are caught in the rotation. The background beyond the center
+      is pure black (void). The image should be circular with
+      transparent/dark corners. Used as reference for portal inner
+      material/shader. Concept art style.
+    negative: "square, rectangular, flat, cartoon, text"
+    aspect: "1:1"
+
+  crystal-surface:
+    id: crystal-surface
+    name: "Memory Crystal Surface"
+    type: NANO
+    style: "crystalline material, translucent, concept"
+    prompt: |
+      Close-up of a translucent crystal surface material. The crystal
+      is clear with internal fractures and light paths visible. The
+      internal structure shows geometric growth patterns — hexagonal
+      lattice, like a synthetic crystal grown with purpose. Faint
+      cyan-green (#4af0c0) light pulses along the fracture lines.
+      The surface has a slight frosted quality at edges, clearer in
+      center. Macro photography style, shallow depth of field.
+      This is material reference for memory crystal geometry.
+    negative: "opaque, colored, rough, natural, cartoon, text"
+    aspect: "1:1"

concept-packs/genie-nano-banana/references/palette.md

@@ -0,0 +1,78 @@
+# Nexus Visual Palette Reference
+
+## Primary Colors
+
+| Name | Hex | RGB | Usage |
+|------|-----|-----|-------|
+| Void | #050510 | 5, 5, 16 | Background, deep space, base darkness |
+| Surface | #0a0f28 | 10, 15, 40 | UI panels, platform base metal |
+| Primary | #4af0c0 | 74, 240, 192 | Main accent, grid lines, active elements, cyan-green glow |
+| Secondary | #7b5cff | 123, 92, 255 | Supporting accent, purple energy, archive data |
+| Gold | #ffd700 | 255, 215, 0 | Sacred/highlight, chapel, sovereignty pillar |
+| Danger | #ff4466 | 255, 68, 102 | Warnings, gate portal, error states |
+| Text | #e0f0ff | 224, 240, 255 | Primary text color |
+| Text Muted | #8a9ab8 | 138, 154, 184 | Secondary text, labels |
+
+## Portal Colors
+
+| Portal | Hex | Source |
+|--------|-----|--------|
+| Morrowind | #ff6600 | Volcanic orange |
+| Bannerlord | #ffd700 | Battle gold |
+| Workshop | #4af0c0 | Creative cyan |
+| Archive | #0066ff | Deep blue |
+| Chapel | #ffd700 | Sacred gold |
+| Courtyard | #4af0c0 | Social cyan |
+| Gate | #ff4466 | Transit red |
+
+## Nebula Colors
+
+| Layer | Hex | Opacity |
+|-------|-----|---------|
+| Nebula primary | #1a0a3e | Low — background wash |
+| Nebula secondary | #0a1a3e | Low — background wash |
+| Nebula accent | #4af0c0 | Very low — wisps only |
+| Star cluster | #ffd700 | Very low — distant points |
+
+## Material Properties
+
+| Surface | Color | Roughness | Metalness | Emissive |
+|---------|-------|-----------|-----------|----------|
+| Platform base | #0a0f28 | 0.6 | 0.8 | none |
+| Platform grid | #4af0c0 | 0.3 | 0.4 | #4af0c0, 0.3 |
+| Portal ring | varies | 0.4 | 0.7 | portal color, 0.5 |
+| Crystal (active) | #4af0c0 | 0.1 | 0.2 | #4af0c0, 0.6 |
+| Crystal (archive) | #7b5cff | 0.1 | 0.2 | #7b5cff, 0.4 |
+| Crystal (sacred) | #ffd700 | 0.1 | 0.2 | #ffd700, 0.8 |
+| Energy barrier | transparent | 0.0 | 0.0 | #4af0c0, 0.4 |
+| Sovereignty pillar | layered crystal | 0.1 | 0.3 | #ffd700, 0.5 |
+
+## Lighting Reference
+
+| Light Type | Color | Intensity | Position (relative) |
+|-----------|-------|-----------|-------------------|
+| Ambient | #0a0f28 | 0.15 | Global |
+| Hub key light | #4af0c0 | 0.8 | Above center, slightly forward |
+| Hub fill | #7b5cff | 0.3 | Below, scattered |
+| Portal light | portal color | 0.6 | At each portal ring |
+| Crystal glow | crystal color | 0.4 | At crystal position |
+| Chapel warm | #ffd700 | 0.5 | From holographic windows |
+
+## Post-Processing Targets
+
+| Effect | Value | Purpose |
+|--------|-------|---------|
+| Bloom threshold | 0.7 | Only bright emissives bloom |
+| Bloom strength | 0.8 | Strong but not overwhelming |
+| Bloom radius | 0.4 | Soft falloff |
+| SMAA | enabled | Anti-aliasing |
+| Fog color | #050510 | Match void background |
+| Fog density | 0.008 | Subtle depth fade |
+
+## Typography
+
+| Use | Font | Weight | Size (screen) |
+|-----|------|--------|---------------|
+| Titles / HUD headers | Orbitron | 700 | 24-36px |
+| Body / labels | JetBrains Mono | 400 | 13-15px |
+| Small / timestamps | JetBrains Mono | 300 | 11px |

concept-packs/genie-nano-banana/shot-list.yaml

@@ -0,0 +1,143 @@
+# Shot List — First Concept Batch
+# Ordered by priority. Each shot maps to a prompt in prompts/*.yaml.
+#
+# GENIE = Project Genie world prototype (explorable 3D, screenshot/video)
+# NANO  = Nano Banana Pro image generation (static concept art)
+
+batch: 1
+target: "Nexus core environments + portal gallery"
+generated_by: "mimo-build-680"
+
+shots:
+  # ═══ PRIORITY 1: CORE ENVIRONMENTS ═══
+  - id: env-core-hub
+    name: "The Hub — Central Nexus"
+    type: NANO
+    prompt_ref: "environments.yaml#core-hub"
+    count: 4
+    purpose: "Establish the primary landing space. Player spawn, portal ring visible."
+    threejs_target: "Main scene — platform, portal ring, particle field"
+
+  - id: env-core-hub-world
+    name: "The Hub — Genie Walkthrough"
+    type: GENIE
+    prompt_ref: "environments.yaml#core-hub-world"
+    count: 1
+    purpose: "Explorable prototype of the hub. Validate scale, sightlines, portal placement."
+    threejs_target: "Reference for camera height, movement speed, spatial layout"
+
+  - id: env-batcave
+    name: "Batcave Terminal"
+    type: NANO
+    prompt_ref: "environments.yaml#batcave"
+    count: 4
+    purpose: "Timmy's command center. Holographic displays, terminal consoles, data streams."
+    threejs_target: "Batcave area — terminal mesh, HUD panels, data visualization"
+
+  - id: env-chapel
+    name: "The Chapel"
+    type: NANO
+    prompt_ref: "environments.yaml#chapel"
+    count: 3
+    purpose: "Sacred space for reflection. Softer lighting, gold accents, quiet energy."
+    threejs_target: "Chapel zone — stained-glass shader, warm point lights"
+
+  - id: env-archive
+    name: "The Archive"
+    type: NANO
+    prompt_ref: "environments.yaml#archive"
+    count: 3
+    purpose: "Knowledge repository. Floating data crystals, scroll-like projections."
+    threejs_target: "Archive room — crystal geometry, ambient data particles"
+
+  # ═══ PRIORITY 2: PORTALS ═══
+  - id: portal-morrowind
+    name: "Morrowind Portal"
+    type: NANO
+    prompt_ref: "portals.yaml#morrowind"
+    count: 2
+    purpose: "Ash-storm gateway. Orange glow, volcanic textures."
+    threejs_target: "Portal ring material + particle effect for morrowind portal"
+
+  - id: portal-bannerlord
+    name: "Bannerlord Portal"
+    type: NANO
+    prompt_ref: "portals.yaml#bannerlord"
+    count: 2
+    purpose: "Medieval war gateway. Gold/brown, shield motifs, dust."
+    threejs_target: "Portal ring material for bannerlord portal"
+
+  - id: portal-workshop
+    name: "Workshop Portal"
+    type: NANO
+    prompt_ref: "portals.yaml#workshop"
+    count: 2
+    purpose: "Creative forge. Cyan glow, geometric construction lines."
+    threejs_target: "Portal ring material + particle effect for workshop portal"
+
+  - id: portal-gallery
+    name: "Portal Gallery — Genie Prototype"
+    type: GENIE
+    prompt_ref: "portals.yaml#gallery-world"
+    count: 1
+    purpose: "Walk through a space with multiple portals. Validate distances and visual hierarchy."
+    threejs_target: "Portal placement spacing, FOV, scale reference"
+
+  # ═══ PRIORITY 3: LANDMARKS ═══
+  - id: land-memory-crystal
+    name: "Memory Crystal Cluster"
+    type: NANO
+    prompt_ref: "landmarks.yaml#memory-crystal"
+    count: 3
+    purpose: "Floating crystalline data stores. Glow pulses with activity."
+    threejs_target: "Memory crystal geometry, emissive material, pulse animation"
+
+  - id: land-sovereignty-pillar
+    name: "Pillar of Sovereignty"
+    type: NANO
+    prompt_ref: "landmarks.yaml#sovereignty-pillar"
+    count: 2
+    purpose: "Monument at hub center. Inscribed with Timmy's SOUL values."
+    threejs_target: "Central monument mesh, text shader or decal system"
+
+  - id: land-nebula-skybox
+    name: "Nebula Skybox Variants"
+    type: NANO
+    prompt_ref: "skyboxes.yaml#nebula-void"
+    count: 4
+    purpose: "Background environment. Deep space nebula, subtle color gradients."
+    threejs_target: "Cubemap/equirectangular skybox texture"
+
+  - id: land-nebula-genie
+    name: "Nebula Skybox — Genie Environment"
+    type: GENIE
+    prompt_ref: "skyboxes.yaml#nebula-world"
+    count: 1
+    purpose: "Feel the scale of the void. Standing on a platform in deep space."
+    threejs_target: "Skybox mood reference, fog density calibration"
+
+  # ═══ PRIORITY 4: TEXTURES ═══
+  - id: tex-platform
+    name: "Platform Surface Textures"
+    type: NANO
+    prompt_ref: "textures.yaml#platform"
+    count: 3
+    purpose: "Walkable surfaces. Dark metal, subtle grid lines, neon edge trim."
+    threejs_target: "Diffuse + normal map reference for platform materials"
+
+  - id: tex-energy-field
+    name: "Energy Field / Force Wall"
+    type: NANO
+    prompt_ref: "textures.yaml#energy-field"
+    count: 2
+    purpose: "Translucent barrier material. Holographic, shimmering."
+    threejs_target: "Shader reference for translucent energy barriers"
+
+  # ═══ PRIORITY 5: GENIE FULL-WORLD PROTOTYPE ═══
+  - id: world-full-nexus
+    name: "Full Nexus Prototype"
+    type: GENIE
+    prompt_ref: "environments.yaml#full-nexus-world"
+    count: 1
+    purpose: "Complete explorable world with hub, portals visible in distance, floating platforms, skybox. Record walkthrough video."
+    threejs_target: "Master layout reference. Spatial relationships between all zones."

concept-packs/genie-nano-banana/storage-policy.md

@@ -0,0 +1,65 @@
+# Storage Policy — Repo vs. Local
+
+## What Goes In The Repo
+
+These are lightweight, versionable, text-based artifacts:
+
+| Artifact | Path | Format |
+|----------|------|--------|
+| README | `concept-packs/genie-nano-banana/README.md` | Markdown |
+| Shot list | `concept-packs/genie-nano-banana/shot-list.yaml` | YAML |
+| Prompt packs | `concept-packs/genie-nano-banana/prompts/*.yaml` | YAML |
+| Pipeline docs | `concept-packs/genie-nano-banana/pipeline.md` | Markdown |
+| This policy | `concept-packs/genie-nano-banana/storage-policy.md` | Markdown |
+| Palette reference | `concept-packs/genie-nano-banana/references/palette.md` | Markdown |
+| Design notes | `concept-packs/genie-nano-banana/references/design-*.md` | Markdown |
+| Selected thumbnails | `concept-packs/genie-nano-banana/references/*_thumb.jpg` | JPEG, max 200KB each |
+
+Thumbnails are low-res (max 480px wide, JPEG quality 60) versions of
+selected concept art — enough to show which image a design note
+references, not enough to serve as actual texture data.
+
+## What Stays Local (NOT in Repo)
+
+These are binary, heavy, or ephemeral:
+
+| Artifact | Local Path | Reason |
+|----------|-----------|--------|
+| Nano Banana full-res PNGs | `~/nexus-concepts/nano-banana/` | Binary, 2-10MB each |
+| Genie walkthrough videos | `~/nexus-concepts/genie-worlds/` | Binary, 50-500MB each |
+| Genie full-res screenshots | `~/nexus-concepts/genie-worlds/` | Binary, 5-20MB each |
+| Raw texture maps (PBR) | `~/nexus-concepts/textures/` | Binary, 2-8MB each |
+| Cubemap face images | `~/nexus-concepts/skyboxes/` | Binary, 6x2-10MB |
+
+## Why This Split
+
+1. **Git is for text.** Binary blobs bloat history, slow clones, and
+   can't be diffed. The repo should remain fast to clone.
+
+2. **Concepts are reference, not source.** The actual Nexus lives in
+   JavaScript code. Concept art informs the code but isn't shipped
+   to users. Keeping it local avoids shipping a 500MB repo.
+
+3. **Regeneration is cheap.** If a local concept is lost, re-run the
+   prompt. The prompt is in the repo; the output can be regenerated.
+   The prompt is the durable artifact.
+
+4. **Selected references survive.** When a concept image directly
+   informs a design decision, a low-res thumbnail and design note
+   go into the repo — enough context to understand the decision,
+   not enough to replace the original.
+
+## Thumbnail Generation
+
+To create a repo-safe thumbnail from a concept image:
+
+```bash
+# macOS
+sips -Z 480 -s format jpeg -s formatOptions 60 input.png --out output_thumb.jpg
+
+# Linux (ImageMagick)
+convert input.png -resize 480x -quality 60 output_thumb.jpg
+```
+
+Max 5 thumbnails per shot. Only commit the ones that are actively
+referenced in design notes.

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 +1,302 @@
+"""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 graph_data(
+        self,
+        topic_filter: Optional[str] = None,
+    ) -> dict:
+        """Export the full connection graph for 3D constellation visualization.
+
+        Returns a dict with:
+        - nodes: list of {id, title, topics, source, created_at}
+        - edges: list of {source, target, weight} from holographic links
+
+        Args:
+            topic_filter: If set, only include entries matching this topic
+                and edges between them.
+        """
+        entries = list(self._entries.values())
+
+        if topic_filter:
+            topic_lower = topic_filter.lower()
+            entries = [
+                e for e in entries
+                if topic_lower in [t.lower() for t in e.topics]
+            ]
+
+        entry_ids = {e.id for e in entries}
+
+        nodes = [
+            {
+                "id": e.id,
+                "title": e.title,
+                "topics": e.topics,
+                "source": e.source,
+                "created_at": e.created_at,
+            }
+            for e in entries
+        ]
+
+        # Build edges from links, dedup (A→B and B→A become one edge)
+        seen_edges: set[tuple[str, str]] = set()
+        edges = []
+        for e in entries:
+            for linked_id in e.links:
+                if linked_id not in entry_ids:
+                    continue
+                pair = (min(e.id, linked_id), max(e.id, linked_id))
+                if pair in seen_edges:
+                    continue
+                seen_edges.add(pair)
+                # Compute weight via linker for live similarity score
+                linked = self._entries.get(linked_id)
+                if linked:
+                    weight = self.linker.compute_similarity(e, linked)
+                    edges.append({
+                        "source": pair[0],
+                        "target": pair[1],
+                        "weight": round(weight, 4),
+                    })
+
+        return {"nodes": nodes, "edges": edges}
+
+    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,
+        }

nexus/mnemosyne/cli.py

@@ -0,0 +1,140 @@
+"""CLI interface for Mnemosyne.
+
+Provides: mnemosyne ingest, mnemosyne search, mnemosyne link, mnemosyne stats,
+          mnemosyne topics, mnemosyne remove, mnemosyne export
+"""
+
+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 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")
+
+    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,
+    }
+    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 +1,345 @@
+"""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_graph_data_empty_archive():
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        archive = MnemosyneArchive(archive_path=path)
+        data = archive.graph_data()
+        assert data == {"nodes": [], "edges": []}
+
+
+def test_graph_data_nodes_and_edges():
+    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", topics=["code"])
+        e2 = ingest_event(archive, title="Python scripting", content="Writing automation scripts using Python", topics=["code"])
+        e3 = ingest_event(archive, title="Cooking", content="Making pasta carbonara", topics=["food"])
+
+        data = archive.graph_data()
+        assert len(data["nodes"]) == 3
+        # All node fields present
+        for node in data["nodes"]:
+            assert "id" in node
+            assert "title" in node
+            assert "topics" in node
+            assert "source" in node
+            assert "created_at" in node
+
+        # e1 and e2 should be linked (shared Python/automation tokens)
+        edge_pairs = {(e["source"], e["target"]) for e in data["edges"]}
+        e1e2 = (min(e1.id, e2.id), max(e1.id, e2.id))
+        assert e1e2 in edge_pairs or (e1e2[1], e1e2[0]) in edge_pairs
+
+        # All edges have weights
+        for edge in data["edges"]:
+            assert "weight" in edge
+            assert 0 <= edge["weight"] <= 1
+
+
+def test_graph_data_topic_filter():
+    with tempfile.TemporaryDirectory() as tmp:
+        path = Path(tmp) / "test_archive.json"
+        archive = MnemosyneArchive(archive_path=path)
+        e1 = ingest_event(archive, title="A", content="code stuff", topics=["code"])
+        e2 = ingest_event(archive, title="B", content="more code", topics=["code"])
+        ingest_event(archive, title="C", content="food stuff", topics=["food"])
+
+        data = archive.graph_data(topic_filter="code")
+        node_ids = {n["id"] for n in data["nodes"]}
+        assert e1.id in node_ids
+        assert e2.id in node_ids
+        assert len(data["nodes"]) == 2
+
+
+def test_graph_data_deduplicates_edges():
+    """Bidirectional links should produce a single edge, not two."""
+    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")
+
+        data = archive.graph_data()
+        # Count how many edges connect e1 and e2
+        e1e2_edges = [
+            e for e in data["edges"]
+            if {e["source"], e["target"]} == {e1.id, e2.id}
+        ]
+        assert len(e1e2_edges) <= 1, "Should not have duplicate bidirectional edges"
+
+
+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"}

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 ---');