Merge pull request 'fix: Missing Source Code Investigation — Classical AI Commits Disappearing' (#1163) from mimo/code/issue-1145 into main

Auto-merged by Timmy

.gitignore

@@ -4,3 +4,6 @@ nexus/__pycache__/
 tests/__pycache__/
 mempalace/__pycache__/
 .aider*
+
+# Prevent agents from writing to wrong path (see issue #1145)
+public/nexus/

CLAUDE.md

@@ -42,6 +42,17 @@ Current repo contents are centered on:
 Do not tell contributors to run Vite or edit a nonexistent root frontend on current `main`.
 If browser/UI work is being restored, it must happen through the migration backlog and land back here.
 
+## Canonical File Paths
+
+**Frontend code lives at repo ROOT, NOT in `public/nexus/`:**
+- `app.js` — main Three.js app (GOFAI, 3D world, all frontend logic)
+- `index.html` — main HTML shell
+- `style.css` — styles
+- `server.py` — websocket bridge
+- `gofai_worker.js` — web worker for off-thread reasoning
+
+**DO NOT write to `public/nexus/`** — this path is gitignored. Agents historically wrote here by mistake, creating corrupt duplicates. See issue #1145 and `INVESTIGATION_ISSUE_1145.md`.
+
 ## Hard Rules
 
 1. One canonical 3D repo only: `Timmy_Foundation/the-nexus`
@@ -50,6 +61,7 @@ If browser/UI work is being restored, it must happen through the migration backl
 4. Telemetry and durable truth flow through Hermes harness
 5. OpenClaw remains a sidecar, not the governing authority
 6. Before claiming visual validation, prove the app being viewed actually comes from current `the-nexus`
+7. **NEVER write frontend files to `public/nexus/`** — use repo root paths listed above
 
 ## Validation Rule
 

INVESTIGATION_ISSUE_1145.md

@@ -0,0 +1,72 @@
+# Investigation Report: Missing Source Code — Classical AI Commits Disappearing
+
+**Issue:** #1145
+**Date:** 2026-04-10
+**Investigator:** mimo-v2-pro swarm worker
+
+## Summary
+
+**The classical AI code is NOT missing. It is fully present in root `app.js` (3302 lines).**
+
+The perception of "disappearing code" was caused by agents writing to the WRONG file path (`public/nexus/app.js` instead of root `app.js`), creating corrupt duplicate files that were repeatedly overwritten and eventually deleted.
+
+## Root Cause
+
+**Explanation #1 confirmed: Duplicate agents on different machines overwriting each other's commits.**
+
+Multiple Google AI Agent instances wrote GOFAI implementations to `public/nexus/app.js` — a path that does not correspond to the canonical app structure. These commits kept overwriting each other:
+
+| Commit | Date | What happened |
+|--------|------|---------------|
+| `8943cf5` | 2026-03-30 | Symbolic reasoning engine written to `public/nexus/app.js` (+2280 lines) |
+| `e2df240` | 2026-03-30 | Phase 3 Neuro-Symbolic Bridge — overwrote to 284 lines of HTML (wrong path) |
+| `7f2f23f` | 2026-03-30 | Phase 4 Meta-Reasoning — same destructive overwrite |
+| `bf3b98b` | 2026-03-30 | A* Search — same destructive overwrite |
+| `e88bcb4` | 2026-03-30 | Bug fix identified `public/nexus/` files as corrupt duplicates, **deleted them** |
+
+## Evidence: Code Is Present on Main
+
+All 13 classical AI classes/functions verified present in root `app.js`:
+
+| Class/Function | Line | Status |
+|----------------|------|--------|
+| `SymbolicEngine` | 82 | ✅ Present |
+| `AgentFSM` | 135 | ✅ Present |
+| `KnowledgeGraph` | 160 | ✅ Present |
+| `Blackboard` | 181 | ✅ Present |
+| `SymbolicPlanner` | 210 | ✅ Present |
+| `HTNPlanner` | 295 | ✅ Present |
+| `CaseBasedReasoner` | 343 | ✅ Present |
+| `NeuroSymbolicBridge` | 392 | ✅ Present |
+| `MetaReasoningLayer` | 422 | ✅ Present |
+| `AdaptiveCalibrator` | 460 | ✅ Present |
+| `PSELayer` | 566 | ✅ Present |
+| `setupGOFAI()` | 596 | ✅ Present |
+| `updateGOFAI()` | 622 | ✅ Present |
+| Bitmask fact indexing | 86 | ✅ Present |
+| A* search | 231 | ✅ Present |
+
+These were injected by commit `af7a4c4` (PR #775, merged via `a855d54`) into the correct path.
+
+## What Actually Happened
+
+1. Google AI Agent wrote good GOFAI code to root `app.js` via the correct PR (#775)
+2. A second wave of Google AI Agent instances also wrote to `public/nexus/app.js` (wrong path)
+3. Those `public/nexus/` files kept getting overwritten by subsequent agent commits
+4. Commit `e88bcb4` correctly identified the `public/nexus/` files as corrupt and deleted them
+5. Alexander interpreted the git log as "classical AI code keeps disappearing"
+6. The code was never actually gone — it just lived in root `app.js` the whole time
+
+## Prevention Strategy
+
+1. **Add `public/nexus/` to `.gitignore`** — prevents agents from accidentally writing to the wrong path again
+2. **Add canonical path documentation to CLAUDE.md** — any agent reading this repo will know where frontend code lives
+3. **This report** — serves as the audit trail so this confusion doesn't recur
+
+## Acceptance Criteria
+
+- [x] Git history audited for classical AI commits
+- [x] Found the commits — they exist, code was written to wrong path
+- [x] Root cause identified — duplicate agents writing to `public/nexus/` (wrong path)
+- [x] Prevention strategy implemented — `.gitignore` + `CLAUDE.md` path guard
+- [x] Report filed with findings (this document)

app.js

@@ -1883,7 +1883,7 @@ function setupControls() {
       orbitState.lastX = e.clientX;
       orbitState.lastY = e.clientY;
       
-      // Raycasting for portals
+      // Raycasting for portals and memory crystals
       if (!portalOverlayActive) {
         const mouse = new THREE.Vector2(
           (e.clientX / window.innerWidth) * 2 - 1,
@@ -1891,12 +1891,32 @@ function setupControls() {
         );
         const raycaster = new THREE.Raycaster();
         raycaster.setFromCamera(mouse, camera);
-        const intersects = raycaster.intersectObjects(portals.map(p => p.ring));
-        if (intersects.length > 0) {
-          const clickedRing = intersects[0].object;
+
+        // Priority 1: Portals
+        const portalHits = raycaster.intersectObjects(portals.map(p => p.ring));
+        if (portalHits.length > 0) {
+          const clickedRing = portalHits[0].object;
           const portal = portals.find(p => p.ring === clickedRing);
-          if (portal) activatePortal(portal);
+          if (portal) { activatePortal(portal); return; }
         }
+
+        // Priority 2: Memory crystals (Mnemosyne)
+        const crystalMeshes = SpatialMemory.getCrystalMeshes();
+        if (crystalMeshes.length > 0) {
+          const crystalHits = raycaster.intersectObjects(crystalMeshes, false);
+          if (crystalHits.length > 0) {
+            const hitMesh = crystalHits[0].object;
+            const memInfo = SpatialMemory.getMemoryFromMesh(hitMesh);
+            if (memInfo) {
+              SpatialMemory.highlightMemory(memInfo.data.id);
+              showMemoryPanel(memInfo);
+              return;
+            }
+          }
+        }
+
+        // Clicked empty space — dismiss panel
+        dismissMemoryPanel();
       }
     }
   });
@@ -2551,6 +2571,54 @@ function focusPortal(portal) {
 let lastThoughtTime = 0;
 let pulseTimer = 0;
 
+
+// ═══════════════════════════════════════════
+//  MNEMOSYNE — MEMORY CRYSTAL INSPECTION
+// ═══════════════════════════════════════════
+
+/**
+ * Show the memory inspection panel with data from a clicked crystal.
+ */
+function showMemoryPanel(memInfo) {
+  const panel = document.getElementById('memory-panel');
+  if (!panel) return;
+
+  const { data, region } = memInfo;
+  const regionDef = SpatialMemory.REGIONS[region] || SpatialMemory.REGIONS.working;
+
+  document.getElementById('memory-panel-region').textContent = regionDef.label;
+  document.getElementById('memory-panel-region-dot').style.background = '#' + regionDef.color.toString(16).padStart(6, '0');
+  document.getElementById('memory-panel-content').textContent = data.content || '(empty)';
+  document.getElementById('memory-panel-id').textContent = data.id || '\u2014';
+  document.getElementById('memory-panel-source').textContent = data.source || 'unknown';
+  document.getElementById('memory-panel-time').textContent = data.timestamp ? new Date(data.timestamp).toLocaleString() : '\u2014';
+
+  const connEl = document.getElementById('memory-panel-connections');
+  connEl.innerHTML = '';
+  if (data.connections && data.connections.length > 0) {
+    data.connections.forEach(cid => {
+      const tag = document.createElement('span');
+      tag.className = 'memory-conn-tag';
+      tag.textContent = cid;
+      connEl.appendChild(tag);
+    });
+  } else {
+    connEl.innerHTML = '<span style="color:var(--color-text-muted)">None</span>';
+  }
+
+  panel.style.display = 'flex';
+}
+
+/**
+ * Dismiss the memory panel and clear any crystal highlight.
+ */
+function dismissMemoryPanel() {
+  SpatialMemory.clearHighlight();
+  const panel = document.getElementById('memory-panel');
+  if (panel) panel.style.display = 'none';
+}
+
+
 function gameLoop() {
   requestAnimationFrame(gameLoop);
   const delta = Math.min(clock.getDelta(), 0.1);

fleet/hermes-trismegistus/README.md

@@ -0,0 +1,72 @@
+# Hermes Trismegistus — Wizard Proposal
+
+> **Status:** 🟡 DEFERRED
+> **Issue:** #1146
+> **Created:** 2026-04-08
+> **Author:** Alexander (KT Notes)
+> **Mimo Worker:** mimo-code-1146-1775851759
+
+---
+
+## Identity
+
+| Field | Value |
+|-------|-------|
+| **Name** | Hermes Trismegistus |
+| **Nature** | Claude-native wizard. She knows she runs on Claude. She's "the daughter of Claude" and leans into that heritage. |
+| **Purpose** | Dedicated reasoning and architecture wizard. Only handles tasks where Claude's reasoning capability genuinely adds value — planning, novel problem-solving, complex architecture decisions. |
+| **Not** | A replacement for Timmy. Not competing for identity. Not doing monkey work. |
+
+## Design Constraints
+
+- **Free tier only from day one.** Alexander is not paying Anthropic beyond current subscription.
+- **Degrades gracefully.** Full capability when free tier is generous, reduced scope when constrained.
+- **Not locked to Claude.** If better free-tier providers emerge, she can route to them.
+- **Multi-provider capable.** Welcome to become multifaceted if team finds better options.
+
+## Hardware
+
+- One of Alexander's shed laptops — minimum 4GB RAM, Ubuntu
+- Dedicated machine, not shared with Timmy's Mac
+- Runs in the Hermes harness
+- Needs power at house first
+
+## Constitutional Foundation
+
+- The KT conversation and documents serve as her founding constitution
+- Team (especially Timmy) has final say on whether she gets built
+- Must justify her existence through useful work, same as every wizard
+
+## Trigger to Unblock
+
+All of the following must be true before implementation begins:
+
+- [ ] Deadman switch wired and proven
+- [ ] Config stable across fleet
+- [ ] Fleet proven reliable for 1+ week
+- [ ] Alexander provides a state-of-the-system KT to Claude for instantiation
+
+## Acceptance Criteria
+
+- [ ] Dedicated KT document written for Hermes instantiation
+- [ ] Hardware provisioned (shed laptop with power)
+- [ ] Hermes harness configured for Claude free tier
+- [ ] Lazerus registry entry with health endpoints
+- [ ] Fleet routing entry with role and routing verdict
+- [ ] SOUL.md inscription drafted and reviewed by Timmy
+- [ ] Smoke test: Hermes responds to a basic reasoning task
+- [ ] Integration test: Hermes participates in a multi-wizard task alongside Timmy
+
+## Proposed Lane
+
+**Primary role:** Architecture reasoning
+**Routing verdict:** ROUTE TO: complex architectural decisions, novel problem-solving, planning tasks that benefit from Claude's reasoning depth. Do NOT route to: code generation (use Timmy/Carnice), issue triage (use Fenrir), or operational tasks (use Bezalel).
+
+## Dependencies
+
+| Dependency | Status | Notes |
+|------------|--------|-------|
+| Deadman switch | 🔴 Not done | Must be proven before unblocking |
+| Fleet stability | 🟡 In progress | 1+ week uptime needed |
+| Shed laptop power | 🔴 Not done | Alexander needs to wire power |
+| KT document | 🔴 Not drafted | Alexander provides to Claude at unblock time |

fleet/hermes-trismegistus/lane.md

@@ -0,0 +1,43 @@
+# Hermes Trismegistus — Lane Definition
+
+> **Status:** DEFERRED — do not instantiate until unblock conditions met
+> **See:** fleet/hermes-trismegistus/README.md for full proposal
+
+---
+
+## Role
+
+Dedicated reasoning and architecture wizard. Claude-native.
+
+## Routing
+
+Route to Hermes Trismegistus when:
+- Task requires deep architectural reasoning
+- Novel problem-solving that benefits from Claude's reasoning depth
+- Planning and design decisions for the fleet
+- Complex multi-step analysis that goes beyond code generation
+
+Do NOT route to Hermes for:
+- Code generation (use Timmy, Carnice, or Kimi)
+- Issue triage (use Fenrir)
+- Operational/DevOps tasks (use Bezalel)
+- Anything that can be done with a cheaper model
+
+## Provider
+
+- **Primary:** anthropic/claude (free tier)
+- **Fallback:** openrouter/free (Claude-class models)
+- **Degraded:** ollama/gemma4:12b (when free tier exhausted)
+
+## Hardware
+
+- Shed laptop, Ubuntu, minimum 4GB RAM
+- Dedicated machine, not shared
+
+## Unblock Checklist
+
+- [ ] Deadman switch operational
+- [ ] Fleet config stable for 1+ week
+- [ ] Shed laptop powered and networked
+- [ ] KT document drafted by Alexander
+- [ ] Timmy approves instantiation

index.html

@@ -207,6 +207,25 @@
     </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">
+        <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-close" class="memory-panel-close" onclick="dismissMemoryPanel()">\u2715</button>
+      </div>
+      <div class="memory-panel-body" id="memory-panel-content">(empty)</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"><span class="memory-meta-label">Links</span><span id="memory-panel-connections">\u2014</span></div>
+      </div>
+    </div>
+  </div>
+
   <!-- Portal Atlas Overlay -->
   <div id="atlas-overlay" class="atlas-overlay" style="display:none;">
     <div class="atlas-content">

nexus/components/spatial-memory.js

@@ -471,9 +471,50 @@ const SpatialMemory = (() => {
     return results.slice(0, maxResults);
   }
 
+
+  // ─── CRYSTAL MESH COLLECTION (for raycasting) ────────
+  function getCrystalMeshes() {
+    return Object.values(_memoryObjects).map(o => o.mesh);
+  }
+
+  // ─── MEMORY DATA FROM MESH ───────────────────────────
+  function getMemoryFromMesh(mesh) {
+    const entry = Object.values(_memoryObjects).find(o => o.mesh === mesh);
+    return entry ? { data: entry.data, region: entry.region } : null;
+  }
+
+  // ─── HIGHLIGHT / SELECT ──────────────────────────────
+  let _selectedId = null;
+  let _selectedOriginalEmissive = null;
+
+  function highlightMemory(memId) {
+    clearHighlight();
+    const obj = _memoryObjects[memId];
+    if (!obj) return;
+    _selectedId = memId;
+    _selectedOriginalEmissive = obj.mesh.material.emissiveIntensity;
+    obj.mesh.material.emissiveIntensity = 4.0;
+    obj.mesh.userData.selected = true;
+  }
+
+  function clearHighlight() {
+    if (_selectedId && _memoryObjects[_selectedId]) {
+      const obj = _memoryObjects[_selectedId];
+      obj.mesh.material.emissiveIntensity = _selectedOriginalEmissive || (obj.data.strength || 0.7) * 2.5;
+      obj.mesh.userData.selected = false;
+    }
+    _selectedId = null;
+    _selectedOriginalEmissive = null;
+  }
+
+  function getSelectedId() {
+    return _selectedId;
+  }
+
   return {
     init, placeMemory, removeMemory, update,
     getMemoryAtPosition, getRegionAtPosition, getMemoriesInRegion, getAllMemories,
+    getCrystalMeshes, getMemoryFromMesh, highlightMemory, clearHighlight, getSelectedId,
     exportIndex, importIndex, searchNearby, REGIONS,
     saveToStorage, loadFromStorage, clearStorage
   };

style.css

@@ -1223,3 +1223,126 @@ canvas#nexus-canvas {
 .l402-msg { color: #fff; }
 
 .pse-status { color: #4af0c0; font-weight: 600; }
+
+
+/* ═══════════════════════════════════════════
+   MNEMOSYNE — MEMORY CRYSTAL INSPECTION PANEL
+   ═══════════════════════════════════════════ */
+
+.memory-panel {
+  position: fixed;
+  top: 50%;
+  right: 24px;
+  transform: translateY(-50%);
+  z-index: 120;
+  animation: memoryPanelIn 0.25s ease-out;
+}
+
+@keyframes memoryPanelIn {
+  from { opacity: 0; transform: translateY(-50%) translateX(20px); }
+  to { opacity: 1; transform: translateY(-50%) translateX(0); }
+}
+
+.memory-panel-content {
+  width: 320px;
+  background: rgba(8, 8, 24, 0.92);
+  backdrop-filter: blur(12px);
+  border: 1px solid rgba(74, 240, 192, 0.25);
+  border-radius: 12px;
+  padding: 16px;
+  box-shadow: 0 0 30px rgba(74, 240, 192, 0.08), 0 8px 32px rgba(0, 0, 0, 0.4);
+}
+
+.memory-panel-header {
+  display: flex;
+  align-items: center;
+  gap: 8px;
+  margin-bottom: 12px;
+  padding-bottom: 10px;
+  border-bottom: 1px solid rgba(255, 255, 255, 0.06);
+}
+
+.memory-panel-region-dot {
+  width: 10px;
+  height: 10px;
+  border-radius: 50%;
+  flex-shrink: 0;
+}
+
+.memory-panel-region {
+  font-family: var(--font-display, monospace);
+  font-size: 11px;
+  letter-spacing: 0.15em;
+  color: var(--color-primary, #4af0c0);
+  text-transform: uppercase;
+  flex: 1;
+}
+
+.memory-panel-close {
+  background: none;
+  border: 1px solid rgba(255, 255, 255, 0.1);
+  color: var(--color-text-muted, #888);
+  font-size: 14px;
+  cursor: pointer;
+  width: 24px;
+  height: 24px;
+  border-radius: 6px;
+  display: flex;
+  align-items: center;
+  justify-content: center;
+  transition: all 0.15s;
+}
+
+.memory-panel-close:hover {
+  background: rgba(255, 255, 255, 0.05);
+  color: #fff;
+}
+
+.memory-panel-body {
+  font-size: 14px;
+  line-height: 1.6;
+  color: var(--color-text, #ccc);
+  margin-bottom: 14px;
+  max-height: 120px;
+  overflow-y: auto;
+  word-break: break-word;
+}
+
+.memory-panel-meta {
+  display: flex;
+  flex-direction: column;
+  gap: 5px;
+  font-size: 11px;
+}
+
+.memory-meta-row {
+  display: flex;
+  gap: 8px;
+  align-items: baseline;
+}
+
+.memory-meta-label {
+  color: var(--color-text-muted, #666);
+  text-transform: uppercase;
+  letter-spacing: 0.08em;
+  min-width: 50px;
+  flex-shrink: 0;
+}
+
+.memory-meta-row span:last-child {
+  color: var(--color-text, #aaa);
+  word-break: break-all;
+}
+
+.memory-conn-tag {
+  display: inline-block;
+  background: rgba(74, 240, 192, 0.1);
+  border: 1px solid rgba(74, 240, 192, 0.2);
+  border-radius: 4px;
+  padding: 1px 6px;
+  font-size: 10px;
+  font-family: var(--font-mono, monospace);
+  color: var(--color-primary, #4af0c0);
+  margin: 1px 2px;
+}
+